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PubMed2004

MathSBML: a package for manipulating SBML-based biological models.

UNLABELLED: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. AVAILABILITY: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml

Cell Physiological Phenomena↗
PubMed2005

Hypospadias: a transgenerational effect of diethylstilbestrol?

BACKGROUND: In 2002, an increased risk of hypospadias was reported for sons of women exposed to diethylstilbestrol (DES) in utero, suggesting transgenerational effects of DES. The aim of this study was to further assess the association between parental DES exposure and hypospadias in a case-referent study. METHODS: Cases with hypospadias were retrieved from the hospital information system. Referents were recruited via the parents of cases. Both parents completed postal questionnaires. Associations were estimated by odds ratios (OR) with 95% confidence intervals (CI). Additionally, conditional logistic regression analyses were performed for a matched subset of parents. RESULTS: The final database included 583 cases and 251 referents. In the initial analyses, an indication was found for an increased risk of hypospadias when mothers were exposed to DES in utero: OR=2.3 (95% CI 0.7-7.9). Conditional logistic regression resulted in a stronger risk estimate: OR=4.9 (95% CI 1.1-22.3). Paternal exposure to DES did not increase the risk. CONCLUSIONS: The results confirm an increased risk of hypospadias when mothers were exposed to DES in utero. However, the excess risk appears to be of much smaller magnitude than in the 2002 study. Further research on the potential health risks for the third generation is of great importance.

Diethylstilbestrol↗
PubMed2005

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.

Amino Acid Sequence↗
PubMed2005

Clinical variables related to propofol effect-site concentrations at recovery of consciousness after neurosurgical procedures.

Target controlled infusion (TCI) systems and computer data acquisition software are increasingly used in anesthesia. It was hypothesized that the use of such systems might allow retrieval of information useful to anticipate the effect-site concentrations of propofol at which patients would recover from anesthesia. The goal of the study was to identify variables related to propofol effect-site concentrations at recovery of consciousness (ROC). Sixteen patients with a Glasgow of 15, ASA 1 or 2, subjected to neurosurgical procedures, received TIVA with TCI propofol and remifentanil. Data were collected every 5 seconds from Datex AS3 and Aspect A200XP (BIS). Effect-site TCI was used for propofol (initial effect target 5.0 microg/ml) and for remifentanil (initial plasma target 2.5 ng/ml). All clinical events were noted. Variables possibly related to propofol effect-site concentration at ROC were selected. Data are expressed as mean +/- SD. Effect-site propofol concentration at ROC was 1.3 +/- 0.5 microg/ml. A positive correlation was found between propofol effect-site concentration at ROC and: age (49.3 +/- 17 years) (P = 0.003); mean remifentanil dose during surgery (0.11 +/- 0.05 microg/kg/min) (P = 0.003); mean propofol dose during surgery (0.12 +/- 0.03 mg/kg/min) (P = 0.046); and remifentanil effect-site concentration at ROC (2.85 +/- 2.06 ng/ml) (P = 0.002). Propofol effect-site concentrations were not correlated with: weight, height, LBM, duration of anesthesia, minimum BIS at induction (30.4 +/- 6.8), time till minimum BIS (4.7 +/- 2.2 min), mean and median BIS during surgery (38.2 +/- 4.5 and 37.8 +/- 5.3). BIS-related variables were not useful as ROC predictors. Only drug variables and age correlated with propofol effect-site concentrations at ROC.

Adult↗
PubMed2006

Use of health care databases in pharmacoepidemiology.

Pharmacoepidemiology is the study of the use and effects of medications in populations. Large health care databases are often used to address research questions within pharmacoepidemiology. This paper briefly describes the kinds of research questions that can be addressed using pharmacoepidemiology databases, provides an overview of pharmacoepidemiologic databases, describes some differences between medical records and administrative databases, discusses factors that should be considered when choosing a database for a particular study, and considers what the future holds.

Databases, Factual↗
PubMed2005

The REALAB project: a new method for the formulation of reference intervals based on current data.

BACKGROUND: In a primary healthcare center concerned more with maintaining wellness than with diagnosing and monitoring illness, it is particularly important to compare patients' results with reference intervals derived from a matched population by use of defined statistical methods. METHODS: Laboratory results over a 3-year period (approximately 15,000,000 records; 197,350 individuals) were retrieved from our laboratory information system. An inclusion/exclusion procedure for individual patients was applied based on (a) presence of at least 1 of 23 previously defined "basic tests"; (b) only 1 measurement per test by the laboratory over the 3-year period; (c) for each test, absence of any abnormality in the correlated tests. Before the third step, correlations among quantities were assessed by a Spearman correlation matrix, comparing each of the 23 basic tests with all remaining tests by use of a novel multivariate algorithm. RESULTS: The initial sample group (n = 197,350) was reduced stepwise by the selection criteria outlined above to 166,027, then to 93,649, and finally to 61 246 individuals constituting our reference sample group. Results from the last 2 groups were used to calculate sex-specific, and in some cases age-related, reference limits for the 23 basic tests and for 13 additional quantities. Reference limits were calculated throughout this study by nonparametric estimation of percentiles. CONCLUSION: Reference values derived by retrospective analysis of large samples of data obtained at a given institution are particularly suitable for the evaluation of results for the presenting patient population at that institution.

Adolescent↗
PubMed2006

Use of total patient data for indirect estimation of reference intervals for 40 clinical chemical analytes in Turkey.

In the present study we used patient data to calculate laboratory-specific indirect reference intervals. These values were compared with reference intervals obtained for a healthy group according to recommendations of the International Federation of Clinical Chemistry and Laboratory Medicine and manufacturer suggestions. Laboratory results (422,919 records) from all subjects of 18-45 years of age over a 1-year period were retrieved from our laboratory information system and indirect reference intervals for 40 common analytes were estimated using a modified Bhattacharya procedure. Indirect reference intervals for most of the biochemical analytes were comparable, with small differences in lower [alkaline phosphatase (ALP) (male), alanine aminotransferase (ALT), creatine kinase, iron (male), total iron-binding capacity, folic acid, calcium (female), lactate dehydrogenase (LDH), lipoprotein (a) [Lp(a)], thyroid-stimulating hormone (TSH), total triiodothyronine (T(3)), direct bilirubin, apolipoprotein A-I (apoA-I), glucose, homocysteine, total cholesterol, ferritin, total protein, ceruloplasmin, sodium, blood urea nitrogen (BUN) and uric acid (female)] and/or upper limits [albumin, ALP (male), amylase, apoA-I, creatine kinase-MB (CK-MB), total iron-binding capacity, phosphorus, glucose, total cholesterol, gamma-glutamyltransferase (gamma-GT), magnesium, total protein, high-density lipoprotein cholesterol (HDL-C), total T(3), ALP (male), ALT, aspartate aminotransferase (AST) (male), direct bilirubin (male), creatine kinase, iron, folic acid (female), Lp(a), uric acid and triglycerides], to the reference intervals determined for healthy subjects in our laboratory. The indirect reference intervals, with the exception of a few parameters (creatinine, direct total bilirubin, calcium, BUN and potassium), were not similar to the reference intervals suggested by the manufacturers. We conclude that laboratory-specific reference intervals can be determined from stored data with a relatively easy and inexpensive method. Indirect reference intervals derived from stored data may be particularly suitable for the evaluation of results for the presenting population.

Adolescent↗
PubMed1997

Putting a new SPIN (Sentara Physician Information System) on information systems. When was the last time you invested in your system's future?

Once you have a vision and strategy for the future, an information system will probably be your biggest and most important investment. Information systems that can track clinical data are critical to providing employers with the data they're demanding and doctors with the data they need. See how and why Sentara Health System developed the Sentara Physician Information System (SPIN).

Computer Communication Networks↗
PubMed1997

Implementation of standardized nursing languages (NIC, NOC) in on-line care planning and documentation.

At the University of Iowa Hospitals and Clinics (UIHC), the Standardized Nursing Languages (SNLs) of Nursing Interventions Classification (NIC) and Nursing-sensitive Outcomes Classification (NOC) are being implemented in on-line care planning and documentation. NIC and NOC are being integrated in the INFORMM NIS (Information Network For Retrieval & Medical Management Nursing Information System). The implementation process for SNLs includes six components: objectives, programming, database content, education, utilization, and evaluation. This process has been used successfully in NIC implementation and will be applied in NOC field testing.

Humans↗