Dictated versus database-generated discharge summaries: a randomized clinical trial. (17/10211)

BACKGROUND: Hospital discharge summaries communicate information necessary for continuing patient care. They are most commonly generated by voice dictation and are often of poor quality. The objective of this study was to compare discharge summaries created by voice dictation with those generated from a clinical database. METHODS: A randomized clinical trial was performed in which discharge summaries for patients discharged from a general internal medicine service at a tertiary care teaching hospital in Ottawa were created by voice dictation (151 patients) or from a database (142 patients). Patients had been admitted between September 1996 and June 1997. The trial was preceded by a baseline cohort study in which all summaries were created by dictation. For the database group, information on forms completed by housestaff was entered into a database and collated into a discharge summary. For the dictation group, housestaff dictated narrative letters. The proportion of patients for whom a summary was generated within 4 weeks of discharge was recorded. Physicians receiving the summary rated its quality, completeness, organization and timeliness on a 100-mm visual analogue scale. Housestaff preference was also determined. RESULTS: Patients in the database group and the dictation group were similar. A summary was much more likely to be generated within 4 weeks of discharge for patients in the database group than for those in the dictation group (113 [79.6%] v. 86 [57.0%]; p < 0.001). Summary quality was similar (mean rating 72.7 [standard deviation (SD) 19.3] v. 74.9 [SD 16.6]), as were assessments of completeness (73.4 [SD 19.8] v. 78.2 [SD 14.9]), organization (77.4 [SD 16.3] v. 79.3 [SD 17.2]) and timeliness (70.3 [SD 21.9] v. 66.2 [SD 25.6]). Many information items of interest were more likely to be included in the database-generated summaries. The database system created summaries faster and was preferred by housestaff. Dictated summaries in the baseline and randomized studies were similar, which indicated that the control group was not substantially different from the baseline cohort. INTERPRETATION: The database system significantly increased the likelihood that a discharge summary was created. Housestaff preferred the database system for summary generation. Physicians thought that the quality of summaries generated by the 2 methods was similar. The use of computer databases to create hospital discharge summaries is promising and merits further study and refinement.  (+info)

Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. (18/10211)

In order to search for a common structural motif in the phosphate-binding sites of protein-mononucleotide complexes, we investigated the structural variety of phosphate-binding schemes by an all-against-all comparison of 491 binding sites found in the Protein Data Bank. We found four frequently occurring structural motifs composed of protein atoms interacting with phosphate groups, each of which appears in different protein superfamilies with different folds. The most frequently occurring motif, which we call the structural P-loop, is shared by 13 superfamilies and is characterized by a four-residue fragment, GXXX, interacting with a phosphate group through the backbone atoms. Various sequence motifs, including Walker's A motif or the P-loop, turn out to be a structural P-loop found in a few specific superfamilies. The other three motifs are found in pairs of superfamilies: protein kinase and glutathione synthetase ATPase domain like, actin-like ATPase domain and nucleotidyltransferase, and FMN-linked oxidoreductase and PRTase.  (+info)

A neural network based predictor of residue contacts in proteins. (19/10211)

We describe a method based on neural networks for predicting contact maps of proteins using as input chemicophysical and evolutionary information. Neural networks are trained on a data set comprising the contact maps of 200 non-homologous proteins of well resolved three-dimensional structures. The systems learn the association rules between the covalent structure of each protein and its correspondent contact map by means of a standard back propagation algorithm. Validation of the predictor on the training set and on 408 proteins of known structure which are not homologous to those contained in the training set indicate that this method scores higher than statistical approaches previously described and based on correlated mutations and sequence information.  (+info)

Amino acid composition of protein termini are biased in different manners. (20/10211)

An exhaustive statistical analysis of the amino acid sequences at the carboxyl (C) and amino (N) termini of proteins and of coding nucleic acid sequences at the 5' side of the stop codons was undertaken. At the N ends, Met and Ala residues are over-represented at the first (+1) position whereas at positions 2 and 5 Thr is preferred. These peculiarities at N-termini are most probably related to the mechanism of initiation of translation (for Met) and to the mechanisms governing the life-span of proteins via regulation of their degradation (for Ala and Thr). We assume that the C-terminal bias facilitates fixation of the C ends on the protein globule by a preference for charged and Cys residues. The terminal biases, a novel feature of protein structure, have to be taken into account when molecular evolution, three-dimensional structure, initiation and termination of translation, protein folding and life-span are concerned. In addition, the bias of protein termini composition is an important feature which should be considered in protein engineering experiments.  (+info)

Recognizing misfolded and distorted protein structures by the assumption-based similarity score. (21/10211)

A new similarity score (sigma-score) is proposed which is able to find the correct protein structure among the very close alternatives and to distinguish between correct and deliberately misfolded structures. This score is based on the general principle 'similar likes similar', and it favors hydrophobic and hydrophilic contacts, and disfavors hydrophobic-to-hydrophilic contacts in proteins. The values of sigma-scores calculated for the high-resolution protein structures from the representative set are compared with those of alternatives: (i) very close alternatives which are only slightly distorted by conformational energy minimization in vacuo; (ii) alternatives with subsequently growing distortions, generated by molecular dynamics simulations in vacuo; (iii) structures derived by molecular dynamics simulation in solvent at 300 K; (iv) deliberately misfolded protein models. In nearly all tested cases the similarity score can successfully distinguish between experimental structure and its alternatives, even if the root mean square displacement of all heavy atoms is less than 1 A. The confidence interval of the similarity score was estimated using the high-resolution X-ray structures of domain pairs related by non-crystallographic symmetry. The similarity score can be used for the evaluation of the general quality of the protein models, choosing the correct structures among the very close alternatives, characterization of models simulating folding/unfolding, etc.  (+info)

Imagene: an integrated computer environment for sequence annotation and analysis. (22/10211)

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene  (+info)

RFX-B is the gene responsible for the most common cause of the bare lymphocyte syndrome, an MHC class II immunodeficiency. (23/10211)

The bare lymphocyte syndrome (BLS) is characterized by the absence of MHC class II transcription and humoral- and cellular-mediated immune responses to foreign antigens. Three of the four BLS genetic complementation groups have defects in the activity of the MHC class II transcription factor RFX. We have purified the RFX complex and sequenced its three subunits. The sequence of the smallest subunit describes a novel gene, termed RFX-B. RFX-B complements the predominant BLS complementation group (group B) and was found to be mutant in cell lines from this BLS group. The protein has no known DNA-binding domain but does contain three ankyrin repeats that are likely to be important in protein-protein interactions.  (+info)

Primary structure, tissue distribution, and expression of mouse phosphoinositide-dependent protein kinase-1, a protein kinase that phosphorylates and activates protein kinase Czeta. (24/10211)

Phosphoinositide-dependent protein kinase-1 (PDK1) is a recently identified serine/threonine kinase that phosphorylates and activates Akt and p70(S6K), two downstream kinases of phosphatidylinositol 3-kinase. To further study the potential role of PDK1, we have screened a mouse liver cDNA library and identified a cDNA encoding the enzyme. The predicted mouse PDK1 (mPDK1) protein contained 559 amino acids and a COOH-terminal pleckstrin homology domain. A 7-kilobase mPDK1 mRNA was broadly expressed in mouse tissues and in embryonic cells. In the testis, a high level expression of a tissue-specific 2-kilobase transcript was also detected. Anti-mPDK1 antibody recognized multiple proteins in mouse tissues with molecular masses ranging from 60 to 180 kDa. mPDK1 phosphorylated the conserved threonine residue (Thr402) in the activation loop of protein kinase C-zeta and activated the enzyme in vitro and in cells. Our findings suggest that there may be different isoforms of mPDK1 and that the protein is an upstream kinase that activates divergent pathways downstream of phosphatidylinositol 3-kinase.  (+info)