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Re-treatment of chronic hepatitis C with consensus interferon .

A multicenter, open-label, phase 3 study was conducted in 337 patients with chronic hepatitis C virus (HCV) infection who had either not responded to previous interferon therapy or had relapsed after discontinuation of therapy with either consensus interferon (9 microg) or interferon alpha-2b (3 million U) three times a week for 24 weeks. Patients were randomized to receive a higher dose of consensus interferon (15 microg) administered subcutaneously three times a week for 24 or 48 weeks and then were observed for an additional 24 weeks. Patients who had relapsed after prior interferon therapy were more likely to have a sustained alanine aminotransferase response and HCV RNA response (as measured by reverse transcription-polymerase chain reaction with a sensitivity of < 100 copies/mL) than were patients who had not responded to prior interferon therapy. For relapsers, the sustained HCV RNA response rate was 58% (48 weeks) and 28% (24 weeks). The sustained alanine aminotransferase response for relapsers was 52% (48 weeks) and 39% (24 weeks). The sustained HCV RNA response rate among prior nonresponders was 13% (48 weeks) and 5% (24 weeks), and the sustained alanine aminotransferase response rate for nonresponders was 17% (48 weeks) and 12% (24 weeks). The administration of 15 microg of consensus interferon was well tolerated and was not associated with an increase in the incidence of side effects. These data demonstrate that re-treatment with 15 microg of consensus interferon is safe and effective therapy for patients with chronic hepatitis C who have either not responded to previous interferon therapy or relapsed after discontinuation of interferon therapy.

Adult↗

Consensus functions and patterns in molecular sequences.

In recent years, methods of consensus, developed for the solution of problems in the social sciences, have become widely used in molecular biology. We study a method of consensus originally due to Waterman et al. (Waterman, Galas and Arratis. 1984. Pattern recognition in several sequences: consensus and alignment. Bull. math. Biol. 46, 515-527) which is used to identify patterns or features in a molecular sequence where a pattern can vary in position within a given window. We show that some well-known consensus methods of the social sciences, the median and the mean, are special cases of this method for certain choices of the parameters used in it and give a precise account of the parameters for which these special cases arise. We also show that the specific parameters used in the method of Waterman et al. make their method equivalent to the media procedure which is widely used in the social sciences.

Base Sequence↗

Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers.

PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S(1) to S(6) S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S(13), these also amplified S(7) to S(14) and an allele previously referred to as S(x), which we now label S(16). The genomic PCR products were cloned and sequenced. The partial sequence of S(11) matched that of S(7) and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S(7) to S(16), so that allele-specific primers are now available for all 13 S alleles of cherry (S(8), S(11) and S(15) are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S(3) S(16)), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S(6) S(12)), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S(3) S(3)', S(4)' S(6), S(4)' S(9) and S(4)' S(13), were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.

Alleles↗

Resource utilisation for neuropsychiatric disorders in developing countries: a multinational Delphi consensus study.

BACKGROUND: Substantial information is now available at a global and regional level relating to the burden of mental disorders, yet hardly any international data are available on the resources that are needed to respond to this global burden. AIMS: The aim of this study was to develop consensus-driven estimates of resource utilisation, coverage and adherence for key mental health care interventions capable of reducing leading neuropsychiatric causes of disease burden. METHODS: A resource utilisation questionnaire was developed for a series of mental health care interventions for schizophrenia, affective and anxiety disorders, alcohol misuse, epilepsy and Alzheimer's disease. Expert opinion surveys using a Delphi approach were conducted in seven countries (Brazil, China, Egypt, Ghana, India, Mexico and Thailand). Initial results were fed back to participants in order to elicit a second, final set of consensus estimates. Mean and median values were calculated, together with measures of dispersion and agreement. RESULTS: Sixty-seven psychiatrists took part in the first Delphi round and 60 completed the seven consensus panels in the second Delphi round. Expected resource use was highest for acute psychosis, mania, severe depression and severe dementia (at least monthly outpatient visits, and over 25% of cases admitted to hospital with an average length of stay one month). Aggregated estimates for current treatment coverage ranged from below 20% for Alzheimer's disease to 60% for epilepsy. Coverage and adherence levels for affective disorders were both below 50%. CONCLUSION: The Delphi technique proved to be a feasible and efficient method for data collection and consensus generation concerning mental health care resource utilisation. Results provide a set of range estimates for mental health resource planning and evaluation in a variety of developing regions.

Delphi Technique↗

Consensus Seasonal Flood Forecasts and Warning Response System (FFWRS): an alternate for nonstructural flood management in Bangladesh.

Despite advances in short-range flood forecasting and information dissemination systems in Bangladesh, the present system is less than satisfactory. This is because of short lead-time products, outdated dissemination networks, and lack of direct feedback from the end-user. One viable solution is to produce long-lead seasonal forecasts--the demand for which is significantly increasing in Bangladesh--and disseminate these products through the appropriate channels. As observed in other regions, the success of seasonal forecasts, in contrast to short-term forecast, depends on consensus among the participating institutions. The Flood Forecasting and Warning Response System (henceforth, FFWRS) has been found to be an important component in a comprehensive and participatory approach to seasonal flood management. A general consensus in producing seasonal forecasts can thus be achieved by enhancing the existing FFWRS. Therefore, the primary objective of this paper is to revisit and modify the framework of an ideal warning response system for issuance of consensus seasonal flood forecasts in Bangladesh. The five-stage FFWRS-i) Flood forecasting, ii) Forecast interpretation and message formulation, iii) Warning preparation and dissemination, iv) Responses, and v) Review and analysis-has been modified. To apply the concept of consensus forecast, a framework similar to that of the Southern African Regional Climate Outlook Forum (SARCOF) has been discussed. Finally, the need for a climate Outlook Fora has been emphasized for a comprehensive and participatory approach to seasonal flood hazard management in Bangladesh.

Bangladesh↗

Using Dynamic Modeling to Scope Environmental Problems and Build Consensus

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

Journal Article↗

Genotyping new BXD recombinant inbred mouse strains and comparison of BXD and consensus maps.

Nine additional BXD recombinant inbred (RI) strains have been developed from the F2 cross of C57BL/6J and DBA/2J mouse strains. A tenth line stopped breeding in the F12 generation. F20 generation breeding pairs from the nine surviving strains and an F12 pair from the extinct line were genotyped at 319 genetic markers (primarily microsatellites) spanning most of the genome. Where typing data were lacking, the established set of 26 BXD strains also were genotyped at these same loci. The availability of these additional nine strains enhances the value of the BXD RI set for analysis of complex phenotypic traits. The proportion of loci still segregating at the F20 generation was found to closely approximate expectation, suggesting that selection favoring the retention of heterozygosity is not a strong factor. However, the number of crossovers between adjacent markers was frequently less than predicted from consensus map distances. A significant deficiency of recombinants was observed on Chrs 3, 4, 14, and X. On Chr 14, the estimated cumulative BXD map distance between the most proximal and distal markers was only 30.2 cM, compared with a distance of 60.0 cM in the consensus map. On the X Chr, the estimated and predicted cumulative distances were 38.8 and 69.5 cM, respectively. Over all chromosomes, the BXD RI map is 14.5% shorter than predicted from the consensus map. It is suggested that distances in some of the consensus maps are inflated. Alternatively, recombinant genotypes could be selected against during inbreeding owing to allelic interactions affecting fitness. The latter interpretation implies that relatively strong intrachromosomal epistasis is common.

Animals↗

Consensus statement on the use of breastfeeding as a family planning method.

An interdisciplinary international group of researchers in the area of lactational infertility gathered with the purpose of coming to a consensus about the conditions under which breastfeeding can be used as a safe and effective method of family planning. The consensus of the group was that the maximum birth spacing effect of breastfeeding is achieved when a mother "fully" or nearly fully breastfeeds and remains amenorrheic. When these two conditions are fulfilled, breastfeeding provides more than 98% protection from pregnancy in the first six months. Data are reviewed from thirteen prospective studies in both developed and developing countries supporting the consensus. The rationale for the consensus is given in detail. Recommendations are made based on what is currently known of the antifertility effects of breastfeeding. Research should continue to measure a broad spectrum of variables so that these guidelines can be refined as new information becomes available.

Breast Feeding↗

Detecting homology of distantly related proteins with consensus sequences.

A simple protocol is described that is suitable for the detection of distantly related members of a protein family. In this procedure, similarity to a consensus sequence is used to distinguish chance similarity from similarity due to common ancestry. The consensus sequence is constructed from the sequences of established members of a protein family and it incorporates features characteristic of the protein fold of this family: conserved residues, the pattern of variable and conserved segments, preferred location of gaps etc. The database is searched with the consensus sequence, using the unitary matrix or log odds matrix for scoring the alignments, with variable gap penalty. The advantage of the method is that it weights key residues, ignores sequence similarity in variable segments (thus partially eliminating "background noise" coming from chance similarity), distinguishes gaps disrupting conserved segments from those occurring in positions known to be tolerant of gap events. The utility of the method was demonstrated in the case of the protein family homologous with the internal repeats of complement B as well as the internal repeats identified in fibroblast proteoglycan PG40. The consensus sequence method succeeded in finding some new members of these protein families that could not be detected by earlier methods of sequence comparison.

Algorithms↗

Consensus methods for finding and ranking DNA binding sites. Application to Escherichia coli promoters.

There have been many different approaches employed to define the "consensus" sequence of various DNA binding sites and to use the definition obtained to locate and rank members of a given sequence family. The analysis presented here enlists two of these approaches, each in modified form, to develop a highly efficient search protocol for Escherichia coli promoters and to provide a relative ranking of these sites showing good agreement with in vitro measurements of promoter strength. Schneider et al. have applied Shannon's index of information content to evaluate the significance of each position within the consensus of a family of aligned sequences. In a formal sense, this index is only applicable to a group of sequences, providing at each position a negative entropy value between zero (random) and two bits (total conservation of a single base) for sequences in which all bases are equally represented. A method for evaluating how well an individual sequence conforms to the information content pattern of the consensus is described. A function is derived, by analogy to the information content of the sequence family, for application to individual sequences. Since this function is a measure of conformity, it can be used in a search protocol to identify new members of the family represented by the consensus. A protocol for locating E. coli promoters is presented. The Berg-von Hippel statistical-mechanical function is also tested in a similar application. While the information content function provides a superior search protocol, the Berg-von Hippel function, when scaled at each position by the information content, does well at ranking promoters according to their strength as measured in vitro.

Base Composition↗

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

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

Biological Evolution↗

ProteinParser--a community based tool for the generation of a detailed protein consensus and FASTA output.

Comparison of bioinformatic data is a common application in the life sciences and beyond. In this communication, a novel Java based software tool, ProteinParser, is outlined. This software tool calculates a detailed consensus, or most common, amino acid at a given position in an aligned protein set, whilst also generating a full consensus protein FASTA output. A second application of this software tool, computing a consensus amino acid given a tolerance threshold, is also demonstrated. The phytase and the common bacterial beta-lactamase proteins are analysed as 'proof of concept' examples. Consensus proteins, as generated by ProteinParser, are regularly utilised in the selection of residues for protein stabilisation mutagenesis; however, this widely applicable software tool will find many alternative applications in areas such as protein homology modelling.

Amino Acid Sequence↗

Integrating conflict analysis and consensus reaching in a decision support system for water resource management.

The importance of shared decision processes in water management derives from the awareness of the inadequacy of traditional--i.e. engineering--approaches in dealing with complex and ill-structured problems. It is becoming increasingly obvious that traditional problem solving and decision support techniques, based on optimisation and factual knowledge, have to be combined with stakeholder based policy design and implementation. The aim of our research is the definition of an integrated decision support system for consensus achievement (IDSS-C) able to support a participative decision-making process in all its phases: problem definition and structuring, identification of the possible alternatives, formulation of participants' judgments, and consensus achievement. Furthermore, the IDSS-C aims at structuring, i.e. systematising the knowledge which has emerged during the participative process in order to make it comprehensible for the decision-makers and functional for the decision process. Problem structuring methods (PSM) and multi-group evaluation methods (MEM) have been integrated in the IDSS-C. PSM are used to support the stakeholders in providing their perspective of the problem and to elicit their interests and preferences, while MEM are used to define not only the degree of consensus for each alternative, highlighting those where the agreement is high, but also the consensus label for each alternative and the behaviour of individuals during the participative decision-making. The IDSS-C is applied experimentally to a decision process regarding the use of treated wastewater for agricultural irrigation in the Apulia Region (southern Italy).

Agriculture↗

Ethnopharmacological evaluation of the informant consensus model on anti-tuberculosis claims among the Manus.

Ethnobotanists often utilize predictive models to analyze the potential of indigenously used medicinal plants. The most common of these prognostic models is the informant consensus model. This study evaluates use of this model through the analytical ethnopharmacology of Manus Province, Papua New Guinea (PNG). The informant consensus model enables researchers to prioritize plants for pharmacognostic evaluation, based on the relative frequency of plants cited in anthropological interviews. Fieldwork on Manus Island, PNG, led to the identification of 43 species of plants used in traditional medicine for persistent respiratory symptoms. Plants were collected, dried, micro-extracted using a new technique generated in our laboratory, and evaluated in vitro against Mycobacterium tuberculosis. The results, in the form of IC(50) values and modified selectivity indices (SI), were compared to the results of the anthropological models of informant consensus, and statistically compared through linear regression and t-tests. Results were not statistically significant (alpha=0.1), leading to the conclusions that the informant consensus assumptions were inaccurate in predicting anti-mycobacterial activity among the Manus for anti-TB claims.

Anti-Bacterial Agents↗

[Hybrid Capture 2 vs HPV Consensus kit: comparison of 2 assays for human papillomavirus detection and typing].

BACKGROUND: Many laboratories use the DNA Hybrid Capture 2 HPV-high risk assay (Digene) to detect and type oncogenic HPV. The aim of this work was to compare this assay with a new HPV genotyping assay: HPV Consensus kit (Argène). Actually, this assay is not commercially available. MATERIALS AND METHODS: Ninety-four cervical samples were tested with both the routine assay Hybrid Capture 2 and the HPV Consensus kit. Discordant results were analysed by amplification with a nested PCR and sequencing of amplified products. RESULTS: Only 81 results could be analysed concerning the oncogenic risk. The overall concordance was 92,6%. But we find 13 "generic" results with the HPV Consensus kit, the generic probe including high risk and low risk genotypes. CONCLUSION: HPV Consensus kit results showed a better detection sensitivity for this assay than Hybrid Capture 2 assay. Nevertheless, "generic" results give no information about the oncogenic risk of the HPV detected in a sample.

DNA Primers↗

CT-based delineation of lymph node levels and related CTVs in the node-negative neck: DAHANCA, EORTC, GORTEC, NCIC,RTOG consensus guidelines.

BACKGROUND AND PURPOSE: The appropriate application of 3-D CRT and IMRT for HNSCC requires a standardization of the procedures for the delineation of the target volumes. Over the past few years, two proposals--the so-called Brussels guidelines from Grégoire et al., and the so-called Rotterdam guidelines from Nowak et al.--emerged from the literature for the delineation of the neck node levels. Detailed examination of these proposals however revealed some important discrepancies. MATERIALS AND METHODS: Within this framework, the Brussels and Rotterdam groups decided to review their guidelines and derive a common set of recommendations for delineation of neck node levels. This proposal was then discussed with representatives of major cooperative groups in Europe (DAHANCA, EORTC, GORTEC) and in North America (NCIC, RTOG), which, after some additional refinements, have endorsed them. The objective of the present article is to present the consensus guidelines for the delineation of the node levels in the node-negative neck. RESULTS AND CONCLUSIONS: First a short discussion of the discrepancies between the previous Brussels and the Rotterdam guidelines is presented. The general philosophy of the consensus guidelines and the methodology used to resolve the various discrepancies are then described. The consensus proposal is then presented and representative CTVs that are consistent with these guidelines are illustrated on CT sections. Last, the limitations of the consensus guidelines are discussed and some concerns about the direct applications of these guidelines to the node-positive neck and the post-operative neck are described.

Head and Neck Neoplasms↗

[Consensus on care for the users of the Maintenance Program with Methadone at the health centers of the province of Cádiz].

OBJECTIVES: To reach a consensus on primary care actions concerning transmissible illnesses in users of the methadone maintenance programme. To promote coordination between levels. To find the needs of primary care professionals. DESIGN: Qualitative study based on the nominal group technique. SETTING: Cádiz province, including primary care districts, NHS hospitals and county drug-dependency centres. PARTICIPANTS: 76 health professionals: two doctors and a nurse from each health centre, selected for their experience and motivation; hospital specialists in preventive medicine and internal medicine also with experience and motivation, and with knowledge of primary care; a doctor from each county drug-dependency centre, chosen by the Provincial Drug-Dependency Management. INTERVENTIONS: The study had two phases: a) nominal group technique with homogeneous groups for each professional environment; b) modified nominal group with heterogeneous groups of professionals from all environments by hospital areas. MEASUREMENTS AND MAIN RESULTS: The final result of the study was the overall consensus in the four areas. The prioritized activities focused on "recruitment and study of patients and contacts", "educational and health promotion interventions", "immunisation programme", "monitoring therapy compliance", and "unified record of actions". What was needed to put into practice the interventions was agreed by consensus. CONCLUSIONS: Consensus techniques are a useful tool for planning primary care activities. A high degree of reproducibility can be reached if the participants are properly selected. Restrictions in being able to introduce some of the agreed interventions could be avoided with user participation and involvement of the health authorities.

Humans↗

Consensus temporal order of amino acids and evolution of the triplet code.

Forty different single-factor criteria and multi-factor hypotheses about chronological order of appearance of amino acids in the early evolution are summarized in consensus ranking. All available knowledge and thoughts about origin and evolution of the genetic code are thus combined in a single list where the amino acids are ranked chronologically. Due to consensus nature of the chronology it has several important properties not visible in individual rankings by any of the initial criteria. Nine amino acids of the Miller's imitation of primordial environment are all ranked as topmost (G, A, V, D, E, P, S, L, T). This result does not change even after several criteria related to Miller's data are excluded from calculations. The consensus order of appearance of the 20 amino acids on the evolutionary scene also reveals a unique and strikingly simple chronological organization of 64 codons, that could not be figured out from individual criteria: New codons appear in descending order of their thermostability, as complementary pairs, with the complements recruited sequentially from the codon repertoires of the earlier or simultaneously appearing amino acids. These three rules (Thermostability, Complementarity and Processivity) hold strictly as well as leading position of the earliest amino acids according to Miller. The consensus chronology of amino acids, G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W, and the derived temporal order for codons may serve, thus, as a justified working model of choice for further studies on the origin and evolution of the genetic code.

Amino Acids↗