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At least 955 records · Page 53Linked to original sources
PubMed2003

Atypical recognition consensus of CIN85/SETA/Ruk SH3 domains revealed by target-assisted iterative screening.

Target-assisted iterative screening applied to random peptide libraries unveiled a novel and atypical recognition consensus shared by CIN85/SETA/Ruk SH3 domains, PX(P/A)XXR. Confirmed by mutagenesis and in vitro binding experiments, the novel consensus allowed for the accurate mapping of CIN85 SH3 binding sites within known CIN85 interactors, c-Cbl, BLNK, Cbl-b, AIP1/Alix, SB1, and CD2 proteins, as well as the prediction of CIN85 novel-interacting partners in protein databases. Synaptojanin 1, PAK2, ZO-2, and TAFII70, which contain CIN85 SH3 recognition consensus sites, were selectively precipitated from mouse brain lysates by CIN85 SH3 domains in glutathione S-transferase pull-down experiments. A direct interaction of synaptojanin 1 and PAK2 with CIN85 SH3 domains was confirmed by Far Western blotting.

Adaptor Proteins, Signal Transducing↗
PubMed1993

Generalizability of the false consensus effect in chronic psychiatric patients.

The selective exposure hypothesis argues that the false consensus effect occurs because people base their estimates about the prevalence of behaviors, beliefs, and traits on a mental sample of those around them, overrepresenting others who are similar. It was hypothesized that psychiatric patients would be less subject to the false consensus effect because they would recognize the deviance of their peers and avoid using them to make estimates. Sixty male and female college students and 32 psychiatric patients estimated the percentage of average Americans who endorsed 32 behaviors, beliefs, and self-descriptive traits. Contrary to prediction, the psychiatric patients' estimates were no less likely than the college students' to exhibit false consensus effects.

Adolescent↗
PubMed1987

Structure and conformation of the duplex consensus 5'-splice site d[(CpApGpGpTpApApGpT).(ApCpTpTpApCpCpTpG)] deduced from high field 1H-NMR of the non-exchangeable and imino protons.

The complementary consensus donor exon intron junction d(ApCpTpTpApCpCpTpG) has been synthesized by a solid phase procedure. The non-exchangeable proton assignments were obtained using one- and two-dimensional NMR techniques including NOE, COSY, NOESY and 1H-1H-INADEQUATE. The non self-complementary nonamer exists as a random coil form in aqueous buffer at 21 degrees C as evidenced by the temperature variable 1H-NMR and NOE measurements. The nonamer was annealed to the primary consensus donor junction d(CpApGpGpTpApApGpT) and confirmation of complete annealing was obtained by detection and assignment of base pair imino protons in D2O/H2O mixtures. Application of one- and two-dimensional NMR techniques permitted the complete assignment of all the non-exchangeable protons in the duplex nonamer. These data, together with determination of vicinal coupling constants in the individual deoxyribose moieties, permits the following conclusions on the structure and conformation of the consensus donor junction: (i) it exists in aqueous solution in a conformation that belongs to the B family (ii) the sugar-base orientations are anti (iii) the deoxyribose units exist predominantly in the S conformation (2'-endo-3'-exo) (iv) the contiguous A.T base pairs d[T(5)-A(6)-A(7)].d[T(12)-T(13)-A(14)], two positions removed downstream from the splice site (5'-CAG decreases GTAAGT-3'), are uniquely propeller twisted. The propeller twisting occurs in the region in which there is partial complementarity with the branch site splice signal TACTAAC. The cross-correlation rates were used to derive the interproton distances between adjacent AH2 protons of 4.00 A in the T(5)-A(6).T(13)-A(14) step and of 3.87 A in the A(6)-A(7).T(12)-T(13) step. This structural and conformational feature if carried over into the primary RNA transcripts may serve as a recognition signal for this critical site in the genome.

DNA↗
PubMedDate not supplied

War and peace in phylogenetics: a rejoinder on total evidence and consensus.

For more than 10 years, systematists have been debating the superiority of character or taxonomic congruence in phylogenetic analysis. In this paper, we demonstrate that the competing approaches can converge to the same solution when a consensus method that accounts for branch lengths is selected. Thus, we propose to use both methods in combination, as a way to corroborate the results of combined and separate analyses. This so-called "global congruence" approach is tested with a wide variety of examples sampled from the literature, and the results are compared with those obtained by standard consensus methods. Our analyses show that when the total evidence and consensus trees differ topologically, collapsing weakly supported nodes with low bootstrap support usually improves "global congruence".

Animals↗
PubMed2005

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

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

Animals↗
PubMedDate not supplied

Consensus and variation between speech and language therapists in the assessment and selection of preschool children for intervention: a body of knowledge or idiosyncratic decisions?

The aim was to investigate consensus between speech and language therapists (SLT) during the initial assessment of preschool children. A multimethod design was used. The qualitative component provided SLT's own views of the process as the starting point for the study. Data were generated from semistructured interviews and focus group discussions. The interviews investigated factors considered during an initial assessment of a preschool child. The focus groups discussed the process and content of a videotaped initial assessment carried out by the author. Quantitative data was generated from six case analyses and from a card sorting exercise. In the former, SLT were asked to record important features of newly referred cases. In the latter, SLT sorted statements about preschool children according to a simple concern/not concerned decision. Data collection tasks and analysis took place successively to build a composite and triangulated picture. The main subjects were 11 SLT, experienced in childrens' work with a further six acting as a broader reference group. The results show an interacting pattern of consensus and variation. SLT agreed about the relative priority of children, categories that informed the assessment; they made similar interpretations of incoming information. There was variation in their preferred assessment methods, in the thresholds of concern and in the interventions offered. Sources of variation that were identified included individual confidence in and access to assessments, personal levels of concern and in the approach to the SLT's role, as well as the influence of workplace policies. The study concluded that, consensus and variation both exist within the context of SLT's initial assessment of preschool children, but that there are discernible patterns to the variation. While such variation may be inevitable, it is suggested that any variation should be made explicit and used to challenge and develop the shared knowledge base of the speech and language therapy profession.

Child, Preschool↗
PubMedDate not supplied

Preparation and examination of proposed consensus reference standards for fiber-counting.

This study provided standard reference materials for fiber-counting by phase-contrast microscopy (PCM). PCM is subject to many sources of variation, including those dependent on the microscopist, so reference standards cannot be produced that are traceable to national or international standard units. Consensus standards using a "true value" agreed on by a number of laboratories may be acceptable. Reference slides for fiber-counting can be prepared using a proprietary process of grid overlay in which the fields of view defined by the grids are identifiable and relocatable. Multiple microscopists then can examine exactly the same areas of samples, reducing one source of potential variation. Twelve slides prepared from proficiency test samples of the American Industrial Hygiene Association (AIHA) Industrial Hygiene Laboratory Quality Program were used in this study, four each of chrysotile asbestos, amosite asbestos, and man-made mineral fibers. Five microscopists from AIHA-accredited laboratories, plus the inventor of the grid process, examined the slides in a blind study. This group represented commercial analytical companies, in-house corporate laboratories, research institutions, and universities. The six microscopists met to obtain consensus agreement on the fibers in each designated field classified as countable under National Institute for Occupational Safety and Health Method 7400. Slides and documentation were forwarded to AIHA for training or other purposes. Examination of the results by statistical methods showed that some microscopists' results were significantly different from others, even though all analysts would have been considered proficient with respect to the final consensus values. Although the reasons for the outliers are complex, this procedure may have value in selecting reference laboratories in proficiency test schemes, possibly leading to more defensible "true" values and tighter limits of variation.

Air Pollution, Indoor↗
PubMed1999

A multi-epitope synthetic peptide and recombinant protein for the detection of antibodies to Trypanosoma cruzi in radioimmunoprecipitation-confirmed and consensus-positive sera.

Peptide epitopes of Trypanosoma cruzi have been identified through expression cloning. A tripeptide (2/D/E) containing three epitopes (TcD, TcE, PEP-2) was used in ELISA to detect antibodies to T. cruzi in 239 of 240 consensus-positive sera and 41 of 42 sera confirmed positive by radioimmunoprecipitation assay. The 1 discrepant consensus-positive serum was used to expression-clone a novel gene that contained a repeat sequence. A peptide corresponding to this sequence, TcLo1.2, was specific for T. cruzi. This antigen detected the discrepant consensus-positive serum and enhanced reactivity of low-positive sera in the tripeptide assay. A branched synthetic peptide, 2/D/E/Lo1.2, or a linear recombinant, r2/D/E/Lo1.2, realized all of the diagnostic features of the four epitopes, including the ability to boost reactivity of low-reactive sera. These studies show that peptides and recombinants containing multiple repeat epitopes are powerful tools for developing assays for T. cruzi antibody detection and have direct application in blood screening.

Amino Acid Sequence↗
PubMed1985

Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters.

We describe FORTRAN 77 software allowing for convenient searching of any segmented and ambiguous pattern in the currently available protein or nucleotide sequence databanks. For proteins, this software can be instrumental in defining conserved functional domains among non-homologous overall primary structures. For nucleic acids, it is used in detecting complex and/or low consensus structural or regulatory patterns. As first applications we have studied the distribution of short consensus sequences believed to characterize heat-shock and glucocorticoid regulated promoters. This analysis allowed an evaluation of the specificity, probable role and thus biological significance of various regions of these consensus. In addition, the expression of several known genes are predicted to be heat-shock or glucocorticoid sensitive.

Algorithms↗
PubMed1999

Decision tree-based formation of consensus protein secondary structure prediction.

MOTIVATION: Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction constructed from the output of several methods should yield more reliable results than each of the individual methods. METHOD: We present an approach that reveals subtle but systematic differences in the output of different secondary structure prediction methods allowing the derivation of coherent consensus predictions. The method uses a machine learning technique that builds decision trees from existing data. RESULTS: The first results of our analysis show that consensus prediction of protein secondary structure may be improved both quantitatively and qualitatively.

Algorithms↗
PubMed1992

Local multiple alignment by consensus matrix.

A new algorithm for aligning several sequences based on the calculation of a consensus matrix and the comparison of all the sequences using this consensus matrix is described. This consensus matrix contains the preference scores of each nucleotide/amino acid and gaps in every position of the alignment. Two modifications of the algorithm corresponding to the evolutionary and functional meanings of the alignment were developed. The first one solves the best-fitting problem without any penalty for end gaps and with an internal gap penalty function independent on the gap length. This algorithm should be used when comparing evolutionary-related proteins for identifying the most conservative residues. The other modification of the algorithm finds the most similar segments in the given sequences. It can be used for finding those parts of the sequences that are responsible for the same biological function. In this case the gap penalty function was chosen to be proportional to the gap length. The result of aligning amino acid sequences of neutral proteases and a compilation of 65 allosteric effectors and substrates of PEP carboxylase are presented.

Algorithms↗
PubMed2005

Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.

MOTIVATION: Hierarchical and relocation clustering (e.g. K-means and self-organizing maps) have been successful tools in the display and analysis of whole genome DNA microarray expression data. However, the results of hierarchical clustering are sensitive to outliers, and most relocation methods give results which are dependent on the initialization of the algorithm. Therefore, it is difficult to assess the significance of the results. We have developed a consensus clustering algorithm, where the final result is averaged over multiple clustering runs, giving a robust and reproducible clustering, capable of capturing small signal variations. The algorithm preserves valuable properties of hierarchical clustering, which is useful for visualization and interpretation of the results. RESULTS: We show for the first time that one can take advantage of multiple clustering runs in DNA microarray analysis by collecting re-occurring clustering patterns in a co-occurrence matrix. The results show that consensus clustering obtained from clustering multiple times with Variational Bayes Mixtures of Gaussians or K-means significantly reduces the classification error rate for a simulated dataset. The method is flexible and it is possible to find consensus clusters from different clustering algorithms. Thus, the algorithm can be used as a framework to test in a quantitative manner the homogeneity of different clustering algorithms. We compare the method with a number of state-of-the-art clustering methods. It is shown that the method is robust and gives low classification error rates for a realistic, simulated dataset. The algorithm is also demonstrated for real datasets. It is shown that more biological meaningful transcriptional patterns can be found without conservative statistical or fold-change exclusion of data. AVAILABILITY: Matlab source code for the clustering algorithm ClusterLustre, and the simulated dataset for testing are available upon request from T.G. and O.W.

Algorithms↗
PubMed1997

Educational objectives and requirements of an undergraduate clerkship in general practice. The outcome of a consensus procedure.

OBJECTIVES: The main aim of this study was to reach consensus between students, faculty and general practice teachers on the educational objectives and requirements of the clerkship in general practice. METHOD: The consensus procedure consisted of four steps and all active general practice teachers (n = 116) were asked to participate in the study. RESULTS: We identified 189 educational objectives: 127 complaints (problems, symptoms, syndromes), 29 clinical skills and 37 objectives concerning the theoretical dimensions of general practice. Educational requirements crystallized to 16 essential preconditions of a teaching practice and 35 didactic activities to be performed by the general practice teachers. CONCLUSIONS: These consensus results will be used to structure the medical curriculum and as guidelines for the educational process during the clerkship.

Australia↗
PubMed1991

Patient education in family practice: the consensus reached by patients, doctors and experts.

Patient education is a central aspect of the GP's work, but it is not clear what type of information and guidance should be given to patients during consultations. As the existing literature did not offer any clear solutions to this problem, a consensus study was carried out using a panel of GPs, patients and experts/policymakers in the field of health education. After three cycles of questioning involving written questionnaires and written feedback, the panel reached a consensus on 35 priorities and recommendations concerning patient education carried out by the GP. A consensus method of this type is a valuable tool for setting standards when scientific findings are not available, and contrasting views play a role in the definition of what constitutes adequate performance.

Delphi Technique↗
PubMed2003

Analysis and exploration of the use of rule-based algorithms and consensus methods for the inferral of haplotypes.

The difficulty of experimental determination of haplotypes from phase-unknown genotypes has stimulated the development of nonexperimental inferral methods. One well-known approach for a group of unrelated individuals involves using the trivially deducible haplotypes (those found in individuals with zero or one heterozygous sites) and a set of rules to infer the haplotypes underlying ambiguous genotypes (those with two or more heterozygous sites). Neither the manner in which this "rule-based" approach should be implemented nor the accuracy of this approach has been adequately assessed. We implemented eight variations of this approach that differed in how a reference list of haplotypes was derived and in the rules for the analysis of ambiguous genotypes. We assessed the accuracy of these variations by comparing predicted and experimentally determined haplotypes involving nine polymorphic sites in the human apolipoprotein E (APOE) locus. The eight variations resulted in substantial differences in the average number of correctly inferred haplotype pairs. More than one set of inferred haplotype pairs was found for each of the variations we analyzed, implying that the rule-based approach is not sufficient by itself for haplotype inferral, despite its appealing simplicity. Accordingly, we explored consensus methods in which multiple inferrals for a given ambiguous genotype are combined to generate a single inferral; we show that the set of these "consensus" inferrals for all ambiguous genotypes is more accurate than the typical single set of inferrals chosen at random. We also use a consensus prediction to divide ambiguous genotypes into those whose algorithmic inferral is certain or almost certain and those whose less certain inferral makes molecular inferral preferable.

Algorithms↗
PubMed2003

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

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.

Base Sequence↗
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny.

Although recent studies indicate that estimating phylogenies from alignments of concatenated genes greatly reduces the stochastic error, the potential for systematic error still remains, heightening the need for reliable methods to analyze multigene data sets. Consensus methods provide an alternative, more inclusive, approach for analyzing collections of trees arising from multiple genes. We extend a previously described consensus network method for genome-scale phylogeny (Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. 2004. Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol. 21:1459-1461) to incorporate additional information. This additional information could come from bootstrap analysis, Bayesian analysis, or various methods to find confidence sets of trees. The new methods can be extended to include edge weights representing genetic distance. We use three data sets to illustrate the approach: 61 genes from 14 angiosperm taxa and one gymnosperm, 106 genes from eight yeast taxa, and 46 members of a gene family from 15 vertebrate taxa.

Animals↗
PubMed1983

Essential structure of E. coli promoter: effect of spacer length between the two consensus sequences on promoter function.

A promoter with the consensus sequence(TTGACA and TATAAT) at -35 and -10 regions was constructed, and the distance between the two consensus sequences was independently altered at two restriction sites. In an in vitro transcription system, a maximum activity was observed at the spacer length of 17 base-pairs regardless of the sites of space adjustment. Evidence was also provided that the start point of transcription was fixed by the consensus sequence at the -10 region.

Base Composition↗