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PubMed1982

Autopsy pathology storage and coding by microcomputer.

Storage and coding of anatomic pathology data usually is accomplished by expensive main frame systems. The authors of this article have developed a microcomputer based program package for autopsy pathology which stores patient demographic data, provisional or final anatomic diagnoses, and coded diagnoses obtained from an on-line Systematized Nomenclature of Pathology (SNOP) code lexicon. The system includes limited text editor functions as well as rapid data retrieval with the generation of final reports. Data files containing SNOP codes and diagnoses are searched easily by a variety of parameters, making data retrieval of autopsy material simple and efficient.

Abstracting and Indexing↗
PubMed1988

Determinants of financially burdensome family health expenses: United States, 1980.

This report focuses on two questions of current interest to policymakers. First, "What percent of U.S. families experience financially burdensome health expenses?" and, second, "What are the determinants of financially burdensome health expenses among U.S. families?" The first question is addressed by examining how the distribution in the United States of families with financially burdensome health expenses is affected by six different possible measures of financial burden. The second question is addressed by using multiple regression techniques on one of the measures selected as a preferred measure. The data used are from the family data files of the 1980 National Medical Care Utilization and Expenditure Survey (NMCUES). This report presents data on approximately 5,000 multiple-person families interviewed in this longitudinal survey. It provides a separate analysis for each of three socioeconomic family populations that have consistently been of interest to policymakers. These are (1) older families (defined for this report as all U.S. multiple-person families with a member 65 years of age or over); (2) younger, lower-income families (defined as all U.S. multiple-person families below 200 percent of the poverty level in 1980 and with all members under 65 years of age); and (3) younger, better-off families (defined as all U.S. multiple-person families at 200 percent of the poverty level or higher in 1980 and with all members under 65 years of age). Two general conceptual approaches have been used in the literature to assess financially burdensome health expenses. The first approach measures financial burden by the size of a family's health bill in dollars. The second approach focuses on a family's ability to pay its health bill, and it measures financial burden as a ratio of health expenses to family income. There is no agreement on which of the two approaches is preferable and also no agreement on which of several operational measures in each category is the most appropriate. In order to shed light on this controversy, this report compares six potentially useful operational measures of financially burdensome health expenses. Three are dollar measures and three are ratio measures. The three dollar measures are (1) total charges for health care (irrespective of who pays the bill or whether or not the bill is paid), (2) out-of-pocket expenses for health care services (family-paid premiums for health insurance are not included), and (3) total out-of-pocket expenses for health (the previous measure plus out-of-pocket premiums).(ABSTRACT TRUNCATED AT 400 WORDS)

Data Collection↗
PubMed1999

Major complications of laparoscopy: a follow-up Finnish study.

OBJECTIVE: To examine recent figures on major laparoscopic complications in Finland. METHODS: This was a nationwide record-linkage study from January 1995 through December 1996 including all Finnish hospitals performing gynecologic laparoscopies. Data files of the National Patient Insurance Association and the Finnish Hospital Discharge Register were used. Data were compared with previous results from 1990 to 1994. RESULTS: Among 32,205 gynecologic laparoscopies, 130 major complications were noted. The total complication rate was 4.0 per 1000 procedures: 0.6 per 1000 in diagnostic laparoscopies, 0.5 per 1000 in sterilization, and 12.6 per 1000 in operative laparoscopies. Intestinal injuries were reported in 0.7 per 1000, incisional hernias in 0.3 per 1000, urinary tract injuries in 2.5 per 1000, major vascular injuries in 0.1 per 1000, and other injuries in 0.5 per 1000 gynecologic laparoscopic procedures. Seventy-five percent (88 of 118) of the major complications in operative laparoscopies occurred during hysterectomies. The total major complication rate decreased from 4.9% in 1993 to 2.3% in 1996 (chi2 = 8.55, P = .003), but the incidence of ureteral injuries remained stable, at about 1% of laparoscopic hysterectomies. Ureteral injuries were most common in local hospitals (2.6%), followed by central (1.1%) and university hospitals (0.9%). From 1990 through 1996, the relative risk for ureteral injury in laparoscopic hysterectomies, compared with other operative laparoscopies was 29.0 (95% confidence interval [CI] 13.3, 63.0), for bladder injury 13.0 (95% CI 6.0, 28.2), for intestinal injury 1.3 (95% CI 0.6, 2.5), and for major vascular injury 0.4 (95% CI 0.1, 3.6). Compared with the figures for 1990-1994, all major complications in operative laparoscopies increased, from 0 per 1000 in 1990 to 14.0 per 1000 in 1996 (chi2 = 20.28, P<.001), but part of this increase was due to the increased proportion of laparoscopic hysterectomies. CONCLUSION: Laparoscopic hysterectomies are still associated with a stable 1% risk of ureteral injury, whereas other major complications were decreasing until 1996. Complications in other laparoscopic procedures generally are rare.

Female↗
PubMedDate not supplied

A computerized system for equipment control and preventive maintenance.

The Medical Engineering Laboratory of the University of Rochester-Strong Memorial Hospital is responsible for service of and scheduled preventive maintenance on approximately 6000 pieces of patient-care and laboratory equipment. A database management computer program has been developed t increase the efficiency and accuracy with which equipment control records are maintained. The program has three major divisions: data files, update programs, and report programs. The date files are for storage of all records and tables; the update programs are for convenient data entry, corrections, and changes; the report programs are for creating all the forms, records, and reports associated with the equipment control program. Besides maintaining all of the identifying information, inspection results, and service reports on all of the medical equipment, the system can maintain the department's parts inventory records and prepare itemized bills.

Computers↗
PubMed2025

Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.

Biobank-scale whole-genome sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume and complexity presents significant challenges. We highlight the annotated genomic data structure (aGDS) format, substantially reducing the WGS data file size while enabling seamless integration of genomic and functional information for comprehensive WGS analyses. The aGDS format yielded 23 chromosome-specific files for the UK Biobank 500k WGS dataset, occupying only 1.10 tebibytes of storage. We develop the vcf2agds toolkit that streamlines the conversion of WGS data from VCF to aGDS format. Additionally, the STAARpipeline equipped with the aGDS files enabled scalable, comprehensive, and functionally informed WGS analysis, facilitating the detection of common and rare coding and noncoding phenotype-genotype associations. Overall, the vcf2agds toolkit and STAARpipeline provide a streamlined solution that facilitates efficient data management and analysis of biobank-scale WGS data across hundreds of thousands of samples.

Humans↗
PubMed1989

BUMP: a FORTRAN program for identifying dose-response curves subject to downturns.

BUMP is a FORTRAN implementation of a modified Jonckheere-Terpstra test, proposed by Simpson and Margolin, to test nonparametrically for a dose-response curve when a downturn is possible at high doses. The Jonckheere-Terpstra statistic is commonly used to test for increasing or decreasing trends in dose-response relationships. In many experimental settings, however, a test agent has more than one effect, and a "bump"-shaped dose-response can occur. For instance, increasing the concentration of a certain nutrient on a petri dish may increase the growth rate at low doses yet decrease the growth rate at high doses because of toxicity. The modified test allows one to assess the significance of the initial increase in the dose-response curve and yet to minimize the effect on the conclusions of any downturn at higher doses. A complete system which operates directly on SYSTAT/MYSTAT files is available for the IBM-PC and compatibles; it includes a utility which converts ASCII data files to the SYSTAT/MYSTAT format. The FORTRAN 77 source code is available for those who would like to run BUMP on other machines.

Data Interpretation, Statistical↗
PubMed1975

Quantification of ventricular performance: a computer-based system for the analysis of angiographic data.

A computer-based quantitative angiography system for the acquisition and analysis of ventriculographic data has been developed. In addition to the apparatus normally required for angiography and left ventricular pressure recording, a digitizing tablet, PDP 11/20 mini computer, and TV monitor with a hard-copy device is employed. Four modes of operation are currently in use: data acquisition, analysis, mini cine, and data tape editor. Data acquisition facilitates forming a magnetic tape record of the digitized pressure, timing, and event identification, together with anywhere from 4 to 100 digitilized LV contours. A number of error checks and feedbacks are incorporated to provide some measure of quality control. In the event an error is written onto the magnetic tape record, the data tape editor can be used to review the record and correct most errors. Analysis of the generated data tape consists of several options which include: pump function, muscle function, pressure derived indices of contractility and systolic time intervals, and contour pattern recognition which is still under development. If the complete analysis option is chosen, a summary of the analysis, referred to as the quick-sight list, is also presented. The so called mini cine option employs a separate and independent acquisition-analysis program. This requires only the end-diastolic (with a segment of wall) and end-systolic contours (without pressure data) to extract the most essential parameters (EDV, EF, CI, HR, and wall mass). As a result of the relative straightforward processing and inherent simplicity, the mini cine option is most frequently used. This system has done much to reduce the time required for analysis of angiographic data, while at the same time maintaining and even improving the quality of the results. Other less tangible benefits include: the possibility to build a readily accessible library of patient data files facilitating a posteriori studies, precise and uniform definition of the rules to input and analyze data, and finally providing a useful step towards fully automatic ventriculographic processing.

Angiocardiography↗
PubMed1999

Private patients in NHS hospitals: comparison of two sources of information.

BACKGROUND: The use of National Health Service (NHS) hospitals to treat private patients is debatable on the grounds of equity of access. Hospital Episodes Statistics (HES) annual reports are the only routine source of information on the scale of this activity. The accuracy of the information is doubted. This enquiry tested the completeness of HES data against information obtained directly from private patient unit managers. METHOD: Managers of the 71 pay bed units in NHS hospitals in England were asked to supply from local registers and accounts the numbers of in-patients and day cases admitted in 1995-1996. Their reports were matched with the numbers of first consultant episodes for private in-patients and day cases shown for those hospitals in the HES data file for that year. RESULTS: Of the 71 units 62 responded; 53 of these gave usable data. The 53 included, and 18 excluded from the comparison, matched on median and range of bed numbers. Managers identified 16 per cent more total admissions than did HES, 62,572 against 54,131; 13 per cent more in-patient admissions, 39,776 against 35,319; and 21 per cent more day cases, 22,796 against 18,812. More total admissions were reported by managers of 38 pay bed units than were recorded in HES, fewer by 12, and equal numbers by three. Similar sized discrepancies were noted for in-patient admissions and day cases. Reasons for the under-reporting of private patients in HES included the use of separate patient administration systems for private patients with a failure to feed data to HES, and the omission of some provider units altogether by a minority of trusts from the returns made to the Department of Health. CONCLUSION: Overall, HES underestimates the amount of private patient activity reported directly by NHS hospitals. No method of validating private patient data is currently available. An amendment to an existing statistical return would provide a check on numbers. Central guidance on the inclusion of private patient activity in data transmitted by providers to the HES processing agency should be reinforced.

England↗
PubMed2005

An improved photo-absorption cross section model for the physics models regime in MCNPX.

The photo-nuclear physics model capabilities utilising the CEM2k model implemented in the MCNPX code were improved > 100 MeV photon energy by basing the photon transport on experimental photo-absorption cross sections of nuclides rather than on free nucleon cross sections. Below 100 MeV, the photo-nuclear physics model now uses isotope-specific giant dipole resonance (GDR) photo-absorption cross sections that are provided to the code in a parameterised form on a data file. Adjustments of the photo-fission cross sections were implemented to match the BOFOD evaluated data through a CEM2k internal parameter. The physics models with these improvements are better equipped to supplement the tabulated data based photo-nuclear MCNPX capability for isotopes with missing tabulated data evaluations especially in the GDR region, and has improved its predictive power at energies above the GDR resonances.

Absorption↗
PubMed1995

Continuous pO2 monitoring during dual perfusion of the term human placenta in vitro.

A computerized system has been developed to continuously monitor, collect and display pO2 in real time from the maternal and fetal arteries and veins in the dually perfused term placenta. Oxygen electrodes were installed in flow-through chambers in the tubing of the perfusion system. The signal from the O2 electrodes was digitized, acquired, analyzed and displayed in real time during the perfusions using a personal computer. Output from the O2 electrodes was linearly proportional to pO2 (33-502 mm Hg; r2 = 0.99). Running average pO2 values (mean +/- SD) were also calculated for every minute and stored. The captured data files can be recalled and analyzed after completion of the perfusion experiment and compared with other data collected during perfusion. One of the unique capabilities of the pO2 electrodes is their ability to respond rapidly to changing perfusion conditions. For example, as the fetal circulation begins to break down the change is noted before volume loss in the fetal circuit by decreasing fetal vein pO2.

Biological Transport↗
PubMed2005

EXPANDER--an integrative program suite for microarray data analysis.

BACKGROUND: Gene expression microarrays are a prominent experimental tool in functional genomics which has opened the opportunity for gaining global, systems-level understanding of transcriptional networks. Experiments that apply this technology typically generate overwhelming volumes of data, unprecedented in biological research. Therefore the task of mining meaningful biological knowledge out of the raw data is a major challenge in bioinformatics. Of special need are integrative packages that provide biologist users with advanced but yet easy to use, set of algorithms, together covering the whole range of steps in microarray data analysis. RESULTS: Here we present the EXPANDER 2.0 (EXPression ANalyzer and DisplayER) software package. EXPANDER 2.0 is an integrative package for the analysis of gene expression data, designed as a 'one-stop shop' tool that implements various data analysis algorithms ranging from the initial steps of normalization and filtering, through clustering and biclustering, to high-level functional enrichment analysis that points to biological processes that are active in the examined conditions, and to promoter cis-regulatory elements analysis that elucidates transcription factors that control the observed transcriptional response. EXPANDER is available with pre-compiled functional Gene Ontology (GO) and promoter sequence-derived data files for yeast, worm, fly, rat, mouse and human, supporting high-level analysis applied to data obtained from these six organisms. CONCLUSION: EXPANDER integrated capabilities and its built-in support of multiple organisms make it a very powerful tool for analysis of microarray data. The package is freely available for academic users at http://www.cs.tau.ac.il/~rshamir/expander.

Algorithms↗
PubMed1994

The urge to merge: linking vital statistics records and Medicaid claims.

This paper describes a procedure used to link Medicaid claims data to California vital statistics records for very low birthweight infants. The linkage involved about 53,000 infants born from 1980 to 1987 and 1.46 million claims for delivery/birth-related hospital admissions during the same period. Because the two data files did not share a unique identifier, record linkage required combining evidence across several linking variables: delivery hospital, delivery/birth date or hospitalization period, names, mother's age, and zip code. To combine the various pieces of evidence, we used record linkage theory to compute scores that measure the likelihood of a match, i.e., that two records correspond to the same delivery. These scores appropriately weight the various pieces of evidence for or against a match. Implementation required dealing with large amounts of missing data in one of the files, errors and variations in reported names, and the need to minimize the number of incorrect links. The approach applies to a wide range of linkage problems. The ability to combine existing datasets to form new datasets containing analysis variables from each facilitates analyses that would otherwise be impossible, or prohibitively expensive.

Bias↗
PubMed2003

e-Phys: a suite of intracellular neurophysiology programs integrating COM (component object model) technologies.

Current computer programs for intracellular recordings often lack advanced data management, are usually incompatible with other applications and are also difficult to adapt to new experiments. We have addressed these shortcomings in e-Phys, a suite of electrophysiology applications for intracellular recordings. The programs in e-Phys use Component Object Model (COM) technologies available in the Microsoft Windows operating system to provide enhanced data storage, increased interoperability between e-Phys and other COM-aware applications, and easy customization of data acquisition and analysis thanks to a script-based integrated programming environment. Data files are extensible, hierarchically organized and integrated in the Windows shell by using the Structured Storage technology. Data transfers to and from other programs are facilitated by implementing the ActiveX Automation standard and distributed COM (DCOM). ActiveX Scripting allows experimenters to write their own event-driven acquisition and analysis programs in the VBScript language from within e-Phys. Scripts can reuse components available from other programs on other machines to create distributed meta-applications. This paper describes the main features of e-Phys and how this package was used to determine the effect of the atypical antipsychotic drug clozapine on synaptic transmission at the neuromuscular junction.

Intracellular Fluid↗
PubMedDate not supplied

A prototype object database for mitochondrial DNA variation.

Surveys of biochemical and molecular genetic variation in natural populations have generated a wealth of data, but this valuable resource has not been adequately preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype for animal mitochondrial DNA (mtDNA) surveys. This prototype includes the specification of a format for data files that are to be submitted to the database, an open-source object database that encapsulates data with methods to display and analyze data, and a website where data can be retrieved in either its original form or extensible markup language (XML). Data from more than 50 published surveys of mtDNA variation were retrieved from the literature and entered into the database. We hope that the population genetics community will support this project by contributing both data and expertise.

Animals↗
PubMed2005

MRS: a fast and compact retrieval system for biological data.

The biological data explosion of the 'omics' era requires fast access to many data types in rapidly growing data banks. The MRS server allows for very rapid queries in a large number of flat-file data banks, such as EMBL, UniProt, OMIM, dbEST, PDB, KEGG, etc. This server combines a fast and reliable backend with a very user-friendly implementation of all the commonly used information retrieval facilities. The MRS server is freely accessible at http://mrs.cmbi.ru.nl/. Moreover, the MRS software is freely available at http://mrs.cmbi.ru.nl/download/ for those interested in making their own data banks available via a web-based server.

Databases, Genetic↗
PubMedDate not supplied

A data base management system for clinical records of renal failure.

This paper describes a computerized data-base management system (DBMS) for keeping medical records of kidney failure patients. The system allows simple data entry by untrained medical personnel as well as automatic feeding of data from computer generated data files. The system allows easy retrieval which is enhanced by graphic displays and statistical analyses of the data. The DBMS uses a relational model of data representation and is based on an existing system which was developed to run under the UNIX operating system on DEC PDP 11's. Previous attempts by the authors and others to create such a medical record system are described. A description of the hardware and software environment of the medical record system is provided. The system is then described, and examples of data manipulations are given.

Computers↗
PubMed1997

A deterministic method to calculate the radiation spectra of nuclides.

Recently, the computer program IMRDEC has been developed to determine the radiation spectra due to a single atomic-subshell ionisation of a stable atom by a particle, or due to the atomic deexcitation or decay of nuclides. The data needed to describe the deexcitation or decay scheme are obtained from the Evaluated Nuclear Structure Data File (ENSDF) maintained at Brookhaven National Laboratory; this results in the simplest possible input specification. The atomic data as well as the atomic relaxation probabilities are taken from the Evaluated Atomic Data Library (EADL) from Lawrence Livermore National Laboratory. The program IMRDEC calculates the radiation spectra (inclusively the atomic relaxation cascades) deterministically rather than by the Monte Carlo method; this results in much shorter calculational time per nuclide. Since many assumptions still have to be made in determining the atomic relaxation probabilities and in calculating the atomic relaxation, the deterministic method seems to be a small source of inaccuracy.

Radiation Dosage↗