Technology assessment and the drug use process.
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This activity is designed for pharmacists, physicians, physician assistants, nurses, and other healthcare team members, payers for health services, and healthcare executives. OBJECTIVES: Upon completion of this activity, the participant should be able to: 1. Describe the rationale behind, the development of, and the advantages arising from the formulary process, and discuss the health professionals involved in the creation of formularies. 2. Describe the impact of new drug development and technology on the drug use process. 3. Discuss the functions of the pharmacy and therapeutics committee. 4. Describe the impact of consumers on the drug use process. (+info)
DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts.
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A program is described for automatically generating schematic linear representations of protein chains in terms of their structural domains. The program requires the co-ordinates of the chain, the domain assignment, PROSITE information and a file listing all intermolecular interactions in the protein structure. The output is a PostScript file in which each protein is represented by a set of linked boxes, each box corresponding to all or part of a structural domain. PROSITE motifs and residues involved in ligand interactions are highlighted. The diagrams allow immediate visualization of the domain arrangement within a protein chain, and by providing information on sequence motifs, and metal ion, ligand and DNA binding at the domain level, the program facilitates detection of remote evolutionary relationships between proteins. (+info)
A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm.
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We present a novel method that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The PRED-TMR algorithm described, refines a standard hydrophobicity analysis with a detection of potential termini ('edges', starts and ends) of transmembrane regions. This allows one both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non-homologous transmembrane proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). A WWW server running the PRED-TMR algorithm is available at http://o2.db.uoa. gr/PRED-TMR/ (+info)
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations.
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Sequence weighting techniques are aimed at balancing redundant observed information from subsets of similar sequences in multiple alignments. Traditional approaches apply the same weight to all positions of a given sequence, hence equal efficiency of phylogenetic changes is assumed along the whole sequence. This restrictive assumption is not required for the new method PSIC (position-specific independent counts) described in this paper. The number of independent observations (counts) of an amino acid type at a given alignment position is calculated from the overall similarity of the sequences that share the amino acid type at this position with the help of statistical concepts. This approach allows the fast computation of position-specific sequence weights even for alignments containing hundreds of sequences. The PSIC approach has been applied to profile extraction and to the fold family assignment of protein sequences with known structures. Our method was shown to be very productive in finding distantly related sequences and more powerful than Hidden Markov Models or the profile methods in WiseTools and PSI-BLAST in many cases. The profile extraction routine is available on the WWW (http://www.bork.embl-heidelberg. de/PSIC or http://www.imb.ac.ru/PSIC). (+info)
Fast evaluation of internal loops in RNA secondary structure prediction.
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MOTIVATION: Though not as abundant in known biological processes as proteins, RNA molecules serve as more than mere intermediaries between DNA and proteins. Research in the last 15 years demonstrates that RNA molecules serve in many roles, including catalysis. Furthermore, RNA secondary structure prediction based on free energy rules for stacking and loop formation remains one of the few major breakthroughs in the field of structure prediction, as minimum free energy structures and related quantities can be computed with full mathematical rigor. However, with the current energy parameters, the algorithms used hitherto suffer the disadvantage of either employing heuristics that risk (though highly unlikely) missing the optimal structure or becoming prohibitively time consuming for moderate to large sequences. RESULTS: We present a new method to evaluate internal loops utilizing currently used energy rules. This method reduces the time complexity of this part of the structure prediction from O(n4) to O(n3), thus reducing the overall complexity to O(n3). Even when the size of evaluated internal loops is bounded by k (a commonly used heuristic), the method presented has a competitive edge by reducing the time complexity of internal loop evaluation from O(k2n2) to O(kn2). The method also applies to the calculation of the equilibrium partition function. AVAILABILITY: Source code for an RNA secondary structure prediction program implementing this method is available at ftp://www.ibc.wustl.edu/pub/zuker/zuker .tar.Z (+info)
Health information and interaction on the internet: a survey of female urinary incontinence.
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OBJECTIVE: To evaluate the internet as a source of information about urinary incontinence and to explore interactive facilities. DESIGNLimited survey of internet resources. SUBJECTS: 75 websites providing information about incontinence and an opportunity for interactivity, 25 web doctors, and two news groups. MAIN OUTCOME MEASURES: Quality scores according to predefined general and specific criteria. Internet popularity indexes according to number of links to websites. Correlation between quality scores and popularity indexes. RESULTS: Few sites provided comprehensive information, but the information actually provided was mostly correct. Internet popularity indexes did not correlate with quality scores. The most informative site was easily found with general internet search engines but was not found in any of the medical index sites investigated. Sixty six per cent of sites responded to an email request for advice from a fictitious incontinent woman, half of them within 24 hours. Twelve responders provided vital information that the woman might suffer from drug induced incontinence. CONCLUSIONS: Excellent information about urinary incontinence was found on the internet, but the number of links to a site did not reflect quality of content. Patients may get valuable advice and comfort from using interactive services. (+info)
Construction of a variability map for eukaryotic large subunit ribosomal RNA.
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In this paper, we present a variability map of the eukaryotic large subunit ribosomal RNA, showing the distribution of variable and conserved sites in this molecule. The variability of each site in this map is indicated by means of a colored dot. Construction of the variability map was based on the substitution rate calibration (SRC) method, in which the substitution rate of each nucleotide site is computed by looking at the frequency with which sequence pairs differ at that site as a function of their evolutionary distance. Variability maps constructed by this method provide a much more accurate and objective description of site-to-site variability than visual inspection of sequence alignments. (+info)
Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases.
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In spite of many efforts, the prediction of the location of proteins in eukaryotic cells (cytoplasm, mitochondrion or chloroplast) is still far from straightforward. In some cases (e.g. ribosomal proteins and aminoacyl-tRNA synthetases) both the cytoplasmic proteins and their organellar counterparts are encoded by the nuclear genome. A factorial correspondence analysis of the codon usage in yeast and Caenorhabditis elegans shows that the codon usage of those nuclear genes encoding ribosomal proteins or aminoacyl-tRNA synthetases is markedly different, depending on the final location of the proteins (cytoplasmic or mitochondrial). As a consequence, the location of such proteins-whose sequences are now frequently determined by systematic genomic sequencing-can be easily and quickly predicted. A WWW interface has been developed, aimed at providing a user-friendly tool for codon usage pattern analysis. It is available from http://www.genetique.uvsq.fr/afc.html (+info)