Stem Trace: an interactive visual tool for comparative RNA structure analysis.
MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations. (+info)
Day surgery: development of a national comparative audit service.
OBJECTIVES: To develop software for hospitals to analyse their own survey data on patients' experiences of day surgery and to create and test the feasibility of a national comparative audit service. DESIGN: Software development and testing; database analysis. SETTING: Eleven general hospitals in England. PATIENTS: 1741 day surgery patients undergoing procedures during 1991-2. MAIN MEASURES: Postoperative symptoms, complications, health and functional status, general satisfaction, and satisfaction with specific aspects of care. RESULTS: Software for data entry and analysis by hospitals was successfully used at the pilot sites. The overall response rate for the 11 hospitals using the questionnaire was 60%, ranging from 33% to 90% depending on the way the survey was managed. Data from all 11 hospitals were included in the national comparative audit database. Hospitals showed little variation in measures of patients' overall satisfaction (around 85%), but significant differences were apparent for specific aspects such as receiving adequate written information before admission (range 50%-89%), provision of adequate parking facilities (14%-92%) and experiencing a significant amount of postoperative pain (8%-42%). The proportion of day case patients undergoing procedures that could have been performed in outpatient departments varied from 0 to 27% between hospitals. Further comparisons of outcome, in particular measures of effectiveness, must await the development of validated case mix adjustment methods. CONCLUSION: Establishing a comparative audit database is feasible but several methodological problems remain to be resolved. (+info)
Description of local adaptation of national guidelines and of active feedback for rationalising preoperative screening in patients at low risk from anaesthetics in a French university hospital.
OBJECTIVE: To describe the effect of local adaptation of national guidelines combined with active feedback and organisational analysis on the ordering of preoperative investigations for patients at low risk from anaesthetics. DESIGN: Assessment of preoperative tests ordered over one month, before and after local adaptation of guidelines and feedback of results, combined with an organisational analysis. SETTING: Motivated anaesthetists in 15 surgical wards of Bordeaux University Hospital, Region Aquitain, France. SUBJECTS: 42 anaesthetists, 60 surgeons, and their teams. MAIN OUTCOME MEASURES: Number and type of preoperative tests ordered in June 1993 and 1994, and the estimated savings. RESULTS: Of 536 patients at low risk from anaesthetics studied in 1993 before the intervention 80% had at least one preoperative test. Most (70%) tests were ordered by anaesthetists. Twice the number of preoperative tests were ordered than recommended by national guidelines. Organisational analysis indicated lack of organised consultations and communication within teams. Changes implemented included scheduling of anaesthetic consultations; regular formal multidisciplinary meetings for all staff; preoperative ordering decision charts. Of 516 low risk patients studied in 1994 after the intervention only 48% had one or more preoperative tests ordered (p < 0.05). Estimated mean (SD) saving for one year if changes were applied to all patients at low risk from anaesthesia in the hospital 3.04 (1.23) mFF. CONCLUSIONS: A sharp decrease in tests ordered in low risk patients was found. The likely cause was the package of changes that included local adaptation of national guidelines, feedback, and organisational change. (+info)
COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.
An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial ellipsoid particles [Rallison, J. M., and S.E Harding. (1985). J. Colloid Interface Sci. 103:284-289]. This covolume has the potential to provide a magnitude for the second virial coefficient of macromolecules bearing no net charge. Allowance for a charge-charge contribution is made via an expression based on Debye-Huckel theory and uniform distribution of the net charge over the surface of a sphere with dimensions governed by the Stokes radius of the macromolecule. Ovalbumin, ribonuclease A, and hemoglobin are used as model systems to illustrate application of the COVOL routine. (+info)
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.
MOTIVATION: As databanks grow, sequence classification and prediction of function by searching protein family databases becomes increasingly valuable. The original Blocks Database, which contains ungapped multiple alignments for families documented in Prosite, can be searched to classify new sequences. However, Prosite is incomplete, and families from other databases are now available to expand coverage of the Blocks Database. RESULTS: To take advantage of protein family information present in several existing compilations, we have used five databases to construct Blocks+, a unified database that is built on the PROTOMAT/BLOSUM scoring model and that can be searched using a single algorithm for consistent sequence classification. The LAMA blocks-versus-blocks searching program identifies overlapping protein families, making possible a non-redundant hierarchical compilation. Blocks+ consists of all blocks derived from PROSITE, blocks from Prints not present in PROSITE, blocks from Pfam-A not present in PROSITE or Prints, and so on for ProDom and Domo, for a total of 1995 protein families represented by 8909 blocks, doubling the coverage of the original Blocks Database. A challenge for any procedure aimed at non-redundancy is to retain related but distinct families while discarding those that are duplicates. We illustrate how using multiple compilations can minimize this potential problem by examining the SNF2 family of ATPases, which is detectably similar to distinct families of helicases and ATPases. AVAILABILITY: http://blocks.fhcrc.org/ (+info)
Protein analyst--a distributed object environment for protein sequence and structure analysis.
SUMMARY: Protein Analyst is a flexible tool for the analysis of protein sequences with emphasis on the integration of sequence and structural information. AVAILABILITY: The software will be available from the Oxford Molecular Biolib web site (http://www. oxmol.co.uk/biolib) and will be free to the academic research community. (+info)
Preparing manuscripts for submission to medical journals: the paper trail.
CONTEXT: Preparing a manuscript for publication in a medical journal is hard work. OBJECTIVE: To make it easier to prepare a readable manuscript. APPROACH: Start early--A substantial portion of the manuscript can be written before the project is completed. Even though you will revise it later, starting early will help document the methods and guide the analysis. Focus on high-visibility components--Pay attention to what readers are most likely to look at: the title, abstract, tables, and figures. Strive to develop a set of tables and figures that convey not only the major results but also the basic methods. Develop a systematic approach to the body of the paper--A standard framework can make it easier to write the introduction, methods, results, and discussion. An obvious organization with frequent subheadings and consistent labels makes the paper easier to read. Finish strong--Improve the paper by sharing it with others and by learning how to elicit and receive their feedback. Take the time to incorporate useful feedback by revising frequently. (+info)
A framework and tools for authoring, editing, documenting, sharing, searching, navigating, and executing computer-based clinical guidelines.
With the spread of managed care and integrated delivery networks, an increased emphasis has been placed on the cost-effectiveness of clinical practices. The need has been recognized to use guidelines to support education, and to integrate them into clinical practice. A specification for guideline representation that would facilitate computer-based clinical guideline sharing has been developed by the InterMed Collaboratory. Called GLIF (GuideLine Interchange Format), this specification and its proposed extensions have been the basis for our implementation of a framework and suite of integrated software tools for guideline authoring and editing, packaging in XML, Internet distribution, navigation, eligibility determination, and automatic execution. (+info)