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Sample records for 24-bp consensus sequence

  1. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole-Imidazole Polyamide Probes.

    PubMed

    Kawamoto, Yusuke; Sasaki, Asuka; Chandran, Anandhakumar; Hashiya, Kaori; Ide, Satoru; Bando, Toshikazu; Maeshima, Kazuhiro; Sugiyama, Hiroshi

    2016-10-03

    Synthetic molecules that bind sequence-specifically to DNA have been developed for varied biological applications, including anticancer activity, regulation of gene expression, and visualization of specific genomic regions. Increasing the number of base pairs targeted by synthetic molecules strengthens their sequence specificity. Our group has been working on the development of pyrrole-imidazole polyamides that bind to the minor groove of DNA in a sequence-specific manner without causing denaturation. Recently, we reported a simple synthetic method of fluorescent tandem dimer polyamide probes composed of two hairpin moieties with a linking hinge, which bound to 12 bp in human telomeric repeats (5'-(TTAGGG)n-3') and could be used to specifically visualize telomeres in chemically fixed cells under mild conditions. We also performed structural optimization and extension of the target base pairs to allow more specific stain-ing of telomeres. In the present study, we synthesized tandem tetramer polyamides composed of four hairpin moieties, targeting 24 bp in telomeric repeats, the longest reported binding site for synthetic, non-nucleic-acid-based, sequence-specific DNA-binding molecules. The novel tandem tetramers bound with a nanomolar dissociation constant to 24 bp sequences made up of four telomeric repeats. Fluorescently labeled tandem tetramer polyamide probes could visualize human telomeres in chemically fixed cells with lower background signals than polyamide probes reported previously, suggesting that they had higher specificity for telomeres. Furthermore, high-throughput sequencing of human genomic DNA pulled down by the biotin-labeled tandem tetramer polyamide probe confirmed its effective binding to telomeric repeats in the complex chromatinized genome.

  2. 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.

  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

    2006-05-03

    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.

  4. Optimal treatment sequence in COPD: Can a consensus be found?

    PubMed

    Ferreira, J; Drummond, M; Pires, N; Reis, G; Alves, C; Robalo-Cordeiro, C

    2016-01-01

    There is currently no consensus on the treatment sequence in chronic obstructive pulmonary disease (COPD), although it is recognized that early diagnosis is of paramount importance to start treatment in the early stages of the disease. Although it is fairly consensual that initial treatment should be with an inhaled short-acting beta agonist, a short-acting muscarinic antagonist, a long-acting beta-agonist or a long-acting muscarinic antagonist. As the disease progresses, several therapeutic options are available, and which to choose at each disease stage remains controversial. When and in which patients to use dual bronchodilation? When to use inhaled corticosteroids? And triple therapy? Are the existing non-inhaled therapies, such as mucolytic agents, antibiotics, phosphodiesterase-4 inhibitors, methylxanthines and immunostimulating agents, useful? If so, which patients would benefit? Should co-morbidities be taken into account when choosing COPD therapy for a patient? This paper reviews current guidelines and available evidence and proposes a therapeutic scheme for COPD patients. We also propose a treatment algorithm in the hope that it will help physicians to decide the best approach for their patients. The authors conclude that, at present, a full consensus on optimal treatment sequence in COPD cannot be found, mainly due to disease heterogeneity and lack of biomarkers to guide treatment. For the time being, and although some therapeutic approaches are consensual, treatment of COPD should be patient-oriented.

  5. 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.

  6. To Clone or Not To Clone: Method Analysis for Retrieving Consensus Sequences In Ancient DNA Samples

    PubMed Central

    Winters, Misa; Barta, Jodi Lynn; Monroe, Cara; Kemp, Brian M.

    2011-01-01

    The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from “modern” DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be “gold standards” in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones. To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous. PMID:21738625

  7. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design?

    PubMed

    Novitsky, V; Smith, U R; Gilbert, P; McLane, M F; Chigwedere, P; Williamson, C; Ndung'u, T; Klein, I; Chang, S Y; Peter, T; Thior, I; Foley, B T; Gaolekwe, S; Rybak, N; Gaseitsiwe, S; Vannberg, F; Marlink, R; Lee, T H; Essex, M

    2002-06-01

    An evolving dominance of human immunodeficiency virus type 1 subtype C (HIV-1C) in the AIDS epidemic has been associated with a high prevalence of HIV-1C infection in the southern African countries and with an expanding epidemic in India and China. Understanding the molecular phylogeny and genetic diversity of HIV-1C viruses may be important for the design and evaluation of an HIV vaccine for ultimate use in the developing world. In this study we analyzed the phylogenetic relationships (i) between 73 non-recombinant HIV-1C near-full-length genome sequences, including 51 isolates from Botswana; (ii) between HIV-1C consensus sequences that represent different geographic subsets; and (iii) between specific isolates and consensus sequences. Based on the phylogenetic analyses of 73 near-full-length genomes, 16 "lineages" (a term that is used hereafter for discussion purposes and does not imply taxonomic standing) were identified within HIV-1C. The lineages were supported by high bootstrap values in maximum-parsimony and neighbor-joining analyses and were confirmed by the maximum-likelihood method. The nucleotide diversity between the 73 HIV-1C isolates (mean value of 8.93%; range, 2.9 to 11.7%) was significantly higher than the diversity of the samples to the consensus sequence (mean value of 4.86%; range, 3.3 to 7.2%, P < 0.0001). The translated amino acid distances to the consensus sequence were significantly lower than distances between samples within all HIV-1C proteins. The consensus sequences of HIV-1C proteins accompanied by amino acid frequencies were presented (that of Gag is presented in this work; those of Pol, Vif, Vpr, Tat, Rev, Vpu, Env, and Nef are presented elsewhere [http://www.aids.harvard.edu/lab_research/concensus_sequence.htm]). Additionally, in the promoter region three NF-kappa B sites (GGGRNNYYCC) were identified within the consensus sequences of the entire set or any subset of HIV-1C isolates. This study suggests that the consensus sequence

  8. Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations.

    PubMed Central

    Davis, J P; Janjić, N; Pribnow, D; Zichi, D A

    1995-01-01

    We present a computer-aided approach for identifying and aligning consensus secondary structure within a set of functionally related oligonucleotide sequences aligned by sequence. The method relies on visualization of secondary structure using a generalization of the dot matrix representation appropriate for consensus sequence data sets. An interactive computer program implementing such a visualization of consensus structure has been developed. The program allows for alignment editing, data and display filtering and various modes of base pair representation, including co-variation. The utility of this approach is demonstrated with four sample data sets derived from in vitro selection experiments and one data set comprising tRNA sequences. Images PMID:7501472

  9. The consensus sequence for self-catalyzed site-specific G residue depurination in DNA.

    PubMed

    Amosova, Olga; Smith, Alexander; Fresco, Jacques R

    2011-10-21

    The sequence variation tolerated within the stem-loop-forming genomic consensus sequence for self-catalyzed site-specific depurination of G residues is explored. The variation in self-depurination kinetics with sequence changes in the loop residues and stem base pairs, as well as with pH, provides insights into the self-catalytic mechanism. The observations suggest that self-catalyzed depurination of the 5' G residue of the loop consensus sequence 5'-G(T/A)GG-3' probably involves formation of some intraloop hydrogen-bonded base pair with the 3'-terminal G residue; although the electronic structure of both these G residues is retained, their 2-amino substituents are not critical for that interaction. The strong dependence of the self-depurination kinetics on stem stability suggests that the lifetime of some strained form of the loop is controlled by the integrity of the stem. In addition to the effects of length and base pair sequence on stem stability, there is a base pair requirement at the base of the loop: self-depurination is suppressed by 5'-C·G-3', 5'-A·T-3', or a mismatch but is most favored by 5'T·A3' and less so by 5'-G·C-3'. The occurrence in T and G of a similarly located carbonyl capable of hydrogen-bonding to the water molecule required for glycosyl bond hydrolysis may explain this sequence requirement. In toto, the more complete definition of the consensus sequence provided by this investigation enables a more accurate estimation of their number in the human genome and their distribution among different genes.

  10. Consensus multi-locus sequence typing scheme for Cryptococcus neoformans and Cryptococcus gattii

    PubMed Central

    Meyer, Wieland; Aanensen, David M.; Boekhout, Teun; Cogliati, Massimo; Diaz, Mara R.; Esposto, Maria Carmela; Fisher, Matthew; Gilgado, Felix; Hagen, Ferry; Kaocharoen, Sirada; Litvintseva, Anastasia P.; Mitchell, Thomas G.; Simwami, Sitali P.; Trilles, Luciana; Viviani, Maria Anna; Kwon-Chung, June

    2010-01-01

    This communication describes the consensus multi-locus typing scheme established by the Cryptococcal Working Group I (Genotyping of Cryptococcus neoformans and C. gattii) of the International Society for Human and Animal Mycology (ISHAM) using seven unlinked genetic loci for global strain genotyping. These genetic loci include the housekeeping genes CAP59, GPD1, LAC1, PLB1, SOD1, URA5 and the IGS1 region. Allele and sequence type information are accessible at http://www.mlst.net/. PMID:19462334

  11. Unity in function in the absence of consensus in sequence: role of leader peptides in export.

    PubMed

    Randall, L L; Hardy, S J

    1989-03-03

    Passage of proteins across membranes during export from their site of synthesis to their final destination is mediated by leader peptides that paradoxically exhibit a unity of function in spite of a diversity of sequence. These leader peptides act in at least two stages of the export process: at entry into the pathway and subsequently during translocation across the membrane. How selectivity is imposed on the system in the absence of a consensus among the sequences of leader peptides is the main issue discussed here.

  12. A FRET Biosensor for ROCK Based on a Consensus Substrate Sequence Identified by KISS Technology.

    PubMed

    Li, Chunjie; Imanishi, Ayako; Komatsu, Naoki; Terai, Kenta; Amano, Mutsuki; Kaibuchi, Kozo; Matsuda, Michiyuki

    2017-01-11

    Genetically-encoded biosensors based on Förster/fluorescence resonance energy transfer (FRET) are versatile tools for studying the spatio-temporal regulation of signaling molecules within not only the cells but also tissues. Perhaps the hardest task in the development of a FRET biosensor for protein kinases is to identify the kinase-specific substrate peptide to be used in the FRET biosensor. To solve this problem, we took advantage of kinase-interacting substrate screening (KISS) technology, which deduces a consensus substrate sequence for the protein kinase of interest. Here, we show that a consensus substrate sequence for ROCK identified by KISS yielded a FRET biosensor for ROCK, named Eevee-ROCK, with high sensitivity and specificity. By treating HeLa cells with inhibitors or siRNAs against ROCK, we show that a substantial part of the basal FRET signal of Eevee-ROCK was derived from the activities of ROCK1 and ROCK2. Eevee-ROCK readily detected ROCK activation by epidermal growth factor, lysophosphatidic acid, and serum. When cells stably-expressing Eevee-ROCK were time-lapse imaged for three days, ROCK activity was found to increase after the completion of cytokinesis, concomitant with the spreading of cells. Eevee-ROCK also revealed a gradual increase in ROCK activity during apoptosis. Thus, Eevee-ROCK, which was developed from a substrate sequence predicted by the KISS technology, will pave the way to a better understanding of the function of ROCK in a physiological context.

  13. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences.

    PubMed Central

    Rose, T M; Schultz, E R; Henikoff, J G; Pietrokovski, S; McCallum, C M; Henikoff, S

    1998-01-01

    We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. We demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World Wide Web (http://blocks.fhcrc.org/codehop.html) and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. PMID:9512532

  14. Peptide consensus sequence determination for the enhancement of the antimicrobial activity and selectivity of antimicrobial peptides

    PubMed Central

    Almaaytah, Ammar; Ajingi, Ya’u; Abualhaijaa, Ahmad; Tarazi, Shadi; Alshar’i, Nizar; Al-Balas, Qosay

    2017-01-01

    The rise of multidrug-resistant bacteria is causing a serious threat to the world’s human population. Recent reports have identified bacterial strains displaying pan drug resistance against antibiotics and generating fears among medical health specialists that humanity is on the dawn of entering a post-antibiotics era. Global research is currently focused on expanding the lifetime of current antibiotics and the development of new antimicrobial agents to tackle the problem of antimicrobial resistance. In the present study, we designed a novel consensus peptide named “Pepcon” through peptide consensus sequence determination among members of a highly homologous group of scorpion antimicrobial peptides. Members of this group were found to possess moderate antimicrobial activity with significant toxicity against mammalian cells. The aim of our design method was to generate a novel peptide with an enhanced antimicrobial potency and selectivity against microbial rather than mammalian cells. The results of our study revealed that the consensus peptide displayed potent antibacterial activities against a broad range of Gram-positive and Gram-negative bacteria. Our membrane permeation studies displayed that the peptide efficiently induced membrane damage and consequently led to cell death through the process of cell lysis. The microbial DNA binding assay of the peptide was found to be very weak suggesting that the peptide is not targeting the microbial DNA. Pepcon induced minimal cytotoxicity at the antimicrobial concentrations as the hemolytic activity was found to be zero at the minimal inhibitory concentrations (MICs). The results of our study demonstrate that the consensus peptide design strategy is efficient in generating peptides. PMID:28096686

  15. 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.

  16. Functional annotation of proteomic sequences based on consensus of sequence and structural analysis.

    PubMed

    Kitson, David H; Badretdinov, Azat; Zhu, Zhan-yang; Velikanov, Mikhail; Edwards, David J; Olszewski, Krzysztof; Szalma, Sándor; Yan, Lisa

    2002-03-01

    To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity detection, homology modelling and fold recognition methods. GeneAtlas is described in detail here. To test GeneAtlas, a 'virtual' genome was used, a subset of PDB structures from the SCOP database, in which the functional relationships are known. GeneAtlas detects additional relationships by building 3D models in comparison with the sequence searching method PSI-BLAST. Functionally related proteins with sequence identity below the twilight zone can be recognised correctly.

  17. AMS 4.0: consensus prediction of post-translational modifications in protein sequences.

    PubMed

    Plewczynski, Dariusz; Basu, Subhadip; Saha, Indrajit

    2012-08-01

    We present here the 2011 update of the AutoMotif Service (AMS 4.0) that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The selection of experimentally confirmed modifications is acquired from the latest UniProt and Phospho.ELM databases for training. The sequence vicinity of each modified residue is represented using amino acids physico-chemical features encoded using high quality indices (HQI) obtaining by automatic clustering of known indices extracted from AAindex database. For each type of the numerical representation, the method builds the ensemble of Multi-Layer Perceptron (MLP) pattern classifiers, each optimising different objectives during the training (for example the recall, precision or area under the ROC curve (AUC)). The consensus is built using brainstorming technology, which combines multi-objective instances of machine learning algorithm, and the data fusion of different training objects representations, in order to boost the overall prediction accuracy of conserved short sequence motifs. The performance of AMS 4.0 is compared with the accuracy of previous versions, which were constructed using single machine learning methods (artificial neural networks, support vector machine). Our software improves the average AUC score of the earlier version by close to 7 % as calculated on the test datasets of all 88 PTM types. Moreover, for the selected most-difficult sequence motifs types it is able to improve the prediction performance by almost 32 %, when compared with previously used single machine learning methods. Summarising, the brainstorming consensus meta-learning methodology on the average boosts the AUC score up to around 89 %, averaged over all 88 PTM types. Detailed results for single machine learning methods and the consensus methodology are also provided, together with the comparison to previously published methods and state-of-the-art software tools. The

  18. Dup-24 bp in the CHIT1 Gene in Six Mexican Amerindian Populations.

    PubMed

    Da Silva-José, T D; Juárez-Rendón, K J; Juárez-Osuna, J A; Porras-Dorantes, A; Valladares-Salgado, A; Cruz, M; Gonzalez-Ibarra, M; Soto, A G; Magaña-Torres, M T; Sandoval-Ramírez, L; García-Ortiz, José Elías

    2015-01-01

    Chitotriosidase (CHIT, EC 3.2.1.14) is an enzyme secreted by activated macrophages with the ability to hydrolyze the chitin of pathogens. The high activity of this enzyme has been used as a secondary biomarker of response to treatment in patients with Gaucher disease (OMIM 230800). Within the world's population, approximately 6% is homozygous and 35% is heterozygous for the most common polymorphism in the CHIT1 gene, a 24-bp duplication (dup-24 bp), with homozygosity of this duplication causing inactivation of the enzyme but without major consequences for health. To determine the frequency of the dup-24 bp CHIT1 gene in indigenous populations from Mexico, 692 samples were analyzed: Purepecha (49), Tarahumara (97), Huichol (97), Mayan (139), Tenek (97), and Nahua (213). We found that the groups were in Hardy-Weinberg equilibrium. The dup-24 bp allele frequency was found to be (in order of highest to lowest) 37% (Mayan), 34% (Huichol and Nahua), 33% (Purepecha), 31% (Tenek), and 29% (Tarahumara).

  19. Simple sequence repeat-based consensus linkage map of Bombyx mori.

    PubMed

    Miao, Xue-Xia; Xub, Shi-Jie; Li, Ming-Hui; Li, Mu-Wang; Huang, Jian-Hua; Dai, Fang-Yin; Marino, Susan W; Mills, David R; Zeng, Peiyu; Mita, Kazuei; Jia, Shi-Hai; Zhang, Yong; Liu, Wen-Bin; Xiang, Hui; Guo, Qiu-Hong; Xu, An-Ying; Kong, Xiang-Yin; Lin, Hong-Xuan; Shi, Yao-Zhou; Lu, Gang; Zhang, Xianglin; Huang, Wei; Yasukochi, Yuji; Sugasaki, Toshiyuki; Shimada, Toru; Nagaraju, Javaregowda; Xiang, Zhong-Huai; Wang, Sheng-Yue; Goldsmith, Marian R; Lu, Cheng; Zhao, Guo-Ping; Huang, Yong-Ping

    2005-11-08

    We established a genetic linkage map employing 518 simple sequence repeat (SSR, or microsatellite) markers for Bombyx mori (silkworm), the economically and culturally important lepidopteran insect, as part of an international genomics program. A survey of six representative silkworm strains using 2,500 (CA)n- and (CT)n-based SSR markers revealed 17-24% polymorphism, indicating a high degree of homozygosity resulting from a long history of inbreeding. Twenty-nine SSR linkage groups were established in well characterized Dazao and C108 strains based on genotyping of 189 backcross progeny derived from an F(1) male mated with a C108 female. The clustering was further focused to 28 groups by genotyping 22 backcross progeny derived from an F(1) female mated with a C108 male. This set of SSR linkage groups was further assigned to the 28 chromosomes (established linkage groups) of silkworm aided by visible mutations and cleaved amplified polymorphic sequence markers developed from previously mapped genes, cDNA sequences, and cloned random amplified polymorphic DNAs. By integrating a visible mutation p (plain, larval marking) and 29 well conserved genes of insects onto this SSR-based linkage map, a second generation consensus silkworm genetic map with a range of 7-40 markers per linkage group and a total map length of approximately 3431.9 cM was constructed and its high efficiency for genotyping and potential application for synteny studies of Lepidoptera and other insects was demonstrated.

  20. Splicing signals in Drosophila: intron size, information content, and consensus sequences.

    PubMed Central

    Mount, S M; Burks, C; Hertz, G; Stormo, G D; White, O; Fields, C

    1992-01-01

    A database of 209 Drosophila introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59-67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate introns. However, larger introns have greater pyrimidine-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice sites and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich. PMID:1508718

  1. Enterobacterial Repetitive Intergenic Consensus Sequence Repeats in Yersiniae: Genomic Organization and Functional Properties

    PubMed Central

    De Gregorio, Eliana; Silvestro, Giustina; Petrillo, Mauro; Carlomagno, Maria Stella; Di Nocera, Pier Paolo

    2005-01-01

    Genome-wide analyses carried out in silico revealed that the DNA repeats called enterobacterial repetitive intergenic consensus sequences (ERICs), which are present in several Enterobacteriaceae, are overrepresented in yersiniae. From the alignment of DNA regions from the wholly sequenced Yersinia enterocolitica 8081 and Yersinia pestis CO92 strains, we could establish that ERICs are miniature mobile elements whose insertion leads to duplication of the dinucleotide TA. ERICs feature long terminal inverted repeats (TIRs) and can fold as RNA into hairpin structures. The proximity to coding regions suggests that most Y. enterocolitica ERICs are cotranscribed with flanking genes. Elements which either overlap or are located next to stop codons are preferentially inserted in the same (or B) orientation. In contrast, ERICs located far apart from open reading frames are inserted in the opposite (or A) orientation. The expression of genes cotranscribed with A- and B-oriented ERICs has been monitored in vivo. In mRNAs spanning B-oriented ERICs, upstream gene transcripts accumulated at lower levels than downstream gene transcripts. This difference was abolished by treating cells with chloramphenicol. We hypothesize that folding of B-oriented elements is impeded by translating ribosomes. Consequently, upstream RNA degradation is triggered by the unmasking of a site for the RNase E located in the right-hand TIR of ERIC. A-oriented ERICs may act in contrast as upstream RNA stabilizers or may have other functions. The hypothesis that ERICs act as regulatory RNA elements is supported by analyses carried out in Yersinia strains which either lack ERIC sequences or carry alternatively oriented ERICs at specific loci. PMID:16291667

  2. Weak Palindromic Consensus Sequences Are a Common Feature Found at the Integration Target Sites of Many Retroviruses

    PubMed Central

    Wu, Xiaolin; Li, Yuan; Crise, Bruce; Burgess, Shawn M.; Munroe, David J.

    2005-01-01

    Integration into the host genome is one of the hallmarks of the retroviral life cycle and is catalyzed by virus-encoded integrases. While integrase has strict sequence requirements for the viral DNA ends, target site sequences have been shown to be very diverse. We carefully examined a large number of integration target site sequences from several retroviruses, including human immunodeficiency virus type 1, simian immunodeficiency virus, murine leukemia virus, and avian sarcoma-leukosis virus, and found that a statistical palindromic consensus, centered on the virus-specific duplicated target site sequence, was a common feature at integration target sites for these retroviruses. PMID:15795304

  3. Generation and Characterization of HIV-1 Transmitted and Founder Virus Consensus Sequence from Intravenous Drug Users in Xinjiang, China.

    PubMed

    Li, Fan; Ma, Liying; Feng, Yi; Hu, Jing; Ni, Na; Ruan, Yuhua; Shao, Yiming

    2017-03-02

    HIV-1 transmission in intravenous drug users (IDUs) has been characterized by high genetic multiplicity and suggests a greater challenge for HIV-1 infection blocking. We investigated a total of 749 sequences of full-length gp160 gene obtained by single genome sequencing (SGS) from 22 HIV-1 early infected IDUs in Xinjiang province, northwest China, and generated a transmitted and founder virus (T/F virus) consensus sequence (IDU.CON). The T/F virus was classified as subtype CRF07_BC and predicted to be CCR5-tropic virus. The variable region (V1, V2, and V4 loop) of IDU.CON showed length variation compared with the heterosexual T/F virus consensus sequence (HSX.CON) and homosexual T/F virus consensus sequence (MSM.CON). A total of 26 N-linked glycosylation sites were discovered in the IDU.CON sequence, which is less than that of MSM.CON and HSX.CON. Characterization of T/F virus from IDUs highlights the genetic make-up and complexity of virus near the moment of transmission or in early infection preceding systemic dissemination and is important toward the development of an effective HIV-1 preventive methods, including vaccines.

  4. Mutations in the mariner transposase: The D,D(35)E consensus sequence is nonfunctional

    PubMed Central

    Lohe, Allan R.; De Aguiar, Daniel; Hartl, Daniel L.

    1997-01-01

    Genetic analysis of eukaryote transposases and comparison with their prokaryote counterparts have been greatly hindered by difficulty in isolating mutations. We describe a simple eye-color screen that facilitates isolation and analysis of mutations in the mariner transposase in Drosophila melanogaster. Use of ethyl methanesulfonate and site-directed mutagenesis has identified 18 residues that are critical for in vivo excision of a target mariner element. When the mutations were examined in heterozygous mutant/nonmutant genotypes, more than half of the mutant transposase proteins were found to reduce the activity of the wild-type transposase, as assayed by the frequency of germline excision of a target element. Remarkably, transposase function is obliterated when the D,D(34)D acidic, ion-binding domain is replaced with the consensus sequence D,D(34)E found in the nematode Tc1 transposase and in many other transposases in the superfamily. A number of mutations strongly complement wild-type transposase in a dominant-negative manner, suggestive of subunit interactions in the excision reaction; these mutations are located in a small region that includes part of the D,D(34)D motif. Transposase function also is eliminated by a mutation in the inferred initiation codon and by a mutation in a putative nuclear localization signal. PMID:9037046

  5. 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

  6. 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

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

    PubMed

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

    2003-11-01

    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.

  8. Does 24bp Duplication of Human CHIT1 Gene (Chitotriosidase1) Predispose to Filarial Chyluria? A Case-Control Study

    PubMed Central

    Pant, Shriya; Agarwal, Jyotsna; Gangwar, Pravin K; Waseem, Mohammad; Gupta, Prashant; Sankhwar, Satya N; Purkait, Bimalesh

    2016-01-01

    Introduction Chyluria which is endemic in many parts of the world is mainly caused by Wuchereria bancrofti. CHIT1 (chitotriosidase) is produced by macrophages and plays an important role in the defense against chitin containing pathogen such as filarial parasite. Variation in the coding region with 24 bp duplication allele results in reduced CHIT1 activity that enhance the survival of parasite which may play a role in the occurrence of disease. Aim To examine the role of 24bp duplication of CHIT1 gene in patients of filarial chyluria (FC). Materials and Methods A case-control study was carried out where 155 confirmed FC patients and equal number of age-, sex- and residence-matched controls without any symptoms or signs of lymphatic filariasis, confirmed by negative immunochromatographic card test (ICT) and IgG/IgM combo rapid antibody test, from a hospital-based population were enrolled. Filarial aetiology was confirmed on the basis of DEC-provocative test (Giemsa staining), ICT and IgG/IgM- antifiarial antibody test. The patients positive by either of these tests were enrolled as FC cases. 24bp duplication in CHIT1 gene in FC was detected by the product size 99bp of amplified gene using polymerase chain reaction. Results The mean ages of patients and controls were 38.25±12.09 and 35.45±12.53 years, respectively while male: female ratio was 2.4:1. The mean duration of illness in chyluria patients was 62.81±60.83 months and mean number of episodes was 2.54±1.11. Homozygous wild type, heterozygous and homozygous mutant frequencies were 10.3%, 81.3% and 8.4% in FC patients and 18.7%, 75.5%, and 5.8% in controls, respectively. The 24bp duplication in CHIT1 gene showed a significant association in Heterozygous (HT) genotype with Odd Ratio (OR) of 1.95, 95% Confidence Interval (CI) (1.01-3.77); p=0.04. However, the homozygous mutant genotype (TT) was found to be non-significant with OR of 2.61, 95% CI (0.91-7.45); p=0.07. The combination of both HT+TT was also found

  9. Characterization of N-glycosylation consensus sequences in the Kv3.1 channel.

    PubMed

    Brooks, Natasha L; Corey, Melissa J; Schwalbe, Ruth A

    2006-07-01

    N-Glycosylation is a cotranslational and post-translational process of proteins that may influence protein folding, maturation, stability, trafficking, and consequently cell surface expression of functional channels. Here we have characterized two consensus N-glycosylation sequences of a voltage-gated K+ channel (Kv3.1). Glycosylation of Kv3.1 protein from rat brain and infected Sf9 cells was demonstrated by an electrophoretic mobility shift assay. Digestion of total brain membranes with peptide N glycosidase F (PNGase F) produced a much faster-migrating Kv3.1 immunoband than that of undigested brain membranes. To demonstrate N-glycosylation of wild-type Kv3.1 in Sf9 cells, cells were treated with tunicamycin. Also, partially purified proteins were digested with either PNGase F or endoglycosidase H. Attachment of simple-type oligosaccharides at positions 220 and 229 was directly shown by single (N229Q and N220Q) and double (N220Q/N229Q) Kv3.1 mutants. Functional measurements and membrane fractionation of infected Sf9 cells showed that unglycosylated Kv3.1s were transported to the plasma membrane. Unitary conductance of N220Q/N229Q was similar to that of the wild-type Kv3.1. However, whole cell currents of N220Q/N229Q channels had slower activation rates, and a slight positive shift in voltage dependence compared to wild-type Kv3.1. The voltage dependence of channel activation for N229Q and N220Q was much like that for N220Q/N229Q. These results demonstrate that the S1-S2 linker is topologically extracellular, and that N-glycosylation influences the opening of the voltage-dependent gate of Kv3.1. We suggest that occupancy of the sites is critical for folding and maturation of the functional Kv3.1 at the cell surface.

  10. Molecular characterization of high plant species using PCR with primers designed from consensus branch point signal sequences.

    PubMed

    Xiong, Faqian; Jiang, Jing; Han, Zhuqiang; Zhong, Ruichun; He, Liangqiong; Zhuang, Weijian; Tang, Ronghua

    2011-06-01

    A novel method is introduced for producing molecular markers in plants using single 15- to 18-mer PCR primers designed from the short conserved consensus branch point signal sequences and standard agarose gel electrophoresis. This method was tested on cultivated peanut and verified to give good fingerprinting results in other plant species (mango, banana, and longan). These single primers, designed from relatively conserved branch point signal sequences within gene introns, should be universal across other plant species. The method is rapid, simple, and efficient, and it requires no sequence information of the plant genome of interest. It could be used in conjunction with, or as a substitute for, conventional RAPD or ISSR techniques for applications including genetic diversity analysis, phylogenetic tree construction, and quantitative trait locus mapping. This technique provides a new way to develop molecular markers for assessing genetic diversity of germplasm in diverse species based on conserved branch point signal sequences.

  11. iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences

    PubMed Central

    Boyce, Richard; Chilana, Parmit; Rose, Timothy M.

    2009-01-01

    PCR amplification using COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) has proven to be highly effective for identifying unknown pathogens and characterizing novel genes. We describe iCODEHOP; a new interactive web application that simplifies the process of designing and selecting CODEHOPs from multiply-aligned protein sequences. iCODEHOP intelligently guides the user through the degenerate primer design process including uploading sequences, creating a multiple alignment, deriving CODEHOPs and calculating their annealing temperatures. The user can quickly scan over an entire set of degenerate primers designed by the program to assess their relative quality and select individual primers for further analysis. The program displays phylogenetic information for input sequences and allows the user to easily design new primers from selected sequence sub-clades. It also allows the user to bias primer design to favor specific clades or sequences using sequence weights. iCODEHOP is freely available to all interested researchers at https://icodehop.cphi.washington.edu/i-codehop-context/Welcome. PMID:19443442

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

    PubMed Central

    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.

    2015-01-01

    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

  13. DNA consensus sequence motif for binding response regulator PhoP, a virulence regulator of Mycobacterium tuberculosis.

    PubMed

    He, Xiaoyuan; Wang, Shuishu

    2014-12-30

    Tuberculosis has reemerged as a serious threat to human health because of the increasing prevalence of drug-resistant strains and synergetic infection with HIV, prompting an urgent need for new and more efficient treatments. The PhoP-PhoR two-component system of Mycobacterium tuberculosis plays an important role in the virulence of the pathogen and thus represents a potential drug target. To study the mechanism of gene transcription regulation by response regulator PhoP, we identified a high-affinity DNA sequence for PhoP binding using systematic evolution of ligands by exponential enrichment. The sequence contains a direct repeat of two 7 bp motifs separated by a 4 bp spacer, TCACAGC(N4)TCACAGC. The specificity of the direct-repeat sequence for PhoP binding was confirmed by isothermal titration calorimetry and electrophoretic mobility shift assays. PhoP binds to the direct repeat as a dimer in a highly cooperative manner. We found many genes previously identified to be regulated by PhoP that contain the direct-repeat motif in their promoter sequences. Synthetic DNA fragments at the putative promoter-binding sites bind PhoP with variable affinity, which is related to the number of mismatches in the 7 bp motifs, the positions of the mismatches, and the spacer and flanking sequences. Phosphorylation of PhoP increases the affinity but does not change the specificity of DNA binding. Overall, our results confirm the direct-repeat sequence as the consensus motif for PhoP binding and thus pave the way for identification of PhoP directly regulated genes in different mycobacterial genomes.

  14. Immunogenic Consensus Sequence T helper Epitopes for a Pan-Burkholderia Biodefense Vaccine

    PubMed Central

    De Groot, Anne S.; Ardito, Matthew; Moise, Leonard; Gustafson, Eric A.; Spero, Denice; Tejada, Gloria; Martin, William

    2014-01-01

    Background Biodefense vaccines against Category B bioterror agents Burkholderia pseudomallei (BPM) and Burkholderia mallei (BM) are needed, as they are both easily accessible to terrorists and have strong weaponization potential. Burkholderia cepaciae (BC), a related pathogen, causes chronic lung infections in cystic fibrosis patients. Since BPM, BM and BC are all intracellular bacteria, they are excellent targets for T cell-based vaccines. However, the sheer volume of available genomic data requires the aid of immunoinformatics for vaccine design. Using EpiMatrix, ClustiMer and EpiAssembler, a set of immunoinformatic vaccine design tools, we screened the 31 available Burkholderia genomes and performed initial tests of our selections that are candidates for an epitope-based multi-pathogen vaccine against Burkholderia species. Results Immunoinformatics analysis of 31 Burkholderia genomes yielded 350,004 9-mer candidate vaccine peptides of which 133,469 had perfect conservation across the 10 BM genomes, 175,722 had perfect conservation across the 11 BPM genomes and 40,813 had perfect conservation across the 10 BC genomes. Further screening with EpiMatrix yielded 54,010 high-scoring Class II epitopes; these were assembled into 2,880 longer highly conserved ‘immunogenic consensus sequence’ T helper epitopes. 100% of the peptides bound to at least one HLA class II allele in vitro, 92.7% bound to at least two alleles, 82.9% to three, and 75.6% of the binding results were consistent with the immunoinformatics analysis. Conclusions Our results show it is possible to rapidly identify promiscuous T helper epitopes conserved across multiple Burkholderia species and test their binding to HLA ligands in vitro. The next step in our process will be to test the epitopes ex vivo using peripheral leukocytes from BC, BPM infected humans and for immunogenicity in human HLA transgenic mice. We expect that this approach will lead to development of a licensable, pan

  15. Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences.

    PubMed

    Karouzou, Maria V; Spyropoulos, Yannis; Iconomidou, Vassiliki A; Cornman, R S; Hamodrakas, Stavros J; Willis, Judith H

    2007-08-01

    The majority of cuticular protein sequences identified to date from a diversity of arthropods have a conserved region known as the Rebers and Riddiford Consensus (R&R Consensus). This consensus region has been used to query the whole genome sequence of Drosophila melanogaster. One hundred one putative cuticular proteins have been annotated. Of these, 29 had been annotated previously, and for several their authenticity as cuticular proteins had been verified by protein sequence data from isolated cuticles or by localization of their transcripts in epidermis when cuticle synthesis was occurring. The original names have been retained, and the 72 newly annotated proteins have been given names beginning with Cpr followed by the chromosomal band in which the gene is located. Proteins with the R&R Consensus can be split into three groups RR-1, RR-2 and RR-3, with some correlation to the type or region of the cuticle in which they occur. Previous classification was manual and subjective. We now have developed a tool using profile hidden Markov models that allows more objective classification. We describe the development and verification of the validity of this tool that is available at the cuticleDB website http://bioinformatics2.biol.uoa.gr/cuticleDB/index.jsp.

  16. Performing Accurate Rigid Kinematics Measurements from 3D in vivo Image Sequences through Median Consensus Simultaneous Registration.

    PubMed

    Cresson, T; Jacq, J; Burdin, V; Roux, Ch

    2005-01-01

    While focusing at accurate 3D joint kinematics, this paper explores the problem of how to perform a robust rigid registration for a sequence of object surfaces observed using standard 3D medical imaging techniques. Each object instance is assumed to give access to a polyhedral encoding of its boundary. We consider the case where object instances are noised with significant truncations and segmentation errors. The proposed method aims to tackle this problem in a global way, fully exploiting the duality between redundancy and complementarity of the available instances set. The algorithm operates through robust and simultaneous registration of all geometrical instances on a virtual instance accounting for their median consensus. When compared with standard robust techniques, trials reveal significant gains, as much in robustness as in accuracy. The considered applications are mainly focused on generating highly accurate kinematics in relation to the bone structures of the most complex joints - the tarsus and the carpus - for which no alternative examination techniques exist, enabling fine morphological analysis as well as access to internal joint motions.

  17. Performing accurate joint kinematics from 3-D in vivo image sequences through consensus-driven simultaneous registration.

    PubMed

    Jacq, Jean-José; Cresson, Thierry; Burdin, Valérie; Roux, Christian

    2008-05-01

    This paper addresses the problem of the robust registration of multiple observations of the same object. Such a problem typically arises whenever it becomes necessary to recover the trajectory of an evolving object observed through standard 3-D medical imaging techniques. The instances of the tracked object are assumed to be variously truncated, locally subject to morphological evolutions throughout the sequence, and imprinted with significant segmentation errors as well as significant noise perturbations. The algorithm operates through the robust and simultaneous registration of all surface instances of a given object through median consensus. This operation consists of two interwoven processes set up to work in close collaboration. The first one progressively generates a median and implicit shape computed with respect to current estimations of the registration transformations, while the other refines these transformations with respect to the current estimation of their median shape. When compared with standard robust techniques, tests reveal significant improvements, both in robustness and precision. The algorithm is based on widely-used techniques, and proves highly effective while offering great flexibility of utilization.

  18. 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.

  19. The consensus sequence YGTGTTYY located downstream from the AATAAA signal is required for efficient formation of mRNA 3' termini.

    PubMed Central

    McLauchlan, J; Gaffney, D; Whitton, J L; Clements, J B

    1985-01-01

    Our previous DNA sequence comparisons of 3' terminal portions from equivalent herpes simplex virus type 1 (HSV-1) and HSV-2 genes identified a conserved sequence (consensus YGTGTTYY; Y = pyrimidine) located approximately 30bp downstream from the AATAAA signal. We report here that this signal is located downstream from 67% of the mammalian mRNA 3' termini examined. Using constructions with the bacterial chloramphenicol acetyl transferase (CAT) gene linked to an HSV 'terminator' fragment, we show that deletions in the 'terminator' reduce CAT activities and the levels of CAT mRNA 3' termini. Specifically: (1) deletions of downstream sequences which extend up to the consensus YGTGTTYY signal reduce CAT levels to values 35% of those obtained with undeleted plasmids, (2) a deletion of a further 14bp, which removes the YGTGTTYY consensus but not the poly A site, reduces CAT activities to 1%-4%. The levels of CAT mRNA 3' termini reflect the reductions in CAT activities however, levels of mRNA 5' termini are unaffected by these deletions. The RNA produced in the absence of the YGTGTTYY signal is present in the cytoplasm although no CAT activity is detectable. Images PMID:2987822

  20. 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

  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. 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

  3. 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.

  4. Genetic interactions between the 5' and 3' splice site consensus sequences and U6 snRNA during the second catalytic step of pre-mRNA splicing.

    PubMed Central

    Collins, C A; Guthrie, C

    2001-01-01

    The YAG/ consensus sequence at the 3' end of introns (the slash indicates the location of the 3' splice site) is essential for catalysis of the second step of pre-mRNA splicing. Little is known about the interactions formed by these three nucleotides in the spliceosome. Although previous observations have suggested that the G of the YAG/ interacts with the first nucleotide of the /GUA consensus sequence at the 5' end of the intron, additional interactions have not been identified. Here we report several striking genetic interactions between A+3 of the 5' /GUA with Y-3 of the 3' YAG/ and G50 of the highly conserved ACAGAG motif in U6 snRNA. Two mutations in U6 G50 of the ACAGAG can weakly suppress two mutations in A+3 of the 5' /GUA. This suppression is significantly enhanced upon the inclusion of a specific mutation Y-3 in the 3' YAG/. RNA analysis confirmed that the severe splicing defect observed in A+3 and Y-3 double mutants can be rescued to near wild-type levels by the mutations in U6 G50. The contributions of each mutation to the genetic interaction and the strong position specificity of suppression, combined with previous findings, support a model in which the 5' /GUA and the GAG of U6 function in binding the 3' YAG/ during the second catalytic step. PMID:11780639

  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.

  6. Full trans-activation mediated by the immediate-early protein of equine herpesvirus 1 requires a consensus TATA box, but not its cognate binding sequence.

    PubMed

    Kim, Seong K; Shakya, Akhalesh K; O'Callaghan, Dennis J

    2016-01-04

    The immediate-early protein (IEP) of equine herpesvirus 1 (EHV-1) has extensive homology to the IEP of alphaherpesviruses and possesses domains essential for trans-activation, including an acidic trans-activation domain (TAD) and binding domains for DNA, TFIIB, and TBP. Our data showed that the IEP directly interacted with transcription factor TFIIA, which is known to stabilize the binding of TBP and TFIID to the TATA box of core promoters. When the TATA box of the EICP0 promoter was mutated to a nonfunctional TATA box, IEP-mediated trans-activation was reduced from 22-fold to 7-fold. The IEP trans-activated the viral promoters in a TATA motif-dependent manner. Our previous data showed that the IEP is able to repress its own promoter when the IEP-binding sequence (IEBS) is located within 26-bp from the TATA box. When the IEBS was located at 100 bp upstream of the TATA box, IEP-mediated trans-activation was very similar to that of the minimal IE(nt -89 to +73) promoter lacking the IEBS. As the distance from the IEBS to the TATA box decreased, IEP-mediated trans-activation progressively decreased, indicating that the IEBS located within 100 bp from the TATA box sequence functions as a distance-dependent repressive element. These results indicated that IEP-mediated full trans-activation requires a consensus TATA box of core promoters, but not its binding to the cognate sequence (IEBS).

  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.

  8. Model peptide studies of sequence regions in the elastomeric biomineralization protein, Lustrin A. I. The C-domain consensus-PG-, -NVNCT-motif.

    PubMed

    Zhang, Bo; Wustman, Brandon A; Morse, Daniel; Evans, John Spencer

    2002-05-01

    The lustrin superfamily represents a unique group of biomineralization proteins localized between layered aragonite mineral plates (i.e., nacre layer) in mollusk shell. Recent atomic force microscopy (AFM) pulling studies have demonstrated that the lustrin-containing organic nacre layer in the abalone, Haliotis rufescens, exhibits a typical sawtooth force-extension curve with hysteretic recovery. This force extension behavior is reminiscent of reversible unfolding and refolding in elastomeric proteins such as titin and tenascin. Since secondary structure plays an important role in force-induced protein unfolding and refolding, the question is, What secondary structure(s) exist within the major domains of Lustrin A? Using a model peptide (FPGKNVNCTSGE) representing the 12-residue consensus sequence found near the N-termini of the first eight cysteine-rich domains (C-domains) within the Lustrin A protein, we employed CD, NMR spectroscopy, and simulated annealing/minimization to determine the secondary structure preferences for this sequence. At pH 7.4, we find that the 12-mer sequence adopts a loop conformation, consisting of a "bend" or "turn" involving residues G3-K4 and N7-C8-T9, with extended conformations arising at F1-G3; K4-V6; T9-S10-G11 in the sequence. Minor pH-dependent conformational effects were noted for this peptide; however, there is no evidence for a salt-bridge interaction between the K4 and E12 side chains. The presence of a loop conformation within the highly conserved -PG-, -NVNCT- sequence of C1-C8 domains may have important structural and mechanistic implications for the Lustrin A protein with regard to elastic behavior.

  9. A four-nucleotide translation enhancer in the 3'-terminal consensus sequence of the nonpolyadenylated mRNAs of rotavirus.

    PubMed Central

    Chizhikov, V; Patton, J T

    2000-01-01

    The 5' cap and poly(A) tail of eukaryotic mRNAs work synergistically to enhance translation through a process that requires interaction of the cap-associated eukaryotic initiation factor, eIF-4G, and the poly(A)-binding protein, PABP. Because the mRNAs of rotavirus, and other members of the Reoviridae, contain caps but lack poly(A) tails, their translation may be enhanced through a unique mechanism. To identify translation-enhancement elements in the viral mRNAs that stimulate translation in vivo, chimeric RNAs were prepared that contained an open reading frame for luciferase and the 5' and 3' untranslated regions (UTRs) of a rotavirus mRNA or of a nonviral mRNA. Transfection of the chimeric RNAs into rotavirus-infected cells showed that the viral 3' UTR contained a translation-enhancement element that promoted gene expression. The element did not enhance gene expression in uninfected cells and did not affect the stability of the RNAs. Mutagenesis showed that the conserved sequence GACC located at the 3' end of rotavirus mRNAs operated as an enhancement element. The 3'-GACC element stimulated protein expression independently of the sequence of the 5' UTR, although efficient expression required the RNA to contain a cap. The results indicate that the expression of viral proteins in rotavirus-infected cells is specifically up-regulated by the activity of a novel 4-nt 3' translation enhancer (TE) common to the 11 nonpolyadenylated mRNAs of the virus. The 4-nt sequence of the rotavirus 3' TE represents by far the shortest of any of the sequence enhancers known to stimulate translation. PMID:10864041

  10. The Complete Mitochondrial DNA Sequence of the Bichir (Polypterus Ornatipinnis), a Basal Ray-Finned Fish: Ancient Establishment of the Consensus Vertebrate Gene Order

    PubMed Central

    Noack, K.; Zardoya, R.; Meyer, A.

    1996-01-01

    The evolutionary position of bichirs is disputed, and they have been variously aligned with ray-finned fish (Actinopterygii) or lobe-finned fish (Sarcopterygii), which also include tetrapods. Alternatively, they have been placed into their own group, the Brachiopterygii. The phylogenetic position of bichirs as possibly the most primitive living bony fish (Osteichthyes) made knowledge about their mitochondrial genome of considerable evolutionary interest. We determined the complete nucleotide sequence (16,624 bp) of the mitochondrial genome of a bichir, Polypterus ornatipinnis. Its genome contains 13 protein-coding genes, 22 tRNAs, two rRNAs and one major noncoding region. The genome's structure and organization show that this is the most basal vertebrate that conforms to the consensus vertebrate mtDNA gene order. Bichir mitochondrial protein-coding and ribosomal RNA genes have greater sequence similarity to ray-finned fish than to either lamprey or lungfish. Phylogenetic analyses suggest the bichir's placement as the most basal living member of the ray-finned fish and rule out its classification as a lobe-finned fish. Hence, its lobe-fins are probably not a shared-derived trait with those of lobe-finned fish (Sarcopterygii). PMID:8913758

  11. Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method.

    PubMed

    Debourgogne, Anne; Gueidan, Cécile; de Hoog, Sybren; Lozniewski, Alain; Machouart, Marie

    2012-10-01

    Multilocus sequence typing (MLST) is a widely used approach for differentiating microbial isolates presenting many advantages such as easy access through online databases and straightforward interpretation. For the Fusarium solani species complex (FSSC), three gene regions have been widely used to investigate phylogenetic relationships at the interspecific level (ITS-nuLSU, EF1a, RPB2) and a nomenclature system has been proposed for the different known haplotypes. More recently, a MLST scheme was proposed for this species complex based on the polymorphisms of five housekeeping genes (ACC, ICL, GDP, MDP, SOD). Here, we compare the phylogenetic resolution and sequence discriminatory powers of these two sets of loci on 50 epidemiologically unrelated FSSC strains. Although the widely used gene set offers better phylogenetic resolution, the newly developed gene set is slightly better at discriminating isolates using a MLST method. A consensus scheme of eight loci is proposed for typing FSSC strains combining the advantages of the two previous gene sets and offering the best typing efficiency.

  12. The 3'-terminal consensus sequence of rotavirus mRNA is the minimal promoter of negative-strand RNA synthesis.

    PubMed Central

    Wentz, M J; Patton, J T; Ramig, R F

    1996-01-01

    We used an in vitro template-dependent replicase assay (D. Chen, C. Zeng, M. Wentz, M. Gorziglia, M. Estes, and R. Ramig. J. Virol. 68:7030-7039, 1994) to identify the cis-acting signals required for replication of a genome segment 9 template from the group A rotavirus strain OSU. The replicase phenotypes for a panel of templates with internal deletions or 3'-terminal truncations indicated that no essential replication signals were present within the open reading frame and that key elements were present in the 5' and 3' noncoding regions. Chimeric constructs containing portions of viral sequence ligated to a nonviral backbone were generated to further map the regions required for in vitro replication of segment 9. The data from these constructs showed that the 3'-terminal seven nucleotides of the segment 9 mRNA provided the minimum requirement for replication (minimal promoter). Analysis of additional chimeric templates demonstrated that sequences capable of enhancing replication from the minimal promoter were located immediately upstream of the minimal promoter and at the extreme 5' terminus of the template. Mutational analysis of the minimal promoter revealed that the 3'-terminal -CC residues are required for efficient replication. Comparison of the replication levels for templates with guanosines and uridines at nucleotides -4 to -6 from the 3' terminus compared with levels for templates containing neither of these residues at these positions indicated that either or both residues must be present in this region for efficient replication in vitro. PMID:8892905

  13. The tumor suppressor gene HIC1 (hypermethylated in cancer 1) is a sequence-specific transcriptional repressor: definition of its consensus binding sequence and analysis of its DNA binding and repressive properties.

    PubMed

    Pinte, Sébastien; Stankovic-Valentin, Nicolas; Deltour, Sophie; Rood, Brian R; Guérardel, Cateline; Leprince, Dominique

    2004-09-10

    HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene located at chromosome 17p13.3, a region frequently hypermethylated or deleted in human tumors and in a contiguous-gene syndrome, the Miller-Dieker syndrome. HIC1 is a transcriptional repressor containing five Krüppel-like C(2)H(2) zinc fingers and an N-terminal dimerization and autonomous repression domain called BTB/POZ. Although some of the HIC1 transcriptional repression mechanisms have been recently deciphered, target genes are still to be discovered. In this study, we determined the consensus binding sequence for HIC1 and investigated its DNA binding properties. Using a selection and amplification of binding sites technique, we identified the sequence 5'-(C)/(G)NG(C)/(G)GGGCA(C)/(A) CC-3' as an optimal binding site. In silico and functional analyses fully validated this consensus and highlighted a GGCA core motif bound by zinc fingers 3 and 4. The BTB/POZ domain inhibits the binding of HIC1 to a single site but mediates cooperative binding to a probe containing five concatemerized binding sites, a property shared by other BTB/POZ proteins. Finally, full-length HIC1 proteins transiently expressed in RK13 cells and more importantly, endogenous HIC1 proteins from the DAOY medulloblastoma cell line, repress the transcription of a reporter gene through their direct binding to these sites, as confirmed by chromatin immunoprecipitation experiments. The definition of the HIC1-specific DNA binding sequence as well as the requirement for multiple sites for optimal binding of the full-length protein are mandatory prerequisites for the identification and analyses of bona fide HIC1 target genes.

  14. Interaction of heparin with internally quenched fluorogenic peptides derived from heparin-binding consensus sequences, kallistatin and anti-thrombin III.

    PubMed

    Pimenta, Daniel C; Nantes, Iseli L; de Souza, Eduardo S; Le Bonniec, Bernard; Ito, Amando S; Tersariol, Ivarne L S; Oliveira, Vitor; Juliano, Maria A; Juliano, Luiz

    2002-09-01

    Internally quenched fluorogenic (IQF) peptides bearing the fluorescence donor/acceptor pair o-aminobenzoic acid (Abz)/N-(2,4-dinitrophenyl)ethylenediamine (EDDnp) at N- and C-terminal ends were synthesized containing heparin-binding sites from the human serpins kallistatin and antithrombin, as well as consensus heparin-binding sequences (Cardin clusters). The dissociation constant (K(d)), as well as the stoichiometry for the heparin-peptide complexes, was determined directly by measuring the decrease in fluorescence of the peptide solution. Experimental procedures were as sensitive as those used to follow the fluorescence change of tryptophan in heparin-binding proteins. The conformation of the peptides and the heparin-peptide complexes were obtained from measurements of time-resolved fluorescence decay and CD spectra. Kallistatin (Arg(300)-Pro(319))-derived peptide (HC2) and one derived from antithrombin III helix D [(AT3D), corresponding to Ser(112)-Lys(139)], which are the heparin-binding sites in these serpins, showed significant affinity for 4500 Da heparin, for which K(d) values were 17 nM and 100 nM respectively. The CD spectra of the heparin-HC2 peptide complex did not show any significant alpha-helix content, different from the situation with peptide AT3D, for which complex-formation with heparin resulted in 24% alpha-helix content. The end-to-end distance distribution and the time-resolved fluorescence-decay measurements agree with the CD spectra and K(d) values. The synthetic alpha-methyl glycoside pentasaccharide AGA*IA(M) (where A represents N,6-O-sulphated alpha-d-glucosamine; G, beta-d-glucuronic acid; A*, N,3,6-O-sulphated alpha-d-glucosamine; I, 2-O-sulphated alpha-l-iduronic acid; and A(M), alpha-methyl glycoside of A) also binds to AT3D and other consensus heparin-binding sequences, although with lower affinity. The interaction of IQF peptides with 4500 Da heparin was displaced by protamine. In conclusion, IQF peptides containing Abz/EDDnp as the

  15. Interaction of heparin with internally quenched fluorogenic peptides derived from heparin-binding consensus sequences, kallistatin and anti-thrombin III.

    PubMed Central

    Pimenta, Daniel C; Nantes, Iseli L; de Souza, Eduardo S; Le Bonniec, Bernard; Ito, Amando S; Tersariol, Ivarne L S; Oliveira, Vitor; Juliano, Maria A; Juliano, Luiz

    2002-01-01

    Internally quenched fluorogenic (IQF) peptides bearing the fluorescence donor/acceptor pair o-aminobenzoic acid (Abz)/N-(2,4-dinitrophenyl)ethylenediamine (EDDnp) at N- and C-terminal ends were synthesized containing heparin-binding sites from the human serpins kallistatin and antithrombin, as well as consensus heparin-binding sequences (Cardin clusters). The dissociation constant (K(d)), as well as the stoichiometry for the heparin-peptide complexes, was determined directly by measuring the decrease in fluorescence of the peptide solution. Experimental procedures were as sensitive as those used to follow the fluorescence change of tryptophan in heparin-binding proteins. The conformation of the peptides and the heparin-peptide complexes were obtained from measurements of time-resolved fluorescence decay and CD spectra. Kallistatin (Arg(300)-Pro(319))-derived peptide (HC2) and one derived from antithrombin III helix D [(AT3D), corresponding to Ser(112)-Lys(139)], which are the heparin-binding sites in these serpins, showed significant affinity for 4500 Da heparin, for which K(d) values were 17 nM and 100 nM respectively. The CD spectra of the heparin-HC2 peptide complex did not show any significant alpha-helix content, different from the situation with peptide AT3D, for which complex-formation with heparin resulted in 24% alpha-helix content. The end-to-end distance distribution and the time-resolved fluorescence-decay measurements agree with the CD spectra and K(d) values. The synthetic alpha-methyl glycoside pentasaccharide AGA*IA(M) (where A represents N,6-O-sulphated alpha-d-glucosamine; G, beta-d-glucuronic acid; A*, N,3,6-O-sulphated alpha-d-glucosamine; I, 2-O-sulphated alpha-l-iduronic acid; and A(M), alpha-methyl glycoside of A) also binds to AT3D and other consensus heparin-binding sequences, although with lower affinity. The interaction of IQF peptides with 4500 Da heparin was displaced by protamine. In conclusion, IQF peptides containing Abz/EDDnp as the

  16. 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.

  17. Comparative analysis of seven viral nuclear export signals (NESs) reveals the crucial role of nuclear export mediated by the third NES consensus sequence of nucleoprotein (NP) in influenza A virus replication.

    PubMed

    Chutiwitoonchai, Nopporn; Kakisaka, Michinori; Yamada, Kazunori; Aida, Yoko

    2014-01-01

    The assembly of influenza virus progeny virions requires machinery that exports viral genomic ribonucleoproteins from the cell nucleus. Currently, seven nuclear export signal (NES) consensus sequences have been identified in different viral proteins, including NS1, NS2, M1, and NP. The present study examined the roles of viral NES consensus sequences and their significance in terms of viral replication and nuclear export. Mutation of the NP-NES3 consensus sequence resulted in a failure to rescue viruses using a reverse genetics approach, whereas mutation of the NS2-NES1 and NS2-NES2 sequences led to a strong reduction in viral replication kinetics compared with the wild-type sequence. While the viral replication kinetics for other NES mutant viruses were also lower than those of the wild-type, the difference was not so marked. Immunofluorescence analysis after transient expression of NP-NES3, NS2-NES1, or NS2-NES2 proteins in host cells showed that they accumulated in the cell nucleus. These results suggest that the NP-NES3 consensus sequence is mostly required for viral replication. Therefore, each of the hydrophobic (Φ) residues within this NES consensus sequence (Φ1, Φ2, Φ3, or Φ4) was mutated, and its viral replication and nuclear export function were analyzed. No viruses harboring NP-NES3 Φ2 or Φ3 mutants could be rescued. Consistent with this, the NP-NES3 Φ2 and Φ3 mutants showed reduced binding affinity with CRM1 in a pull-down assay, and both accumulated in the cell nucleus. Indeed, a nuclear export assay revealed that these mutant proteins showed lower nuclear export activity than the wild-type protein. Moreover, the Φ2 and Φ3 residues (along with other Φ residues) within the NP-NES3 consensus were highly conserved among different influenza A viruses, including human, avian, and swine. Taken together, these results suggest that the Φ2 and Φ3 residues within the NP-NES3 protein are important for its nuclear export function during viral

  18. 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…

  19. The human clotting factor VIII cDNA contains an autonomously replicating sequence consensus- and matrix attachment region-like sequence that binds a nuclear factor, represses heterologous gene expression, and mediates the transcriptional effects of sodium butyrate.

    PubMed Central

    Fallaux, F J; Hoeben, R C; Cramer, S J; van den Wollenberg, D J; Briët, E; van Ormondt, H; van Der Eb, A J

    1996-01-01

    Expression of the human blood-clotting factor VIII (FVIII) cDNA is hampered by the presence of sequences located in the coding region that repress transcription. We have previously identified a 305-bp fragment within the FVIII cDNA that is involved in the repression (R.C. Hoeben, F.J. Fallaux, S.J. Cramer, D.J.M. van den Wollenberg, H. van Ormondt, E. Briet, and A.J. van der Eb, Blood 85:2447-2454, 1995). Here, we show that this 305-bp region of FVIII cDNA contains sequences that resemble the yeast (Saccharomyces cerevisiae) autonomously replicating sequence consensus. Two of these DNA elements coincide with AT-rich sequences that are often found in matrix attachment regions or scaffold-attached regions. One of these elements, consisting of nucleotides 1569 to 1600 of the FVIII cDNA (nucleotide numbering is according to the system of Wood et al. (W.I. Wood, D.J. Capon, C.C. Simonsen, D.L. Eaton, J. Gitschier, D. Keyt, P.H. Seeburg, D.H. Smith, P. Hollingshead, K.L. Wion, et al., Nature [London] 312:330-337,1984), binds a nuclear factor in vitro but loses this capacity after four of its base pairs have been changed. A synthetic heptamer of this segment can repress the expression of a chloramphenicol acetyltransferase (CAT) reporter gene and also loses this capacity upon mutation. Furthermore, we demonstrate that repression by FVIII sequences can be relieved by sodium butyrate. We demonstrate that the synthetic heptamer (FVIII nucleotides 1569 to 1600), when placed upstream of the Moloney murine leukemia virus long terminal repeat promoter that drives the CAT reporter, can render the CAT reporter inducible by butyrate. This effect was absent when the same element was mutated. The stimulatory effect of butyrate could not be attributed to butyrate-responsive elements in the studied long terminal repeat promoters. Our data provide a functional characterization of the sequences that repress expression of the FVIII cDNA. These data also suggest a link between

  20. Replacement of amino acid sequence features of a- and c-subunits of ATP synthases of Alkaliphilic Bacillus with the Bacillus consensus sequence results in defective oxidative phosphorylation and non-fermentative growth at pH 10.5.

    PubMed

    Wang, ZhenXiong; Hicks, David B; Guffanti, Arthur A; Baldwin, Katisha; Krulwich, Terry Ann

    2004-06-18

    Mitchell's (Mitchell, P. (1961) Nature 191, 144-148) chemiosmotic model of energy coupling posits a bulk electrochemical proton gradient (Deltap) as the sole driving force for proton-coupled ATP synthesis via oxidative phosphorylation (OXPHOS) and for other bioenergetic work. Two properties of proton-coupled OXPHOS by alkaliphilic Bacillus species pose a challenge to this tenet: robust ATP synthesis at pH 10.5 that does not correlate with the magnitude of the Deltap and the failure of artificially imposed potentials to substitute for respiration-generated potentials in energizing ATP synthesis at high pH (Krulwich, T. (1995) Mol. Microbiol. 15, 403-410). Here we show that these properties, in alkaliphilic Bacillus pseudofirmus OF4, depend upon alkaliphile-specific features in the proton pathway through the a- and c-subunits of ATP synthase. Site-directed changes were made in six such features to the corresponding sequence in Bacillus megaterium, which reflects the consensus sequence for non-alkaliphilic Bacillus. Five of the six single mutants assembled an active ATPase/ATP synthase, and four of these mutants exhibited a specific defect in non-fermentative growth at high pH. Most of these mutants lost the ability to generate the high phosphorylation potentials at low bulk Deltap that are characteristic of alkaliphiles. The aLys(180) and aGly(212) residues that are predicted to be in the proton uptake pathway of the a-subunit were specifically implicated in pH-dependent restriction of proton flux through the ATP synthase to and from the bulk phase. The evidence included greatly enhanced ATP synthesis in response to an artificially imposed potential at high pH. The findings demonstrate that the ATP synthase of extreme alkaliphiles has special features that are required for non-fermentative growth and OXPHOS at high pH.

  1. The 5'-terminal sequence of U1 RNA complementary to the consensus 5' splice site of hnRNA is single-stranded in intact U1 snRNP particles.

    PubMed Central

    Rinke, J; Appel, B; Blöcker, H; Frank, R; Lührmann, R

    1984-01-01

    The 5'-terminal region of U1 snRNA is highly complementary to the consensus exon-intron regions of hnRNA and it has been suggested that U1 snRNP might play a role in the splicing of the pre-mRNA by intermolecular base-pairing between these regions. Here the secondary structure of the 5' terminus of U1 RNA in the isolated native U1 snRNP particle has been investigated by site-directed enzymatic cleavage of the RNA. Individual oligodeoxynucleotides complementary to various sequences within the first 15 nucleotides of the 5' terminus of U1 RNA have been tested for their ability to form stable DNA X RNA hybrids, with subsequent cleavage of the U1 RNA by RNase H. Our results show unequivocally that the 9 nucleotides at the 5' terminus which are complementary to a consensus 5' splice site are indeed single-stranded in the intact U1 snRNP particle, and are not protected by snRNP proteins. However, they also indicate that the U1 sequence complementary to an intron's consensus 3' end is not readily available for intermolecular base-pairing, either in the intact U1 snRNP particle or in the deproteinized U1 RNA molecule. Therefore our data favour the possibility that U1 snRNP plays a role only in the recognition of a 5' splice site of hnRNA, rather than being involved in the alignment of both ends of an intron for splicing. Images PMID:6203096

  2. Arg-Pro-X-Ser/Thr is a Consensus Phosphoacceptor Sequence for the Meiosis-Specific Ime2 Protein Kinase in Saccharomyces cerevisiae†

    PubMed Central

    Moore, Michael; Shin, Marcus; Bruning, Adrian; Schindler, Karen; Vershon, Andrew; Winter, Edward

    2008-01-01

    Ime2 is a meiosis-specific protein kinase in Saccharomyces cerevisiae that is functionally related to cyclin-dependent kinase. Although Ime2 regulates multiple steps in meiosis, only a few of its substrates have been identified. Here we show that Ime2 phosphorylates Sum1, a repressor of meiotic gene transcription, on Thr-306. Ime2 protein kinase assays on Sum1 mutants and synthetic peptides define a consensus motif Arg-Pro-X-Ser/Thr that is required for efficient phosphorylation by Ime2. The carboxyl residue adjacent to the phosphoacceptor (+1 position) also influences the efficiency of Ime2 phosphorylation with alanine being a preferred residue. This information has predictive value in identifying new potential Ime2 targets as shown by the ability of Ime2 to phosphorylate Sgs1 and Gip1 in vitro, and could be important in differentiating mitotic and meiotic regulatory pathways. PMID:17198398

  3. Detection of HIV-1 Drug Resistance in Women Following Administration of a Single Dose of Nevirapine: Comparison of Plasma RNA to Cellular DNA by Consensus Sequencing and by Oligonucleotide Ligation Assay▿

    PubMed Central

    Wagner, Thor A.; Kress, Catherine M.; Beck, Ingrid; Techapornroong, Malee; Wittayapraparat, Pakorn; Tansuphasawasdikul, Somboon; Jourdain, Gonzague; Ngo-Giang-Huong, Nicole; Lallemant, Marc; Frenkel, Lisa M.

    2010-01-01

    A single dose of nevirapine (sdNVP) to prevent mother-to-child transmission of HIV-1 increases the risk of failure of subsequent NVP-containing antiretroviral therapy (ART), especially when initiated within 6 months of sdNVP administration, emphasizing the importance of understanding the decay of nevirapine-resistant mutants. Nevirapine-resistant HIV-1 genotypes (with the mutations K103N, Y181C, and/or G190A) from 21 women were evaluated 10 days and 6 weeks after sdNVP administration and at the initiation of ART. Resistance was assayed by consensus sequencing and by a more sensitive assay (oligonucleotide ligation assay [OLA]) using plasma-derived HIV-1 RNA and cell-associated HIV-1 DNA. OLA detected nevirapine resistance in more specimens than consensus sequencing did (63% versus 33%, P < 0.01). When resistance was detected only by OLA (n = 45), the median mutant concentration was 18%, compared to 61% when detected by both sequencing and OLA (n = 51) (P < 0.0001). The proportion of women whose nevirapine resistance was detected by OLA 10 days after sdNVP administration was higher when we tested their HIV-1 RNA (95%) than when we tested their HIV-1 DNA (88%), whereas at 6 weeks after sdNVP therapy, the proportion was greater with DNA (85%) than with RNA (67%) and remained higher with DNA (33%) than with RNA (11%) at the initiation of antiretroviral treatment (median, 45 weeks after sdNVP therapy). Fourteen women started NVP-ART more than 6 months after sdNVP therapy; resistance was detected by OLA in 14% of the women but only in their DNA. HIV-1 resistance to NVP following sdNVP therapy persists longer in cellular DNA than in plasma RNA, as determined by a sensitive assay using sufficient copies of virus, suggesting that DNA may be superior to RNA for detecting resistance at the initiation of ART. PMID:20181911

  4. 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 Central

    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.

    2015-01-01

    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 paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) 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 CAP 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 Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). 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 CLIA

  5. 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...

  6. 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

  7. WT1 exon deletion/insertion mutations in Wilms tumor patients associated with di- and trinucleotide repeats and deletion hotspot consensus sequences

    SciTech Connect

    Huff, V.; Saunders, G.F.; Strong, L.C.

    1994-09-01

    The genetic etiology of Wilms tumor (WT), a childhood kidney tumor, is known to be heterogeneous. One WT gene, WT1 located on chromosomal band 11p13, has been isolated, and mutations specific to the WT1 locus have been identified in some WT patients, demonstrating its importance in the etiology of at least some WT cases. Because of the patient populations selected for study and a focus on specific regions of the gene in identifying WT1 mutations, most mutations described to date are single base substitutions and have occurred in the 3{prime} portion of the gene in exons 7-10 which encode the zinc finger domains of the protein. DNA mutations at the WT1 locus have been reported to be infrequent in WT patients, implying that post-transcriptional modification of the WT1 gene product or alterations at other distinct loci perhaps more commonly play a role in tumorigenesis than do WT1 DNA mutations. We report here the occurrence in four WT patients of inactivating frameshift mutations, three somatic deletions and one germline insertion, in exon 1. This exon is GC-rich (>70%) and contains regions of both di- and trinucleotide direct repeats and ten copies of the sequence, CCTG (CAGG), which has been described as a deletion hotspot in mammalian DNA. The four WT1 exon 1 deletion/insertions range in size from four to 34 bases, are flanked by bi- and/or trinucleotide repeats, and occur in a general context of repetitive sequences. Furthermore, all breakpoints occur at or within five nucleotides of the tetranucleotide sequence, CCTG (CAGG). These data suggest that a mutational mechanism previously unrecognized in WT patients is operating in this repetitive portion of the WT1 gene. The frequency with which mutations of this type are observed in WT patients awaits the complete evaluation of a series of patients. Nevertheless these data indicate that WT1 mutations are more frequent in WT patients than previously thought.

  8. WT1 exon 1 deletion/insertion mutations in Wilms tumor patients, associated with di- and trinucleotide repeats and deletion hotspot consensus sequences.

    PubMed Central

    Huff, V; Jaffe, N; Saunders, G F; Strong, L C; Villalba, F; Ruteshouser, E C

    1995-01-01

    The WT1 gene is known to play a role in at least some cases of Wilms tumor (WT). The first exon of the gene is highly GC rich and contains many short tandem di- and trinucleotide repeats, interrupted direct repeats, and CCTG (CAGG) motifs that have been identified as hotspots for DNA deletions. We have analyzed 80 WT patient samples for mutations in the first exon of WT1, either by SSCP analysis of the first 131 bp of the coding portion of WT1 exon 1 or by size analysis of a PCR product encompassing the coding region of exon 1 in addition to flanking noncoding regions. We report here the occurrence of somatic and germ-line deletion and insertion mutations in this portion of the gene in four WT patients. The mutations are flanked by short direct repeats, and the breakpoints are within 5 nt of a CCTG (CAGG) sequence. These data suggest that a distinctive mutational mechanism, previously unrecognized for this gene, is important for the generation of DNA mutations at the WT1 locus. Images Figure 2 Figure 3 Figure 4 PMID:7825606

  9. Aljoya Consensus Statement

    EPA Pesticide Factsheets

    A consensus statement of 100 experts meeting at the Aljoya Conference Center in Seattle, Washington in July 2000 for the First International Conference on Trans-Pacific Transport of Atmospheric Contaminants.

  10. Transcriptional status of known and novel genes tagged with consensus of 33.15 repeat loci employing minisatellite-associated sequence amplification (MASA) and real-time PCR in water buffalo, Bubalus bubalis.

    PubMed

    Srivastava, Jyoti; Premi, Sanjay; Pathak, Deepali; Ahsan, Zaid; Tiwari, Madhulika; Garg, Lalit C; Ali, Sher

    2006-01-01

    We conducted minisatellite-associated sequence amplification (MASA) with an oligo (5' CACCTCTCCACCTGCC 3') based on consensus of 33.15 repeat loci using cDNA from the testis, ovary, spleen, kidney, heart, liver, and lung of water buffalo Bubalus bubalis and uncovered 25 amplicons of six different sizes (1,263, 846/847, 602, 576, 487, and 324 base pairs). These fragments, cloned and sequenced, were found to represent several functional, regulatory, and structural genes. Blast search of all the 25 amplicons showed homologies with 43 transcribing genes across the species. Of these, the 846/847-bp fragment, having homology with the adenylate kinase gene, showed nucleotide changes at six identical places in the ovary and testis. The 1,263; 324; and 487-bp fragments showed homology with the secreted modular calcium binding protein (SMOC-1), leucine-rich repeat neuronal 6A (LRRN6A) mRNA, and human TTTY5 mRNA, respectively. Real-time PCR showed maximum expression of AKL, LRRN6A, and T-cell receptor gamma (TCR-gamma)-like genes in the testis, SMOC-1 in the liver, and the T-cell receptor-like (TCRL) gene in the spleen compared to those used as endogenous control. We construe that these genes have evolved from a common progenitor and conformed to various biological functions during the course of evolution. MASA approach coupled with real-time PCR has potentials to uncover accurate expression of a large number of genes within and across the species circumventing the screening of cDNA library.

  11. Consensus Protein Design Without Phylogenetic Bias

    PubMed Central

    Jäckel, Christian; Bloom, Jesse D; Kast, Peter; Arnold, Frances H; Hilvert, Donald

    2010-01-01

    Consensus design is an appealing strategy for the stabilization of proteins. It exploits amino acid conservation in sets of homologous proteins to identify likely beneficial mutations. Nevertheless, its success depends on the phylogenetic diversity of the sequence set available. Here we show that randomization of a single protein represents a reliable alternative source of sequence diversity essentially free of phylogenetic bias. A small number of functional protein sequences selected from binary-patterned libraries suffices as input for consensus design of active enzymes that are easier to produce and substantially more stable than individual members of the starting data set. Although catalytic activity correlates less consistently with sequence conservation in these extensively randomized proteins, less extreme mutagenesis strategies might be adopted in practice to augment stability while maintaining function. PMID:20433850

  12. Critique, Contextualism and Consensus

    ERIC Educational Resources Information Center

    Green, Jane

    2004-01-01

    In an epistemology of contextualism, how robust does consensus need to be for critique to be practically effective? In 'Relativism and the Critical Potential of Philosophy of Education,' Frieda Heyting proposes a form of contextualism, but her argument raises a number of problems. The kinds of criteria that her version of contextualism will…

  13. Consensus Statement Immunonutrition and Exercise.

    PubMed

    Bermon, Stephane; Castell, Lindy M; Calder, Philip C; Bishop, Nicolette C; Blomstrand, Eva; Mooren, Frank C; Krüger, Karsten; Kavazis, Andreas N; Quindry, John C; Senchina, David S; Nieman, David C; Gleeson, Michael; Pyne, David B; Kitic, Cecilia M; Close, Graeme L; Larson-Meyer, D Enette; Marcos, Ascension; Meydani, Simin N; Walsh, Neil P; Nagatomi, Ryochi

    2017-01-01

    In this consensus statement on immunonutrition and exercise, a panel of knowledgeable contributors from across the globe provides a consensus of updated science, including the background, the aspects for which a consensus actually exists, the controversies and, when possible, suggested directions for future research.

  14. 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

  15. 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

    2015-01-01

    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

  16. 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.

  17. 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

    2015-03-07

    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.

  18. 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.

  19. Brazilian consensus on photoprotection.

    PubMed

    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; Cunha, José Antônio Jabur da; 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; Reis, Vitor Manoel Silva dos; 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.

  20. 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.

  1. 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

  2. ncRNA consensus secondary structure derivation using grammar strings.

    PubMed

    Achawanantakun, Rujira; Sun, Yanni; Takyar, Seyedeh Shohreh

    2011-04-01

    Many noncoding RNAs (ncRNAs) function through both their sequences and secondary structures. Thus, secondary structure derivation is an important issue in today's RNA research. The state-of-the-art structure annotation tools are based on comparative analysis, which derives consensus structure of homologous ncRNAs. Despite promising results from existing ncRNA aligning and consensus structure derivation tools, there is a need for more efficient and accurate ncRNA secondary structure modeling and alignment methods. In this work, we introduce a consensus structure derivation approach based on grammar string, a novel ncRNA secondary structure representation that encodes an ncRNA's sequence and secondary structure in the parameter space of a context-free grammar (CFG) and a full RNA grammar including pseudoknots. Being a string defined on a special alphabet constructed from a grammar, grammar string converts ncRNA alignment into sequence alignment. We derive consensus secondary structures from hundreds of ncRNA families from BraliBase 2.1 and 25 families containing pseudoknots using grammar string alignment. Our experiments have shown that grammar string-based structure derivation competes favorably in consensus structure quality with Murlet and RNASampler. Source code and experimental data are available at http://www.cse.msu.edu/~yannisun/grammar-string.

  3. Is There a Consensus on Consensus Methodology? Descriptions and Recommendations for Future Consensus Research.

    PubMed

    Waggoner, Jane; Carline, Jan D; Durning, Steven J

    2016-05-01

    The authors of this article reviewed the methodology of three common consensus methods: nominal group process, consensus development panels, and the Delphi technique. The authors set out to determine how a majority of researchers are conducting these studies, how they are analyzing results, and subsequently the manner in which they are reporting their findings. The authors conclude with a set of guidelines and suggestions designed to aid researchers who choose to use the consensus methodology in their work.Overall, researchers need to describe their inclusion criteria. In addition to this, on the basis of the current literature the authors found that a panel size of 5 to 11 members was most beneficial across all consensus methods described. Lastly, the authors agreed that the statistical analyses done in consensus method studies should be as rigorous as possible and that the predetermined definition of consensus must be included in the ultimate manuscript. More specific recommendations are given for each of the three consensus methods described in the article.

  4. Wait-Free Consensus

    DTIC Science & Technology

    1992-07-24

    wn, and a conslanI 1H", scuh hal 1. Each Ui is Fi -L’measuTblf. 2. For all i, I.¥,I < w, with pm/r bily I. and 3. En < W with probability 1, then...Discrete Algorithms, pages 351 -362, 1991. [MV61 Miklos Santha and Umiesh V. Vazirani. Generating quasi-random sequences from semi-random sources. Journal

  5. Consensus development for healthcare professionals.

    PubMed

    Kea, Bory; Sun, Benjamin Chih-An

    2015-04-01

    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 overcome the challenges of consensus development while reaping its rewards. Consensus allows for a group approach of 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 different approaches and how it will affect the overall input, approach, and outcome.

  6. Consensus Algorithms Over Fading Channels

    DTIC Science & Technology

    2010-10-01

    studying the effect of fading and collisions on the performance of wireless consensus gossiping and in comparing its cost (measured in terms of number of...not assumed to be symmetric under A2. III. RELATED WORK There has been a resurgence of interest in characterizing consen- sus and gossip algorithms...tree, and then distribute the consensus value, with a finite number of exchanges. The price paid is clearly that of finding the appropriate routing

  7. 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

  8. Decreased Degradation of Internalized Follicle-Stimulating Hormone Caused by Mutation of Aspartic Acid 6.30550 in a Protein Kinase-CK2 Consensus Sequence in the Third Intracellular Loop of Human Follicle-Stimulating Hormone Receptor1

    PubMed Central

    Kluetzman, Kerri S.; Thomas, Richard M.; Nechamen, Cheryl A.; Dias, James A.

    2011-01-01

    A naturally occurring mutation in follicle-stimulating hormone receptor (FSHR) gene has been reported: an amino acid change to glycine occurs at a conserved aspartic acid 550 (D550, D567, D6.30567). This residue is contained in a protein kinase-CK2 consensus site present in human FSHR (hFSHR) intracellular loop 3 (iL3). Because CK2 has been reported to play a role in trafficking of some receptors, the potential roles for CK2 and D550 in FSHR function were evaluated by generating a D550A mutation in the hFSHR. The hFSHR-D550A binds hormone similarly to WT-hFSHR when expressed in HEK293T cells. Western blot analyses showed lower levels of mature hFSHR-D550A. Maximal cAMP production of both hFSHR-D550A as well as the naturally occurring mutation hFSHR-D550G was diminished, but constitutive activity was not observed. Unexpectedly, when 125I-hFSH bound to hFSHR-D550A or hFSHR-D550G, intracellular accumulation of radiolabeled FSH was observed. Both sucrose and dominant-negative dynamin blocked internalization of radiolabeled FSH and its commensurate intracellular accumulation. Accumulation of radiolabeled FSH in cells transfected with hFSHR-D550A is due to a defect in degradation of hFSH as measured in pulse chase studies, and confocal microscopy imaging revealed that FSH accumulated in large intracellular structures. CK2 kinase activity is not required for proper degradation of internalized FSH because inhibition of CK2 kinase activity in cells expressing hFSHR did not uncouple degradation of internalized radiolabeled FSH. Additionally, the CK2 consensus site in FSHR iL3 is not required for binding because CK2alpha coimmunoprecipitated with hFSHR-D550A. Thus, mutation of D550 uncouples the link between internalization and degradation of hFSH. PMID:21270425

  9. C3 glomerulopathy: consensus report.

    PubMed

    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

    2013-12-01

    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.

  10. Automated protein classification using consensus decision.

    PubMed

    Can, Tolga; Camoğlu, Orhan; Singh, Ambuj K; Wang, Yuan-Fang

    2004-01-01

    We propose a novel technique for automatically generating the SCOP classification of a protein structure with high accuracy. High accuracy is achieved by combining the decisions of multiple methods using the consensus of a committee (or an ensemble) classifier. Our technique is rooted in machine learning which shows that by judicially employing component classifiers, an ensemble classifier can be constructed to outperform its components. We use two sequence- and three structure-comparison tools as component classifiers. Given a protein structure, using the joint hypothesis, we first determine if the protein belongs to an existing category (family, superfamily, fold) in the SCOP hierarchy. For the proteins that are predicted as members of the existing categories, we compute their family-, superfamily-, and fold-level classifications using the consensus classifier. We show that we can significantly improve the classification accuracy compared to the individual component classifiers. In particular, we achieve error rates that are 3-12 times less than the individual classifiers' error rates at the family level, 1.5-4.5 times less at the superfamily level, and 1.1-2.4 times less at the fold level.

  11. 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.

  12. 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.

  13. Consensus standard requirements and guidance

    SciTech Connect

    Putman, V.L.

    1995-12-01

    This report presents information from the ANS Criticality Alarm System Workshop relating to the consensus standard requirements and guidance. Topics presented include: definition; nomenclature; requirements and recommendations; purpose of criticality alarms; design criteria; signal characteristics; reliability, dependability and durability; tests; and emergency preparedness and planning.

  14. Confrontation--Catalyst for Consensus.

    ERIC Educational Resources Information Center

    Barnett, Vincent M., Jr.

    The main question discussed in this paper is whether the confrontations which have been taking place on college campuses these past few years provide the basis for a new consensus which will enable all to move forward with confidence and a renewed sense of achievement. In discussing these confrontations, however, several fallacies need to be…

  15. Expert consensus document: Semantics in active surveillance for men with localized prostate cancer - results of a modified Delphi consensus procedure.

    PubMed

    Bruinsma, Sophie M; Roobol, Monique J; Carroll, Peter R; Klotz, Laurence; Pickles, Tom; Moore, Caroline M; Gnanapragasam, Vincent J; Villers, Arnauld; Rannikko, Antti; Valdagni, Riccardo; Frydenberg, Mark; Kakehi, Yoshiyuki; Filson, Christopher P; Bangma, Chris H

    2017-03-14

    Active surveillance (AS) is broadly described as a management option for men with low-risk prostate cancer, but semantic heterogeneity exists in both the literature and in guidelines. To address this issue, a panel of leading prostate cancer specialists in the field of AS participated in a consensus-forming project using a modified Delphi method to reach international consensus on definitions of terms related to this management option. An iterative three-round sequence of online questionnaires designed to address 61 individual items was completed by each panel member. Consensus was considered to be reached if ≥70% of the experts agreed on a definition. To facilitate a common understanding among all experts involved and resolve potential ambiguities, a face-to-face consensus meeting was held between Delphi survey rounds two and three. Convenience sampling was used to construct the panel of experts. In total, 12 experts from Australia, France, Finland, Italy, the Netherlands, Japan, the UK, Canada and the USA participated. By the end of the Delphi process, formal consensus was achieved for 100% (n = 61) of the terms and a glossary was then developed. Agreement between international experts has been reached on relevant terms and subsequent definitions regarding AS for patients with localized prostate cancer. This standard terminology could support multidisciplinary communication, reduce the extent of variations in clinical practice and optimize clinical decision making.

  16. 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.

  17. Cost Sensitive Moving Target Consensus

    SciTech Connect

    Duan, Sisi; Li, Yun; Levitt, Karl N.

    2016-01-01

    Consensus is a fundamental approach to implementing fault-tolerant services through replication where there exists a tradeoff between the cost and the resilience. For instance, Crash Fault Tolerant (CFT) protocols have a low cost but can only handle crash failures while Byzantine Fault Tolerant (BFT) protocols handle arbitrary failures but have a higher cost. Hybrid protocols enjoy the benefits of both high performance without failures and high resiliency under failures by switching among different subprotocols. However, it is challenging to determine which subprotocols should be used. We propose a moving target approach to switch among protocols according to the existing system and network vulnerability. At the core of our approach is a formalized cost model that evaluates the vulnerability and performance of consensus protocols based on real-time Intrusion Detection System (IDS) signals. Based on the evaluation results, we demonstrate that a safe, cheap, and unpredictable protocol is always used and a high IDS error rate can be tolerated.

  18. 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.

  19. 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.

  20. American Burn Association Consensus Statements

    DTIC Science & Technology

    2013-08-01

    finally allow us to follow the ACS program in bariatric surgery and link quality-based purchasing with verification. For this col- laborative...University of Washington Medicine Department of Surgery , Seattle, Washington. See under consensus statements for author affiliations. The 2012 ABA burn...correspondence to Nicole S. Gibran MD, FACS, UW Medicine Regional Burn Center, UW Medicine Department of Surgery , Seattle, Washington 98104. Copyright

  1. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    PubMed Central

    2010-01-01

    Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS") but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) not to be biological transcription factor binding sites ("empirical TFBS"). We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation. PMID:20875111

  2. Consensus formation on adaptive networks

    NASA Astrophysics Data System (ADS)

    Kozma, Balazs; Barrat, Alain

    2008-01-01

    The structure of a network can significantly influence the properties of the dynamical processes that take place on them. While many studies have been paid to this influence, much less attention has been devoted to the interplay and feedback mechanisms between dynamical processes and network topology on adaptive networks. Adaptive rewiring of links can happen in real life systems such as acquaintance networks, where people are more likely to maintain a social connection if their views and values are similar. In our study, we consider different variants of a model for consensus formation. Our investigations reveal that the adaptation of the network topology fosters cluster formation by enhancing communication between agents of similar opinion, although it also promotes the division of these clusters. The temporal behavior is also strongly affected by adaptivity: while, on static networks, it is influenced by percolation properties, on adaptive networks, both the early and late time evolutions of the system are determined by the rewiring process. The investigation of a variant of the model reveals that the scenarios of transitions between consensus and polarized states are more robust on adaptive networks.

  3. Consensus statement: Virus taxonomy in the age of metagenomics.

    PubMed

    Simmonds, Peter; Adams, Mike J; Benkő, Mária; Breitbart, Mya; Brister, J Rodney; Carstens, Eric B; Davison, Andrew J; Delwart, Eric; Gorbalenya, Alexander E; Harrach, Balázs; Hull, Roger; King, Andrew M Q; Koonin, Eugene V; Krupovic, Mart; Kuhn, Jens H; Lefkowitz, Elliot J; Nibert, Max L; Orton, Richard; Roossinck, Marilyn J; Sabanadzovic, Sead; Sullivan, Matthew B; Suttle, Curtis A; Tesh, Robert B; van der Vlugt, René A; Varsani, Arvind; Zerbini, F Murilo

    2017-03-01

    The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

  4. Consensus of Hybrid Multi-Agent Systems.

    PubMed

    Zheng, Yuanshi; Ma, Jingying; Wang, Long

    2017-01-27

    In this brief, we consider the consensus problem of hybrid multiagent systems. First, the hybrid multiagent system is proposed, which is composed of continuous-time and discrete-time dynamic agents. Then, three kinds of consensus protocols are presented for the hybrid multiagent system. The analysis tool developed in this brief is based on the matrix theory and graph theory. With different restrictions of the sampling period, some necessary and sufficient conditions are established for solving the consensus of the hybrid multiagent system. The consensus states are also obtained under different protocols. Finally, simulation examples are provided to demonstrate the effectiveness of our theoretical results.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome.

    PubMed Central

    Huang, R Y; Kowalski, D

    1993-01-01

    We have defined a replication origin, ORI305, within chromosome III of Saccharomyces cerevisiae by means of mutational analysis. cis-acting elements required for origin activity in the chromosome, as assayed by two-dimensional gel electrophoresis of replication intermediates, are the same as those required for the function of an autonomously replicating sequence, ARS305, in a plasmid. Essential elements include (i) an 11 bp sequence that is a near match to the ARS consensus and (ii) a broad sequence directly 3' to the consensus near match. Origin function is inactivated by point mutations in the essential near match sequence, suggesting that the sequence contributes to specifying the origin in the chromosome. Other consensus near matches with different sequences are present but are not required. The essential 3'-flanking sequence exhibits DNA helical instability and is sensitive to deletion mutations that stabilize the DNA helix. The wild-type 3'-flanking sequence can be functionally substituted by dissimilar sequences that also exhibit helical instability. The requirement for DNA helical instability indicates that the essential 3'-flanking sequence serves as a DNA unwinding element in the chromosome. Images PMID:8223462

  10. Questioning the Consensus Definition of Validity

    ERIC Educational Resources Information Center

    Newton, Paul E.

    2012-01-01

    This focus article provided the author with an opportunity to unpack the consensus definition of validity and to explore its implications in the light of recent debates. He proposed an elaboration of the consensus definition, which was intended to express the spirit of the "Standards for Educational and Psychological Testing" with increased…

  11. 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)

  12. 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

  13. [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.

  14. 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

  15. [Argentine Consensus of Respiratory Rehabilitation].

    PubMed

    Sívori, Martín; Benzo, Roberto; Rhodius, Edgardo; Jolly, Enrique; Boim, Clarisa; Saadia, Marcela; Conti, Ernesto; Guevara, Ivan; Carles, Daniel; Victorio, Carlos; Santini, Fabian; Ratto, Patricia; Capparelli, Ignacio; Prieto, Ernesto; Azvalinsky, Marcos; Alais, Maria

    2004-01-01

    A group of pulmonologists and physical therapists from the Asociacion Argentina de Medicina Respiratoria revised the scientific literature on Respiratory Rehabilitation (RR) to elaborate evidence-based national recommendations to promote its use. RR is a multidisciplinary program of care for patients with chronic respiratory impairment, individually tailored, designed to optimize physical and social performance and autonomy of patients. It is particularly indicated in patients with Chronic Obstructive Pulmonary Disease (COPD) with exercise intolerance. Inclusion and exclusion criteria, guidelines for initial evaluation and follow up have been defined. The resources needed were defined. It was recommended a hospital ambulatory program with domiciliary complement. A pulmonologist and physical therapist were required for the program as minimum. Aerobic training was recommended for lower limb (LL) (Evidence A) and upper limb (UL) (Evidence B), strength training for LL and UL (Evidence C), as well as respiratory muscles training by resistive inspiratory threshold load (Evidence D) and other physiotherapy techniques were recommended for specific patients. In addition recommendations have been made for educational objectives of the program, nutritional and psychological support. The positive impact of RR on health care was analyzed through the reduction in exacerbation of COPD, length of hospital stay and cost. RR is a key component in the treatment of COPD patients. This evidenced-based consensus statement was prepared to provide recommendations to be implemented nationally.

  16. Consensus Paper: Cerebellum and Emotion.

    PubMed

    Adamaszek, M; D'Agata, F; Ferrucci, R; Habas, C; Keulen, S; Kirkby, K C; Leggio, M; Mariën, P; Molinari, M; Moulton, E; Orsi, L; Van Overwalle, F; Papadelis, C; Priori, A; Sacchetti, B; Schutter, D J; Styliadis, C; Verhoeven, J

    2017-04-01

    Over the past three decades, insights into the role of the cerebellum in emotional processing have substantially increased. Indeed, methodological refinements in cerebellar lesion studies and major technological advancements in the field of neuroscience are in particular responsible to an exponential growth of knowledge on the topic. It is timely to review the available data and to critically evaluate the current status of the role of the cerebellum in emotion and related domains. The main aim of this article is to present an overview of current facts and ongoing debates relating to clinical, neuroimaging, and neurophysiological findings on the role of the cerebellum in key aspects of emotion. Experts in the field of cerebellar research discuss the range of cerebellar contributions to emotion in nine topics. Topics include the role of the cerebellum in perception and recognition, forwarding and encoding of emotional information, and the experience and regulation of emotional states in relation to motor, cognitive, and social behaviors. In addition, perspectives including cerebellar involvement in emotional learning, pain, emotional aspects of speech, and neuropsychiatric aspects of the cerebellum in mood disorders are briefly discussed. Results of this consensus paper illustrate how theory and empirical research have converged to produce a composite picture of brain topography, physiology, and function that establishes the role of the cerebellum in many aspects of emotional processing.

  17. [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.

  18. Phylogenetic Trees From Sequences

    NASA Astrophysics Data System (ADS)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  19. 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

  20. Consensus of population systems with community structures.

    PubMed

    Wang, Jing; Wu, Bin; Wang, Long; Fu, Feng

    2008-11-01

    Multicommunity population systems may reach a consensus state where the fractions of each species in different communities agree on a common value. In this paper, by analyzing the evolutionary dynamics based on an extended replicator equation incorporating community effects, the consensus problem of population systems with n communities is studied. In particular, the simple case of two communities is investigated in detail. In general, for n communities, a sufficient and necessary condition for population systems to reach a consensus of coexistent state is provided. Regarding the population dynamics for the four different types of games, whether the population systems can achieve consensus is determined. The dynamics of community-structured populations shows richer features than nonstructured populations, and some nontrivial phenomena arising from different community-structured population systems are illustrated with concrete numerical examples.

  1. Leader selection for fast consensus in networks

    NASA Astrophysics Data System (ADS)

    Wang, Ying; Yang, Wen; Wang, Lin; Wang, Xiaofan

    2015-12-01

    This paper considers a leader-follower system with the aim to select an optimal leader so as to drive the remaining nodes to reach the desired consensus with the fastest convergence speed. An index called consensus centrality (CC) is proposed to quantify how fast a leader could guide the network to achieve the desired consensus. The experiment results explored the big similarities between the distributions of CC and degree in the network, which suggest that the suboptimal leader selected by the maximum degree can approximately approach the optimal leader in heterogeneous networks. Combining the degree-based k-shell decomposition with consensus centrality, a leader selection algorithm is proposed to reduce the computational complexity in large-scale networks. Finally, the convergence time of an equivalent discrete-time model is given to illustrate the properties of the suboptimal solutions.

  2. Diagnostic and therapeutic consensus on acromegaly.

    PubMed

    Doga, M; Bonadonna, S; Gola, M; Nuzzo, M; Giustina, A

    2005-01-01

    In February 1999 and May 2000, two workshops were held in Cortina, Italy and Montecarlo, respectively, to develop a consensus defining the diagnosis and treatment of acromegaly. The workshops were sponsored by the Italian Society of Endocrinology, the Pituitary Society and European Neuroendocrine Association. Partecipants from all over the world included endocrinologists, neurosurgeons and radiotherapists skilled in the management of acromegaly. This review paper summarizes the main points of the two consensus statements published following these two workshops.

  3. 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

  4. In vitro and in vivo replication of a chemically synthesized consensus genome of hepatitis B virus genotype B.

    PubMed

    Zhang, Zhenhua; Xia, Jianbo; Sun, Binghu; Dai, Yu; Li, Xu; Schlaak, Joerg F; Lu, Mengji

    2015-03-01

    Hepatitis B virus (HBV) genotypes vary in their geographical distribution and virological features. Previous investigations have shown that HBV genotype B is a predominant HBV genotype in China. Studies on HBV concerning different isolates frequently meet the question about the HBV reference strain and its representativeness. Although HBV consensus sequences can be generated easily by sequence alignment, they may not exist in nature or could not usually be isolated from patient samples. Thus, the construction of a consensus HBV genome has been proposed. In this study, an HBV genotype B consensus sequence was established by comparing 42 full-length HBV genotype B sequences and the genome was generated by chemical synthesis. This consensus genome was fully replication competent by in vitro transfection into hepatoma cells. The plasmid pHBV1.3B carrying a 1.3× full-length HBV consensus genome was hydrodynamically injected into Balb/c mice. HBsAg, anti-HBs, HBeAg, anti-HBe, and anti-HBc detection indicated expression and replication of this HBV genome in mice, similar to other HBV isolates. This approach represents a strategy to design and create consensus HBV genomes for future studies.

  5. Population conference: consensus and conflict.

    PubMed

    Willson, P D

    1984-01-01

    The United Nations-sponsored International Conference on Population held in Mexico City was both a rejection and an affirmation of a new policy of the Reagan administration. The policy denies international family planning funds to nongovernmental organizations that perform or actively promote abortion as a family planning method in other nations. A compromise statement was accepted urging governments to take appropriate measures to discourage abortion as a family planning method and when possible to provide for the humane treatment and counseling of women ho resorted to abortion. The statement on abortion was 1 of 88 reccomendations approved by the conference. The commitment expressed in the 10-year-old World Population Plan of Action to the rights and responsiblity to all people as reaffirmed. The conference also endorsed family life education and sex education as well as suitable family planning, information and services for adolescents, with due consideration given to the role, rights and obligations of parents. Increased support for international population and family planning programs was urged and World Bank President, Clausen, urged a 4-fold increase in international funding by the year 2000. Most of the conference's recommendations re devoted to the broad range of population policy issues, including morbidity and mortality, international and internal migration, the relationship between population and economic development and the status of women. The purpose of the recommendations is to increase the momentum of international support. The Mexico City conference was characterized by a remarkable degree of consensus about population policies with respect to integration with economic development, the need to respect individual rights and the recognition that all nations have sovereign rights to develop and implement their own population policies. Conflict and controversy arose in the areas of the arms race and the Middle East. The US position on abortion funding

  6. 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

  7. 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

  8. 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...

  9. Sequence specific binding of chlamydial histone H1-like protein.

    PubMed Central

    Kaul, R; Allen, M; Bradbury, E M; Wenman, W M

    1996-01-01

    Chlamydia trachomatis is one of the few prokaryotic organisms known to contain proteins that bear homology to eukaryotic histone H1. Changes in macromolecular conformation of DNA mediated by the histone H1-like protein (Hc1) appear to regulate stage specific differentiation. We have developed a cross-linking immunoprecipitation protocol to examine in vivo protein-DNA interaction by immune precipitating chlamydial Hc1 cross linked to DNA. Our results strongly support the presence of sequence specific binding sites on the chlamydial plasmid and hc1 gene upstream of its open reading frame. The preferential binding sites were mapped to 520 bp BamHI-XhoI and 547 bp BamHI-DraI DNA fragments on the plasmid and hc1 respectively. Comparison of these two DNA sequences using Bestfit program has identified a 24 bp region with >75% identity that is unique to the chlamydial genome. Double-stranded DNA prepared by annealing complementary oligonucleotides corresponding to the conserved 24 bp region bind Hc1, in contrast to control sequences with similar A+T ratios. Further, Hc1 binds to DNA in a strand specific fashion, with preferential binding for only one strand. The site specific affinity to plasmid DNA was also demonstrated by atomic force microscopy data images. Binding was always followed by coiling, shrinking and aggregation of the affected DNA. Very low protein-DNA ratio was required if incubations were carried out in solution. However, if DNA was partially immobilized on mica substrate individual strands with dark foci were still visible even after the addition of excess Hc1. PMID:8760883

  10. [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.

  11. 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.

  12. Thailand Consensus on Helicobacter pylori Treatment 2015.

    PubMed

    Mahachai, Varocha; Vilaichone, Ratha-Korn; Pittayanon, Rapat; Rojborwonwitaya, Jarin; Leelakusolvong, Somchai; Kositchaiwat, Chomsri; Mairiang, Pisaln; Praisontarangkul, Ong-Ard; Ovartlarnporn, Buncha; Sottisuporn, Jaksin; Pisespongsa, Pises; Maneerattanaporn, Monthira; Sony, Ravin; Sirinthornpunya, Siam; Chaiyamahapurk, Orawan; Wiwattanachang, Olarn; Sansak, Inchaya; Harnsomboon, Piyathida; Chitapanarux, Taned; Chuenrattanakul, Surapon

    2016-01-01

    Management of Helicobacter pylori infection is an important aspect of many upper gastrointestinal tract diseases, such as chronic gastritis, peptic ulcer disease, gastric cancer and mucosa-associated lymphoid tissue (MALT) lymphoma. The Thailand Consensus on H. pylori treatment 2015 consisted of 22 national experts who took active roles, discussed all important clinical information and investigated clinical aspects in four workshops, focuising on: (1) Diagnosis (2) Treatment (3) Follow-up after eradication and (4) H. pylori infection and special conditions. Experts were invited to participate on the basis of their expertise and contribution to H. pylori works and/or consensus methodology. The results of each workshop were taken to a final consensus vote by all experts. Recommendations were developed from the best evidence and availability to guide clinicians in management of this specific infection associated with variety of clinical outcomes.

  13. 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

  14. 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.

  15. Eastern Canadian Gastrointestinal Cancer Consensus Conference 2016

    PubMed Central

    Bossé, D.; Ng, T.; Ahmad, C.; Alfakeeh, A.; Alruzug, I.; Biagi, J.; Brierley, J.; Chaudhury, P.; Cleary, S.; Colwell, B.; Cripps, C.; Dawson, L.A.; Dorreen, M.; Ferland, E.; Galiatsatos, P.; Girard, S.; Gray, S.; Halwani, F.; Kopek, N.; Mahmud, A.; Martel, G.; Robillard, L.; Samson, B.; Seal, M.; Siddiqui, J.; Sideris, L.; Snow, S.; Thirwell, M.; Vickers, M.; Goodwin, R.; Goel, R.; Hsu, T.; Tsvetkova, E.; Ward, B.; Asmis, T.

    2016-01-01

    The annual Eastern Canadian Gastrointestinal Cancer Consensus Conference 2016 was held in Montreal, Quebec, 5–7 February. Experts in radiation oncology, medical oncology, surgical oncology, and infectious diseases involved in the management of patients with gastrointestinal malignancies participated in presentations and discussion sessions for the purpose of developing the recommendations presented here. This consensus statement addresses multiple topics: ■ Follow-up and survivorship of patients with resected colorectal cancer■ Indications for liver metastasectomy■ Treatment of oligometastases by stereotactic body radiation therapy■ Treatment of borderline resectable and unresectable pancreatic cancer■ Transarterial chemoembolization in hepatocellular carcinoma■ Infectious complications of antineoplastic agents PMID:28050151

  16. Photopatch testing: a consensus methodology for Europe.

    PubMed

    Bruynzeel, D P; Ferguson, J; Andersen, K; Gonçalo, M; English, John; Goossens, A; Holzle, E; Ibbotson, S H; Lecha, M; Lehmann, P; Leonard, F; Moseley, Harry; Pigatto, P; Tanew, A

    2004-11-01

    A group of interested European Contact Dermatologists/Photobiologists met to produce a consensus statement on methodology, test materials and interpretation of photopatch testing. While it is recognized that a range of local variables operate throughout Europe, the underlying purpose of the work is to act as an essential preamble to a Pan European Photopatch Test Study focusing particularly on sunscreen chemicals.

  17. 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)…

  18. 3rd Brazilian Consensus on Helicobacter pylori.

    PubMed

    Coelho, Luiz Gonzaga; Maguinilk, Ismael; Zaterka, Schlioma; Parente, José Miguel; do Carmo Friche Passos, Maria; Moraes-Filho, Joaquim Prado P

    2013-04-01

    Signicant progress has been obtained since the Second Brazilian Consensus Conference on Helicobacter pylori Infection held in 2004, in São Paulo, SP, Brazil, and justify a third meeting to establish updated guidelines on the current management of H. pylori infection. The Third Brazilian Consensus Conference on H pylori Infection was organized by the Brazilian Nucleus for the Study of Helicobacter, a Department of the Brazilian Federation of Gastroenterology and took place on April 12-15, 2011, in Bento Gonçalves, RS, Brazil. Thirty-one delegates coming from the five Brazilian regions and one international guest, including gastroenterologists, pathologists, epidemiologists, and pediatricians undertook the meeting. The participants were allocated in one of the five main topics of the meeting: H pylori, functional dyspepsia and diagnosis; H pylori and gastric cancer; H pylori and other associated disorders; H pylori treatment and retreatment; and, epidemiology of H pylori infection in Brazil. The results of each subgroup were submitted to a final consensus voting to all participants. Relevant data were presented, and the quality of evidence, strength of recommendation, and level of consensus were graded. Seventy per cent and more votes were considered as acceptance for the final statement. This article presents the main recommendations and conclusions to guide Brazilian doctors involved in the management of H pylori infection.

  19. 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…

  20. 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…

  1. Adaptive bipartite consensus on coopetition networks

    NASA Astrophysics Data System (ADS)

    Hu, Jiangping; Zhu, Hong

    2015-07-01

    In this paper, a bipartite consensus tracking problem is considered for a group of autonomous agents on a coopetition network, on which the agents interact cooperatively and competitively simultaneously. The coopetition network involves positive and negative edges and is conveniently modeled by a signed graph. Additionally, the dynamics of all the agents are subjected to unknown disturbances, which are represented by linearly parameterized models. An adaptive estimation scheme is designed for each agent by virtue of the relative position measurements and the relative velocity measurements from its neighbors. Then a consensus tracking law is proposed for a new distributed system, which uses the relative measurements as the new state variables. The convergence of the consensus tracking error and the parameter estimation are analyzed even when the coopetition network is time-varying and no more global information about the bounds of the unknown disturbances is available to all the agents. Finally, some simulation results are provided to demonstrate the formation of the bipartite consensus on the coopetition network.

  2. 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…

  3. Statistical Inference for Cultural Consensus Theory

    DTIC Science & Technology

    2014-02-24

    Facts on Aging Quiz ”. Covariates were also incorporated into the model, and it was shown that a consensus answer key that corresponded to the...Structural balance: a generalization of Heider’s theory. Psychological Review, 63, 277-293. Palmore, E. (1998). Facts on aging quiz , second edition

  4. The Overreliance of Accreditors on Consensus Standards.

    ERIC Educational Resources Information Center

    Murray, Frank B.

    2001-01-01

    Argues that the legitimacy of accreditation in teacher education is rooted in political consensus, power, and scholarship. Because these roots are fragile, there is no accepted concept of educational malpractice. The legitimacy of accreditation should be rooted in scholarly evidence that the program has fulfilled the claim that its graduates are…

  5. 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…

  6. Report of the Consensus Planning Project.

    ERIC Educational Resources Information Center

    Council of Chief State School Officers, Washington, DC.

    This third report of the National Assessment Planning Project concentrates on the consensus planning process used in the project. The project is an outgrowth of National Assessment of Educational Progress (NAEP) program expansion, whose original task was to produce state-by-state comparisons of student achievement. The report is organized in four…

  7. 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

  8. Report on the consensus workshop on formaldehyde

    SciTech Connect

    Gough, M.; Hart, R.; Karrh, B.W.; Koestner, A.; Neal, R.; Parkinson, D.; Perera, F.; Powell, K.E.; Rosenkranz, S.

    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. 264 references.

  9. 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

  10. Sampled-Data Consensus of Linear Multi-agent Systems With Packet Losses.

    PubMed

    Zhang, Wenbing; Tang, Yang; Huang, Tingwen; Kurths, Jurgen

    2016-08-17

    In this paper, the consensus problem is studied for a class of multi-agent systems with sampled data and packet losses, where random and deterministic packet losses are considered, respectively. For random packet losses, a Bernoulli-distributed white sequence is used to describe packet dropouts among agents in a stochastic way. For deterministic packet losses, a switched system with stable and unstable subsystems is employed to model packet dropouts in a deterministic way. The purpose of this paper is to derive consensus criteria, such that linear multi-agent systems with sampled-data and packet losses can reach consensus. By means of the Lyapunov function approach and the decomposition method, the design problem of a distributed controller is solved in terms of convex optimization. The interplay among the allowable bound of the sampling interval, the probability of random packet losses, and the rate of deterministic packet losses are explicitly derived to characterize consensus conditions. The obtained criteria are closely related to the maximum eigenvalue of the Laplacian matrix versus the second minimum eigenvalue of the Laplacian matrix, which reveals the intrinsic effect of communication topologies on consensus performance. Finally, simulations are given to show the effectiveness of the proposed results.

  11. [Argentine consensus on the treatment of bipolar disorders].

    PubMed

    Vázquez, Gustavo Héctor; Strejilevich, Sergio; García Bonetto, Gerardo; Cetkovich-Bakmas, Marcelo; Zaratiegui, Rodolfo; Lagomarsino, Alejandro; Goldchluk, Aníbal; Kalina, Eduardo; Herbst, Luis; Gutiérrez, Benigno

    2005-01-01

    The consensus guidelines of argentine experts in the treatment of bipolar disorders are the result of three days of work of the 10 main local experts under the organization of the Argentine Association of Biological Psychiatry (AAPB). It was adopted a mixed criterion for its preparation: all the recent data of the evidence medicine based published until now were discussed and were balanced with the knowledge acquired from clinical experience of the local experts on the bipolar field. It presents general recommendations and suggested therapeutic sequences for the phase of maintenance, the manic/hypomanic or mixed episode and the depressive episode. These have been divided according to the classification in type I and II; with or without rapid cycling. Since the group of experts identified the delay and miss-diagnoses like the most important barrier for a suitable treatment enclosed a series of recommendations for differential diagnosis of bipolar disorders.

  12. Consensus Prediction of Charged Single Alpha-Helices with CSAHserver.

    PubMed

    Dudola, Dániel; Tóth, Gábor; Nyitray, László; Gáspári, Zoltán

    2017-01-01

    Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.

  13. Expert consensus document: A consensus on the medical treatment of acromegaly.

    PubMed

    Giustina, Andrea; Chanson, Philippe; Kleinberg, David; Bronstein, Marcello D; Clemmons, David R; Klibanski, Anne; van der Lely, Aart J; Strasburger, Christian J; Lamberts, Steven W; Ho, Ken K Y; Casanueva, Felipe F; Melmed, Shlomo

    2014-04-01

    In March 2013, the Acromegaly Consensus Group met to revise and update guidelines for the medical treatment of acromegaly. The meeting comprised experts skilled in the medical management of acromegaly. The group considered treatment goals covering biochemical, clinical and tumour volume outcomes, and the place in guidelines of somatostatin receptor ligands, growth hormone receptor antagonists and dopamine agonists, and alternative modalities for treatment including combination therapy and novel treatments. This document represents the conclusions of the workshop consensus.

  14. Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions.

    PubMed Central

    Ulyanov, A V; Stormo, G D

    1995-01-01

    A method for the identification and characterization of protein-DNA interactions is presented. We have developed an approach for finding unknown multiple patterns that occur imperfectly in a set of several sequences. The pattern may contain letters from the nucleotide alphabet (A, C, G and T) including ambiguous characters (A/C, A/G, A/T; A/C/G, etc.). This method reveals weak DNA signals on an unaligned set of DNA fragments known to be functionally related and assumes no prior information on the sequences' alignment. It determines the locations of the signals from only the information intrinsic to the sequences themselves. We have applied this method to analyze the binding sites of cAMP receptor protein (CRP). The consensus based on these data are discussed and a comparison of the consensus with the crystal structure of CAP-DNA complex is presented. We further show that in a mixture of DNA sequences, containing binding sites for two different proteins, both classes of binding sites can be discovered simultaneously by this method. The DNA sequences of nucleosome cores from chicken erythrocyte and a set of the other known nucleosomal sequences show existence of symmetrical features in nucleosome-binding DNA sequences. We also show multi-alphabet patterns that can play a role in the phasing signal on the nucleosome DNA molecule and have compared the results with existing models of nucleosome positioning. PMID:7753637

  15. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... carry out those plans and activities. For the purposes of this Part, consensus-based management involves..., whenever practicable, use a consensus-based management approach to the NEPA process. (d) If the Responsible... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Incorporating consensus-based...

  16. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... carry out those plans and activities. For the purposes of this Part, consensus-based management involves..., whenever practicable, use a consensus-based management approach to the NEPA process. (d) If the Responsible... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Incorporating consensus-based...

  17. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... carry out those plans and activities. For the purposes of this Part, consensus-based management involves..., whenever practicable, use a consensus-based management approach to the NEPA process. (d) If the Responsible... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Incorporating consensus-based...

  18. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... carry out those plans and activities. For the purposes of this Part, consensus-based management involves..., whenever practicable, use a consensus-based management approach to the NEPA process. (d) If the Responsible... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Incorporating consensus-based...

  19. 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…

  20. Lack of Consensus on Education: What Are Its Dimensions?

    ERIC Educational Resources Information Center

    Rozycki, Edward G.

    2010-01-01

    This article offers an analysis of the dimensions of consensus on education using Diane Ravitch's statement: "The single biggest problem in American education is that no one agrees on why they educate." The interesting problem is to determine which consensus on educational issues varies, whose consensus it is, and how and why it varies. The author…

  1. 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.

  2. Bruxism defined and graded: an international consensus.

    PubMed

    Lobbezoo, F; Ahlberg, J; Glaros, A G; Kato, T; Koyano, K; Lavigne, G J; de Leeuw, R; Manfredini, D; Svensson, P; Winocur, E

    2013-01-01

    To date, there is no consensus about the definition and diagnostic grading of bruxism. A written consensus discussion was held among an international group of bruxism experts as to formulate a definition of bruxism and to suggest a grading system for its operationalisation. The expert group defined bruxism as a repetitive jaw-muscle activity characterised by clenching or grinding of the teeth and/or by bracing or thrusting of the mandible. Bruxism has two distinct circadian manifestations: it can occur during sleep (indicated as sleep bruxism) or during wakefulness (indicated as awake bruxism). For the operationalisation of this definition, the expert group proposes a diagnostic grading system of 'possible', 'probable' and 'definite' sleep or awake bruxism. The proposed definition and grading system are suggested for clinical and research purposes in all relevant dental and medical domains.

  3. Consensus and transitions in coupled Sznajd networks

    NASA Astrophysics Data System (ADS)

    Ludden, Matthew

    2013-03-01

    In this work we investigate two coupled square lattice networks undergoing Sznajd model dynamics. The coupling between the networks is quantified by a coupling strength p. Monte Carlo simulations indicate that the exit probability of each network (to reach either all spins up or all down) depends on p and the initial density of up spins d in the other network. For fixed initial densities, we find a critical coupling pc, above which no further changes in the exit probability are observed. We also find pc to decrease linearly with increasing d. The consensus time scales with system size as Lα, where α = α(p, d). The conditions that must be met for the two networks to reach consensus are also considered. Thomas E. Stone: Husson University, Susan R. McKay: University of Maine

  4. [Consensus on safe infant's furniture: brief version].

    PubMed

    2016-04-01

    Several products that are used for support, transportation or recreation in infants and children can cause non intentional injuries. This consensus tries to provide pediatricians and families with the necessary elements to recognize and choose safe infant's furniture. A group of 24 experts developed a consensus according to Delphi's method, which consists in successiverounds of questions. Recommendations are supported with bibliography. Infant walkers are not recommended, as they are considered useless and dangerous. Guidelines are given to choose appropriate child restraint systems, when and how to use them, and how to install them in a safe way. Injuries and prevention measures related to strollers, high chairs, cribs and bunk beds are described. Risks and the way to avoid them are diagrammed in figures that can be used to transmit recommendations to families.

  5. 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

  6. 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.

  7. Shoulder biomechanics: today's consensus and tomorrow's perspectives.

    PubMed

    Cutti, Andrea Giovanni; Veeger, H E J DirkJan

    2009-05-01

    Shoulder biomechanics is a fast growing field, which is progressively expanding its focus to include more applied research. The papers included in this Special Issue confirm this trend. After a classification of the papers as dealing with fundamental or applied research through theoretical or experimental methods, in this Editorial we tried to summarize the elements of consensus and the open issues discussed during the last International Shoulder Group meeting, held in Bologna (Italy) in 2008.

  8. 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...

  9. Consensus contact prediction by linear programming.

    PubMed

    Gao, Xin; Bu, Dongbo; Li, Shuai Cheng; Li, Ming; Xu, Jinbo

    2007-01-01

    Protein inter-residue contacts are of great use for protein structure determination or prediction. Recent CASP events have shown that a few accurately predicted contacts can help improve both computational efficiency and prediction accuracy of the ab inito folding methods. This paper develops an integer linear programming (ILP) method for consensus-based contact prediction. In contrast to the simple "majority voting" method assuming that all the individual servers are equal and independent, our method evaluates their correlations using the maximum likelihood method and constructs some latent independent servers using the principal component analysis technique. Then, we use an integer linear programming model to assign weights to these latent servers in order to maximize the deviation between the correct contacts and incorrect ones; our consensus prediction server is the weighted combination of these latent servers. In addition to the consensus information, our method also uses server-independent correlated mutation (CM) as one of the prediction features. Experimental results demonstrate that our contact prediction server performs better than the "majority voting" method. The accuracy of our method for the top L/5 contacts on CASP7 targets is 73.41%, which is much higher than previously reported studies. On the 16 free modeling (FM) targets, our method achieves an accuracy of 37.21%.

  10. Molecular subgroups of medulloblastoma: the current consensus.

    PubMed

    Taylor, Michael D; Northcott, Paul A; Korshunov, Andrey; Remke, Marc; Cho, Yoon-Jae; Clifford, Steven C; Eberhart, Charles G; Parsons, D Williams; Rutkowski, Stefan; Gajjar, Amar; Ellison, David W; Lichter, Peter; Gilbertson, Richard J; Pomeroy, Scott L; Kool, Marcel; Pfister, Stefan M

    2012-04-01

    Medulloblastoma, a small blue cell malignancy of the cerebellum, is a major cause of morbidity and mortality in pediatric oncology. Current mechanisms for clinical prognostication and stratification include clinical factors (age, presence of metastases, and extent of resection) as well as histological subgrouping (classic, desmoplastic, and large cell/anaplastic histology). Transcriptional profiling studies of medulloblastoma cohorts from several research groups around the globe have suggested the existence of multiple distinct molecular subgroups that differ in their demographics, transcriptomes, somatic genetic events, and clinical outcomes. Variations in the number, composition, and nature of the subgroups between studies brought about a consensus conference in Boston in the fall of 2010. Discussants at the conference came to a consensus that the evidence supported the existence of four main subgroups of medulloblastoma (Wnt, Shh, Group 3, and Group 4). Participants outlined the demographic, transcriptional, genetic, and clinical differences between the four subgroups. While it is anticipated that the molecular classification of medulloblastoma will continue to evolve and diversify in the future as larger cohorts are studied at greater depth, herein we outline the current consensus nomenclature, and the differences between the medulloblastoma subgroups.

  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.

  12. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  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.

  14. Diabetes and cancer: a consensus report.

    PubMed

    Giovannucci, Edward; Harlan, David M; Archer, Michael C; Bergenstal, Richard M; Gapstur, Susan M; Habel, Laurel A; Pollak, Michael; Regensteiner, Judith G; Yee, Douglas

    2010-01-01

    Epidemiologic evidence suggests that cancer incidence is associated with diabetes as well as certain diabetes risk factors and treatments. This consensus statement of experts assembled jointly by the American Diabetes Association and the American Cancer Society reviews the state of science concerning 1) the association between diabetes and cancer incidence or prognosis; 2) risk factors common to both diabetes and cancer; 3) possible biologic links between diabetes and cancer risk; and 4) whether diabetes treatments influence the risk of cancer or cancer prognosis. In addition, key unanswered questions for future research are posed.

  15. Distributed Estimation using Bayesian Consensus Filtering

    DTIC Science & Technology

    2014-06-06

    22] and Bayesian programming [23]. This paper focuses on developing a consensus framework for distributed Bayesian filters. The statistics literature...denote the set of inclusive neighbors. Let N, R, and Rm×n be the sets of natural numbers (positive integers ), real numbers, and m by n matrices. Let λ and...the bounded integral (´ X |f(x)| pdµ(x) )1/p , where µ is a measure on X . II. PRELIMINARIES In this section, we first state four assumptions used

  16. A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.

    PubMed

    Sen, Taner Z; Cheng, Haitao; Kloczkowski, Andrzej; Jernigan, Robert L

    2006-11-01

    The major aim of tertiary structure prediction is to obtain protein models with the highest possible accuracy. Fold recognition, homology modeling, and de novo prediction methods typically use predicted secondary structures as input, and all of these methods may significantly benefit from more accurate secondary structure predictions. Although there are many different secondary structure prediction methods available in the literature, their cross-validated prediction accuracy is generally <80%. In order to increase the prediction accuracy, we developed a novel hybrid algorithm called Consensus Data Mining (CDM) that combines our two previous successful methods: (1) Fragment Database Mining (FDM), which exploits the Protein Data Bank structures, and (2) GOR V, which is based on information theory, Bayesian statistics, and multiple sequence alignments (MSA). In CDM, the target sequence is dissected into smaller fragments that are compared with fragments obtained from related sequences in the PDB. For fragments with a sequence identity above a certain sequence identity threshold, the FDM method is applied for the prediction. The remainder of the fragments are predicted by GOR V. The results of the CDM are provided as a function of the upper sequence identities of aligned fragments and the sequence identity threshold. We observe that the value 50% is the optimum sequence identity threshold, and that the accuracy of the CDM method measured by Q(3) ranges from 67.5% to 93.2%, depending on the availability of known structural fragments with sufficiently high sequence identity. As the Protein Data Bank grows, it is anticipated that this consensus method will improve because it will rely more upon the structural fragments.

  17. 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

  18. 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.

  19. 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.

  20. Consensus document on allergic conjunctivitis (DECA).

    PubMed

    Sánchez-Hernández, M C; Montero, J; Rondon, C; Benitez del Castillo, J M; Velázquez, E; Herreras, J M; Fernández-Parra, B; Merayo-Lloves, J; Del Cuvillo, A; Vega, F; Valero, A; Panizo, C; Montoro, J; Matheu, V; Lluch-Bernal, M; González, M L; González, R; Dordal, M T; Dávila, I; Colás, C; Campo, P; Antón, E; Navarro, A

    2015-01-01

    Allergic conjunctivitis (AC) is an inflammatory disease of the conjunctiva caused mainly by an IgE-mediated mechanism. It is the most common type of ocular allergy. Despite being the most benign form of conjunctivitis, AC has a considerable effect on patient quality of life, reduces work productivity, and increases health care costs. No consensus has been reached on its classification, diagnosis, or treatment. Consequently, the literature provides little information on its natural history, epidemiological data are scarce, and it is often difficult to ascertain its true morbidity. The main objective of the Consensus Document on Allergic Conjunctivitis (Documento dE Consenso sobre Conjuntivitis Alérgica [DECA]), which was drafted by an expert panel from the Spanish Society of Allergology and Spanish Society of Ophthalmology, was to reach agreement on basic criteria that could prove useful for both specialists and primary care physicians and facilitate the diagnosis, classification, and treatment of AC. This document is the first of its kind to describe and analyze aspects of AC that could make it possible to control symptoms.

  1. 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.

  2. 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.

  3. Frailty Consensus: A Call to Action

    PubMed Central

    Morley, John E.; Vellas, Bruno; van Kan, G. Abellan; Anker, Stefan D.; Bauer, Juergen M.; Bernabei, Roberto; Cesari, Matteo; Chumlea, W.C.; Doehner, Wolfram; Evans, Jonathan; Fried, Linda P.; Guralnik, Jack M.; Katz, Paul R.; Malmstrom, Theodore K.; McCarter, Roger J.; Gutierrez Robledo, Luis M.; Rockwood, Ken; von Haehling, Stephan; Vandewoude, Maurits F.; Walston, Jeremy

    2014-01-01

    Frailty is a clinical state in which there is an increase in an individual’s vulnerability for developing increased dependency and/or mortality when exposed to a stressor. Frailty can occur as the result of a range of diseases and medical conditions. A consensus group consisting of delegates from 6 major international, European, and US societies created 4 major consensus points on a specific form of frailty: physical frailty. Physical frailty is an important medical syndrome. The group defined physical frailty as “a medical syndrome with multiple causes and contributors that is characterized by diminished strength, endurance, and reduced physiologic function that increases an individual’s vulnerability for developing increased dependency and/or death.”Physical frailty can potentially be prevented or treated with specific modalities, such as exercise, protein-calorie supplementation, vitamin D, and reduction of polypharmacy.Simple, rapid screening tests have been developed and validated, such as the simple FRAIL scale, to allow physicians to objectively recognize frail persons.For the purposes of optimally managing individuals with physical frailty, all persons older than 70 years and all individuals with significant weight loss (≥5%) due to chronic disease should be screened for frailty. PMID:23764209

  4. Dialogic Consensus In Clinical Decision-Making.

    PubMed

    Walker, Paul; Lovat, Terry

    2016-12-01

    This paper is predicated on the understanding that clinical encounters between clinicians and patients should be seen primarily as inter-relations among persons and, as such, are necessarily moral encounters. It aims to relocate the discussion to be had in challenging medical decision-making situations, including, for example, as the end of life comes into view, onto a more robust moral philosophical footing than is currently commonplace. In our contemporary era, those making moral decisions must be cognizant of the existence of perspectives other than their own, and be attuned to the demands of inter-subjectivity. Applicable to clinical practice, we propose and justify a Habermasian approach as one useful means of achieving what can be described as dialogic consensus. The Habermasian approach builds around, first, his discourse theory of morality as universalizable to all and, second, communicative action as a cooperative search for truth. It is a concrete way to ground the discourse which must be held in complex medical decision-making situations, in its actual reality. Considerations about the theoretical underpinnings of the application of dialogic consensus to clinical practice, and potential difficulties, are explored.

  5. 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

  6. [SECOT consensus on painful knee replacement].

    PubMed

    Vaquero, J; Macule, F; Bello, S; Chana, F; Forriol, F

    2013-01-01

    The opinions of 21 experts in knee surgery were evaluated in this study, using a DELPHI questionnaire method in two successive rounds, on 64 controversial scenarios that covered both the diagnosis and possible treatment of painful knee replacements. The level of consensus was significantly unanimous in 42 items and of the design in 5, with no agreement in 17 of the questions presented. light of the published scientific evidence, the surgeons who took part showed to have a notable level of information on the most effective diagnostic tests, although, it should be pointed out that there was a lack of confidence in the possibility of ruling out an infection when the erythrocyte sedimentation rate and the C-reactive protein were within normal values, which have been demonstrated in the literature to have a high negative predictive value As regards the treatments to employ in the different situations, the responses of the expert panel were mainly in agreement with the data in the literature. The conclusions of this consensus may help other surgeons when they are faced with a painful knee prosthesis.

  7. Universal full-length nucleosome mapping sequence probe.

    PubMed

    Tripathi, Vijay; Salih, Bilal; Trifonov, Edward N

    2015-01-01

    For the computational sequence-directed mapping of the nucleosomes, the knowledge of the nucleosome positioning motifs - 10-11 base long sequences - and respective matrices of bendability, is not sufficient, since there is no justified way to fuse these motifs in one continuous nucleosome DNA sequence. Discovery of the strong nucleosome (SN) DNA sequences, with visible sequence periodicity allows derivation of the full-length nucleosome DNA bendability pattern as matrix or consensus sequence. The SN sequences of three species (A. thaliana, C. elegans, and H. sapiens) are aligned (512 sequences for each species), and long (115 dinucleotides) matrices of bendability derived for the species. The matrices have strong common property - alternation of runs of purine-purine (RR) and pyrimidine-pyrimidine (YY) dinucleotides, with average period 10.4 bases. On this basis the universal [R,Y] consensus of the nucleosome DNA sequence is derived, with exactly defined positions of respective penta- and hexamers RRRRR, RRRRRR, YYYYY, and YYYYYY.

  8. Consensus and Stability Analysis of Networked Multiagent Predictive Control Systems.

    PubMed

    Liu, Guo-Ping

    2016-03-17

    This paper is concerned with the consensus and stability problem of multiagent control systems via networks with communication delays and data loss. A networked multiagent predictive control scheme is proposed to achieve output consensus and also compensate for the communication delays and data loss actively. The necessary and sufficient conditions of achieving both consensus and stability of the closed-loop networked multiagent control systems are derived. An important result that is obtained is that the consensus and stability of closed-loop networked multiagent predictive control systems are not related to the communication delays and data loss. An example illustrates the performance of the networked multiagent predictive control scheme.

  9. Rural/urban elderly and siblings: their value consensus.

    PubMed

    Suggs, P K; Kivett, V R

    Consensus is the level of agreement about life felt among kin and has been identified as a dimension of family solidarity with important implications for the family network. This investigation studied the factors contributing to the consensus between older adults (age sixty-five and older) and the sibling with whom they had the most contact. Respondents (N = 275) lived in a rural/urban area. Seven independent variables were entered into a multiple-regression model to determine their relative importance to consensus of the sibling relationship. Results showed that 7 percent of the variance in consensus could be explained. Filial expectations, educational disparity, and the brother/sister link were the only variables of relative importance to older adult/sibling consensus. There was greater consensus when there were fewer expectations of the sibling, similarity of educational backgrounds, and when the respondent was male and his sibling was female. Brother/sister and brother/brother links, residential proximity, communication by mail or telephone, helping behaviors, and marital status were of no relative importance to consensus. The results suggest that factors previously found to be associated with intergenerational consensus may vary in their importance to intragenerational consensus.

  10. 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.

  11. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

    PubMed Central

    Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S.; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M.; Bhak, Jong

    2016-01-01

    Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. PMID:27882922

  12. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes.

    PubMed

    Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M; Bhak, Jong

    2016-11-24

    Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

  13. Current level of consensus on probiotic science

    PubMed Central

    Capurso, Lucio; Collins, Kevin; Cummings, John; Delzenne, Nathalie; Goulet, Olivier; Guarner, Francisco; Marteau, Philippe; Meier, Rémy

    2010-01-01

    The present paper summarizes the consensus views of a group of 9 European clinicians and scientists on the current state of scientific knowledge on probiotics, covering those areas where there is substantial evidence for beneficial effects and those where the evidence base is poor or inconsistent. There was general agreement that probiotic effects were species and often strain specific. The experts agreed that some probiotics were effective in reducing the incidence and duration of rotavirus diarrhea in infants, antibiotic-associated diarrhea in adults and, for certain probiotics, Clostridium difficile infections. Some probiotics are associated with symptomatic improvements in irritable bowel syndrome and alleviation of digestive discomfort. Probiotics can reduce the frequency and severity of necrotizing enterocolitis in premature infants and have been shown to regulate intestinal immunity. Several other clinical effects of probiotics, including their role in inflammatory bowel disease, atopic dermatitis, respiratory or genito-urinary infections or H. pylori adjuvant treatment were thought promising but inconsistent. PMID:21637035

  14. 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.

  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. [Neonatal screening: trends, debates and consensus].

    PubMed

    Vailly, Joëlle

    2007-03-01

    This study focuses on the social and political implications of the substantial expansion of genetic tests and neonatal screening. The introduction of neonatal screening for cystic fibrosis is one of the significant developments that have fuelled debate on their appropriateness. It has raised a series of questions on the pros and cons, the role of evidence in biomedicine, and the articulation between the therapeutic approach and foetal selection. In this respect France provides an ideal research field as it was one of the first countries to generalize this screening, launched in January 2002. Several questions arise: What were the terms of the debate in France and their underlying logics? How was consensus reached? More generally, what does this screening tell us about policies on life forms today?

  17. Consensus control of flexible-joint robots

    NASA Astrophysics Data System (ADS)

    Avila-Becerril, Sofía; Espinosa-Pérez, Gerardo; Panteley, Elena; Ortega, Romeo

    2015-06-01

    Synchronisation of networks composed by fully actuated robot manipulators has received a lot of attention from the control theory community. Unfortunately, the case of under-actuated robots has not been deeply studied. The aim of this paper is to extend previous results reported by the authors addressing the particular (but of practical interest) case of networks composed by flexible-joint robots. The main feature of the contribution is to consider a change of coordinates, first introduced in Nuno, Ortega, Basanes and Hill, to solve the consensus problem assuming the existence of unknown delays in the communication channels. The extension is twofold, namely: the presentation of a control scheme that, in contrast to the one considered in Avila-Becerril and Espinosa-Perez, does not require knowledge of the initial conditions and the proof that the controller can also be implemented in Cartesian coordinates. The usefulness of the contribution is illustrated through numerical simulations.

  18. 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

  19. Toward a consensus in protein structure nomenclature

    PubMed Central

    DaSilva, Linder C; Gurry, Thomas; Stultz, Collin M

    2014-01-01

    In a recent article, published in Intrinsically Disordered Proteins, a valuable consensus view regarding the nomenclature for disordered proteins was presented.1 In this work the authors present a thoughtful and systemic review of terms that have been used in the literature to describe proteins that sample a heterogeneous set of structures during their biological lifetime. We agree that the term “intrinsically disordered proteins” (IDPs) is an appropriate single descriptor to refer to this particular class of proteins, although it does not fully capture much of the nuanced complexities that are inherent to this class. In what follows we suggest a refinement to this nomenclature based on an analysis of the underlying ensemble that describes the thermally accessible states of a given IDP.

  20. 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

  1. Early Gnathostome Phylogeny Revisited: Multiple Method Consensus

    PubMed Central

    Qiao, Tuo; King, Benedict; Long, John A.; Ahlberg, Per E.; Zhu, Min

    2016-01-01

    A series of recent studies recovered consistent phylogenetic scenarios of jawed vertebrates, such as the paraphyly of placoderms with respect to crown gnathostomes, and antiarchs as the sister group of all other jawed vertebrates. However, some of the phylogenetic relationships within the group have remained controversial, such as the positions of Entelognathus, ptyctodontids, and the Guiyu-lineage that comprises Guiyu, Psarolepis and Achoania. The revision of the dataset in a recent study reveals a modified phylogenetic hypothesis, which shows that some of these phylogenetic conflicts were sourced from a few inadvertent miscodings. The interrelationships of early gnathostomes are addressed based on a combined new dataset with 103 taxa and 335 characters, which is the most comprehensive morphological dataset constructed to date. This dataset is investigated in a phylogenetic context using maximum parsimony (MP), Bayesian inference (BI) and maximum likelihood (ML) approaches in an attempt to explore the consensus and incongruence between the hypotheses of early gnathostome interrelationships recovered from different methods. Our findings consistently corroborate the paraphyly of placoderms, all ‘acanthodians’ as a paraphyletic stem group of chondrichthyans, Entelognathus as a stem gnathostome, and the Guiyu-lineage as stem sarcopterygians. The incongruence using different methods is less significant than the consensus, and mainly relates to the positions of the placoderm Wuttagoonaspis, the stem chondrichthyan Ramirosuarezia, and the stem osteichthyan Lophosteus—the taxa that are either poorly known or highly specialized in character complement. Given that the different performances of each phylogenetic approach, our study provides an empirical case that the multiple phylogenetic analyses of morphological data are mutually complementary rather than redundant. PMID:27649538

  2. A healthy bladder: a consensus statement.

    PubMed

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

    2011-10-01

    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

  3. 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.

  4. Case definitions integrating empiric and consensus perspectives

    PubMed Central

    Jason, Leonard A.; McManimen, Stephanie; Sunnquist, Madison; Brown, Abigail; Furst, Jacob; Newton, Julia L.; Strand, Elin Bolle

    2016-01-01

    Background There has been considerable controversy regarding how to name and define the illnesses known as myalgic encephalomyelitis (ME) and chronic fatigue syndrome (CFS). The IOM report has proposed a new clinical criteria and name for this illness, but aspects of these recommendations have been scrutinized by patients and scientists. Purpose It is possible that both empiric and consensus approaches could be used to help settle some of these diagnostic challenges. Using patient samples collected in the United States, Great Britain, and Norway (N=556), the current study attempted to categorize patients using more general as well as more restricted case definitions. Results Overall, the outcomes suggest that there might be four groupings of patients, with the broadest category involving those with chronic fatigue (N=62), defined by 6 or more months of fatigue which can be cannot be explained by medical or psychiatric conditions. A second category involves those patients that have chronic fatigue that can be explained by a medical or psychiatric condition (N=47). A third category involves more specific criteria that have been posited both by the IOM report, a Canadian Clinical Case criteria, a ME-ICC criteria and a more empiric approach. These efforts have specified domains of substantial reductions of activity, post-exertional malaise, neurocognitive impairment, and sleep dysfunction (N=346). Patients with these characteristics were more functionally impaired than those meeting just chronic fatigue criteria, p < .05. Finally, those meeting even more restrictive ME criteria proposed by Ramsay, identified a smaller and even more impaired group, p < .05. Discussion The advantages of using such empirical and consensus approaches to develop reliable classification and diagnostic efforts are discussed. PMID:27088059

  5. A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

    PubMed Central

    Uitdewilligen, Jan G. A. M. L.; Wolters, Anne-Marie A.; D’hoop, Bjorn B.; Borm, Theo J. A.; Visser, Richard G. F.; van Eck, Herman J.

    2013-01-01

    Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and

  6. Methodological Quality of Consensus Guidelines in Implant Dentistry

    PubMed Central

    Faggion, Clovis Mariano; Apaza, Karol; Ariza-Fritas, Tania; Málaga, Lilian; Giannakopoulos, Nikolaos Nikitas; Alarcón, Marco Antonio

    2017-01-01

    Background Consensus guidelines are useful to improve clinical decision making. Therefore, the methodological evaluation of these guidelines is of paramount importance. Low quality information may guide to inadequate or harmful clinical decisions. Objective To evaluate the methodological quality of consensus guidelines published in implant dentistry using a validated methodological instrument. Methods The six implant dentistry journals with impact factors were scrutinised for consensus guidelines related to implant dentistry. Two assessors independently selected consensus guidelines, and four assessors independently evaluated their methodological quality using the Appraisal of Guidelines for Research & Evaluation (AGREE) II instrument. Disagreements in the selection and evaluation of guidelines were resolved by consensus. First, the consensus guidelines were analysed alone. Then, systematic reviews conducted to support the guidelines were included in the analysis. Non-parametric statistics for dependent variables (Wilcoxon signed rank test) was used to compare both groups. Results Of 258 initially retrieved articles, 27 consensus guidelines were selected. Median scores in four domains (applicability, rigour of development, stakeholder involvement, and editorial independence), expressed as percentages of maximum possible domain scores, were below 50% (median, 26%, 30.70%, 41.70%, and 41.70%, respectively). The consensus guidelines and consensus guidelines + systematic reviews data sets could be compared for 19 guidelines, and the results showed significant improvements in all domain scores (p < 0.05). Conclusions Methodological improvement of consensus guidelines published in major implant dentistry journals is needed. The findings of the present study may help researchers to better develop consensus guidelines in implant dentistry, which will improve the quality and trust of information needed to make proper clinical decisions. PMID:28107405

  7. 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

  8. 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

    1999-04-02

    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.

  9. 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…

  10. The Search for a Value Consensus. Working Papers.

    ERIC Educational Resources Information Center

    Rockefeller Foundation, New York, NY.

    These papers by four social scientists were prepared for a conference to analyze the current absence of a value consensus in American life and to examine grounds for a consensus. Further, the contribution of education and the media to the shaping and dissemination of values is explored. Kenneth Boulding contends that underlying moral diversity is…

  11. 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…

  12. Evidentiary Standards for Consensus Standards in Teacher Education

    ERIC Educational Resources Information Center

    Murray, Frank B.

    2011-01-01

    The standards that currently define a quality teacher or teacher education program derive their authority from the consensus of experts, who negotiate and craft statements that codify their views of best practice. In education, these consensus statements are rarely rooted in the field's established scholarship (as is the case for many standards in…

  13. 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…

  14. 43 CFR 46.110 - Incorporating consensus-based management.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... OF THE NATIONAL ENVIRONMENTAL POLICY ACT OF 1969 Protection and Enhancement of Environmental Quality... a course of action. (b) In incorporating consensus-based management in the NEPA process, bureaus... reasonable consensus-based alternative, if any, is reflected in the evaluation of the proposed action...

  15. 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)

  16. DASACT: A decision aiding software for axiomatic consensus theory.

    PubMed

    Domenach, Florent; Tayari, Ali

    2016-01-01

    There have been various attempts, solutions, and approaches towards constructing an appropriate consensus tree based on a given set of phylogenetic trees. However, for practitioners, it is not always clear, for a given data set, which of these would create the most relevant consensus tree. In this paper, we introduce an open-source software called DASACT (Decision Aiding Software for Axiomatic Consensus Theory) created to assist practitioners on choosing the most appropriate consensus function. It is based on an exhaustive evaluation of axiomatic properties and consensus functions, which define the knowledge space as a concept lattice. Using a selection of axiomatic properties provided by the user, it is able to aid the user in choosing the most suitable function. DASACT is freely available at http://www.cs.unic.ac.cy/florent/software.htm.

  17. Consensus preferred hydration sites in six FKBP12-drug complexes.

    PubMed

    Faerman, C H; Karplus, P A

    1995-09-01

    A set of consensus hydration sites for the FK506-FKBP12 complex are derived by comparing six FKBP12-drug complexes. These hydration sites include a subset of the observed water molecules plus some sites that are occupied by neighboring protein atoms in the FK506-FKBP12 crystal structure. Two hydration prediction algorithms, AUTO-SOL and AQUARIUS2, showed significant increases in apparent efficacy using these consensus water sites, suggesting that our proposed set of consensus hydration sites is truly a better representation of the hydration properties of FKBP12 in solution. Predictably, the consensus hydration sites include all buried water molecules. Otherwise, the features of solvation sites included in the consensus list versus those discarded reveal no distinctive features that would allow them to be selected unambiguously without reference to multiple crystal forms. We suggest that analyses such as this one are a crucial prelude to any theoretical analysis aimed at understanding hydration properties.

  18. The "golden section" and bias in perceptions of social consensus.

    PubMed

    Gross, S R; Miller, N

    1997-01-01

    Meta-analytic examination of I28 false consensus effect issues supports the hypothesis that the "Golden Section" (61.8% group size) approximates the level of actual consensus that separates overestimation of consensus (group size < 61.8%) from underestimation (group size > 61.8%). Overestimation of the actual percentage of others who endorse one's own view increases as actual consensus decreases from 61.8%, and underestimation increases as it exceeds 61.8%. The form of the response (viz, a yes or no answer to a question) moderates this conclusion. The Golden Section holds for majorities and minorities defined by agreement with an issue. For majority and minority groups defined by disagreement, the inflection point is higher. Contrary to Mullen and Hu (1988), for agreeing majorities, the slope for consensus underestimation as a function of increased majority size does not differ from that of minority overestimation.

  19. 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.

  20. Compilation and analysis of Escherichia coli promoter DNA sequences.

    PubMed Central

    Hawley, D K; McClure, W R

    1983-01-01

    The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence. PMID:6344016

  1. 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.

  2. 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.

  3. 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

  4. Bleeding avoidance strategies. Consensus and controversy.

    PubMed

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

    2011-06-28

    Bleeding complications after coronary intervention are associated with prolonged hospitalization, increased hospital costs, patient dissatisfaction, morbidity, and 1-year mortality. Bleeding avoidance strategies is 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 suggest 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), pharmacological (multiple agents), and technological (vascular closure devices) approaches to improved access. In this paper, 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.

  5. 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.

  6. 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.

  7. Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.

    PubMed

    Kandoi, Gaurav; Leelananda, Sumudu P; Jernigan, Robert L; Sen, Taner Z

    2017-01-01

    Predicting the secondary structure of a protein from its sequence still remains a challenging problem. The prediction accuracies remain around 80 %, and for very diverse methods. Using evolutionary information and machine learning algorithms in particular has had the most impact. In this chapter, we will first define secondary structures, then we will review the Consensus Data Mining (CDM) technique based on the robust GOR algorithm and Fragment Database Mining (FDM) approach. GOR V is an empirical method utilizing a sliding window approach to model the secondary structural elements of a protein by making use of generalized evolutionary information. FDM uses data mining from experimental structure fragments, and is able to successfully predict the secondary structure of a protein by combining experimentally determined structural fragments based on sequence similarities of the fragments. The CDM method combines predictions from GOR V and FDM in a hierarchical manner to produce consensus predictions for secondary structure. In other words, if sequence fragment are not available, then it uses GOR V to make the secondary structure prediction. The online server of CDM is available at http://gor.bb.iastate.edu/cdm/ .

  8. Event-Triggered Distributed Average Consensus Over Directed Digital Networks With Limited Communication Bandwidth.

    PubMed

    Li, Huaqing; Chen, Guo; Huang, Tingwen; Dong, Zhaoyang; Zhu, Wei; Gao, Lan

    2016-12-01

    In this paper, we consider the event-triggered distributed average-consensus of discrete-time first-order multiagent systems with limited communication data rate and general directed network topology. In the framework of digital communication network, each agent has a real-valued state but can only exchange finite-bit binary symbolic data sequence with its neighborhood agents at each time step due to the digital communication channels with energy constraints. Novel event-triggered dynamic encoder and decoder for each agent are designed, based on which a distributed control algorithm is proposed. A scheme that selects the number of channel quantization level (number of bits) at each time step is developed, under which all the quantizers in the network are never saturated. The convergence rate of consensus is explicitly characterized, which is related to the scale of network, the maximum degree of nodes, the network structure, the scaling function, the quantization interval, the initial states of agents, the control gain and the event gain. It is also found that under the designed event-triggered protocol, by selecting suitable parameters, for any directed digital network containing a spanning tree, the distributed average consensus can be always achieved with an exponential convergence rate based on merely one bit information exchange between each pair of adjacent agents at each time step. Two simulation examples are provided to illustrate the feasibility of presented protocol and the correctness of the theoretical results.

  9. The Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of prostate carcinoma.

    PubMed

    McNeel, Douglas G; Bander, Neil H; Beer, Tomasz M; Drake, Charles G; Fong, Lawrence; Harrelson, Stacey; Kantoff, Philip W; Madan, Ravi A; Oh, William K; Peace, David J; Petrylak, Daniel P; Porterfield, Hank; Sartor, Oliver; Shore, Neal D; Slovin, Susan F; Stein, Mark N; Vieweg, Johannes; Gulley, James L

    2016-01-01

    Prostate cancer is the most commonly diagnosed malignancy and second leading cause of cancer death among men in the United States. In recent years, several new agents, including cancer immunotherapies, have been approved or are currently being investigated in late-stage clinical trials for the management of advanced prostate cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) convened a multidisciplinary panel, including physicians, nurses, and patient advocates, to develop consensus recommendations for the clinical application of immunotherapy for prostate cancer patients. To do so, a systematic literature search was performed to identify high-impact papers from 2006 until 2014 and was further supplemented with literature provided by the panel. Results from the consensus panel voting and discussion as well as the literature review were used to rate supporting evidence and generate recommendations for the use of immunotherapy in prostate cancer patients. Sipuleucel-T, an autologous dendritic cell vaccine, is the first and currently only immunotherapeutic agent approved for the clinical management of metastatic castrate resistant prostate cancer (mCRPC). The consensus panel utilized this model to discuss immunotherapy in the treatment of prostate cancer, issues related to patient selection, monitoring of patients during and post treatment, and sequence/combination with other anti-cancer treatments. Potential immunotherapies emerging from late-stage clinical trials are also discussed. As immunotherapy evolves as a therapeutic option for the treatment of prostate cancer, these recommendations will be updated accordingly.

  10. Event-triggered nonlinear consensus in directed multi-agent systems with combinational state measurements

    NASA Astrophysics Data System (ADS)

    Li, Huaqing; Chen, Guo; Xiao, Li

    2016-10-01

    Event-triggered sampling control is motivated by the applications of embedded microprocessors equipped in the agents with limited computation and storage resources. This paper studied global consensus in multi-agent systems with inherent nonlinear dynamics on general directed networks using decentralised event-triggered strategy. For each agent, the controller updates are event-based and only triggered at its own event times by only utilising the locally current sampling data. A high-performance sampling event that only needs local neighbours' states at their own discrete time instants is presented. Furthermore, we introduce two kinds of general algebraic connectivity for strongly connected networks and strongly connected components of the directed network containing a spanning tree so as to describe the system's ability for reaching consensus. A detailed theoretical analysis on consensus is performed and two criteria are derived by virtue of algebraic graph theory, matrix theory and Lyapunov control approach. It is shown that the Zeno behaviour of triggering time sequence is excluded during the system's whole working process. A numerical simulation is given to show the effectiveness of the theoretical results.

  11. BRAZILIAN CONSENSUS FOR MULTIMODAL TREATMENT OF COLORECTAL LIVER METASTASES. MODULE 3: CONTROVERSIES AND UNRESECTABLE METASTASES

    PubMed Central

    TORRES, Orlando Jorge Martins; MARQUES, Márcio Carmona; SANTOS, Fabio Nasser; de FARIAS, Igor Correia; COUTINHO, Anelisa Kruschewsky; de OLIVEIRA, Cássio Virgílio Cavalcante; KALIL, Antonio Nocchi; de MELLO, Celso Abdon Lopes; KRUGER, Jaime Arthur Pirola; FERNANDES, Gustavo dos Santos; QUIREZE JR, Claudemiro; MURAD, André M.; SILVA, Milton José de BARROS E; ZURSTRASSEN, Charles Edouard; FREITAS, Helano Carioca; CRUZ, Marcelo Rocha; WESCHENFELDER, Rui; LINHARES, Marcelo Moura; CASTRO, Leonaldson dos Santos; VOLLMER, Charles; DIXON, Elijah; RIBEIRO, Héber Salvador de Castro; COIMBRA, Felipe José Fernandez

    2016-01-01

    ABSTRACT In the last module of this consensus, controversial topics were discussed. Management of the disease after progression during first line chemotherapy was the first discussion. Next, the benefits of liver resection in the presence of extra-hepatic disease were debated, as soon as, the best sequence of treatment. Conversion chemotherapy in the presence of unresectable liver disease was also discussed in this module. Lastly, the approach to the unresectable disease was also discussed, focusing in the best chemotherapy regimens and hole of chemo-embolization. PMID:27759781

  12. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  13. Finding Optimal Alignment and Consensus of Circular Strings

    NASA Astrophysics Data System (ADS)

    Lee, Taehyung; Na, Joong Chae; Park, Heejin; Park, Kunsoo; Sim, Jeong Seop

    We consider the problem of finding the optimal alignment and consensus (string) of circular strings. Circular strings are different from linear strings in that the first (leftmost) symbol of a circular string is wrapped around next to the last (rightmost) symbol. In nature, for example, bacterial and mitochondrial DNAs typically form circular strings. The consensus string problem is finding a representative string (consensus) of a given set of strings, and it has been studied on linear strings extensively. However, only a few efforts have been made for the consensus problem for circular strings, even though circular strings are biologically important. In this paper, we introduce the consensus problem for circular strings and present novel algorithms to find the optimal alignment and consensus of circular strings under the Hamming distance metric. They are O(n 2logn)-time algorithms for three circular strings and an O(n 3logn)-time algorithm for four circular strings. Our algorithms are O(n/ logn) times faster than the naïve algorithm directly using the solutions for the linear consensus problems, which takes O(n 3) time for three circular strings and O(n 4) time for four circular strings. We achieved this speedup by adopting a convolution and a system of linear equations into our algorithms to reflect the characteristics of circular strings that we found.

  14. 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.

  15. [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.

  16. 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.

  17. 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.

  18. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement.

    PubMed

    Chaffin, Ashley S; Huang, Yung-Fen; Smith, Scott; Bekele, Wubishet A; Babiker, Ebrahiem; Gnanesh, Belaghihalli N; Foresman, Bradley J; Blanchard, Steven G; Jay, Jeremy J; Reid, Robert W; Wight, Charlene P; Chao, Shiaoman; Oliver, Rebekah; Islamovic, Emir; Kolb, Frederic L; McCartney, Curt; Mitchell Fetch, Jennifer W; Beattie, Aaron D; Bjørnstad, Åsmund; Bonman, J Michael; Langdon, Tim; Howarth, Catherine J; Brouwer, Cory R; Jellen, Eric N; Klos, Kathy Esvelt; Poland, Jesse A; Hsieh, Tzung-Fu; Brown, Ryan; Jackson, Eric; Schlueter, Jessica A; Tinker, Nicholas A

    2016-07-01

    Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

  19. Management of Neuroblastoma: ICMR Consensus Document.

    PubMed

    Bansal, Deepak; Totadri, Sidharth; Chinnaswamy, Girish; Agarwala, Sandeep; Vora, Tushar; Arora, Brijesh; Prasad, Maya; Kapoor, Gauri; Radhakrishnan, Venkatraman; Laskar, Siddharth; Kaur, Tanvir; Rath, G K; Bakhshi, Sameer

    2017-04-03

    Neuroblastoma (NBL) is the most common extra-cranial solid tumor in childhood. High-risk NBL is considered challenging and has one of the least favourable outcomes amongst pediatric cancers. Primary tumor can arise anywhere along the sympathetic chain. Advanced disease at presentation is common. Diagnosis is established by tumor biopsy and elevated urinary catecholamines. Staging is performed using bone marrow and mIBG scan (FDG-PET/bone scan if mIBG unavailable or non-avid). Age, stage, histopathological grading, MYCN amplification and 11q aberration are important prognostic factors utilized in risk stratification. Low-risk disease including Stage 1 and asymptomatic Stage 2 disease has an excellent prognosis with non-mutilating surgery alone. Perinatal adrenal neuroblastoma may be managed with close observation alone. Intermediate-risk disease consisting largely of unresectable/symptomatic Stage 2/3 disease and infants with Stage 4 disease has good outcome with few cycles of chemotherapy followed by surgical resection. Paraspinal neuroblastomas with cord compression are treated emergently, typically with upfront chemotherapy. Asymptomatic Stage 4S disease may be followed closely without treatment. Organ dysfunction and age below 3 mo would warrant chemotherapy in 4S. High-risk disease includes older children with Stage 4 disease and MYCN amplified tumors. High-risk disease has a suboptimal outcome, though the survival is improving with multimodality therapy including autologous stem cell transplant and immunotherapy. Relapse after multimodality therapy is difficult to salvage. Late presentation, lack of transplant facility, malnutrition and treatment abandonment are additional hurdles for survival in India. The review provides a consensus document on management of NBL for developing countries, including India.

  20. 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.

  1. Undescended testes: a consensus on management.

    PubMed

    Ritzén, E Martin

    2008-12-01

    The mode of treatment best for undescended testes is controversial, and local traditions often override knowledge gained from randomized controlled studies. In order to reach a consensus within the Nordic countries on the current state-of-the-art of treatment, a group of specialists in testicular physiology, paediatric surgery/urology, endocrinology, andrology, pathology and anaesthesiology from all the Nordic countries met for 2 days. Before the meeting, reviews of the literature had been prepared by the participants. Judging from published meta-analyses, hormonal treatment has low efficacy. Although 15-20% of retained testes descend during hormonal treatment, one-fifth of these re-ascend later on. Also, treatment with human chorionic gonadotropin (hCG) may be harmful to future spermatogenesis through increased apoptosis of germ cells. Orchiopexy, on the contrary, results in about 95% anatomical success, with a low (about 1%) risk of complications. The optimal time for orchiopexy has also been debated. However, a recent randomized controlled study shows that surgery at 9 months of age is followed by a better post-operative growth of the testes than surgery at 3 years, which supports previous arguments for early surgery. The unanimous conclusion of the group was that surgery is generally the preferred mode of treatment, rather than hCG or GnRH treatments. Orchiopexy should be performed between 6 and 12 months of age, or soon after diagnosis, if that occurs later. If a testis is found to be undescended at any age after 6 months, the patient should be referred for surgery. Referral should be to paediatric rather than general surgeons/urologists if the boy is less than 1 year old, if he has bilateral or non-palpable testes, or if he has got relapse of cryptorchidism.

  2. Carotid endarterectomy: current consensus and controversies.

    PubMed

    Meerwaldt, Robbert; Hermus, Linda; Reijnen, Michel M P J; Zeebregts, Clark J

    2010-10-01

    Stroke is the third most common cause of mortality, and carotid artery stenosis causes 8% to 29% of all ischemic strokes. Best medical treatment forms the basis of carotid stenosis treatment, and carotid endarterectomy (CEA) has an additional beneficial effect in high-grade stenosis. Carotid angioplasty and stenting (CAS) has challenged CEA as a primary carotid intervention. At present, CEA remains the gold standard, but in the future, CAS techniques will evolve and might become beneficial for subgroups of patients with carotid stenosis. This chapter briefly describes the history of carotid interventions and current consensus and controversies in CEA. In the last two years, several meta-analyses were published on a variety of aspects of best medical treatment, CEA, and CAS. It is still a matter of debate as to whether asymptomatic patients with carotid stenosis should undergo a carotid intervention. Especially because medical treatment has dramatically evolved since the early carotid trials. On the other hand, it is clear that carotid interventions in symptomatic patients with a high-grade stenosis should be performed as early as possible after the initial neurological event in order to achieve optimal stroke risk reduction. In CEA, the use of patching is advocated above primary closure, while the role of selective patching is still unclear. No differences in stroke and mortality rates are observed for routine versus selective shunting, for conventional versus eversion CEA, or for local versus general anesthesia. It is anticipated that in the future, there will be several interesting developments in carotid interventions such as plaque morphology analysis, acute interventions during stroke in progress, and further evolvement of CAS techniques.

  3. 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

  4. The development of a consensus definition for healthcare improvement science (HIS) in seven European countries: A consensus methods approach

    PubMed Central

    Macrae, Rhoda; Lillo-Crespo, Manuel; Rooney, Kevin D

    2017-01-01

    Abstract Introduction There is a limited body of research in the field of healthcare improvement science (HIS). Quality improvement and ‘change making’ should become an intrinsic part of everyone’s job, every day in all parts of the healthcare system. The lack of theoretical grounding may partly explain the minimal transfer of health research into health policy. Methods This article seeks to present the development of the definition for healthcare improvement science. A consensus method approach was adopted with a two-stage Delphi process, expert panel and consensus group techniques. A total of 18 participants were involved in the expert panel and consensus group, and 153 answers were analysed as a part of the Delphi survey. Participants were researchers, educators and healthcare professionals from Scotland, Slovenia, Spain, Italy, England, Poland, and Romania. Results A high level of consensus was achieved for the broad definition in the 2nd Delphi iteration (86%). The final definition was agreed on by the consensus group: ‘Healthcare improvement science is the generation of knowledge to cultivate change and deliver person-centred care that is safe, effective, efficient, equitable and timely. It improves patient outcomes, health system performance and population health.’ Conclusions The process of developing a consensus definition revealed different understandings of healthcare improvement science between the participants. Having a shared consensus definition of healthcare improvement science is an important step forward, bringing about a common understanding in order to advance the professional education and practice of healthcare improvement science. PMID:28289467

  5. 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.

  6. Efficient Globally Optimal Consensus Maximisation with Tree Search.

    PubMed

    Chin, Tat-Jun; Purkait, Pulak; Eriksson, Anders; Suter, David

    2017-04-01

    Maximum consensus is one of the most popular criteria for robust estimation in computer vision. Despite its widespread use, optimising the criterion is still customarily done by randomised sample-and-test techniques, which do not guarantee optimality of the result. Several globally optimal algorithms exist, but they are too slow to challenge the dominance of randomised methods. Our work aims to change this state of affairs by proposing an efficient algorithm for global maximisation of consensus. Under the framework of LP-type methods, we show how consensus maximisation for a wide variety of vision tasks can be posed as a tree search problem. This insight leads to a novel algorithm based on A* search. We propose efficient heuristic and support set updating routines that enable A* search to efficiently find globally optimal results. On common estimation problems, our algorithm is much faster than previous exact methods. Our work identifies a promising direction for globally optimal consensus maximisation.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Consensus Statement on Standard of Care for Congenital Muscular Dystrophies

    PubMed Central

    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

    2016-01-01

    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

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

    PubMed Central

    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

    2016-01-01

    Summary 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

  14. Consensus algorithm in smart grid and communication networks

    NASA Astrophysics Data System (ADS)

    Alfagee, Husain Abdulaziz

    On a daily basis, consensus theory attracts more and more researches from different areas of interest, to apply its techniques to solve technical problems in a way that is faster, more reliable, and even more precise than ever before. A power system network is one of those fields that consensus theory employs extensively. The use of the consensus algorithm to solve the Economic Dispatch and Load Restoration Problems is a good example. Instead of a conventional central controller, some researchers have explored an algorithm to solve the above mentioned problems, in a distribution manner, using the consensus algorithm, which is based on calculation methods, i.e., non estimation methods, for updating the information consensus matrix. Starting from this point of solving these types of problems mentioned, specifically, in a distribution fashion, using the consensus algorithm, we have implemented a new advanced consensus algorithm. It is based on the adaptive estimation techniques, such as the Gradient Algorithm and the Recursive Least Square Algorithm, to solve the same problems. This advanced work was tested on different case studies that had formerly been explored, as seen in references 5, 7, and 18. Three and five generators, or agents, with different topologies, correspond to the Economic Dispatch Problem and the IEEE 16-Bus power system corresponds to the Load Restoration Problem. In all the cases we have studied, the results met our expectations with extreme accuracy, and completely matched the results of the previous researchers. There is little question that this research proves the capability and dependability of using the consensus algorithm, based on the estimation methods as the Gradient Algorithm and the Recursive Least Square Algorithm to solve such power problems.

  15. Diagnosis and treatment of acromegaly and its complications: consensus guidelines.

    PubMed

    Bonadonna, S; Doga, M; Gola, M; Mazziotti, G; Giustina, A

    2005-01-01

    In February 1999, May 2000 and April 2002, three workshops were held in Cortina, Montecarlo and Versailles, respectively, to develop a consensus defining the diagnosis and treatment of acromegaly and its complications. The workshops were sponsored by the Pituitary Society and European Neuroendocrine Association. Invited international participants included endocrinologists, neurosurgeons and radiotherapists skilled in the management of acromegaly. This review paper summarizes the main points of the three consensus statements published following these three workshops.

  16. 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.

  17. Mapping Replication Origin Sequences in Eukaryotic Chromosomes

    PubMed Central

    Fu, Haiqing; Besnard, Emilie; Desprat, Romain; Ryan, Michael; Kahli, Malik; Lemaitre, Jean-Marc; Aladjem, Mirit I.

    2014-01-01

    Recent advances in genome sequencing technology have led towards the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates the understanding of the relationship between replication initiation events, transcription and chromatin modifications and allows the characterization of consensus sequences of potential replication origins. This unit provides a detailed protocol for isolation and sequence analyses of nascent DNA strands. Two variations of the protocol based on non-overlapping assumptions are described below, addressing potential bias issues for whole genome analyses. PMID:25447077

  18. A consensus opinion model based on the evolutionary game

    NASA Astrophysics Data System (ADS)

    Yang, Han-Xin

    2016-08-01

    We propose a consensus opinion model based on the evolutionary game. In our model, both of the two connected agents receive a benefit if they have the same opinion, otherwise they both pay a cost. Agents update their opinions by comparing payoffs with neighbors. The opinion of an agent with higher payoff is more likely to be imitated. We apply this model in scale-free networks with tunable degree distribution. Interestingly, we find that there exists an optimal ratio of cost to benefit, leading to the shortest consensus time. Qualitative analysis is obtained by examining the evolution of the opinion clusters. Moreover, we find that the consensus time decreases as the average degree of the network increases, but increases with the noise introduced to permit irrational choices. The dependence of the consensus time on the network size is found to be a power-law form. For small or larger ratio of cost to benefit, the consensus time decreases as the degree exponent increases. However, for moderate ratio of cost to benefit, the consensus time increases with the degree exponent. Our results may provide new insights into opinion dynamics driven by the evolutionary game theory.

  19. 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

  20. 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

  1. Improved thermostability of Clostridium thermocellum endoglucanase Cel8A by using consensus-guided mutagenesis.

    PubMed

    Anbar, Michael; Gul, Ozgur; Lamed, Raphael; Sezerman, Ugur O; Bayer, Edward A

    2012-05-01

    The use of thermostable cellulases is advantageous for the breakdown of lignocellulosic biomass toward the commercial production of biofuels. Previously, we have demonstrated the engineering of an enhanced thermostable family 8 cellulosomal endoglucanase (EC 3.2.1.4), Cel8A, from Clostridium thermocellum, using random error-prone PCR and a combination of three beneficial mutations, dominated by an intriguing serine-to-glycine substitution (M. Anbar, R. Lamed, E. A. Bayer, ChemCatChem 2:997-1003, 2010). In the present study, we used a bioinformatics-based approach involving sequence alignment of homologous family 8 glycoside hydrolases to create a library of consensus mutations in which residues of the catalytic module are replaced at specific positions with the most prevalent amino acids in the family. One of the mutants (G283P) displayed a higher thermal stability than the wild-type enzyme. Introducing this mutation into the previously engineered Cel8A triple mutant resulted in an optimized enzyme, increasing the half-life of activity by 14-fold at 85°C. Remarkably, no loss of catalytic activity was observed compared to that of the wild-type endoglucanase. The structural changes were simulated by molecular dynamics analysis, and specific regions were identified that contributed to the observed thermostability. Intriguingly, most of the proteins used for sequence alignment in determining the consensus residues were derived from mesophilic bacteria, with optimal temperatures well below that of C. thermocellum Cel8A.

  2. Towards a European consensus for reporting incidental findings during clinical NGS testing

    PubMed Central

    Hehir-Kwa, Jayne Y; Claustres, Mireille; Hastings, Ros J; van Ravenswaaij-Arts, Conny; Christenhusz, Gabrielle; Genuardi, Maurizio; Melegh, Béla; Cambon-Thomsen, Anne; Patsalis, Philippos; Vermeesch, Joris; Cornel, Martina C; Searle, Beverly; Palotie, Aarno; Capoluongo, Ettore; Peterlin, Borut; Estivill, Xavier; Robinson, Peter N

    2015-01-01

    In 2013, the American College of Medical Genetics (ACMG) examined the issue of incidental findings in whole exome and whole genome sequencing, and introduced recommendations to search for, evaluate and report medically actionable variants in a set of 56 genes. At a debate held during the 2014 European Society for Human Genetics Conference (ESHG) in Milan, Italy, the first author of that paper presented this view in a debate session that did not end with a conclusive vote from the mainly European audience for or against reporting back actionable incidental findings. In this meeting report, we elaborate on the discussions held during a special meeting hosted at the ESHG in 2013 from posing the question ‘How to reach a (European) consensus on reporting incidental findings and unclassified variants in diagnostic next generation sequencing'. We ask whether an European consensus exists on the reporting of incidental findings in genome diagnostics, and present a series of key issues that require discussion at both a national and European level in order to develop recommendations for handling incidental findings and unclassified variants in line with the legal and cultural particularities of individual European member states. PMID:26036857

  3. 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

  4. 2014 consensus statement from the first Economics of Physical Inactivity Consensus (EPIC) conference (Vancouver).

    PubMed

    Davis, Jennifer C; Verhagen, Evert; Bryan, Stirling; Liu-Ambrose, Teresa; Borland, Jeff; Buchner, David; Hendriks, Marike R C; Weiler, Richard; Morrow, James R; van Mechelen, Willem; Blair, Steven N; Pratt, Mike; Windt, Johann; al-Tunaiji, Hashel; Macri, Erin; Khan, Karim M

    2014-06-01

    This article describes major topics discussed from the 'Economics of Physical Inactivity Consensus Workshop' (EPIC), held in Vancouver, Canada, in April 2011. Specifically, we (1) detail existing evidence on effective physical inactivity prevention strategies; (2) introduce economic evaluation and its role in health policy decisions; (3) discuss key challenges in establishing and building health economic evaluation evidence (including accurate and reliable costs and clinical outcome measurement) and (4) provide insight into interpretation of economic evaluations in this critically important field. We found that most methodological challenges are related to (1) accurately and objectively valuing outcomes; (2) determining meaningful clinically important differences in objective measures of physical inactivity; (3) estimating investment and disinvestment costs and (4) addressing barriers to implementation. We propose that guidelines specific for economic evaluations of physical inactivity intervention studies are developed to ensure that related costs and effects are robustly, consistently and accurately measured. This will also facilitate comparisons among future economic evidence.

  5. Characterization of insertion sequence IS892 and related elements from the cyanobacterium Anabaena sp. strain PCC 7120.

    PubMed Central

    Cai, Y

    1991-01-01

    IS892, one of the several insertion sequence (IS) elements discovered in Anabaena sp. strain PCC 7120 (Y. Cai and C. P. Wolk, J. Bacteriol. 172:3138-3145, 1990), is 1,675 bp with 24-bp near-perfect inverted terminal repeats and has two open reading frames (ORFs) that could code for proteins of 233 and 137 amino acids. Upon insertion into target sites, this IS generates an 8-bp directly repeated target duplication. A 32-bp sequence in the region between ORF1 and ORF2 is similar to the sequence of the inverted termini. Similar inverted repeats are found within each of those three segments, and the sequences of these repeats bear some similarity to the 11-bp direct repeats flanking the 11-kb insertion interrupting the nifD gene of this strain (J. W. Golden, S. J. Robinson, and R. Haselkorn, Nature [London] 314:419-423, 1985). A sequence similar to that of a binding site for the Escherichia coli integration host factor is found about 120 bp from the left end of IS892. Partial nucleotide sequences of active IS elements IS892N and IS892T, members of the IS892 family from the same Anabaena strain, were shown to be very similar to the sequence of IS892. Images PMID:1653218

  6. A Consensus on Mantle Potential Temperatures? (Invited)

    NASA Astrophysics Data System (ADS)

    Putirka, K. D.

    2009-12-01

    Recent publications may indicate a mounting consensus regarding mantle temperatures - an agreement that can be crucial for improving our understanding of mantle dynamics. To compare temperatures at various localities, McKenzie & Bickle (1988) proposed the concept of a mantle potential temperature (Tp) as a reference; Tp is the temperature the mantle would have at the surface, if it ascended along an adiabat without undergoing melting. Perhaps the most precise method to estimate Tp involves estimating the conditions of partial melting, and then correcting for the heat of fusion. The several sources of error include estimation of: a parental liquid, an equilibrium mantle olivine, the degree of partial melting (F), and the depth at which the parental melt is generated. There is also model error inherent to any thermometer. And when correcting for the heat of fusion we assume that we are correcting up to the convective adiabat, but if the parental melt was generated within the conductive lithosphere, Tp will be low. In any case, if we accept that the highest Tp estimates at Hawaii are of most interest (since magmas generated away from a plume centerline will not reflect the full heat content of a high T source), then in spite of these sources of error, recent estimates, published over a span of 10 months by three independent research groups, indicate considerable convergence. At Hawaii maximum Tp values are: 1600 deg. C by Herzberg & Asimow (2008), ca. 1630 deg. C by Lee et al. (2009; their Fig. 2B), and using two slightly different equation sets, 1687 deg. C by Putirka (2008; Geology) and 1660 deg. C by Putirka (2008; RiMG volume 69), yielding an average of 1644±38oC. Similarly, there is convergence for mean Tp at MORs (accepting that MORs are not isothermal; Klein and Langmuir, 1987): Herzberg & Asimow (2008) and Lee et al. (2009) estimate that Tp is ca. 1350 deg. C, and Putirka (2008; Geology) estimates a Tp of 1396 deg. C; these estimates average to 1365±26o

  7. Big cat phylogenies, consensus trees, and computational thinking.

    PubMed

    Sul, Seung-Jin; Williams, Tiffani L

    2011-07-01

    Phylogenetics seeks to deduce the pattern of relatedness between organisms by using a phylogeny or evolutionary tree. For a given set of organisms or taxa, there may be many evolutionary trees depicting how these organisms evolved from a common ancestor. As a result, consensus trees are a popular approach for summarizing the shared evolutionary relationships in a group of trees. We examine these consensus techniques by studying how the pantherine lineage of cats (clouded leopard, jaguar, leopard, lion, snow leopard, and tiger) evolved, which is hotly debated. While there are many phylogenetic resources that describe consensus trees, there is very little information, written for biologists, regarding the underlying computational techniques for building them. The pantherine cats provide us with a small, relevant example to explore the computational techniques (such as sorting numbers, hashing functions, and traversing trees) for constructing consensus trees. Our hope is that life scientists enjoy peeking under the computational hood of consensus tree construction and share their positive experiences with others in their community.

  8. 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

  9. Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.

    PubMed

    Li, Zhenyu; Chen, Yanxiang; Mu, Desheng; Yuan, Jianying; Shi, Yujian; Zhang, Hao; Gan, Jun; Li, Nan; Hu, Xuesong; Liu, Binghang; Yang, Bicheng; Fan, Wei

    2012-01-01

    Since the completion of the cucumber and panda genome projects using Illumina sequencing in 2009, the global scientific community has had to pay much more attention to this new cost-effective approach to generate the draft sequence of large genomes. To allow new users to more easily understand the assembly algorithms and the optimum software packages for their projects, we make a detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, from how they match the Lander-Waterman model, to the required sequencing depth and reads length. We also discuss the computational efficiency of each class of algorithm, the influence of repeats and heterozygosity and points of note in the subsequent scaffold linkage and gap closure steps. We hope this review can help further promote the application of second-generation de novo sequencing, as well as aid the future development of assembly algorithms.

  10. Sequencing technologies and genome sequencing.

    PubMed

    Pareek, Chandra Shekhar; Smoczynski, Rafal; Tretyn, Andrzej

    2011-11-01

    The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

  11. 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

  12. Dysglycemias in pregnancy: from diagnosis to treatment. Brazilian consensus statement

    PubMed Central

    2010-01-01

    There is an urgent need to find consensus on screening, diagnosing and treating all degrees of DYSGLYCEMIA that may occur during pregnancies in Brazil, considering that many cases of DYSGLYCEMIA in pregnant women are currently not diagnosed, leading to maternal and fetal complications. For this reason the Brazilian Diabetes Society (SBD) and the Brazilian Federation of Gynecology and Obstetrics Societies (FEBRASGO), got together to introduce this proposal. We present here a joint consensus regarding the standardization of clinical management for pregnant women with any degree of Dysglycemia, on the basis of current information, to improve medical assistance and to avoid related complications of Dysglycemia in pregnancy to the mother and the fetus. This consensus aims to standardize the diagnosis among general practitioners, endocrinologists and obstetricians allowing the dissemination of information in basic health units, public and private services, that are responsible for screening, diagnosing and treating disglycemic pregnant patients. PMID:20416099

  13. 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.

  14. 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.

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

    PubMed

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

    2014-06-03

    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.

  16. Monoclonal gammopathy of undetermined significance: a consensus statement.

    PubMed

    Berenson, James R; Anderson, Kenneth C; Audell, Robert A; Boccia, Ralph V; Coleman, Morton; Dimopoulos, Meletios A; Drake, Matthew T; Fonseca, Rafael; Harousseau, Jean-Luc; Joshua, Douglas; Lonial, Sagar; Niesvizky, Ruben; Palumbo, Antonio; Roodman, G David; San-Miguel, Jesus F; Singhal, Seema; Weber, Donna M; Zangari, Maurizio; Wirtschafter, Eric; Yellin, Ori; Kyle, Robert A

    2010-07-01

    On February 25, 2009, a panel of international experts on plasma cell dyscrasia and skeletal disease met to discuss monoclonal gammopathy of undetermined significance (MGUS). This non-malignant B-cell disorder is the most common plasma cell dyscrasia and is associated with an increased risk of developing serious B-cell disorders. Individuals with MGUS also have an increased risk of osteoporosis and osteopenia associated with an increased likelihood of developing fractures especially in the vertebral column, peripheral neuropathy and thromboembolic events. The goal of the meeting was to develop a consensus statement regarding the appropriate tests to screen, evaluate and follow-up patients with MGUS. The panel also addressed the identification and treatment of MGUS-related skeletal problems, thromboembolic events and neurological complications. The following consensus statement outlines the conclusions and marks the first time that a consensus statement for the screening and treatment of MGUS has been clearly stated.

  17. Consensus of synchronization-preferential scale-free networks

    NASA Astrophysics Data System (ADS)

    Hongyong, Yang; Lan, Lu; Siying, Zhang

    2010-08-01

    In this paper, the relations of the scale-free network topology and the moving consensus of multi-agent systems are studied. A synchronization-preferential BA (SPBA) network with the combinatorial preferential attachment is presented for the prestissimo consensus. The effects of the SPBA network on the algebraic connectivity of the topology graph are compared with the standard BA network. The robustness gain to delay is analyzed for variable network topologies with the same size. The characteristics of dramatic increase for the algebraic connectivity and slightly increase for the robustness gain to delay are unfolded in SPBA network. By comparing the convergence time of the different network structures, the consensuses are studied for multiagent systems with and without communication delays.

  18. The importance of assessing and communicating scientific consensus

    NASA Astrophysics Data System (ADS)

    Maibach, Edward W.; van der Linden, Sander L.

    2016-09-01

    The spread of influential misinformation, such as conspiracy theories about the existence of a secret, large-scale atmospheric spraying program (SLAP), is contributing to the politicization of science. In an important recent study, Shearer et al (2016 Environ. Res. Lett. 11 084011) employ a novel methodology to quantify the expert consensus of popular SLAP assertions. The authors find that 99% (76/77) of surveyed experts have not encountered any evidence that would support the existence of such a program. Here we argue that this finding is important because a growing body of research has shown that the public’s perception of expert consensus on key societal issues acts an important ‘gateway’ to science acceptance. Furthermore, communicating normative agreement among experts, such as the strong scientific consensus against the existence of a SLAP, can help limit the spread of misinformation and promote more effective public decision-making about science and society.

  19. 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

  20. Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome

    PubMed Central

    Hüser, Daniela; Gogol-Döring, Andreas; Lutter, Timo; Weger, Stefan; Winter, Kerstin; Hammer, Eva-Maria; Cathomen, Toni; Reinert, Knut; Heilbronn, Regine

    2010-01-01

    Adeno-associated virus type 2 (AAV) is known to establish latency by preferential integration in human chromosome 19q13.42. The AAV non-structural protein Rep appears to target a site called AAVS1 by simultaneously binding to Rep-binding sites (RBS) present on the AAV genome and within AAVS1. In the absence of Rep, as is the case with AAV vectors, chromosomal integration is rare and random. For a genome-wide survey of wildtype AAV integration a linker-selection-mediated (LSM)-PCR strategy was designed to retrieve AAV-chromosomal junctions. DNA sequence determination revealed wildtype AAV integration sites scattered over the entire human genome. The bioinformatic analysis of these integration sites compared to those of rep-deficient AAV vectors revealed a highly significant overrepresentation of integration events near to consensus RBS. Integration hotspots included AAVS1 with 10% of total events. Novel hotspots near consensus RBS were identified on chromosome 5p13.3 denoted AAVS2 and on chromsome 3p24.3 denoted AAVS3. AAVS2 displayed seven independent junctions clustered within only 14 bp of a consensus RBS which proved to bind Rep in vitro similar to the RBS in AAVS3. Expression of Rep in the presence of rep-deficient AAV vectors shifted targeting preferences from random integration back to the neighbourhood of consensus RBS at hotspots and numerous additional sites in the human genome. In summary, targeted AAV integration is not as specific for AAVS1 as previously assumed. Rather, Rep targets AAV to integrate into open chromatin regions in the reach of various, consensus RBS homologues in the human genome. PMID:20628575

  1. High-Performance Consensus Control in Networked Systems With Limited Bandwidth Communication and Time-Varying Directed Topologies.

    PubMed

    Li, Huaqing; Chen, Guo; Huang, Tingwen; Dong, Zhaoyang

    2016-02-08

    Communication data rates and energy constraints are two important factors that have to be considered in the coordination control of multiagent networks. Although some encoder-decoder-based consensus protocols are available, there still exists a fundamental theoretical problem: how can we further reduce the update rate of control input for each agent without the changing consensus performance? In this paper, we consider the problem of average consensus over directed and time-varying digital networks of discrete-time first-order multiagent systems with limited communication data transmission rates. Each agent has a real-valued state but can only exchange binary symbolic sequence with its neighbors due to bandwidth constraints. A class of novel event-triggered dynamic encoding and decoding algorithms is proposed, based on which a kind of consensus protocol is presented. Moreover, we develop a scheme to select the numbers of time-varying quantization levels for each connected communication channel in the time-varying directed topologies at each time step. The analytical relation among system and network parameters is characterized explicitly. It is shown that the asymptotic convergence rate is related to the scale of the network, the number of quantization levels, the system parameter, and the network structure. It is also found that under the designed event-triggered protocol, for a directed and time-varying digital network, which uniformly contains a spanning tree over a time interval, the average consensus can be achieved with an exponential convergence rate based on merely 1-b information exchange between each pair of adjacent agents at each time step.

  2. 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.

  3. 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.

  4. 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

  5. Distributed Consensus Optimization in Multiagent Networks With Time-Varying Directed Topologies and Quantized Communication.

    PubMed

    Li, Huaqing; Huang, Chicheng; Chen, Guo; Liao, Xiaofeng; Huang, Tingwen

    2017-03-31

    This paper considers solving a class of optimization problems which are modeled as the sum of all agents' convex cost functions and each agent is only accessible to its individual function. Communication between agents in multiagent networks is assumed to be limited: each agent can only interact information with its neighbors by using time-varying communication channels with limited capacities. A technique which overcomes the limitation is to implement a quantization process to the interacted information. The quantized information is first encoded as a binary sequence at the side of each agent before sending. After the binary sequence is received by the neighboring agent, corresponding decoding scheme is utilized to resume the original information with a certain degree of error which is caused by the quantization process. With the availability of each agent's encoding states (associated with its out-channels) and decoding states (associated with its in-channels), we devise a set of distributed optimization algorithms that generate two iterative sequences, one of which converges to the optimal solution and the other of which reaches to the optimal value. We prove that if the parameters satisfy some mild conditions, the quantization errors are bounded and the consensus optimization can be achieved. How to minimize the number of quantization level of each connected communication channel in fixed networks is also explored thoroughly. It is found that, by properly choosing system parameters, one bit information exchange suffices to ensure consensus optimization. Finally, we present two numerical simulation experiments to illustrate the efficacy of the algorithms as well as to validate the theoretical findings.

  6. Management of asthma: a consensus statement.

    PubMed Central

    Warner, J O; Götz, M; Landau, L I; Levison, H; Milner, A D; Pedersen, S; Silverman, M

    1989-01-01

    In developing these international guidelines there were several unifying themes in the diagnosis and simple management of childhood asthma. For the purposes of the meeting, asthma was operationally defined as 'episodic wheeze and/or cough in a clinical setting where asthma is likely and other rarer conditions have been excluded'. In making a diagnosis of asthma, a full history is a prerequisite. Additional tests are only used to support clinical impression and to provide objective evidence for therapeutic recommendations. General features of a multidisciplinary approach include an appreciation of the importance of psychosocial factors, counselling, and education. Drugs should be prescribed in a rational sequence: beta 2-stimulants for mild episodic wheeze; sodium cromoglycate for mild to moderate asthma; inhaled steroids for moderate to severe asthma; with xanthines, ipratropium bromide, and oral steroids having their place in more persistent and severe cases. Children and their parents should be reassured that if asthma is properly controlled there is no reason why the child should not lead a normal and physically active life. The management of asthma is rewarding and return to 'normal' lifestyle is nearly always possible with active participation in sporting activities. Images Fig 1 Fig 2 Fig 3 Fig 4 Fig 5 Fig 6 Fig 7 PMID:2698121

  7. Conservation of sequence in recombination signal sequence spacers.

    PubMed Central

    Ramsden, D A; Baetz, K; Wu, G E

    1994-01-01

    The variable domains of immunoglobulins and T cell receptors are assembled through the somatic, site specific recombination of multiple germline segments (V, D, and J segments) or V(D)J rearrangement. The recombination signal sequence (RSS) is necessary and sufficient for cell type specific targeting of the V(D)J rearrangement machinery to these germline segments. Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif. The heptamer and nonamer motifs are separated by a 'spacer' that was not thought to possess significant sequence conservation, however the length of the spacer could be either 12 +/- 1 bp or 23 +/- 1 bp long. In this report we have assembled and analyzed an extensive data base of published RSS. We have derived, through extensive consensus comparison, a more detailed description of the RSS than has previously been reported. Our analysis indicates that RSS spacers possess significant conservation of sequence, and that the conserved sequence in 12 bp spacers is similar to the conserved sequence in the first half of 23 bp spacers. PMID:8208601

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

    PubMed

    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 consensual

  9. 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

  10. Consensus siRNA for inhibition of HCV genotype-4 replication

    PubMed Central

    Zekri, Abdel Rahman N; Bahnassy, Abeer A; El-Din, Hanaa M Alam; Salama, Hosny M

    2009-01-01

    Background HCV is circulating as a heterogeneous group of quasispecies. It has been addressed that siRNA can inhibit HCV replication in-vitro using HCV clone and/or replicon which have only one genotype. The current study was conducted to assess whether siRNA can inhibit different HCV genotypes with many quasispecies and to assess whether consensus siRNA have the same effect as regular siRNA. Methods We generated two chemically synthesized consensus siRNAs (Z3 and Z5) which cover most known HCV genotype sequences and quasispecies using Ambium system. Highly positive HCV patient's serum with nine quasispecies was transfected in-vitro to Huh-7 cell line which supports HCV genotype-4 replication. siRNA (Z3&Z5) were transfected according to Qiagen Porta-lipid technique and subsequently cultured for eight days. HCV replication was monitored by RT-PCR for detection of plus and minus strands. Real-time PCR was used for quantification of HCV, whereas detection of the viral core protein was performed by western blot. Results HCV RNA levels decreased 18-fold (P = 0.001) and 25-fold (P = 0.0005) in cells transfected with Z3 and Z5, respectively, on Day 2 post transfection and continued for Day 3 by Z3 and Day 7 by Z5. Reduction of core protein expression was reported at Day 2 post Z3 siRNA transfection and at Day 1 post Z5 siRNA, which was persistent for Day 4 for the former and for Day 6 for the latter. Conclusion Consensus siRNA could be used as a new molecular target therapy to effectively inhibit HCV replication in the presence of more than one HCV quasispecies. PMID:19173711

  11. Goal-directed Focused Ultrasound Milestones Revised: A Multiorganizational Consensus.

    PubMed

    Nelson, Mathew; Abdi, Amin; Adhikari, Srikar; Boniface, Michael; Bramante, Robert M; Egan, Daniel J; Matthew Fields, J; Leo, Megan M; Liteplo, Andrew S; Liu, Rachel; Nomura, Jason T; Pigott, David C; Raio, Christopher C; Ruskis, Jennifer; Strony, Robert; Thom, Chris; Lewiss, Resa E

    2016-11-01

    In 2012 the Accreditation Council for Graduate Medical Education and the American Board of Emergency Medicine released the emergency medicine milestones. The Patient Care 12 (PC12) subcompetency delineates staged and progressive accomplishment in emergency ultrasound. While valuable as an initial framework for ultrasound resident education, there are limitations to PC12. This consensus paper provides a revised description of criteria to define the subcompetency. A multiorganizational task force was formed between the American College of Emergency Physicians Ultrasound Section, the Council of Emergency Medicine Residency Directors, and the Academy of Emergency Ultrasound of the Society for Academic Emergency Medicine. Representatives from each organization created this consensus document and revision.

  12. 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.

  13. [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.

  14. Standardised neonatal parenteral nutrition formulations - an Australasian group consensus 2012.

    PubMed

    Bolisetty, Srinivas; Osborn, David; Sinn, John; Lui, Kei

    2014-02-18

    Standardised parenteral nutrition formulations are routinely used in the neonatal intensive care units in Australia and New Zealand. In 2010, a multidisciplinary group was formed to achieve a consensus on the formulations acceptable to majority of the neonatal intensive care units. Literature review was undertaken for each nutrient and recommendations were developed in a series of meetings held between November 2010 and April 2011. Three standard and 2 optional amino acid/dextrose formulations and one lipid emulsion were agreed by majority participants in the consensus. This has a potential to standardise neonatal parenteral nutrition guidelines, reduce costs and prescription errors.

  15. Necessary and sufficient conditions of stationary average consensus for second-order multi-agent systems

    NASA Astrophysics Data System (ADS)

    Pei, Yongquan; Sun, Jitao

    2016-11-01

    This paper investigates the stationary average consensus problem for second-order discrete-time multi-agent systems (SDMAS). A stationary consensus problem is to find a control algorithm that brings the state of a group of agents to a common constant value which is called the collective decision. We introduce the concept of stationary average consensus of SDMAS and propose a consensus algorithm. Based on the polynomial stability and the graph theory, we obtain two necessary and sufficient conditions of stationary average consensus of SDMAS. The last theorem provides an algebraic criterion of stationary average consensus, and can help us to determine the parameters in the consensus algorithm. Furthermore, in this consensus algorithm, only the states of the agents are transferred among the agents. Therefore, this algorithm can not only solve the stationary average consensus problem but also reduce the amount of transferred data. A numerical example is provided to illustrate the efficiency of our results.

  16. 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

  17. 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

  18. Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.

    PubMed

    Pal, Ayon; Banerjee, Rachana; Mondal, Uttam K; Mukhopadhyay, Subhasis; Bothra, Asim K

    2015-01-01

    A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.

  19. Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus.

    PubMed

    Sonnante, Gabriella; Gatto, Angela; Morgese, Anita; Montemurro, Francesco; Sarli, Giulio; Blanco, Emanuela; Pignone, Domenico

    2011-11-01

    An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.

  20. My Identical Twin Sequenced our Genome.

    PubMed

    Schilit, Samantha L P; Schilit Nitenson, Arielle

    2017-04-01

    With rapidly declining costs, whole genome sequencing is becoming feasible for widespread use. Although cost-effectiveness is driving increased use of the technology, comprehensive recommendations on how to handle ethical dilemmas have yet to reach a consensus. In this article, Sam shares her experience of undergoing whole genome sequencing. Despite the deeply private nature of the test, the results do not solely belong to Sam; her identical twin sister, Arielle, shares virtually the same genome and received results without a formal consent process. This article explores their parallel experiences as a way of highlighting the controversial ethics of a private test with familial implications.

  1. 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.

  2. DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys).

    PubMed

    Matson, C W; Baker, R J

    2001-08-01

    The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.

  3. 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…

  4. 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

  5. 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…

  6. Brain Hemispheric Consensus and the Quality of Investment Decisions.

    ERIC Educational Resources Information Center

    Boyd, Michael

    This on-going study explores the hypothesis that stock fund managers who underperform do so because they make bad decisions, and examines whether their choices can be improved by using a decision model that invokes principles of brain hemispheric consensus. The study, begun in fall 1999, involves two groups of business students: the control group…

  7. 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…

  8. 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.

  9. [Consensus for the prevention of cervical cancer in Mexico].

    PubMed

    Kably Ambe, Alberto; Ruiz Moreno, José Antonio; Ponce, Eduardo Lazcano; Vargas Hernández, Victor Manuel; Aguado Pérez, Rogelio A; Alonso de Ruiz, Patricia

    2011-12-01

    Cervical cancer remains a serious public health problem in the world; that is why the Mexican Federation of Schools of Obstetrics and Gynecology convened the elaboration of a consensus that is devoted this number of Ginecologia y Obstetricia de Mexico. In recent years has strengthened perceptions (public and private) in the need for preventive strategies in the medium and long terms. The development of effective vaccines against the human papilloma virus and the application of new methods of detection from viral DNA (completely automated for personal application) allow some degree of optimism. It is proposed a consensus with general recommendations in two consecutive stages: (a) primary prevention consisting of education for the prevention of cervical cancer and universal immunization and (b) secondary prevention by early detection of infections or injuries that could favor carcinogenesis. The consensus reviewed characteristics of available vaccines in detail and proposes strategies for implementation in Mexican population. Also, check out main methods of early detection of infection (or predisposing lesions) and suggests public and private strategies for implementation. Consensus places particular emphasis on early immunization for female population and correct use of methods for detection of infections or injuries that might cause cervical cancer.

  10. 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…

  11. 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... Light-Sport Aircraft rule issued July 16, 2004, and effective September 1, 2004. ASTM International Committee F37 on Light Sport Aircraft developed the new and revised standards with Federal...

  12. 76 FR 45647 - Consensus Standards, Light-Sport Aircraft

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-29

    ... 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, and effective September 1, 2004. ASTM International Committee F37 on Light Sport Aircraft developed the...

  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... and Light-Sport Aircraft rule issued July 16, 2004, and effective September 1, 2004. ASTM International Committee F37 on Light Sport Aircraft developed the new and revised standards with...

  14. 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...

  15. IV Spanish Consensus Conference on Helicobacter pylori infection treatment.

    PubMed

    Gisbert, Javier P; Molina-Infante, Javier; Amador, Javier; Bermejo, Fernando; Bujanda, Luis; Calvet, Xavier; Castro-Fernández, Manuel; Cuadrado-Lavín, Antonio; Elizalde, J Ignasi; Gene, Emili; Gomollón, Fernando; Lanas, Ángel; Martín de Argila, Carlos; Mearin, Fermín; Montoro, Miguel; Pérez-Aisa, Ángeles; Pérez-Trallero, Emilio; McNicholl, Adrián G

    2016-12-01

    Helicobacter pylori approximately infect 50% of Spanish population and causes chronic gastritis, peptic ulcer and gastric cancer. Until now, three consensus meetings on H.pylori infection had been performed in Spain (the last in 2012). The changes in the treatment schemes, and the increasing available evidence, have justified organizing the IVSpanish Consensus Conference (March 2016), focused on the treatment of this infection. Nineteen experts participated, who performed a systematic review of the scientific evidence and developed a series of recommendation that were subjected to an anonymous Delphi process of iterative voting. Scientific evidence and the strength of the recommendation were classified using GRADE guidelines. As starting point, this consensus increased the minimum acceptable efficacy of recommended treatments that should reach, or preferably surpass, the 90% cure rate when prescribed empirically. Therefore, only quadruple therapies (with or without bismuth), and generally lasting 14 days, are recommended both for first and second line treatments. Non-bismuth quadruple concomitant regimen, including a proton pump inhibitor, clarithromycin, amoxicillin and metronidazole, is recommended as first line. In the present consensus, other first line alternatives and rescue treatments are also reviewed and recommended.

  16. 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,…

  17. 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…

  18. Eisenhower: Decision-making and Consensus in an Unfamiliar Context

    DTIC Science & Technology

    2015-05-17

    modern design theory in action, particularly managing the interests of multiple stakeholders, building consensus, and confronting complex problems...The creation of a National Security Council, provided many of the foundational materials for Eisenhower’s national security strategy. Project...Solarium, a planning exercise directed by Eisenhower during the creation of his administration’s national security policy, illustrates an approach to

  19. Educational Standards, Assessment, and the Search for Consensus.

    ERIC Educational Resources Information Center

    Moss, Pamela A.; Schutz, Aaron

    2001-01-01

    Examines the nature of the "consensus" reflected in educational standards used to orient high-stakes assessment programs and considers the discourse of standards creation and how standards are used to orient assessment development and performance judgments. Discusses the theoretical perspectives of J. Habermas and H. Gadamer. (Author/SLD)

  20. European consensus statement on "HPV Vaccination and Colposcopy".

    PubMed

    Shafi, Mahmood I; Petry, Ulrich; Bosch, Xavier F; Gissman, Lutz; Kocken, Marielle; Helmerhorst, Theo J M; Stanley, Margaret; Nazeer, Saloney; European Federation for Colposcopy

    2011-10-01

    We have developed a Europe-wide consensus statement on "HPV Vaccination and Colposcopy" under the aegis of the European Federation for Colposcopy. We look at the historical perspective, the currently available vaccines, cervical vaccination programs, future perspectives, and the impact all this will have on cervical cancer screening and colposcopy services.

  1. 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

  2. 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)

  3. 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…

  4. 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…

  5. 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…

  6. A consensus on protein structure accuracy in NMR?

    PubMed

    Billeter, Martin

    2015-02-03

    The precision of an NMR structure may be manipulated by calculation parameters such as calibration factors. Its accuracy is, however, a different issue. In this issue of Structure, Buchner and Güntert present "consensus structure bundles," where precision analysis allows estimation of accuracy.

  7. Nurses' Perceptions of Consensus Reports Containing Recommendations for Practice.

    ERIC Educational Resources Information Center

    Fitzgerald, Sheila T.; Hill, Martha N.; Santamaria, Barbara; Howard, Cheryl; Jadack, Rose

    1997-01-01

    Responses from 1,107 nurses working with asthma patients showed positive to neutral views of consensus reports with practice recommendations from professional associations, government, and health agencies. Most felt the reports were a better source of information than colleagues, textbooks, or journals. However, 75% were unaware of one major set…

  8. 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.

  9. Consensus and Difference: American Students' Perspectives on the National History

    ERIC Educational Resources Information Center

    Dan, Yongjun; Todd, Reese; Lan, William

    2010-01-01

    The purpose of this study was to re-examine the consensus and difference in American students' understanding of national history, on which there were divergent research results. With three sets of questions that examined students' perspectives of the collective memory, historical significance, and credibility of historical sources, we found that…

  10. Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens

    NASA Astrophysics Data System (ADS)

    Huang, Shan-Han; Tung, Chun-Wei

    2017-01-01

    The assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation.

  11. Consensus tracking for multiagent systems with nonlinear dynamics.

    PubMed

    Dong, Runsha

    2014-01-01

    This paper concerns the problem of consensus tracking for multiagent systems with a dynamical leader. In particular, it proposes the corresponding explicit control laws for multiple first-order nonlinear systems, second-order nonlinear systems, and quite general nonlinear systems based on the leader-follower and the tree shaped network topologies. Several numerical simulations are given to verify the theoretical results.

  12. National consensus on the management of constipation in indonesia 2010.

    PubMed

    2011-10-01

    Constipation is a common complaint in our daily practice, which may occur in young adult or elderly patients. Recently, the incidence has been increasing; however, most patients try to have self-medication using over-the-counter (OTC) drugs, which is usually inappropriate. Moreover, there has been unequal distribution of knowledge and vigilance of medical practitioners, both general physician and specialist doctors on the constipation issue. Therefore, patients usually present with greater complications. The Organizing Committee of Indonesian Society of Gastroenterology or Pengurus Besar Perkumpulan Gastroenterologi Indonesia (PB PGI) considers that it is important to compose a National Consensus on the Management of Constipation in Indonesia. The Consensus is expected to be a guideline for doctors to deal with patients who have constipation in their daily practice, so that optimal results could be achieved. Nowadays, there are new data on definition, pathophysiology, diagnosis and management of constipation; thus, the Organizing Committee of ISG feels that it is necessary to revise the established consensus. We expect that the consensus may bring advantages for medical practitioners in Indonesia and in general, it may cause community health improvement.

  13. Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens

    PubMed Central

    Huang, Shan-Han; Tung, Chun-Wei

    2017-01-01

    The assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation. PMID:28117354

  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.

  15. 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…

  16. 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

    2015-06-11

    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.

  17. 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.

  18. Consensus on the standardization of terminology in thrombotic thrombocytopenic purpura and related thrombotic microangiopathies.

    PubMed

    Scully, M; Cataland, S; Coppo, P; de la Rubia, J; Friedman, K D; Kremer Hovinga, J; Lämmle, B; Matsumoto, M; Pavenski, K; Sadler, E; Sarode, R; Wu, H

    2017-02-01

    Essentials An international collaboration provides a consensus for clinical definitions. This concerns thrombotic microangiopathies and thrombotic thrombocytopenic purpura (TTP). The consensus defines diagnosis, disease monitoring and response to treatment. Requirements for ADAMTS-13 are given.

  19. 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.

  20. 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.

  1. Definition of a consensus DNA-binding site for the Escherichia coli pleiotropic regulatory protein, FruR.

    PubMed

    Nègre, D; Bonod-Bidaud, C; Geourjon, C; Deléage, G; Cozzone, A J; Cortay, J C

    1996-07-01

    The FruR regulator of Escherichia coli controls the initiation of transcription of several operons encoding a variety of proteins involved in carbon and energy metabolism. The sequence determinants of the FruR-binding site were analysed by using 6x His-tagged FruR and a series of double-stranded randomized oligonucleotides. FruR consensus binding sites were selected and characterized by several consecutive rounds of the polymerase chain reaction-assisted binding-site selection method (BSS) using nitrocellulose-immobilized DNA-binding protein. FruR was demonstrated to require, for binding, an 8 bp left half-site motif and a 3 bp conserved right half-site with the following sequence: 5'-GNNGAATC/GNT-3'. In this sequence, the left half-site AATC/ consensus tetranucleotide is a typical motif of the DNA-binding site of the regulators of the GalR-Lacl family. On the other hand, the high degree of degeneracy found in the right half-site of this palindrome-like structure indicated that FruR, which is a tetramer in solution, interacts asymmetrically with the two half-sites of its operator. However, potentially FruR-target sites showing a high degree of symmetry were detected in 13 genes/operons. Among these, we have focused our interest on the pfkA gene, encoding phosphofructo-kinase-1, which is negatively regulated by FruR.

  2. 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.

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

    PubMed Central

    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

  4. Characterization of minisatellites in Arabidopsis thaliana with sequence similarity to the human minisatellite core sequence.

    PubMed Central

    Tourmente, S; Deragon, J M; Lafleuriel, J; Tutois, S; Pélissier, T; Cuvillier, C; Espagnol, M C; Picard, G

    1994-01-01

    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. Images PMID:8078766

  5. 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

    2016-04-01

    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.

  6. Optimal Topology Control and Power Allocation for Minimum Energy Consumption in Consensus Networks

    DTIC Science & Technology

    2011-12-16

    network topology can be modeled as a random graph model. It can be shown [22], [23] that the system in (3) converges to consensus almost surely, i.e...Terms— Consensus algorithms, minimum energy con- sumption, random graphs, sensor networks, topology control. I. INTRODUCTION A VERAGE consensus ...network context, it is necessary to minimize the en- ergy consumption necessary to reach consensus . Clearly, the network topology plays a fundamental role

  7. Genome Sequence of a Novel Archaeal Rudivirus Recovered from a Mexican Hot Spring

    PubMed Central

    Peng, Xu; Garrett, Roger A.; Martínez-Romero, Esperanza

    2013-01-01

    We report the consensus genome sequence of a novel GC-rich rudivirus, designated SMR1 (Sulfolobales Mexican rudivirus 1), assembled from a high-throughput sequenced environmental sample from a hot spring in Los Azufres National Park in western Mexico. PMID:23405288

  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. 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...

  11. 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

  12. 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…

  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. 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.

  15. Consensus Guidelines for the Management and Treatment of Neuroendocrine Tumors

    PubMed Central

    Kunz, Pamela L.; Reidy-Lagunes, Diane; Anthony, Lowell B.; Bertino, Erin M.; Brendtro, Kari; Chan, Jennifer A.; Chen, Herbert; Jensen, Robert T.; Kim, Michelle Kang; Klimstra, David S.; Kulke, Matthew H.; Liu, Eric H.; Metz, David C.; Phan, Alexandria T.; Sippel, Rebecca S.; Strosberg, Jonathan R.; Yao, James C.

    2014-01-01

    Neuroendocrine tumors (NETs) are a heterogeneous group of tumors originating in various anatomic locations. The management of this disease poses a significant challenge because of the heterogeneous clinical presentations and varying degree of aggressiveness. The recent completion of several phase III trials, including those evaluating octreotide, sunitinib, and everolimus, demonstrate that rigorous evaluation of novel agents in this disease is possible and can lead to practice-changing outcomes. Nevertheless, there are many aspects to the treatment of NETs that remain unclear and controversial. The North American Neuroendocrine Tumor Society (NANETS) published a set of consensus guidelines in 2010 which provided an overview for the treatment of patients with these malignancies. Here, we present a set of consensus tables intended to complement these guidelines and serve as a quick, accessible reference for the practicing physician. PMID:23591432

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

    PubMed

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

    2016-01-07

    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.

  17. [Neuroendocrine dysfunction and brain damage. A consensus statement].

    PubMed

    Leal-Cerro, Alfonso; Rincón, María Dolores; Domingo, Manel Puig

    2009-01-01

    This consensus statement aims to enhance awareness of the incidence and risks of hypopituitarism in patients with traumatic brain injury (TBI) and/or brain hemorrhages among physicians treating patients with brain damage. The importance of this problem is related not only to the frequency of TBI but also to its prevalence in younger populations. The consequences of TBI are characterized by a series of symptoms that depend on the type of sequels related to neuroendocrine dysfunction. The signs and symptoms of hypopituitarism are often confused with those of other sequels of TBI. Consequently, patients with posttraumatic hypopituitarism may receive suboptimal rehabilitation unless the underlying hormone deficiency is identified and treated. This consensus is based on the recommendation supported by expert opinion that patients with a TBI and/or brain hemorrhage should undergo endocrine evaluation in order to assess pituitary function and, if deficiency is detected, should receive hormone replacement therapy.

  18. Bias, belief, and consensus: Collective opinion formation on fluctuating networks

    NASA Astrophysics Data System (ADS)

    Ngampruetikorn, Vudtiwat; Stephens, Greg J.

    2016-11-01

    With the advent of online networks, societies have become substantially more interconnected with individual members able to easily both maintain and modify their own social links. Here, we show that active network maintenance exposes agents to confirmation bias, the tendency to confirm one's beliefs, and we explore how this bias affects collective opinion formation. We introduce a model of binary opinion dynamics on a complex, fluctuating network with stochastic rewiring and we analyze these dynamics in the mean-field limit of large networks and fast link rewiring. We show that confirmation bias induces a segregation of individuals with different opinions and stabilizes the consensus state. We further show that bias can have an unusual, nonmonotonic effect on the time to consensus and this suggests a novel avenue for large-scale opinion manipulation.

  19. 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.

  20. Link-Prediction Enhanced Consensus Clustering for Complex Networks.

    PubMed

    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.

  1. Expert Consensus for Discharge Referral Decisions Using Online Delphi

    PubMed Central

    Bowles, Kathy H.; Holmes, John H.; Naylor, Mary D.; Liberatore, Matthew; Nydick, Robert

    2003-01-01

    This paper describes the results of using a modified Delphi approach designed to achieve consensus from eight discharge planning experts regarding the decision to refer hospitalized older adults for post-discharge follow-up. Experts reviewed 150 cases using an online website designed to facilitate their interaction and efforts to reach agreement on the need for a referral for post-discharge care and the appropriate site for such care. In contrast to an average of eight weeks to complete just 50 cases using the traditional mail method, the first online Delphi round for 150 cases were completed in six weeks. Data provided by experts suggest that online Delphi is a time efficient and acceptable methodology for reaching group consensus. Other benefits include instant access to Delphi decision results, live knowledge of the time requirements and progress of each expert, and cost savings in postage, paper, copying, and storage of paper documents. This online Delphi methodology is highly recommended. PMID:14728143

  2. 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

  3. Design and evaluation of consensus PCR assays for henipaviruses.

    PubMed

    Feldman, K S; Foord, A; Heine, H G; Smith, I L; Boyd, V; Marsh, G A; Wood, J L N; Cunningham, A A; Wang, L-F

    2009-10-01

    Henipaviruses were first discovered in the 1990s, and their potential threat to public health is of increasing concern with increasing knowledge. Old-world fruit bats are the reservoir hosts for these viruses, and spill-over events cause lethal infections in a wide range of mammalian species, including humans. In anticipation of these spill-over events, and to investigate further the geographical range of these genetically diverse viruses, assays for detection of known and potentially novel strains of henipaviruses are required. The development of multiple consensus PCR assays for the detection of henipaviruses, including both SYBR Green and TaqMan real-time PCRs and a conventional heminested PCR is described. The assays are highly sensitive and have defined specificity. In addition to being useful tools for detection of known and novel henipaviruses, evaluation of assay efficiency and sensitivity across both biological and synthetic templates has provided valuable insight into consensus PCR design and use.

  4. Boltzmann-type control of opinion consensus through leaders.

    PubMed

    Albi, G; Pareschi, L; Zanella, M

    2014-11-13

    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.

  5. Consensus statement from the 2014 International Microdialysis Forum.

    PubMed

    Hutchinson, Peter J; Jalloh, Ibrahim; Helmy, Adel; Carpenter, Keri L H; Rostami, Elham; Bellander, Bo-Michael; Boutelle, Martyn G; Chen, Jeff W; Claassen, Jan; Dahyot-Fizelier, Claire; Enblad, Per; Gallagher, Clare N; Helbok, Raimund; Hillered, Lars; Le Roux, Peter D; Magnoni, Sandra; Mangat, Halinder S; Menon, David K; Nordström, Carl-Henrik; O'Phelan, Kristine H; Oddo, Mauro; Perez Barcena, Jon; Robertson, Claudia; Ronne-Engström, Elisabeth; Sahuquillo, Juan; Smith, Martin; Stocchetti, Nino; Belli, Antonio; Carpenter, T Adrian; Coles, Jonathan P; Czosnyka, Marek; Dizdar, Nil; Goodman, J Clay; Gupta, Arun K; Nielsen, Troels H; Marklund, Niklas; Montcriol, Ambroise; O'Connell, Mark T; Poca, Maria A; Sarrafzadeh, Asita; Shannon, Richard J; Skjøth-Rasmussen, Jane; Smielewski, Peter; Stover, John F; Timofeev, Ivan; Vespa, Paul; Zavala, Elizabeth; Ungerstedt, Urban

    2015-09-01

    Microdialysis enables the chemistry of the extracellular interstitial space to be monitored. Use of this technique in patients with acute brain injury has increased our understanding of the pathophysiology of several acute neurological disorders. In 2004, a consensus document on the clinical application of cerebral microdialysis was published. Since then, there have been significant advances in the clinical use of microdialysis in neurocritical care. The objective of this review is to report on the International Microdialysis Forum held in Cambridge, UK, in April 2014 and to produce a revised and updated consensus statement about its clinical use including technique, data interpretation, relationship with outcome, role in guiding therapy in neurocritical care and research applications.

  6. 2 nd Brazilian Consensus on Chagas Disease, 2015.

    PubMed

    Dias, João Carlos Pinto; Ramos, Alberto Novaes; Gontijo, Eliane Dias; Luquetti, Alejandro; Shikanai-Yasuda, Maria Aparecida; Coura, José Rodrigues; Torres, Rosália Morais; Melo, José Renan da Cunha; Almeida, Eros Antonio de; Oliveira, Wilson de; Silveira, Antônio Carlos; Rezende, Joffre Marcondes de; Pinto, Fabiane Scalabrini; Ferreira, Antonio Walter; Rassi, Anis; Fragata, Abílio Augusto; Sousa, Andréa Silvestre de; Correia, Dalmo; Jansen, Ana Maria; Andrade, Glaucia Manzan Queiroz; Britto, Constança Felícia De Paoli de Carvalho; Pinto, Ana Yecê das Neves; Rassi, Anis; Campos, Dayse Elisabeth; Abad-Franch, Fernando; Santos, Silvana Eloi; Chiari, Egler; Hasslocher-Moreno, Alejandro Marcel; Moreira, Eliane Furtado; Marques, Divina Seila de Oliveira; Silva, Eliane Lages; Marin-Neto, José Antonio; Galvão, Lúcia Maria da Cunha; Xavier, Sergio Salles; Valente, Sebastião Aldo da Silva; Carvalho, Noêmia Barbosa; Cardoso, Alessandra Viana; Silva, Rafaella Albuquerque E; Costa, Veruska Maia da; Vivaldini, Simone Monzani; Oliveira, Suelene Mamede; Valente, Vera da Costa; Lima, Mayara Maia; Alves, Renato Vieira

    2016-12-01

    Chagas disease is a neglected chronic condition with a high burden of morbidity and mortality. It has considerable psychological, social, and economic impacts. The disease represents a significant public health issue in Brazil, with different regional patterns. This document presents the evidence that resulted in the Brazilian Consensus on Chagas Disease. The objective was to review and standardize strategies for diagnosis, treatment, prevention, and control of Chagas disease in the country, based on the available scientific evidence. The consensus is based on the articulation and strategic contribution of renowned Brazilian experts with knowledge and experience on various aspects of the disease. It is the result of a close collaboration between the Brazilian Society of Tropical Medicine and the Ministry of Health. It is hoped that this document will strengthen the development of integrated actions against Chagas disease in the country, focusing on epidemiology, management, comprehensive care (including families and communities), communication, information, education, and research .

  7. Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease.

    PubMed Central

    McNearney, T; Hornickova, Z; Markham, R; Birdwell, A; Arens, M; Saah, A; Ratner, L

    1992-01-01

    V3 envelope sequences were determined from amplified human immunodeficiency virus type 1 (HIV-1) sequences of uncultivated leukocytes obtained sequentially from four infected adults over the course of infection. Lower levels of sequence heterogeneity were noted in samples obtained early in HIV-1 infection, prior to CD4 depletion, than in samples obtained at later times during disease. The pattern of amino acid sequence divergence included nonrandom changes, with evidence of sequence variants arising from HIV-1 quasi-species present earlier in infection. Consensus sequences for isolates obtained early after infection from different patients demonstrated a high level of conservation with one another and a consensus sequence for macrophage-tropic HIV-1 isolates. These findings suggest that a highly restricted subset of HIV-1 quasi-species can be transmitted and can establish infection. PMID:1438212

  8. Persistence of opinion in the Sznajd consensus model: computer simulation

    NASA Astrophysics Data System (ADS)

    Stauffer, D.; de Oliveira, P. M. C.

    2002-12-01

    The density of never changed opinions during the Sznajd consensus-finding process decays with time t as 1/t^θ. We find θ simeq 3/8 for a chain, compatible with the exact Ising result of Derrida et al. In higher dimensions, however, the exponent differs from the Ising θ. With simultaneous updating of sublattices instead of the usual random sequential updating, the number of persistent opinions decays roughly exponentially. Some of the simulations used multi-spin coding.

  9. The Same Language Speak We Do - Consensus Terminology for Telehealth.

    PubMed

    Scott, Richard E; Mars, Maurice

    2016-01-01

    e-Health has grown to become interjurisdictional in scope and in practice. Central to successful implementation and scaling of e-heath solutions is clear and concise communication of ideas and principles, and instructions during construction. This paper addresses the need for an agreed taxonomy and terminology and focuses on explaining, proposing, and recommending terms and action for an international consensus-based terminology for telehealth.

  10. Interdisciplinary consensus document for the treatment of fibromyalgia.

    PubMed

    de Miquel, C Alegre; Campayo, J García; Flórez, M Tomás; Arguelles, J M Gómez; Tarrio, E Blanco; Montoya, M Gobbo; Martin, Á Pérez; Salio, A Martínez; Fuentes, J Vidal; Alberch, E Altarriba; de la Cámara, A Gómez

    2010-01-01

    Backgrounds. The elevated prevalence and enormous clinical and social impact of fibromyalgia, together with the complexity of its treatment, require action consensuses that guide health care professionals. Although there are some similar documents in our language, most have been made from the perspective of a single discipline.Objective. To develop a consensus on the treatment of fibromyalgia made by selected representatives and supported by the principal medical associations that intervene in its treatment (rheumatology, neurology, psychiatry,rehabilitation and family medicine) and representatives of the associations of patients. On the other hand, understanding the disease not as a homogenous disorders but also as the sum of different clinical subtypes,having specific symptomatic characteristics and different therapeutic needs is stressed. This approach represented a need perceived by the clinicians and a novelty regarding previous consensuses.Methods. The different clinical classifications proposed in fibromyalgia and the scientific evidence of the treatments used in this disease were reviewed. For the selection of the classification used and performance of the therapeutic recommendations, some of the usual techniques to obtain the consensus (nominal group and brainstorming) were used.Conclusion. The classification of Giesecke of fibromyalgia into 3 subgroups seems to have the greatest scientific evidence and the most useful for the clinician. The guide offers a series of general recommendations for all the patients with fibromyalgia. However, in addition, for each subgroup, there are a series of specific pharmacological and psychological-type recommendations and those of modification of the environment, which will make it possible to have a personalized approach to the patient with fibromyalgia in accordance with their individual clinical characteristics (pain, catastrophizing levels, etc.).

  11. Consensus Tracking for Multiagent Systems with Nonlinear Dynamics

    PubMed Central

    2014-01-01

    This paper concerns the problem of consensus tracking for multiagent systems with a dynamical leader. In particular, it proposes the corresponding explicit control laws for multiple first-order nonlinear systems, second-order nonlinear systems, and quite general nonlinear systems based on the leader-follower and the tree shaped network topologies. Several numerical simulations are given to verify the theoretical results. PMID:25197689

  12. Iterative Approximate Byzantine Consensus under a Generalized Fault Model

    DTIC Science & Technology

    2012-05-21

    on Principles of distributed computing , PODC ’05, pages 138–147, New York, NY, USA, 2005. ACM. [3] S. Dasgupta, C. Papadimitriou , and U. Vazirani...Iterative Approximate Byzantine Consensus under a Generalized Fault Model∗ Lewis Tseng1,3, and Nitin Vaidya2,3 1 Department of Computer Science, 2...Department of Electrical and Computer Engineering, and 3 Coordinated Science Laboratory University of Illinois at Urbana-Champaign Email: {ltseng3, nhv

  13. 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.

  14. Inhaled treatment of COPD: a Delphi consensus statement

    PubMed Central

    Ninane, Vincent; Corhay, Jean-Louis; Germonpré, Paul; Janssens, Wim; Joos, Guy F; Liistro, Giuseppe; Vincken, Walter; Gurdain, Sandra; Vanvlasselaer, Evelyne; Lehouck, An

    2017-01-01

    Background Global Initiative for Chronic Obstructive Lung Disease (GOLD) global strategy (2015) provides guidance for the treatment of chronic obstructive pulmonary disease (COPD) with different first-choice options per GOLD category without specification. Objectives To evaluate the level of medical experts’ consensus on their preferred first-choice treatment within different COPD categories. Methods A two-round Delphi Panel consisting of 15 questions was completed by Belgian pulmonologists (n=31) and European (n=10) COPD experts. Results Good consensus was reached by both expert groups for long-acting bronchodilators instead of short-acting bronchodilators as first-choice treatment in GOLD A. Single bronchodilation with long-acting muscarinic antagonist (LAMA) was preferred over long-acting β2-agonist (LABA) and LABA/LAMA as first-choice treatment in GOLD B and GOLD C. For GOLD D patients based on the forced expiratory volume in 1 second (FEV1)<50%, a very good consensus was reached for LAMA/LABA as first-choice treatment. For GOLD D patients based on frequent or severe exacerbations, there was a good consensus for LABA/LAMA/inhaled corticosteroids (ICS) as first choice in the Belgian group. According to the European experts, both LABA/LAMA and LABA/LAMA/ICS could be the first choice for these patients. Conclusion Belgian and European experts recommend long-acting bronchodilators as first-choice treatment. Treatment containing ICS was found only appropriate in patients with FEV1<50% and ≥2 moderate exacerbations or 1 severe exacerbation/year. PMID:28293106

  15. 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

  16. [Atherothrombotic carotid disease: towards a consensus on its prevention].

    PubMed

    Gil, A C

    2004-05-01

    This consensus document was one of the objectives of the I Meeting of the Spanish Society of Angiology and Vascular Surgery, the Spanish Interventional Neuroradiology Group of the Spanish Society of Neuroradiology, and the Cerebrovascular Disease Study Group of the Spanish Society of Neurology, which was held in October 2002 in Cordoba. Atherosclerosis is a chronic vascular disease of true epidemic proportions. It is the first cause of death in developed countries and responsible for one quarter of documented deaths worldwide. Atherothrombotic ischemic stroke, transient ischemic attack and atherothrombotic origin symptomatic or asymptomatic peripheral arterial disease are all associated with a high risk of vascular death, myocardial infarction and recurrent stroke. In this context, vascular disease represents a serious public health problem, particularly if we take into account current forecasts on population ageing. The prevention of atherosclerosis - and its consequences, if its clinical manifestations are already apparent - is therefore a priority. This multidisciplinary consensus document draws on the different medical specialties dealing with these patients and combines efforts to obtain the greatest possible benefit as regards this disease's management. The consensus document makes a global analysis of atherosclerosis prevention, basically in terms of therapeutic objectives, lifestyle change measures, high bloodpressure management, dyslipidemia, other vascular risk factors and platelet antiaggregation. Emphasis is placed on the frequent coexistence of cerebrovascular and peripheral arterial involvement, and the methods of detecting silent involvement. Lastly, consensus is reached on the diagnostic methods and specific management of atherothrombotic carotid disease, including the benefits and risks of and indications for carotid endarterectomy, and the current role of carotid angioplasty.

  17. Comparison of MY09/11 consensus PCR and type-specific PCRs in the detection of oncogenic HPV types.

    PubMed

    Depuydt, C E; Boulet, G A V; Horvath, C A J; Benoy, I H; Vereecken, A J; Bogers, J J

    2007-01-01

    The causal relationship between persistent infection with high-risk HPV and cervical cancer has resulted in the development of HPV DNA detection systems. The widely used MY09/11 consensus PCR targets a 450bp conserved sequence in the HPV L1 gene, and can therefore amplify a broad spectrum of HPV types. However, limitations of these consensus primers are evident, particularly in regard to the variability in detection sensitivity among different HPV types. This study compared MY09/11 PCR with type-specific PCRs in the detection of oncogenic HPV types. The study population comprised 15, 774 patients. Consensus PCR failed to detect 522 (10.9%) HPV infections indicated by type-specific PCRs. A significant correlation between failure of consensus PCR and HPV type was found. HPV types 51, 68 and 45 were missed most frequently. The clinical relevance of the HPV infections missed by MY09/11 PCR was reflected in the fraction of cases with cytological abnormalities and in follow-up, showing 104 (25.4%) CIN2+ cases. The MY09/11 false negativity could be the result of poor sensitivity, mismatch of MY09/11 primers or disruption of L1 target by HPV integration or DNA degradation. Furthermore, MY09/11 PCR lacked specificity for oncogenic HPVs. Diagnostic accuracy of the PCR systems, in terms of sensitivity (MY09/11 PCR: 87.9%; type-specific PCRs: 98.3%) and specificity (MY09/11 PCR: 38.7%; type-specific PCRs: 76.14%), and predictive values for histologically confirmed CIN2+, suggest that type-specific PCRs could be used in a clinical setting as a reliable screening tool.

  18. Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

    PubMed

    Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

    2011-08-05

    Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

  19. 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.

  20. 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

  1. Taiwan consensus of pharmacological treatment for bipolar disorder.

    PubMed

    Bai, Ya-Mei; Chang, Ching-Jui; Tsai, Shang-Ying; Chen, Yi-Chyan; Hsiao, Mei-Chun; Li, Cheng-Ta; Tu, Peichi; Chang, Shang-Wen; Shen, Winston W; Su, Tung-Ping

    2013-10-01

    Bipolar disorder is an important psychiatric disorder with different disease phases. The pharmacological treatment is complicated, and is updated frequently as new research evidence emerges. For the purpose of international collaboration, research, and education, the Taiwan consensus of pharmacological treatment for bipolar disorders was initiated by the Taiwanese Society of Biological Psychiatry and Neuropsychopharmacology (TSBPN) - the Bipolar Chapter, which was established in August 2010 and approved as a member of International Society of Bipolar Disorder. TSBPN is the country member of the World Federation of Societies of Biological Psychiatry (WFSBP). The development of the Taiwan consensus for bipolar disorder was mainly based on the template of WFSBP Guidelines, with references to other international guidelines including the Canadian Network for Mood and Anxiety Treatments, and British Association for Psychopharmacology. We have also added Taiwanese experts' experience, Taiwan national health insurance data, and the indications for the pharmacological treatment of bipolar disorder given by the Taiwan Department of Health, to emphasize the balance between efficacy and safety, and to make this consensus a concise, empirical, and important reference for clinical psychiatric practice.

  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.

  3. Consensus+Innovations Distributed Kalman Filter With Optimized Gains

    NASA Astrophysics Data System (ADS)

    Das, Subhro; Moura, Jose M. F.

    2017-01-01

    In this paper, we address the distributed filtering and prediction of time-varying random fields represented by linear time-invariant (LTI) dynamical systems. The field is observed by a sparsely connected network of agents/sensors collaborating among themselves. We develop a Kalman filter type consensus+innovations distributed linear estimator of the dynamic field termed as Consensus+Innovations Kalman Filter. We analyze the convergence properties of this distributed estimator. We prove that the mean-squared error of the estimator asymptotically converges if the degree of instability of the field dynamics is within a pre-specified threshold defined as tracking capacity of the estimator. The tracking capacity is a function of the local observation models and the agent communication network. We design the optimal consensus and innovation gain matrices yielding distributed estimates with minimized mean-squared error. Through numerical evaluations, we show that, the distributed estimator with optimal gains converges faster and with approximately 3dB better mean-squared error performance than previous distributed estimators.

  4. Insulin Resistance in Children: Consensus, Perspective, and Future Directions

    PubMed Central

    Levy-Marchal, Claire; Arslanian, Silva; Cutfield, Wayne; Sinaiko, Alan; Druet, Celine; Marcovecchio, M. Loredana; Chiarelli, Francesco

    2010-01-01

    Objective: Emerging data indicate that insulin resistance is common among children and adolescents and is related to cardiometabolic risk, therefore requiring consideration early in life. However, there is still confusion on how to define insulin resistance, how to measure it, what its risk factors are, and whether there are effective strategies to prevent and treat it. A consensus conference was organized in order to clarify these points. Participants: The consensus was internationally supported by all the major scientific societies in pediatric endocrinology and 37 participants. Evidence: An independent and systematic search of the literature was conducted to identify key articles relating to insulin resistance in children. Consensus Process: The conference was divided into five themes and working groups: background and definition; methods of measurement and screening; risk factors and consequences; prevention; and treatment. Each group selected key issues, searched the literature, and developed a draft document. During a 3-d meeting, these papers were debated and finalized by each group before presenting them to the full forum for further discussion and agreement. Conclusions: Given the current childhood obesity epidemic, insulin resistance in children is an important issue confronting health care professionals. There are no clear criteria to define insulin resistance in children, and surrogate markers such as fasting insulin are poor measures of insulin sensitivity. Based on current screening criteria and methodology, there is no justification for screening children for insulin resistance. Lifestyle interventions including diet and exercise can improve insulin sensitivity, whereas drugs should be implemented only in selected cases. PMID:20829185

  5. European consensus conference on faecal microbiota transplantation in clinical practice.

    PubMed

    Cammarota, Giovanni; Ianiro, Gianluca; Tilg, Herbert; Rajilić-Stojanović, Mirjana; Kump, Patrizia; Satokari, Reetta; Sokol, Harry; Arkkila, Perttu; Pintus, Cristina; Hart, Ailsa; Segal, Jonathan; Aloi, Marina; Masucci, Luca; Molinaro, Antonio; Scaldaferri, Franco; Gasbarrini, Giovanni; Lopez-Sanroman, Antonio; Link, Alexander; de Groot, Pieter; de Vos, Willem M; Högenauer, Christoph; Malfertheiner, Peter; Mattila, Eero; Milosavljević, Tomica; Nieuwdorp, Max; Sanguinetti, Maurizio; Simren, Magnus; Gasbarrini, Antonio

    2017-04-01

    Faecal microbiota transplantation (FMT) is an important therapeutic option for Clostridium difficile infection. Promising findings suggest that FMT may play a role also in the management of other disorders associated with the alteration of gut microbiota. Although the health community is assessing FMT with renewed interest and patients are becoming more aware, there are technical and logistical issues in establishing such a non-standardised treatment into the clinical practice with safety and proper governance. In view of this, an evidence-based recommendation is needed to drive the practical implementation of FMT. In this European Consensus Conference, 28 experts from 10 countries collaborated, in separate working groups and through an evidence-based process, to provide statements on the following key issues: FMT indications; donor selection; preparation of faecal material; clinical management and faecal delivery and basic requirements for implementing an FMT centre. Statements developed by each working group were evaluated and voted by all members, first through an electronic Delphi process, and then in a plenary consensus conference. The recommendations were released according to best available evidence, in order to act as guidance for physicians who plan to implement FMT, aiming at supporting the broad availability of the procedure, discussing other issues relevant to FMT and promoting future clinical research in the area of gut microbiota manipulation. This consensus report strongly recommends the implementation of FMT centres for the treatment of C. difficile infection as well as traces the guidelines of technicality, regulatory, administrative and laboratory requirements.

  6. 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

  7. Consensus-based recommendations for the management of juvenile dermatomyositis

    PubMed Central

    Enders, Felicitas Bellutti; Bader-Meunier, Brigitte; Baildam, Eileen; Constantin, Tamas; Dolezalova, Pavla; Feldman, Brian M; Lahdenne, Pekka; Magnusson, Bo; Nistala, Kiran; Ozen, Seza; Pilkington, Clarissa; Ravelli, Angelo; Russo, Ricardo; Uziel, Yosef; van Brussel, Marco; van der Net, Janjaap; Vastert, Sebastiaan; Wedderburn, Lucy R; Wulffraat, Nicolaas; McCann, Liza J; van Royen-Kerkhof, Annet

    2017-01-01

    Background In 2012, a European initiative called Single Hub and Access point for pediatric Rheumatology in Europe (SHARE) was launched to optimise and disseminate diagnostic and management regimens in Europe for children and young adults with rheumatic diseases. Juvenile dermatomyositis (JDM) is a rare disease within the group of paediatric rheumatic diseases (PRDs) and can lead to significant morbidity. Evidence-based guidelines are sparse and management is mostly based on physicians' experience. Consequently, treatment regimens differ throughout Europe. Objectives To provide recommendations for diagnosis and treatment of JDM. Methods Recommendations were developed by an evidence-informed consensus process using the European League Against Rheumatism standard operating procedures. A committee was constituted, consisting of 19 experienced paediatric rheumatologists and 2 experts in paediatric exercise physiology and physical therapy, mainly from Europe. Recommendations derived from a validated systematic literature review were evaluated by an online survey and subsequently discussed at two consensus meetings using nominal group technique. Recommendations were accepted if >80% agreement was reached. Results In total, 7 overarching principles, 33 recommendations on diagnosis and 19 recommendations on therapy were accepted with >80% agreement among experts. Topics covered include assessment of skin, muscle and major organ involvement and suggested treatment pathways. Conclusions The SHARE initiative aims to identify best practices for treatment of patients suffering from PRD. Within this remit, recommendations for the diagnosis and treatment of JDM have been formulated by an evidence-informed consensus process to produce a standard of care for patients with JDM throughout Europe. PMID:27515057

  8. 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

  9. 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

  10. 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

  11. Perceptions of a fluid consensus: uniqueness bias, false consensus, false polarization, and pluralistic ignorance in a water conservation crisis.

    PubMed

    Monin, Benoît; Norton, Michael I

    2003-05-01

    A 5-day field study (N = 415) during and right after a shower ban demonstrated multifaceted social projection and the tendency to draw personality inferences from simple behavior in a time of drastic consensus change. Bathers thought showering was more prevalent than did non-bathers (false consensus) and respondents consistently underestimated the prevalence of the desirable and common behavior--be it not showering during the shower ban or showering after the ban (uniqueness bias). Participants thought that bathers and non-bathers during the ban differed greatly in their general concern for the community, but self-reports demonstrated that this gap was illusory (false polarization). Finally, bathers thought other bathers cared less than they did, whereas non-bathers thought other non-bathers cared more than they did (pluralistic ignorance). The study captures the many biases at work in social perception in a time of social change.

  12. Two-phase analysis in consensus genetic mapping.

    PubMed

    Ronin, Y; Mester, D; Minkov, D; Belotserkovski, R; Jackson, B N; Schnable, P S; Aluru, S; Korol, A

    2012-05-01

    Numerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as "synchronized TSP." The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the

  13. 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

  14. Sequence variability of Chrysanthemum stunt viroid in different chrysanthemum cultivars

    PubMed Central

    Yoon, Ju-Yeon; Choi, Seung-Kook

    2017-01-01

    Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein. Chrysanthemum stunt viroid (CSVd), a member of the family Pospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity. PMID:28149699

  15. 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.

  16. [Kyoto global consensus report for treatment of Helicobacter pylori and its implications for China].

    PubMed

    Xie, Chuan; Lyu, Nonghua

    2016-01-01

    Kyoto global consensus report on Helicobacter pylori gastritis (Gut, July 2015) is another important international consensus since the European Maastricht Ⅳ consensus was published. Kyoto consensus will improve the etiology-based classification, the diagnostic assessment of gastritis, and the treatment of H. pylori-associated dyspepsia and H. pylori gastritis. However, because of high rate of H. pylori infection and antibiotic resistance as well as limited health resources in China, we need to develop our own strategies of H. pylori infection control with the reference of the Kyoto global consensus.

  17. 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

  18. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    PubMed

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  19. 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

  20. 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

  1. 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.

  2. A consensus linkage map of oil palm and a major QTL for stem height.

    PubMed

    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

    2015-02-04

    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.

  3. Consensus recommendations for a standardized Brain Tumor Imaging Protocol in clinical trials

    PubMed Central

    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; Al Yung, W.K.; Cloughesy, Timothy F.; Wen, Patrick Y.; Gilbert, Mark R.

    2015-01-01

    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

  4. 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

  5. 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

  6. 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.

  7. Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens

    SciTech Connect

    Bradley, M.K.; Smith, T.F.; Lathrop, R.H.; Livingston, D.M.; Webster, T.A.

    1987-06-01

    The location and sequence composition of a consensus element of the nucleotide binding site in both simian virus 40 (SV40) and polyomavirus (PyV) large tumor antigens (T antigens) can be predicted with the assistance of a computer-based pattern-matching system, ARIADNE. The latter was used to optimally align elements of T antigen primary sequence and predicted secondary structure with a descriptor for a mononucleotide binding fold. Additional consensus elements of the nucleotide binding site in these two proteins were derived from comparisons of T antigen primary and predicted secondary structures with x-ray structures of the nucleotide binding sites in four otherwise unrelated proteins. Each of these elements was predicted to be encompassed within a 110-residue segment that is highly conserved between the two T antigens residues 418-528 in SV 40 T antigen and residues 565-675 in PyV. Results of biochemical and immunologic experiments on the nucleotide binding behavior of these proteins using (/sup 32/P)-Amp-labeled SV40 T antigen, were found to be consistent with these predictions. Taken together, the latter have resulted in a topological model of the ATP binding site in these two oncogene products.

  8. A Shorter Route to Antibody Binders via Quantitative in vitro Bead-Display Screening and Consensus Analysis

    PubMed Central

    Mankowska, Sylwia A.; Gatti-Lafranconi, Pietro; Chodorge, Matthieu; Sridharan, Sudharsan; Minter, Ralph R.; Hollfelder, Florian

    2016-01-01

    Affinity panning of large libraries is a powerful tool to identify protein binders. However, panning rounds are followed by the tedious re-screening of the clones obtained to evaluate binders precisely. In a first application of Bead Surface Display (BeSD) we show successful in vitro affinity selections based on flow cytometric analysis that allows fine quantitative discrimination between binders. Subsequent consensus analysis of the resulting sequences enables identification of clones that bind tighter than those arising directly from the experimental selection output. This is demonstrated by evolution of an anti-Fas receptor single-chain variable fragment (scFv) that was improved 98-fold vs the parental clone. Four rounds of quantitative screening by fluorescence-activated cell sorting of an error-prone library based on fine discrimination between binders in BeSD were followed by analysis of 200 full-length output sequences that suggested a new consensus design with a Kd ∼140 pM. This approach shortens the time and effort to obtain high affinity reagents and its cell-free nature transcends limitations inherent in previous in vivo display systems. PMID:27819305

  9. 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.

  10. Developing a model osteoarthritis consultation: a Delphi consensus exercise

    PubMed Central

    2013-01-01

    Background Osteoarthritis (OA) is a common condition managed in general practice, but often not in line with published guidance. The ideal consultation for a patient presenting with possible OA is not known. The aim of the study was to develop the content of a model OA consultation for the assessment and treatment of older adults presenting in general practice with peripheral joint problems. Methods A postal Delphi consensus exercise was undertaken with two expert groups: i) general practitioners (GPs) with expertise in OA management and ii) patients with experience of living with OA. An advisory group generated 61 possible consultation tasks for consideration in the consensus exercise. Expert groups were asked to consider which tasks should be included in the model OA consultation. The exercise was completed by 15 GPs and 14 patients. The level of agreement for inclusion in the model was set at 90%. Results The model OA consultation included 25 tasks to be undertaken during the initial consultation between a GP and a patient presenting with peripheral joint pain. The 25 tasks provide detailed advice on how the following elements of the consultation should be addressed: i) assessment of chronic joint pain, ii) patient’s ideas and concerns, iii) exclusion of red flags, iv) examination, v) provision of the diagnosis and written information, vi) promotion of exercise and weight loss, vii) initial pain management and viii) arranging a follow-up appointment. Both groups prioritised a bio-medical approach to the consultation, rather than a bio-psycho-social one, suggesting a discordance between current thinking and research evidence. Conclusions This study has enabled the priorities of GPs and patients to be identified for a model OA consultation. The results of this consensus study will inform the development of best practice for the management of OA in primary care and the implementation of evidence-based guidelines for OA in primary care. PMID:23320630

  11. Moving Toward Consensus on a Photovoltaic Generation Capacity Valuation Methodology

    SciTech Connect

    Richard Perez; Mike Taylor; Tom Hoff; JP Ross

    2011-06-22

    Maintaining adequate generating capacity to meet electricity demand at all times is a fundamental principle for the electric utility industry. This is accomplished through a variety of means including providing/purchasing sufficient generation capacity as well as acquiring the associated ancillary services for the electricity grid. The generation capacity of dispatchable resources is assessed based on technology design parameters. While dispatchable resources have some uncertainty in their output due to unforeseen equipment failures, their dispatch is managed around the demand for electricity and their marginal operating costs. Photovoltaic resources are non-dispatchable because their electrical output is based on both technology design parameters (technology selection, installation characteristics, and site conditions) and a solar resource that varies over a range of time periods (seasonal, daily, hourly, second to second). These solar resource variations, however, are not random and there is an intuitively positive relationship between PV system output and summer peak electricity demand for many locations throughout the U.S. This is because system demand peaks for most utilities are driven by heat-wave cooling demand, and because heat waves are indirectly fed by solar gain, i.e., by the fuel for PV generation. Despite this relationship, there is no consensus across the utility or solar industries on a method for calculating PV capacity or its practical use in electricity markets and utility planning. The U.S. Department of Energy’s Solar America Initiative has provided funding to evaluate the variety of photovoltaic capacity valuation methods and to bring the solar industry, electric utility, and research communities together with the goal of moving toward consensus on what is the most appropriate PV generation capacity valuation methodology using a consensus-oriented process. Developing a framework for accurately and appropriately calculating photovoltaic

  12. 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.

  13. The consensus-based approach for gene/enzyme replacement therapies and crystallization strategies: the case of human alanine-glyoxylate aminotransferase.

    PubMed

    Mesa-Torres, Noel; Yunta, Cristina; Fabelo-Rosa, Israel; Gonzalez-Rubio, Juana María; Sánchez-Ruiz, José M; Salido, Eduardo; Albert, Armando; Pey, Angel L

    2014-09-15

    Protein stability is a fundamental issue in biomedical and biotechnological applications of proteins. Among these applications, gene- and enzyme-replacement strategies are promising approaches to treat inherited diseases that may benefit from protein engineering techniques, even though these beneficial effects have been largely unexplored. In the present study we apply a sequence-alignment statistics procedure (consensus-based approach) to improve the activity and stability of the human AGT (alanine-glyoxylate aminotransferase) protein, an enzyme which causes PH1 (primary hyperoxaluria type I) upon mutation. By combining only five consensus mutations, we obtain a variant (AGT-RHEAM) with largely enhanced in vitro thermal and kinetic stability, increased activity, and with no side effects on foldability and peroxisomal targeting in mammalian cells. The structure of AGT-RHEAM reveals changes at the dimer interface and improved electrostatic interactions responsible for increased kinetic stability. Consensus-based variants maintained the overall protein fold, crystallized more easily and improved the expression as soluble proteins in two different systems [AGT and CIPK24 (CBL-interacting serine/threonine-protein kinase) SOS2 (salt-overly-sensitive 2)]. Thus the consensus-based approach also emerges as a simple and generic strategy to increase the crystallization success for hard-to-get protein targets as well as to enhance protein stability and function for biomedical applications.

  14. Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes

    PubMed Central

    Shirasawa, Kenta; Bertioli, David J.; Varshney, Rajeev K.; Moretzsohn, Marcio C.; Leal-Bertioli, Soraya C. M.; Thudi, Mahendar; Pandey, Manish K.; Rami, Jean-Francois; Foncéka, Daniel; Gowda, Makanahally V. C.; Qin, Hongde; Guo, Baozhu; Hong, Yanbin; Liang, Xuanqiang; Hirakawa, Hideki; Tabata, Satoshi; Isobe, Sachiko

    2013-01-01

    The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding. PMID:23315685

  15. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes.

    PubMed

    Shirasawa, Kenta; Bertioli, David J; Varshney, Rajeev K; Moretzsohn, Marcio C; Leal-Bertioli, Soraya C M; Thudi, Mahendar; Pandey, Manish K; Rami, Jean-Francois; Foncéka, Daniel; Gowda, Makanahally V C; Qin, Hongde; Guo, Baozhu; Hong, Yanbin; Liang, Xuanqiang; Hirakawa, Hideki; Tabata, Satoshi; Isobe, Sachiko

    2013-04-01

    The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaënsis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)(4×), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

  16. 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.

  17. 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.

  18. Partial least squares and random sample consensus in outlier detection.

    PubMed

    Peng, Jiangtao; Peng, Silong; Hu, Yong

    2012-03-16

    A novel outlier detection method in partial least squares based on random sample consensus is proposed. The proposed algorithm repeatedly generates partial least squares solutions estimated from random samples and then tests each solution for the support from the complete dataset for consistency. A comparative study of the proposed method and leave-one-out cross validation in outlier detection on simulated data and near-infrared data of pharmaceutical tablets is presented. In addition, a comparison between the proposed method and PLS, RSIMPLS, PRM is provided. The obtained results demonstrate that the proposed method is highly efficient.

  19. [Consensus document on the aetiology, diagnosis and treatment of sinusitis].

    PubMed

    Martinez Campos, L; Albañil Ballesteros, R; de la Flor Bru, J; Piñeiro Pérez, R; Cervera, J; Baquero Artigao, F; Alfayate Miguelez, S; Moraga Llop, F; Cilleruelo Ortega, M J; Calvo Rey, C

    2013-11-01

    The Spanish National Consensus (Spanish Society of Pediatric Infectious Diseases, Spanish Association of Primary Care Pediatrics, Spanish Society of Pediatric Outpatient and Primary Care, Spanish Society of Otorhinolaryngology and Cervical-Facial Pathology) on Sinusitis is presented. Rhinosinusitis is a difficult to diagnose and often unrecognised disease. The document discusses the aetiology, the clinical signs and symptoms, and the diagnostic criteria. A proposal for treatment is made based on the epidemiological situation in our country. Oral amoxicillin is the treatment of choice (80mg/kg/day divided every 8hours). Alternative treatment is proposed in special cases and when amoxicillin is not sufficient. The main complications are reviewed.

  20. 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.

  1. Consensus statements from the Workshop "Probiotics and Health: Scientific evidence".

    PubMed

    Guarner, F; Requena, T; Marcos, A

    2010-01-01

    This report shows the level of scientific consensus on definition, characteristics and health benefits of probiotics. The content of the report has derived from the scientific meeting: Workshop on Probiotics and Health. Scientific evidence, that congregated several Spanish experts, including gastroenterologists, microbiologists, nutritionists, immunologists and food technologists, among others, who have agreed with the statements shown in this document. Each statement has been sustained with the most relevant scientific aspects that were discussed during the Workshop and the following evaluation of the report by all experts who approved and signed it.

  2. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema

    White, Owen [University of Maryland

    2016-07-12

    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. 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.

  4. 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

  5. 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.

  6. Valuing certainty in a consensus-based water allocation mechanism

    NASA Astrophysics Data System (ADS)

    Pande, Saket; McKee, Mac

    2007-02-01

    We present an interdisciplinary approach to attach economic value to model certainty. The central theme of this paper concerns valuing certainty in water resource management, specifically resource allocation. A conceptual framework is developed to study (1) a hypothetical scenario of three water users attempting to mutually agree on allocation of some fixed amount of water amongst themselves and (2) California water policy negotiations along the lines of Adams et al. (1996). We attempt to answer how uncertainty in a policy variable affects the "allocation solution" in such consensus-based decision-making processes. This study finally evolves into economic valuation of uncertainty reduction and willingness to pay for the same.

  7. 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.

  8. Unexplained symptoms after terrorism and war: an expert consensus statement.

    PubMed

    Clauw, Daniel J; Engel, Charles C; Aronowitz, Robert; Jones, Edgar; Kipen, Howard M; Kroenke, Kurt; Ratzan, Scott; Sharpe, Michael; Wessely, Simon

    2003-10-01

    Twelve years of concern regarding a possible "Gulf War syndrome" has now given way to societal concerns of a "World Trade Center syndrome" and efforts to prevent unexplained symptoms following the most recent war in Iraq. These events serve to remind us that unexplained symptoms frequently occur after war and are likely after terrorist attacks. An important social priority is to recognize, define, prevent, and care for individuals with unexplained symptoms after war and related events (eg, terrorism, natural or industrial disasters). An international, multidisciplinary, and multiinstitutional consensus project was completed to summarize current knowledge on unexplained symptoms after terrorism and war.

  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.

  10. Consensus statement on preventive and symptomatic care of leukodystrophy patients.

    PubMed

    Van Haren, Keith; Bonkowsky, Joshua L; Bernard, Genevieve; Murphy, Jennifer L; Pizzino, Amy; Helman, Guy; Suhr, Dean; Waggoner, Jacque; Hobson, Don; Vanderver, Adeline; Patterson, Marc C

    2015-04-01

    Leukodystrophies are inherited disorders whose primary pathophysiology consists of abnormal deposition or progressive disruption of brain myelin. Leukodystrophy patients manifest many of the same symptoms and medical complications despite the wide spectrum of genetic origins. Although no definitive cures exist, all of these conditions are treatable. This report provides the first expert consensus on the recognition and treatment of medical and psychosocial complications associated with leukodystrophies. We include a discussion of serious and potentially preventable medical complications and propose several preventive care strategies. We also outline the need for future research to prioritize clinical needs and subsequently develop, validate, and optimize specific care strategies.

  11. Periodic sequence patterns in human exons

    SciTech Connect

    Baldi, P.; Brunak, S.; Engelbrecht, J.; Chauvin, Y.; Krogh, A.

    1995-12-31

    We analyze the sequential structure of human exons and their flanking introns by hidden Markov models. Together, models of donor site regions, acceptor site regions and flanked internal exons, show that exons -- besides the reading frame -- hold a specific periodic pattern. The pattern, which has the consensus: non-T(A/T)G and a minimal periodicity of roughly 10 nucleotides, is not a consequence of the nucleotide statistics in the three codon positions, nor of the well known nucleosome positioning signal. We discuss the relation between the pattern and other known sequence elements responsible for the intrinsic bending or curvature of DNA.

  12. 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

  13. 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.

  14. 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

  15. 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

  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.

  17. Consensus Paper: Pathological Role of the Cerebellum in Autism

    PubMed Central

    Fatemi, S. Hossein; Aldinger, Kimberly A.; Ashwood, Paul; Bauman, Margaret L.; Blaha, Charles D.; Blatt, Gene J.; Chauhan, Abha; Chauhan, Ved; Dager, Stephen R.; Dickson, Price E.; Estes, Annette M.; Goldowitz, Dan; Heck, Detlef H.; Kemper, Thomas L.; King, Bryan H.; Martin, Loren A.; Millen, Kathleen J.; Mittleman, Guy; Mosconi, Matthew W.; Persico, Antonio M.; Sweeney, John A.; Webb, Sara J.; Welsh, John P.

    2013-01-01

    There has been significant advancement in various aspects of scientific knowledge concerning the role of cerebellum in the etiopathogenesis of autism. In the current consensus paper, we will observe the diversity of opinions regarding the involvement of this important site in the pathology of autism. Recent emergent findings in literature related to cerebellar involvement in autism are discussed, including: cerebellar pathology, cerebellar imaging and symptom expression in autism, cerebellar genetics, cerebellar immune function, oxidative stress and mitochondrial dysfunction, GABAergic and glutamatergic systems, cholinergic, dopaminergic, serotonergic, and oxytocin related changes in autism, motor control and cognitive deficits, cerebellar coordination of movements and cognition, gene-environment interactions, therapeutics in autism and relevant animal models of autism. Points of consensus include presence of abnormal cerebellar anatomy, abnormal neurotransmitter systems, oxidative stress, cerebellar motor and cognitive deficits, and neuroinflammation in subjects with autism. Undefined areas or areas requiring further investigation include lack of treatment options for core symptoms of autism, vermal hypoplasia and other vermal abnormalities as a consistent feature of autism, mechanisms underlying cerebellar contributions to cognition, and unknown mechanisms underlying neuroinflammation. PMID:22370873

  18. [Consensus statement for accreditation of multidisciplinary thyroid cancer units].

    PubMed

    Díez, Juan José; Galofré, Juan Carlos; Oleaga, Amelia; Grande, Enrique; Mitjavila, Mercedes; Moreno, Pablo

    2016-03-01

    Thyroid cancer is the leading endocrine system tumor. Great advances have recently been made in understanding of the origin of these tumors and the molecular biology that makes them grow and proliferate, which have been associated to improvements in diagnostic procedures and increased availability of effective local and systemic treatments. All of the above makes thyroid cancer a paradigm of how different specialties should work together to achieve the greatest benefit for the patients. Coordination of all the procedures and patient flows should continue throughout diagnosis, treatment, and follow-up, and is essential for further optimization of resources and time. This manuscript was prepared at the request of the Working Group on Thyroid Cancer of the Spanish Society of Endocrinology and Nutrition, and is aimed to provide a consensus document on the definition, composition, requirements, structure, and operation of a multidisciplinary team for the comprehensive care of patients with thyroid cancer. For this purpose, we have included contributions by several professionals from different specialties with experience in thyroid cancer treatment at centers where multidisciplinary teams have been working for years, with the aim of developing a practical consensus applicable in clinical practice.

  19. [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.

  20. [Second Brazilian Consensus Conference on Helicobacter pylori infection].

    PubMed

    Coelho, Luiz Gonzaga Vaz; Zaterka, Schlioma

    2005-01-01

    Significant progress has been obtained since the First Brazilian Consensus Conference on H. pylori Infection held in 1995, in Belo Horizonte, MG, and justify a second meeting to establish updated guidelines on the current management of H. pylori infection. The Second Brazilian Consensus Conference on H. pylori Infection was organized by the Brazilian Federation of Gastroenterology and Brazilian Nucleus for the Study of Helicobacter and took place on June, 19-20, 2004 in São Paulo, SP. Thirty six delegates coming from 15 different Brazilian states including gastroenterologists, pathologists, microbiologists and pediatricians undertook the meeting. The participants were allocated in one the five main topics of the meeting: H. pylori and dyspepsia, H. pylori and NSAIDs, H. pylori and gastroesophageal reflux disease, H. pylori treatment, and H. pylori retreatment. Seventy per cent and more votes were considered as acceptance for the final statement. The results were presented during a special session on the VI Brazilian Week of Digestive System, in Recife, PE (October 2004), and this publication represents the summary of the main recommendations and conclusions emerged from the meeting.

  1. 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.

  2. Harmonization of quality indicators in laboratory medicine. A preliminary consensus.

    PubMed

    Plebani, Mario; Astion, Michael L; Barth, Julian H; Chen, Wenxiang; de Oliveira Galoro, César A; Escuer, Mercedes Ibarz; Ivanov, Agnes; Miller, Warren G; Petinos, Penny; Sciacovelli, Laura; Shcolnik, Wilson; Simundic, Ana-Maria; Sumarac, Zorica

    2014-07-01

    Quality indicators (QIs) are fundamental tools for enabling users to quantify the quality of all operational processes by comparing it against a defined criterion. QIs data should be collected over time to identify, correct, and continuously monitor defects and improve performance and patient safety by identifying and implementing effective interventions. According to the international standard for medical laboratories accreditation, the laboratory shall establish and periodically review QIs to monitor and evaluate performance throughout critical aspects of pre-, intra-, and post-analytical processes. However, while some interesting programs on indicators in the total testing process have been developed in some countries, there is no consensus for the production of joint recommendations focusing on the adoption of universal QIs and common terminology in the total testing process. A preliminary agreement has been achieved in a Consensus Conference organized in Padua in 2013, after revising the model of quality indicators (MQI) developed by the Working Group on "Laboratory Errors and Patient Safety" of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). The consensually accepted list of QIs, which takes into consideration both their importance and applicability, should be tested by all potentially interested clinical laboratories to identify further steps in the harmonization project.

  3. Consensus Statement on Standard of Care for Congenital Myopathies

    PubMed Central

    Wang, Ching H.; Dowling, James J.; North, Kathryn; Schroth, Mary K.; Sejersen, Thomas; Shapiro, Frederic; Bellini, Jonathan; Weiss, Hali; Guillet, Marc; Amburgey, Kimberly; Apkon, Susan; Bertini, Enrico; Bonnemann, Carsten; Clarke, Nigel; Connolly, Anne M.; Estournet-Mathiaud, Brigitte; Fitzgerald, Dominic; Florence, Julaine M.; Gee, Richard; Gurgel-Giannetti, Juliana; Glanzman, Allan M.; Hofmeister, Brittany; Jungbluth, Heinz; Koumbourlis, Anastassios C.; Laing, Nigel G.; Main, Marion; Morrison, Leslie A.; Munns, Craig; Rose, Kristy; Schuler, Pamela M.; Sewry, Caroline; Storhaug, Kari; Vainzof, Mariz; Yuan, Nanci

    2016-01-01

    Recent progress in scientific research has facilitated accurate genetic and neuropathological diagnosis of congenital myopathies. However, given their relatively low incidence, congenital myopathies remain unfamiliar to the majority of care providers, and the levels of patient care are extremely variable. This consensus statement aims to provide care guidelines for congenital myopathies. The International Standard of Care Committee for Congenital Myopathies worked through frequent e-mail correspondences, periodic conference calls, 2 rounds of online surveys, and a 3-day workshop to achieve a consensus for diagnostic and clinical care recommendations. The committee includes 59 members from 10 medical disciplines. They are organized into 5 working groups: genetics/diagnosis, neurology, pulmonology, gastroenterology/nutrition/speech/oral care, and orthopedics/rehabilitation. In each care area the authors summarize the committee’s recommendations for symptom assessments and therapeutic interventions. It is the committee’s goal that through these recommendations, patients with congenital myopathies will receive optimal care and improve their disease outcome. PMID:22431881

  4. 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

  5. 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.

  6. Combination therapy in hypertension: an Asia-Pacific consensus viewpoint.

    PubMed

    Abdul Rahman, Abdul Rashid; Reyes, Eugenio B; Sritara, Piyamitr; Pancholia, Arvind; Van Phuoc, Dang; Tomlinson, Brian

    2015-05-01

    Hypertension incurs a significant healthcare burden in Asia-Pacific countries, which have suboptimal rates of blood pressure (BP) treatment and control. A consensus meeting of hypertension experts from the Asia-Pacific region convened in Hanoi, Vietnam, in April 2013. The principal objectives were to discuss the growing problem of hypertension in the Asia-Pacific region, and to develop consensus recommendations to promote standards of care across the region. A particular focus was recommendations for combination therapy, since it is known that most patients with hypertension will require two or more antihypertensive drugs to achieve BP control, and also that combinations of drugs with complementary mechanisms of action achieve BP targets more effectively than monotherapy. The expert panel reviewed guidelines for hypertension management from the USA and Europe, as well as individual Asia-Pacific countries, and devised a treatment matrix/guide, in which they propose the preferred combination therapy regimens for patients with hypertension, both with and without compelling indications. This report summarizes key recommendations from the group, including recommended antihypertensive combinations for specific patient populations. These strategies generally entail initiating therapy with free drug combinations, starting with the lowest available dosage, followed by treatment with single-pill combinations once the BP target has been achieved. A single reference for the whole Asia-Pacific region may contribute to increased consistency of treatment and greater proportions of patients achieving BP control, and hence reducing hypertension-related morbidity and mortality.

  7. Collective learning and optimal consensus decisions in social animal groups.

    PubMed

    Kao, Albert B; Miller, Noam; Torney, Colin; Hartnett, Andrew; Couzin, Iain D

    2014-08-01

    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.

  8. 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

  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. 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

  12. 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

  13. 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.

  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. Distributed Tracking with Consensus on Noisy Time-varying Graphs: Convergence Results and Applications

    DTIC Science & Technology

    2010-12-01

    R. M. Murray, “ Consensus problems in networks of agents with switching topology and time -delays,” IEEE Trans. Autom. Control, vol. 49, no. 9, pp... Distributed Tracking with Consensus on Noisy Time -varying Graphs: Convergence Results and Applications Sudharman K. Jayaweera and Y. Ruan ECE... distributed tracking with consensus on a time -varying graph with noisy communications links and sensing constraints. We develop a framework to handle the

  16. Leader-follower consensus control of Lipschitz nonlinear systems by output feedback

    NASA Astrophysics Data System (ADS)

    Sadhiqin Mohd Isira, Ahmad; Zuo, Zongyu; Ding, Zhengtao

    2016-12-01

    This paper deals with the leader-follower consensus problem of Lipschitz nonlinear systems under fixed directed communication networks. Both state and output feedback control are proposed based on state and output measurements of neighbouring agents, respectively. Laplacian matrix features are explored for the stability analysis, and the sufficient conditions are derived to solve the consensus problem. Finally, simulation results are included to demonstrate the effectiveness of the output-based consensus controller.

  17. Sequence diversity of wheat mosaic virus isolates.

    PubMed

    Stewart, Lucy R

    2016-02-02

    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.

  18. 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.

  19. Higher order finite-time consensus protocol for heterogeneous multi-agent systems

    NASA Astrophysics Data System (ADS)

    Zhou, Yingjiang; Yu, Xinghuo; Sun, Changyin; Yu, Wenwu

    2015-02-01

    This paper studies the higher order finite-time consensus protocol for heterogeneous multi-agent systems (HMASs). By adding a power integrator method and using heterogeneous domination method, two kinds of consensus protocols are proposed with state feedback and output feedback, respectively. First, for the leaderless and leader-follower HMASs, the continuous finite-time consensus protocols are proposed. Then, by designing a finite-time observer, the output-feedback finite-time consensus protocol is developed. Finally, simulations are performed to illustrate the effectiveness of the theoretical results.

  20. 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.

  1. 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.

  2. Critical Resources for Hospital Surge Capacity: An Expert Consensus Panel

    PubMed Central

    Bayram, Jamil D.; Sauer, Lauren M.; Catlett, Christina; Levin, Scott; Cole, Gai; Kirsch, Thomas D.; Toerper, Matthew; Kelen, Gabor

    2013-01-01

    Background: Hospital surge capacity (HSC) is dependent on the ability to increase or conserve resources. The hospital surge model put forth by the Agency for Healthcare Research and Quality (AHRQ) estimates the resources needed by hospitals to treat casualties resulting from 13 national planning scenarios. However, emergency planners need to know which hospital resource are most critical in order to develop a more accurate plan for HSC in the event of a disaster. Objective: To identify critical hospital resources required in four specific catastrophic scenarios; namely, pandemic influenza, radiation, explosive, and nerve gas. Methods: We convened an expert consensus panel comprised of 23 participants representing health providers (i.e., nurses and physicians), administrators, emergency planners, and specialists. Four disaster scenarios were examined by the panel. Participants were divided into 4 groups of five or six members, each of which were assigned two of four scenarios. They were asked to consider 132 hospital patient care resources- extracted from the AHRQ's hospital surge model- in order to identify the ones that would be critical in their opinion to patient care. The definition for a critical hospital resource was the following: absence of the resource is likely to have a major impact on patient outcomes, i.e., high likelihood of untoward event, possibly death. For items with any disagreement in ranking, we conducted a facilitated discussion (modified Delphi technique) until consensus was reached, which was defined as more than 50% agreement. Intraclass Correlation Coefficients (ICC) were calculated for each scenario, and across all scenarios as a measure of participant agreement on critical resources. For the critical resources common to all scenarios, Kruskal-Wallis test was performed to measure the distribution of scores across all scenarios. Results: Of the 132 hospital resources, 25 were considered critical for all four scenarios by more than 50% of

  3. A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

    PubMed Central

    Blenda, Anna; Fang, David D.; Rami, Jean-François; Garsmeur, Olivier; Luo, Feng; Lacape, Jean-Marc

    2012-01-01

    A consensus genetic map of tetraploid cotton was constructed using six high-density 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 cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous AT and DT chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per AT/DT chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton. PMID:23029214

  4. A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs.

    PubMed

    Muchero, Wellington; Diop, Ndeye N; Bhat, Prasanna R; Fenton, Raymond D; Wanamaker, Steve; Pottorff, Marti; Hearne, Sarah; Cisse, Ndiaga; Fatokun, Christian; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

    2009-10-27

    Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops" with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximately 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.

  5. Annotation and analysis of a large cuticular protein family with the R&R Consensus in Anopheles gambiae

    PubMed Central

    Cornman, R Scott; Togawa, Toru; Dunn, W Augustine; He, Ningjia; Emmons, Aaron C; Willis, Judith H

    2008-01-01

    Background The most abundant family of insect cuticular proteins, the CPR family, is recognized by the R&R Consensus, a domain of about 64 amino acids that binds to chitin and is present throughout arthropods. Several species have now been shown to have more than 100 CPR genes, inviting speculation as to the functional importance of this large number and diversity. Results We have identified 156 genes in Anopheles gambiae that code for putative cuticular proteins in this CPR family, over 1% of the total number of predicted genes in this species. Annotation was verified using several criteria including identification of TATA boxes, INRs, and DPEs plus support from proteomic and gene expression analyses. Two previously recognized CPR classes, RR-1 and RR-2, form separate, well-supported clades with the exception of a small set of genes with long branches whose relationships are poorly resolved. Several of these outliers have clear orthologs in other species. Although both clades are under purifying selection, the RR-1 variant of the R&R Consensus is evolving at twice the rate of the RR-2 variant and is structurally more labile. In contrast, the regions flanking the R&R Consensus have diversified in amino-acid composition to a much greater extent in RR-2 genes compared with RR-1 genes. Many genes are found in compact tandem arrays that may include similar or dissimilar genes but always include just one of the two classes. Tandem arrays of RR-2 genes frequently contain subsets of genes coding for highly similar proteins (sequence clusters). Properties of the proteins indicated that each cluster may serve a distinct function in the cuticle. Conclusion The complete annotation of this large gene family provides insight on the mechanisms of gene family evolution and clues about the need for so many CPR genes. These data also should assist annotation of other Anopheles genes. PMID:18205929

  6. Database Independent Protein Sequencing (DiPS) enables full-length de-novo protein and antibody sequence determination.

    PubMed

    Savidor, Alon; Barzilay, Rotem; Elinger, Dalia; Yarden, Yosef; Lindzen, Moshit; Gabashvili, Alexandra; Adiv Tal, Ophir; Levin, Yishai

    2017-03-27

    Traditional 'bottom-up' proteomics approaches use proteolytic digestion, LC-MS/MS and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here we present Database Independent Protein Sequencing (DiPS), a method for unambiguous, rapid, database independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler" (pTA). As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant, monoclonal antibody. Excluding leucine/isoleucine and glutamic-acid/deamidated glutamine ambiguities, end-to-end, full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100% but there was a 23 residue gap in the constant region sequence.

  7. Consensus numbering system for the rifampicin resistance-associated rpoB gene mutations in pathogenic mycobacteria.

    PubMed

    Andre, E; Goeminne, L; Cabibbe, A; Beckert, P; Kabamba Mukadi, B; Mathys, V; Gagneux, S; Niemann, S; Van Ingen, J; Cambau, E

    2017-03-01

    The rpoB gene codes for the RNA polymerase β subunit, which is the target of rifampicin, an essential drug in the treatment of tuberculosis and other mycobacterial infections. This gene is present in all bacteria, but its length and nucleotide sequence vary between bacterial species, including mycobacteria. Mutations in the rpoB gene alter the structure of this protein and cause drug resistance. To describe the resistance-associated mutations, the scientific and medical communities have been using, since 1993, a numbering system based on the Escherichia coli sequence annotation. Using E. coli reference for describing mutations in mycobacteria leads to misunderstandings, particularly with the increasing use of whole genome sequencing, which brought an alternative numbering system based on the Mycobacterium tuberculosis rpoB sequence. We propose using a consensus numbering system for the reporting of resistance mutations based on the reference genomes from the species interrogated (such as strain H37Rv for M. tuberculosis). This manuscript provides the necessary figures and tables allowing researchers, microbiologists and clinicians to easily convert other annotation systems into one common language.

  8. Consistent breakage between consensus recombinase heptamers of chromosome 9 DNA in a recurrent chromosomal translocation of human T cell leukemia

    PubMed Central

    1989-01-01

    Chromosomal translocations in lymphoid tumors frequently result from recombination between a normally rearranging antigen receptor gene and a normally non-rearranging second locus. The possibility that the lymphocyte recombinase apparatus plays a role in determining the position of breakage at the second locus has been a matter of controversy because of the inconsistent presence of heptamer-like recognition sequences adjoining breakpoints at this site. To further investigate this issue, sites of DNA recombination were analyzed in both the der(9) and der(7) products of t(7;9)(q34;q32), a recurrent translocation of human acute lymphoblastic leukemias (T-ALL). In each of three separate cases, the translocation has divided the TCR-beta locus, juxtaposing chromosome 9 DNA 5' to a J-region in the der(9) product and 3' to a D-region in the der(7) product, with variably sized N-insertions and small deletions detectable at the junctions. All three cases contain breakpoints in chromosome 9 DNA tightly clustered between two closely spaced, and oppositely oriented heptamer sequences, CAC(A/T)GTG, which perfectly match the consensus heptamer sequence recognized by the lymphocyte recombinase apparatus in normal antigen receptor gene rearrangement. In no case was there evidence of directly duplicated sequences in the two reciprocal products, as is often associated with recombination involving random staggered breakage of DNA. Taken together, these results support a mechanism for this particular translocation proceeding by recombinase-mediated breakage of both participating chromosomes. PMID:2536065

  9. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

  10. 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.

  11. Management of Pediatric Malignant Germ Cell Tumors: ICMR Consensus Document.

    PubMed

    Agarwala, Sandeep; Mitra, Aparajita; Bansal, Deepak; Kapoor, Gauri; Vora, Tushar; Prasad, Maya; Chinnaswamy, Girish; Arora, Brijesh; Radhakrishnan, Venkatraman; Laskar, Siddharth; Kaur, Tanvir; Dhaliwal, Rupinder Singh; Rath, G K; Bakhshi, Sameer

    2017-04-01

    With the introduction of cisplatin, the outcome of children with malignant germ cell tumors (MGCT) has improved to nearly 90% 5 year survival. Over the years, through the results of various multinational co-operative trials, the chemotherapy and surgical guidelines for both the gonadal and extra-gonadal MGCTs have been refined to decrease the early and late morbidities and at the same time improve survival. Introduction of risk categorization has further added to this effort. There has been no recommendation on how the children with malignant germ cell tumors should be treated in India. The current manuscript is written with the objective of developing a consensus guideline for practitioners at a National level. Based on extensively reviewed literature and personal experience of the major pediatric oncology centres in India, the ICMR Expert group has made recommendations for management of children with MGCT India.

  12. 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.

  13. Italian consensus conference for colonic diverticulosis and diverticular disease.

    PubMed

    Cuomo, Rosario; 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

    2014-10-01

    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.

  14. Science Organizations Remind Senators of Consensus on Climate Change

    NASA Astrophysics Data System (ADS)

    Chell, Kaitlin

    2009-11-01

    AGU and 17 other scientific organizations sent an open letter to the U.S. Senate on 21 October reminding senators of the scientific consensus on anthropogenic climate change. The letter was sent 1 week before the Senate Committee on Environment and Public Works began a series of hearings on climate change legislation, the Clean Energy Jobs and American Power Act (Senate bill 1733). The letter states, “Observations throughout the world make it clear that climate change is occurring, and rigorous scientific research demonstrates that the greenhouse gases emitted by human activities are the primary driver. These conclusions are based on multiple independent lines of evidence, and contrary assertions are inconsistent with an objective assessment of the vast body of peer-reviewed science.”

  15. 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.

  16. A consensus statement on the gender perspective in lung cancer.

    PubMed

    Isla, D; Majem, M; Viñolas, N; Artal, A; Blasco, A; Felip, E; Garrido, P; Remón, J; Baquedano, M; Borrás, J M; Die Trill, M; García-Campelo, R; Juan, O; León, C; Lianes, P; López-Ríos, F; Molins, L; Planchuelo, M Á; Cobo, M; Paz-Ares, L; Trigo, J M; de Castro, J

    2016-11-24

    Lung cancer is the most common cancer globally and has the highest mortality. Although this disease is not associated with a particular gender, its incidence is rising among women, who are diagnosed at an increasingly younger age compared with men. One of the main reasons for this rise is women taking up smoking. However, many non-smoking women also develop this disease. Other risk factors implicated in the differential development of lung cancer in women are genetic predisposition, tumour histology and molecular profile. Proportionally more women than men with lung cancer have a mutation in the EGFR gene. This consensus statement reviews the available evidence about the epidemiological, biological, diagnostic, therapeutic, social and psychological aspects of lung cancer in women.

  17. Consensus statements on occupational therapy ethics related to driving.

    PubMed

    Slater, Deborah Yarett

    2014-04-01

    As part of an expert panel convened to examine evidence and practice related to diverse aspects of driving evaluation and rehabilitation, consensus statements were developed on ethics. This paper provides context for the ethical obligation of practitioners to assess and make recommendations about the ability of clients to safely perform the activity of driving. It highlights key articles from the literature as well as principles from the Occupational Therapy Code of Ethics and Ethics Standards (2010). The statements support the importance of identifying impairments affecting driving, which could result in harm to the client as well as to the public. The ethical and professional obligation of practitioners to evaluate, make recommendations, and possibly report and/or refer to a driver rehabilitation specialist for further services is reinforced.

  18. Consensus statement for diagnosis of subcortical small vessel disease

    PubMed Central

    Wallin, Anders; Wardlaw, Joanna M; Markus, Hugh S; Montaner, Joan; Wolfson, Leslie; Iadecola, Costantino; Zlokovic, Berislav V; Joutel, Anne; Dichgans, Martin; Duering, Marco; Schmidt, Reinhold; Korczyn, Amos D; Grinberg, Lea T; Chui, Helena C; Hachinski, Vladimir

    2016-01-01

    Vascular cognitive impairment (VCI) is the diagnostic term used to describe a heterogeneous group of sporadic and hereditary diseases of the large and small blood vessels. Subcortical small vessel disease (SVD) leads to lacunar infarcts and progressive damage to the white matter. Patients with progressive damage to the white matter, referred to as Binswanger’s disease (BD), constitute a spectrum from pure vascular disease to a mixture with neurodegenerative changes. Binswanger’s disease patients are a relatively homogeneous subgroup with hypoxic hypoperfusion, lacunar infarcts, and inflammation that act synergistically to disrupt the blood–brain barrier (BBB) and break down myelin. Identification of this subgroup can be facilitated by multimodal disease markers obtained from clinical, cerebrospinal fluid, neuropsychological, and imaging studies. This consensus statement identifies a potential set of biomarkers based on underlying pathologic changes that could facilitate diagnosis and aid patient selection for future collaborative treatment trials. PMID:26198175

  19. 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

  20. 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.

  1. Statistical mechanics model for the emergence of consensus

    NASA Astrophysics Data System (ADS)

    Raffaelli, Giacomo; Marsili, Matteo

    2005-07-01

    The statistical properties of pairwise majority voting over S alternatives are analyzed in an infinite random population. We first compute the probability that the majority is transitive (i.e., that if it prefers A to B to C , then it prefers A to C ) and then study the case of an interacting population. This is described by a constrained multicomponent random field Ising model whose ferromagnetic phase describes the emergence of a strong transitive majority. We derive the phase diagram, which is characterized by a tricritical point and show that, contrary to intuition, it may be more likely for an interacting population to reach consensus on a number S of alternatives when S increases. This effect is due to the constraint imposed by transitivity on voting behavior. Indeed if agents are allowed to express nontransitive votes, the agents’ interaction may decrease considerably the probability of a transitive majority.

  2. 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

  3. Melanoma: diagnosis, staging, and treatment. Consensus group recommendations.

    PubMed

    Berrocal, Alfonso; Cabañas, Luis; Espinosa, Enrique; Fernández-de-Misa, Ricardo; Martín-Algarra, Salvador; Martínez-Cedres, José Carlos; Ríos-Buceta, Luis; Rodríguez-Peralto, José Luis

    2014-09-01

    The incidence of malignant melanoma is increasing worldwide. In Spain, its incidence is increasing faster than any other cancer type, with a 5-year survival rate of about 85%. The impact and characteristics of malignant melanoma in the Spanish population can be ascertained from the national melanoma registry of the Academia Española de Dermatología y Venereología. This review presents consensus group recommendations for the diagnosis, staging and treatment of malignant melanoma in Spain. Incidence and mortality are discussed, as well as evaluation of various prevention and treatment strategies. Prognostic factors, such as BRAF and C-KIT mutations, which are expected to become routine staging procedures over the next few years, are outlined, especially in relation to treatment options. The use of recently approved targeted agents such as ipilimumab, a cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) inhibitor, and vemurafenib, a BRAF inhibitor, in metastatic disease are also discussed.

  4. 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

  5. Surgical research in Canada: synopsis of a consensus conference

    PubMed Central

    Warnock, Garth L.; Tator, Charles H.

    1998-01-01

    Canadian surgical research requires careful nurturing if it is to flourish in tomorrow’s environment. A consensus conference organized by the Research Development Committee of the Canadian Association of Surgical Chairs has addressed a number of issues to promote Canadian surgical research. This synopsis is a summary of the proceedings of that conference. It reflects on the meaning of surgical science, elements of establishing a successful research program, leadership in surgical science, identification of talented trainees, and the means to make the most of opportunities for funding. The information contained in the synopsis should not only assist departments of surgery and surgical specialty societies but should challenge them to set goals and innovative approaches to plan for strong surgical research in a changing environment. PMID:9711162

  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.

  7. Decentralized energy planning and consensus in energy policy

    SciTech Connect

    Wilbanks, T. J.

    1980-05-02

    This paper explores the following three propositions and their relationships: (1) that, in our pluralistic policymaking environment, we cannot solve our nation's energy problems unless we can reach agreement among a diverse group of interested parties about specific actions; (2) that, short of a manifest emergency, such a consensus is difficult to reach unless the scale of the decision-making unit is relatively small; and therefore (3) that one of the keys to an effective energy policy in the United states is to rely heavily on local and regional energy planning and decision-making. First, the paper reviews our problem of irresolution and its roots, and it summaries the policy options for resolving it. Then it explores one of those options, decentralized planning, in a little more detail. Finally, it offers some speculations about the viability of a decentralized approach to energy planninng.

  8. Therapeutic monitoring of clozapine in Australia: the need for consensus.

    PubMed

    Oo, Thein Z; Wilson, John F; Naidoo, Divania; Chetty, Manoranjenni

    2006-10-01

    In the absence of well-defined guidelines for the monitoring of plasma concentrations of clozapine, this study examined the practices of seven laboratories from four states in Australia. Laboratories analyzed 5 freeze-dried serum samples containing a mixture of clozapine and norclozapine in varying concentrations and the measurement data were analyzed for accuracy and precision. Additional information on laboratory practices was obtained through questionnaire responses. Measurement precision amongst the laboratories was good but there were significant differences in the accuracy of measurements from one laboratory. There were differences in the ranges for which assays had been validated and in suggested therapeutic ranges. These differences could have a significant impact on the interpretation of measured concentrations and patient care, and emphasize the need for consensus in this area. Repeat concentration measurements are recommended in the case of drug concentration measurements that are inconsistent with clinical observations or previous measurements.

  9. [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.

  10. 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

  11. Recommendations for intra-abdominal infections consensus report

    PubMed Central

    Avkan-Oğuz, Vildan; Baykam, Nurcan; Sökmen, Selman; Güner, Rahmet; Agalar, Fatih; Alp, Emine; Doğrul, Ahmet; Turhan, Özge; Ağalar, Canan; Kurtaran, Behice; Geçim, İbrahim Ethem; Özaras, Reşat; Yılmaz, Gürdal; Akbulut, Ayhan; Koksal, İftihar

    2016-01-01

    Guidelines include the recommendations of experts from various specialties within a topic in consideration of data specific to each country. However, to date there has not been a guideline standardizing the nomenclature and offering recommendations for intra-abdominal infections (IAIs) in Turkey. This is mainly due to the paucity of laboratory studies regarding the clinical diagnosis and treatment of IAIs or the sensitivity of microorganisms isolated from patients with IAIs. However, due to the diversification of host characteristics and advancements in technological treatment methods, it has become imperative to ‘speak a common language’. For this purpose May 2015, a group of 15 experts in intra-abdominal infections, under the leadership of the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey (EKMUD) and with representatives from the Turkish Surgical Association, Turkish Society of Colon and Rectal Surgery, Hernia Society, Turkish Society of Hepato-pancreato-biliary Surgery, and the Turkish Society of Hospital Infections and Control, was formed to analyze relevant studies in the literature. Ultimately, the suggestions for adults found in this consensus report were developed using available data from Turkey, referring predominantly to the 2010 guidelines for diagnosing and managing complicated IAIs in adults and children by the Infectious Diseases Society of America (IDSA) and the Surgical Infection Society. The recommendations are presented in two sections, from the initial diagnostic evaluation of patients to the treatment approach for IAI. This Consensus Report was presented at the EKMUD 2016 Congress in Antalya and was subsequently opened for suggestions on the official websites of the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey and Turkish Surgical Association for one month. The manuscript was revised according to the feedback received. PMID:28149134

  12. 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

  13. Toward a consensus on radiobiology teaching to radiation oncology residents.

    PubMed

    Dynlacht, Joseph R; Dewhirst, Mark W; Hall, Eric J; Rosenstein, Barry S; Zeman, Elaine M

    2002-05-01

    There are approximately 82 radiation oncology residency programs in the United States, which provide training opportunities for about 400 residents. All accredited radiation oncology residency programs must have at least one basic scientist on the faculty, and it is these individuals who often assume, wholly or in part, the responsibility of teaching radiation and cancer biology to radiation oncology residents in preparation for the American College of Radiology (ACR) In-Training Examination in Radiation Oncology and the American Board of Radiology (ABR) written examinations. In response to a perceived lack of uniformity in radiation and cancer biology curricula currently being taught to residents and a perceived lack of guidance for instructors in formulating course content for this population, a special session was presented at the Forty-eighth Annual Radiation Research Society meeting on April 23, 2001. The session, entitled "Toward a Consensus on Radiobiology Teaching to Radiation Oncology Residents", was focused on issues related to teaching radiobiology to radiation oncology residents and targeted for individuals who actively teach radiation and cancer biology as well as coordinators of residency training programs. The speakers addressed current challenges and future problems facing instructors and programs. Among these were lack of feedback on resident performance on ABR and ACR written examinations and on course content, uncertainty about what topics residents must know to pass the ABR examination, and, in the near future, a reduction (due to retirement) of instructors qualified to teach radiobiology. This article provides a synopsis of the information that was presented during that session, offers a glimpse into how the ABR and ACR examinations are prepared and details of the content of past and future examinations, and summarizes the activities of the Joint Working Group on Radiobiology Teaching which was formed to educate instructors, to establish a

  14. 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

  15. A New Measure for Analyzing and Fusing Sequences of Objects.

    PubMed

    Goulermas, John Yannis; Kostopoulos, Alexandros; Mu, Tingting

    2016-05-01

    This work is related to the combinatorial data analysis problem of seriation used for data visualization and exploratory analysis. Seriation re-sequences the data, so that more similar samples or objects appear closer together, whereas dissimilar ones are further apart. Despite the large number of current algorithms to realize such re-sequencing, there has not been a systematic way for analyzing the resulting sequences, comparing them, or fusing them to obtain a single unifying one. We propose a new positional proximity measure that evaluates the similarity of two arbitrary sequences based on their agreement on pairwise positional information of the sequenced objects. Furthermore, we present various statistical properties of this measure as well as its normalized version modeled as an instance of the generalized correlation coefficient. Based on this measure, we define a new procedure for consensus seriation that fuses multiple arbitrary sequences based on a quadratic assignment problem formulation and an efficient way of approximating its solution. We also derive theoretical links with other permutation distance functions and present their associated combinatorial optimization forms for consensus tasks. The utility of the proposed contributions is demonstrated through the comparison and fusion of multiple seriation algorithms we have implemented, using many real-world datasets from different application domains.

  16. Fusion to a highly stable consensus albumin binding domain allows for tunable pharmacokinetics.

    PubMed

    Jacobs, Steven A; Gibbs, Alan C; Conk, Michelle; Yi, Fang; Maguire, Diane; Kane, Colleen; O'Neil, Karyn T

    2015-10-01

    A number of classes of proteins have been engineered for high stability using consensus sequence design methods. Here we describe the engineering of a novel albumin binding domain (ABD) three-helix bundle protein. The resulting engineered ABD molecule, called ABDCon, is expressed at high levels in the soluble fraction of Escherichia coli and is highly stable, with a melting temperature of 81.5°C. ABDCon binds human, monkey and mouse serum albumins with affinity as high as 61 pM. The solution structure of ABDCon is consistent with the three-helix bundle design and epitope mapping studies enabled a precise definition of the albumin binding interface. Fusion of a 10 kDa scaffold protein to ABDCon results in a long terminal half-life of 60 h in mice and 182 h in cynomolgus monkeys. To explore the link between albumin affinity and in vivo exposure, mutations were designed at the albumin binding interface of ABDCon yielding variants that span an 11 000-fold range in affinity. The PK properties of five such variants were determined in mice in order to demonstrate the tunable nature of serum half-life, exposure and clearance with variations in albumin binding affinity.

  17. 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.

  18. A consensus secondary structure of ITS2 in the chlorophyta identified by phylogenetic reconstruction.

    PubMed

    Caisová, Lenka; Marin, Birger; Melkonian, Michael

    2013-07-01

    The definition of species plays a pivotal role in biology. It has been proposed that Compensatory Base Changes (CBCs) in the fast-evolving Internal Transcribed Spacer 2 (ITS2) correlate with speciation and thus can be used to distinguish species. The applicability of CBC - based species concepts using ITS2, however, rests on the homology of the investigated ITS2 positions. We studied the ITS2 molecule of 147 strains of Chlorophyceae (Chlorophyta, Viridiplantae) including 26 new sequences in the order Chaetophorales, and compared their secondary structures to ITS2 in the sister class Ulvophyceae, represented by the order Ulvales. Using a phylogenetic/comparative approach, it was possible to identify 1) the first consensus structure model of the ITS2 molecule that can be applied to two classes of green algae [Ulvophyceae (Ulvales), Chlorophyceae] and 2) landmarks (the spacer regions separating the ITS2 Helices) for more robust prediction of the secondary structures in green algae. Moreover, we found that CBCs in homologous positions in these 147 strains (representing 115 validly described species) are either completely absent or mostly associated with internal branches representing higher order taxonomic levels (genera, families, orders). As reported for the Ulvales, CBCs are not diagnostic at the species level in the dataset used.

  19. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

    PubMed

    Dias, João D; Rito, Tiago; Torlai Triglia, Elena; Kukalev, Alexander; Ferrai, Carmelo; Chotalia, Mita; Brookes, Emily; Kimura, Hiroshi; Pombo, Ana

    2015-12-19

    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.

  20. MemO: a consensus approach to the annotation of a protein's membrane organization.

    PubMed

    Davis, Melissa J; Zhang, Fasheng; Yuan, Zheng; Teasdale, Rohan D

    2006-01-01

    Membrane organization describes the relationship of proteins to the membrane, that is, whether the protein crosses the membrane or is integral to the membrane and its orientation with respect to the membrane. Membrane organization is determined primarily by the presence of two features which target proteins to the secretory pathway: the endoplasmic reticulum signal peptide and the ?-helical transmembrane domain. In order to generate membrane organization annotation of high quality, confidence and throughput, the Membrane Organization (MemO) pipeline was developed, incorporating consensus feature prediction modules with integration and annotation rules derived from biological observations. The pipeline classifies proteins into six categories based on the presence or absence of predicted features: Soluble, intracellular proteins; Soluble, secreted proteins; Type I membrane proteins; Type II membrane proteins; Multi-span membrane proteins and Glycosylphosphatidylinositol anchored membrane proteins. The MemO pipeline represents an integrated strategy for the application of state-of-the-art bioinformatics tools to the annotation of protein membrane organization, a property which adds biological context to the large quantities of protein sequence information available.