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At least 595 records · Page 33Linked to original sources
PubMed1987

Use of consensus oligonucleotides for detecting and isolating nucleic acids encoding calcium binding domains of the troponin C superfamily.

Proteins belonging to the troponin C superfamily (troponin C, calmodulin, myosin light chains, and parvalbumin) are involved in a wide variety of cellular activities mediated by calcium ions. Most of these proteins bind ionic calcium, and all have calcium binding domains that are conserved to some extent at the nucleic acid level. We made use of the conservation in the third calcium binding domain to synthesize two consensus sequence oligonucleotide probes, one 43 bases and the other 25 bases long. By using cDNA and genomic clones encoding calmodulin, troponin C, parvalbumin, and the sea urchin Spec proteins, we show that these probes hybridize with nucleic acid sequences representing calcium binding domains. In an RNA gel blot analysis of embryonic RNA from the sea urchin Strongylocentrotus purpuratus, we show that transcripts which have previously been shown to encode troponin C like proteins hybridize with the consensus sequence probes. Screening sea urchin cDNA and genomic libraries with the 43-base consensus oligonucleotide shows that the probe can be used to isolate cloned nucleic acids. Two such genomic clones from a Lytechinus pictus library were isolated and characterized. One clone encodes part of an L. pictus calmodulin gene, and the other encodes a member of the superfamily that has not been characterized previously. The consensus oligonucleotides should be valuable probes in the diagnosis and isolation of nucleic acids encoding proteins of the troponin C superfamily.

Amino Acid Sequence↗
PubMedDate not supplied

Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes.

Here, the comparisons of performance of nine consensus scoring strategies, in which multiple scoring functions were used simultaneously to evaluate candidate structures for a protein-ligand complex, in combination with nine scoring functions (FlexX score, GOLD score, PMF score, DOCK score, ChemScore, DrugScore, PLP, ScreenScore, and X-Score), were carried out. The systematic naming of consensus scoring strategies was also proposed. Our results demonstrate that choosing the most appropriate type of consensus score is essential for model selection in computational docking; although the vote-by-number strategy was an effective selection method, the number-by-number and rank-by-number strategies were more appropriate when computational tractability was taken into account. By incorporating these consensus scores into the FlexX program, reasonable complex models can be obtained more efficiently than those selected by independent FlexX scores. These strategies might also improve the scoring of other docking programs, and more-effective structure-based drug design should result from these improvements.

Computer Simulation↗
PubMed2001

Knowledge transfer, policymaking and community empowerment: a consensus model approach for providing public mental health and substance abuse services.

An important problem in creating new programs and policies is how to encourage the transfer of knowledge in non-hierarchical ways so that new, relevant and specific knowledge is co-created by all interested parties. In this paper, we suggest that a consensus model of policymaking is one response and identify four key structural elements thought necessary for creating such a consensus infrastructure. These are a) a leadership and facilitating capacity for initiating and promoting such an endeavor, b) a network or consortium of key researchers, practitioners, consumers, and policymakers to empower community ownership of the endeavor, c) a process for consensus building and strategic problem-solving for such a consortium, and d) the continued creation of a multi-directional dialogue through information dissemination. We examine these elements in action by describing a particular problem solving and consensus building model for developing and implementing a program, resolving group differences, and evaluating the group's process and products.

Community Mental Health Services↗
PubMed1999

Relationality and consensus in Japan: implications for bioethics policy.

This paper examines the Japanese notion of relationality, that is, the idea that the individual is defined primarily within a web of relationships. Furthermore, it proposes that this relationality provides an ontological basis for morality, particularly the critical need for achieving consensus. This need for consensus is evident in the dispute over brain death. It was also conspicuous in the long-standing debate regarding heart transplantation. By reviewing key features of relationality, the study also demonstrates that the Japanese approach toward consensus reflects certain cultural values such as the importance of nemawashi. This inquiry thereby evokes the brain death and heart transplantation controversy in order to illustrate the critical need for consensus in the decision-making process.

Brain Death↗
PubMed1983

Depression, social comparison, and the false-consensus effect.

In general, people perceive high consensus for their own attributes (i.e., the false-consensus effect). Depressed and nondepressed college students were asked about the extent to which depression-relevant and depression-irrelevant attributes were true of themselves and true of the "average college student." Subjects were also asked questions assessing the accuracy of their perceptions of others. Depressed subjects showed less false consensus than nondepressed subjects. Although depressives characterized themselves as dissimilar to others, they showed no consistent bias to depreciate themselves relative to others. Nondepressives, on the other hand, consistently enhanced themselves relative to others, although the magnitude of their self-other differences was smaller than that of depressives. Interestingly, the tendency to depreciate themselves relative to others on negative depression-relevant items was a better predictor of severity of depression than self-perceptions or other perceptions alone. Findings regarding the accuracy of perceptions of others were mixed. The study is discussed in terms of its implications for the false-consensus effect, depressive attributional style, nondepressive self-serving biases, and therapy for depression.

Depression↗
PubMed1988

Knowledge-based information acquisition: norms and the functions of consensus information.

Mill's (1872/1973) method of difference prescribes that the lay scientist should use consensus information as a control condition for the person and distinctiveness information as a control condition for the stimulus when analyzing their causal effects on the occurrence of the target event. However, in studies of information acquisition, subjects have shown a consistent preference for distinctiveness information when answering causal questions about the person, and for consensus information when answering causal questions about the stimulus. To explain this discrepancy, we distinguish between the evaluative, contrastive, and corroborative functions of consensus and distinctiveness information. In addition, we suggest that subjects seek consensus information only if it is relevant to the question posed to them, and if they cannot supply it from their own presupposed knowledge of behavioral norms. We report four information acquisition experiments that provide support for our analysis.

Choice Behavior↗
PubMed1990

Differential construal and the false consensus effect.

People's own beliefs, values, and habits tend to bias their perceptions of how widely they are shared. The present research examined whether this "false consensus effect" is partly due to people's failure to recognize that their choices are not solely a function of the "objective" response alternatives, but of their subjective construal of those alternatives. Study 1 provided initial support for the importance of differential construal in people's consensus estimates by showing that larger false consensus effects tend to be obtained on items that permit the most latitude for subjective construal. Study 2 replicated this effect experimentally by asking Ss either a general or specific version of the same question. Larger false consensus effects were obtained on the general version that offered more latitude for construal. Studies 3 & 4 provided further support by showing that (a) Ss who made different choices tended to interpret the response alternatives in ways that reflected the choices they made and (b) subjects who were led to construe the alternatives in the same way tended to make the same choices.

Adult↗
PubMed2000

Climate quality and climate consensus as mediators of the relationship between organizational antecedents and outcomes.

Research has shown that climate quality (average climate ratings) is related to organizational antecedents and outcomes, but researchers have yet to examine climate consensus (the variance of climate ratings). Similarly, studies have investigated typical behavior (members' average performance), but have neglected behavioral similarity (within-group variance). Data from 1,196 members in 180 organizations were used to test relationships of climate quality and consensus with organizational antecedents and outcomes. Climate quality and consensus both had significant correlations with organizational antecedents and outcomes, but climate consensus did not contribute a significant increment to the prediction of organizational outcomes. Finally, quality mediated many relationships between organizational antecedents and outcomes.

Decision Making↗
PubMed2005

Defensive pride and consensus: strength in imaginary numbers.

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

Adult↗
PubMed1999

Long-term survival in severe heart failure in patients treated with enalapril. Ten year follow-up of CONSENSUS I.

BACKGROUND: The CONSENSUS trial was the first study to show prognostic improvement by an ACE inhibitor. Patients in NYHA class IV heart failure were treated with enalapril or placebo. After study completion (average 183 days) all patients were offered open-label enalapril therapy. This paper reports on the survival at the 10-year follow up of the patients randomized in the CONSENSUS trial. METHODS: All 35 participating centres in CONSENSUS I were asked to complete a questionnaire on the survival status at 1 November 1996 of patients randomized in CONSENSUS. RESULTS: At 10-year follow up, one patient was lost to follow-up. Five patients, all in the enalapril group, were long-term survivors (P = 0.004). Averaged over the duration of the trial (double-blind plus open-label extension) the risk reduction was 30% (P = 0.008), with a 95% confidence interval of 11% to 46%. At the end of the double-blind study period, mortality was considerably higher among patients who did not receive open ACE inhibitor therapy compared to those who did. CONCLUSION: After a treatment period of, on average, 6 months, enalapril was shown to be effective. The effect was sustained for at least 4 years i.e. for another 3.5 years. The present follow-up is the first heart failure trial where the full life-cycle has been followed from randomization. In severe heart failure, mortality is significantly reduced by enalapril. On average, the beneficial effect is maintained for several years and overall survival time is prolonged by 50% (from 521 to 781 days).

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2001

Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters.

Assembly of transcription pre-initiation complexes proceeds from the initial complex formed between "TATA" bearing promoter DNA and the TATA-binding protein (TBP). Our laboratory has been investigating the relationships among TATA sequence, TBP center dot TATA solution structure, recognition mechanisms, and transcription efficiency. TBP center dot TATA interactions have been modeled by global analysis of detailed kinetic and thermodynamic data obtained using fluorimetric and fluorometric techniques in conjunction with fluorescence resonance energy transfer. We have reported recently that TBP recognition of two consensus promoters, adenovirus major late (AdMLP: TATAAAAG) and E4 (TATATATA), is well described by a linear two-intermediate mechanism with simultaneous DNA binding and bending. Similar DNA geometries and high transcription efficiencies characterize these TBP x TATA complexes. Here we show that, in contrast to the consensus sequences, TBP recognition of a variant sequence (C7: TATAAACG) is described by a three-step model with two branching pathways. One pathway proceeds through an intermediate having severely bent DNA, reminiscent of the consensus interactions, with the other branch yielding a unique conformer with shallowly bent DNA. The resulting TBP x C7 complex has a dramatically different solution conformation than for TBP x DNA(CONSENSUS) and is correlated with diminished relative transcription activity. The temperature dependence of the TBP x C7 helical bend is postulated to derive from population shifts between the conformers with slightly and severely bent DNA.

DNA↗
PubMed2003

A consensus tetrapeptide selected by phage display adopts the conformation of a dominant discontinuous epitope of a monoclonal anti-VWF antibody that inhibits the von Willebrand factor-collagen interaction.

Monoclonal antibody (mAb) 82D6A3 is an anti-von Willebrand factor (VWF) mAb directed against the A3-domain of VWF that inhibits the VWF binding to fibrillar collagens type I and III in vitro and in vivo. To identify the discontinuous epitope of this mAb, we used phage display, mutant analysis, and peptide modeling. All 82D6A3-binding phages displayed peptides containing the consensus sequence SPWR that could be aligned with P981W982 in the VWF A3-domain. Next, the binding of mAb 82D6A3 to 27 Ala mutants with mutations in the A3-domain of VWF revealed that amino acids Arg963, Pro981, Asp1009, Arg1016, Ser1020, Met1022, and His1023 are part of the epitope of mAb 82D6A3. Inspection of residues Ser1020, Arg1016, Pro981, and Trp982 in the three-dimensional structure of the A3-domain demonstrated that these residues are close together in space, pointing out that the structure of the SPWR consensus sequence might mimic this discontinuous epitope. Modeling of a cyclic 6-mer peptide containing the consensus sequence and superposition of its three-dimensional structure onto the VWF A3-domain demonstrated that the Ser and Arg in the peptide matched the Ser1020 and Arg1016 in the A3-domain. The Pro residue of the peptide served as a spacer, and the side chain of the Trp pointed in the direction of Trp982. In conclusion, to our knowledge, this is the first report where a modeled peptide containing a consensus sequence could be fitted onto the three-dimensional structure of the antigen, indicating that it might adopt the conformation of the discontinuous epitope.

Amino Acid Sequence↗
PubMed1986

Structure and conformation of the duplex consensus acceptor exon:intron junction d[(CpTpApCpApGpGpT). (ApCpCpTpGpTpApG)] deduced from high-field 1H-NMR of non-exchangeable and imino protons.

The complementary consensus acceptor exon:intron junction d(ApCpCpTpGpTpApG) has been synthesized by a modified phosphotriester method. The non self-complementary octamer exists in the random coil form in aqueous buffer at 20 degrees C as evidenced by temperature variable 1H-NMR and NOE measurements. The non-exchangeable proton assignments were secured using a combination of techniques including two-dimensional COSY, NOESY and 1H-1H-INADEQUATE. The octamer was annealed with the primary consensus sequence d(CpTpApCpApGpGpT). Confirmation of complete duplex formation was confirmed by detection and assignment of imino protons in D2O:H2O mixtures. Assignment of the non-exchangeable proton signals in the duplex consensus junction was then secured by a combination of two-dimensional COSY correlations, NOESY and NOE experiments. Determination of individual vicinal coupling constants in the component deoxyribose moieties permitted deduction of the population of S conformations in this sequence. It is concluded that the consensus acceptor junction exists in solution in a conformation belonging to the B family, and that the bases are oriented anti. In addition the deoxyribose moieties in the 5' regions exist predominantly in the S form (2'endo-3'exo) whereas those residues on or adjacent to the junction on the primary strand show more N character (2'exo-3'endo). The contiguous bases A5-G6 (adjacent to the junction) and A15-G16 are stacked more closely than the other neighbor bases in this duplex sequence. These subtle structural and conformational differences in the exon:intron junction may serve as recognition signals for these critical sites in the genome.

Base Composition↗
PubMed1999

Review of the Fifth American College of Chest Physicians Consensus Conference on Antithrombotic Therapy: outpatient management for adults.

The recommendations of the Fifth American College of Chest Physicians (ACCP) Consensus Conference on Antithrombotic Therapy are reviewed, with a focus on outpatient anticoagulation management in adults. Numerous therapeutic recommendations have changed since the Fourth ACCP Consensus Conference on Antithrombotic Therapy. The system of grading recommendations has been modified to emphasize clinically important differences and to take into account the benefit-risk ratio of each treatment option. The International Normalized Ratio (INR) goal is now expressed as a specific target value within a range rather than simply an INR range. The recommendations of the fifth conference cover initiation of warfarin therapy, hemorrhagic complications, management of excessive anticoagulation, interruption of warfarin therapy for patients requiring surgery, nonvalvular atrial fibrillation, cardioversion in patients with atrial fibrillation, valvular heart disease, mechanical and biological prosthetic heart valves, coronary artery disease, saphenous vein and internal mammary artery bypass grafts, peripheral arterial occlusive disease, prevention of venous thromboembolism, treatment of venous thromboembolism, stroke prevention in patients with cerebrovascular disease, and pregnancy. Since the fourth consensus conference, new anticoagulation therapies and indications have emerged; the recommendations of the Fifth ACCP Consensus Conference on Antithrombotic Therapy have provided practitioners with a resource of immense value.

Adult↗
PubMed1994

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

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

Algorithms↗
PubMed2025

Autocycler: long-read consensus assembly for bacterial genomes.

MOTIVATION: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using Trycycler can improve accuracy, but its lack of automation limits scalability. There is a need for an automated method to generate high-quality consensus bacterial genome assemblies from long-read data. RESULTS: We present Autocycler, a command-line tool for generating accurate bacterial genome assemblies by combining multiple alternative long-read assemblies of the same genome. Without requiring user input, Autocycler builds a compacted De Bruijn graph from the input assemblies, clusters and filters contigs, trims overlaps, and resolves consensus sequences by selecting the most common variant at each locus. It also supports manual curation when desired, allowing users to refine assemblies in challenging or important cases. In our evaluation using Oxford Nanopore Technologies reads from five bacterial isolates, Autocycler outperformed individual assemblers, automated pipelines, and other consensus tools, producing assemblies with lower error rates and improved structural accuracy. AVAILABILITY AND IMPLEMENTATION: Autocycler is implemented in Rust, open-source, and freely available at github.com/rrwick/Autocycler. It runs on Linux and macOS and is extensively documented.

Genome, Bacterial↗
PubMed1987

Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates.

The previously presented consensus sequence for eukaryotic translation initiation sites by Kozak was derived substantially from vertebrate mRNA sequences. Drosophila nuclear genes exhibit a significantly different translation start consensus sequence. These differences probably do not represent mechanistic differences in translation initiation inasmuch as both taxa exhibit identical preferences and restrictions at the crucial -3 position. Using more conservative criteria for the assignment of consensus the following consensus sequences were derived: vertebrate--CANCAUG and Drosophila--CAAAACAUG.

Animals↗
PubMed2004

Construction of stabilized proteins by combinatorial consensus mutagenesis.

We constructed stabilized variants of beta-lactamase (BLA) from Enterobacter cloacae by combinatorial recruitment of consensus mutations. By aligning the sequences of 38 BLA homologs, we identified 29 positions where the E.cloacae gene differs from the consensus sequence of lactamases and constructed combinatorial libraries using mixtures of mutagenic oligonucleotides encompassing all 29 positions. Screening of 90 random isolates from these libraries identified 15 variants with significantly increased thermostability. The stability of these isolates suggest that all tested mutations make additive contributions to protein stability. A statistical analysis of sequence and stability data identified 11 mutations that made stabilizing contributions and eight mutations that destabilized the protein. A second-generation library recombining these 11 stabilizing mutations led to the identification of BLA variants that showed further stabilization. The most stable variant had a mid-point of thermal denaturation (Tm) that was 9.1 degrees C higher than the starting molecule and contained eight consensus mutations. Incubation of three stabilized BLA variants with several proteases showed that all tested isolates have significantly increased resistance to proteolysis. Our data demonstrate that combinatorial consensus mutagenesis (CCM) allows the rapid generation of protein variants with improved thermal and proteolytic stability.

Amino Acid Sequence↗