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PubMed1991

Analysis of one-dimensional gels and two-dimensional Serwer-type gels on the basis of the extended Ogston model using personal computers.

This report presents the stand-alone computer application ELPHOFIT, a software package for the analysis of gel electrophoretic data based on Ferguson plots. Either conventional one-dimensional gels or two-dimensional agarose gels (Serwer-type) can be evaluated. Special emphasis is on the latter gel type, which has been applied previously for the separation of DNA, intact viruses and polydisperse meningitis vaccines. ELPHOFIT is designed for Macintosh PCs and for the IBM XT, AT, PS/2 and compatibles. The program operates interactively with the user, who determines the course of evaluation. Data input is in the format of files providing values of gel electrophoretic migration distances or particle mobility (absolute or relative). Data processing involves a simultaneous least-square curve fitting algorithm (Newton-Gauss, Marquardt-Levenberg) which uses equations derived from the extended Ogston model. Functions are fit to the database by adjusting their variables, representing physical parameters of the gel and the electrophoresed particle. The program output consists of tables and graphics accompanied by an explanatory text providing the following information: (i) radius and free mobility of the electrophoresed particle, (ii) fiber radius, length and volume, mean or median pore radius of the gel, (iii) linear Ferguson plots, (iv) iso-free-mobility/iso-size nomogram for two-dimensional gels, (v) confidence ellipses, (vi) required parameters for image processing program GELFIT and (vii) goodness-of-fit and other statistical parameters, such as standard errors, dependency values, root-mean-square (RMS) error and determination coefficient. Other features of the program are (i) simulation of Serwer-type two-dimensional electrophoresis, (ii) standardization according to size, or size and free mobility, (iii) the conversion of particle radii to molecular (or particle) weight and vice versa, (iv) interconversion of DNA size specifications, i.e. the number of base pairs and the geometric mean radii, (v) computation of gel concentration for optimal resolution of two components, (vi) option to obtain a session record, (viii) option to establish a data output file containing the information of generated graphics (IBM only) and (ix) a text editing facility, e.g., for creating data files. Graphics (Macintosh version, PICT format) and text output files (both IBM and Macintosh versions, standard ASCII format) generated by ELPHOFIT are compatible with commercially available software.

Computers↗
PubMed2002

ZTR: a new format for DNA sequence trace data.

MOTIVATION: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth. RESULTS: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive. lmb.cam.ac.uk/pub/staden/io_lib/test_data.

Algorithms↗
PubMed2003

Prevalence and costs of major depression among elderly claimants with diabetes.

OBJECTIVE: To compare the odds of major depression among Medicare claimants with and without diabetes and to test whether annual medical payments are greater for those with both diabetes and major depression than for those with diabetes alone. RESEARCH DESIGN AND METHODS: This retrospective analysis relies on claims data from the 1997 Medicare 5% Standard Analytic Files. Using these data, we statistically determined whether the odds of major depression are greater among elderly claimants with diabetes after controlling for age, race/ethnicity, and sex. We then used regression analysis on a sample of over 220,000 elderly claimants with diabetes to test whether payments for non-mental health-related services are greater for those with both diabetes and major depression (n = 4,203) than for those with diabetes alone. RESULTS: Our findings indicate that the odds of major depression are significantly greater among elderly Medicare claimants with diabetes than among those without diabetes (OR 1.58 +/- 0.05). We also found that elderly claimants with both diabetes and major depression seek treatment for more services and spend more time in inpatient facilities, and as a result incur higher medical costs than claimants with diabetes but without major depression. These results hold even after excluding services related to mental health treatment. CONCLUSIONS: This analysis suggests that treatment for major depression among claimants with diabetes may reduce total medical costs if treatment results in a decrease in utilization for general medical services in the future.

Aged↗
PubMedDate not supplied

The importance of large, high quality clinical databases in nephrology.

While clinical trials constitute an undisputed standard, they are not perfect because they are focused on a well defined segment of patients with a given disease. Generalizability is a problem with these studies because the experimental setting often differs substantially from everyday clinical practice. Clinical files are traditionally the main source of information for clinical medicine. The quality of recorded information in clinical files is often unsatisfactory. Yet clinical files are data-rich and ought to be considered as a valuable resource, particularly when clinical information is stored in electronic format. Clinicians have already started to construct very large, high quality clinical databases. Outcome research based on high quality data retrieved from well organized and exhaustive clinical files is bound to become increasingly important. Standardization is fundamental for these projects to be successful. The task may be daunting but worth while; due to complexity and cost the randomised clinical trial is unlikely to remain the only source of information on which to base clinical decisions about treatments.

Clinical Trials as Topic↗
PubMed1996

Asthma mortality and hospitalization among children and young adults--United States, 1980-1993.

Asthma is the most common chronic illness in childhood and is characterized by variable airflow obstruction with airway hyperresponsiveness. In the United States, asthma affects an estimated 14-15 million persons, including 4.8 million (6.9%) aged < 18 years. In 1993, asthma accounted for an estimated 198,000 hospitalizations and 342 deaths among persons aged < 25 years. To characterize national trends in mortality and hospitalizations attributable to asthma among children and young adults (persons aged < 25 years) during 1980-1993, CDC analyzed mortality data from its multiple cause-of-death files and hospitalization data from the National Hospital Discharge Survey. This report summarizes the results of that analysis, which indicate that asthma-related mortality and hospitalization rates are increasing among persons aged < 25 years.

Adolescent↗
PubMed1998

Surveillance for asthma--United States, 1960-1995.

PROBLEM/CONDITION: Asthma is one of the most common chronic diseases in the United States, and it has increased in importance during the preceding 20 years. Despite its importance, no comprehensive surveillance system has been established that measures asthma trends at the state or local level. REPORTING PERIOD: This report summarizes and reviews national data for specific end-points: self-reported asthma prevalence (1980-1994), asthma office visits (1975-1995), asthma emergency room visits (1992-1995), asthma hospitalizations (1979-1994), and asthma deaths (1960-1995). DESCRIPTION OF SYSTEM: The National Center for Health Statistics (NCHS) annually conducts the National Health Interview Survey, which asks about self-reported asthma in a subset of the sample. NCHS collects physician office visit data with the National Ambulatory Medical Care Survey, emergency room visit data with the National Hospital Ambulatory Medical Care Survey, and hospitalization data with the National Hospital Discharge Survey. NCHS also collects mortality data annually from each state and produces computerized files from these data. We used these datasets to determine self-reported asthma prevalence, asthma office visits, asthma emergency room visits, asthma hospitalizations, and asthma deaths nationwide and in four geographic regions of the United States (i.e., Northeast, Midwest, South, and West). RESULTS: We found an increase in self-reported asthma prevalence rates and asthma death rates in recent years both nationally and regionally. Asthma hospitalization rates have increased in some regions and decreased in others. At the state level, only death data are available for asthma; death rates varied substantially among states within the same region. INTERPRETATION: Both asthma prevalence rates and asthma death rates are increasing nationally. Available surveillance information are inadequate for fully assessing asthma trends at the state or local level. Implementation of better state and local surveillance can increase understanding of this disease and contribute to more effective treatment and prevention strategies.

Adolescent↗
PubMedDate not supplied

NEUROLAB, a comprehensive program for the analysis of neurophysiological and behavioural data.

A comprehensive and versatile computer software for IBM-compatible microcomputers has been developed. It is designed for quantitative off-line analysis of A/D-sampled intracellular or extracellular recordings and behavioural or stimulus data. The program works with single files or file sets. It supports data to be viewed on the monitor and allows sectioning of interesting data for common analysis. It offers 19 filters/operators for data processing and comprehensive possibilities to set and calculate trigger points. Data of trigger points can be exported as ASCII files. Standard neurophysiological histograms like interval-, PST-, phase histograms or auto- and cross-correlograms can be obtained. Time-dependent and phase-dependent averaging is possible for all original and filtered data. All graphical output on the display can directly be copied to a plotter/laser printer or HP-GL file by keyboard commands.

Animals↗
PubMedDate not supplied

[EXPR: a simple computer system for recording animal behavior].

A number of different methods for recording animal behaviour are briefly reviewed and the computer system "EXPR" for the ethological recording of the sequences of behavioural events is described in this article. The main peculiarities of the system are: (a) recorded data are saved to the files created by a data analysis package, (b) it is possible to record simultaneously behaviour of a number of individuals, which is crucial for the analysis of social interactions. The user can specify the options for different recording tasks through the setup file written with using special notation. The program functioning is illustrated by an artificial example.

Animals↗
PubMed1997

Trauma outcome analysis and the development of regional norms.

Early attempts to assess patient outcomes in trauma hospitals included morality reviews and expert panel chart audits. More recently, a statistical methodology combining the Revised Trauma Score and Injury Severity Score has been developed (TRISS). A modification of this methodology--TRISS-like analysis--allows the inclusion of patients who have required endotracheal intubation prior to the time of arrival at the trauma hospital. This study was undertaken to further improve this TRISS-like methodology by developing statistical coefficients based on regional data. It was hypothesized that his would allow the analysis to better identify those hospitals with significantly better worse outcomes than their peers. The Comprehensive Data Set of the Ontario Trauma Registry was accessed, which contains data on severely injured patients from all 11 lead trauma hospitals in the province. Three years' data were obtained, and checked for accuracy and completeness. Analysis was performed using the previously published coefficients. New coefficients were then derived, using regression analysis on the Ontario patient data. 5,258 of 6,389 files were complete and eligible for analysis. TRISS-like analysis resulted in an expected mortality of 21.2% (1115.6/5258) with a z score for the entire province of -14.102. Individual hospital scores were all negative (fewer deaths than expected), and 9/11 hospital scores were < -1.96 (statistically significant). The new coefficients were markedly different from those previously published, and their application resulted in an overall z score of 0.000. Institutional scores ranged from -3.309 to +4.686, with two hospitals < -1.96 and one > +1.96. The old coefficients predicted many more deaths than occurred in all of the hospitals. The new coefficients proved quite accurate overall in predicting outcomes, and identified one institution with significantly more deaths than would have been predicted for other hospitals in the province. Subsequently, a fourth year's data files were obtained, and used as a validation data set. The new coefficients again proved more useful than the original ones.

Humans↗
PubMed1997

The use of a systemic therapy checklist improves the quality of data acquisition and recording in multicentre trials. A study of the EORTC Soft Tissue and Bone Sarcoma Group.

The aim of this study was to verify whether the introduction of a systemic therapy checklist in the performance of multinational multicentre studies improves the quality of data acquisition and recording. We retrospectively analysed the results obtained through the use of this checklist in a study of the EORTC Soft Tissue and Bone Sarcoma Group. During the clinical trial, data were recorded in the hospital record with optional use of a predesigned EORTC Systemic Therapy Checklist. After completion of the study, 11 centres were monitored for the use of this checklist. Monitors were highly experienced medical oncologists. Items checked included all aspects of patient eligibility, drug administration, biochemical and haematological values, variables related to toxicities of treatment and response parameters. Data of 183 cycles given to 51 patients were checked. A total of 8983 items were checked. 91% of the data was reported correctly, 1% was missing and 6% was reported on the case record from (CRF) but could not be retrieved in the hospital record file. Compared with data obtained before the introduction of the checklist (68% correct, 4% incorrect, 0.1% missing and 28% on CRF but not in hospital files), these results show marked improvement generally. In centres where no Systemic Therapy Checklist was used, 85.9% of data were correct 2.8% incorrect, 0.7% missing and 10.6% only on CRF, which compares unfavourably with those where the Systemic Checklist was completely used (97.7% correct, 0.7% incorrect, 1% missing, 0.6% only on CRF). In addition the time required for data checking largely decreased by the use of the checklist-without this, a median of 3.5 cycles could be checked per hour, whilst if the checklist was used, this number increased to 6.5 cycles per hour. The use of a Systemic Therapy Checklist as an integral part of the hospital file for data recording in multicentre multinational trials is highly recommended and leads to a major improvement in data quality.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1988

Microcomputer-assisted filing system of cardiac catheterization records using a relational database management system.

To efficiently store and retrieve cardiac catheterization records, we have developed a computer-assisted database, which comprises a 16-bit microcomputer with dual floppy disk drives, a 20 MB random-access memory, hard disk drive, and a line printer. All programmings were accomplished using a relational database management system (R:base 5000, Microrim, Inc.). Data inquiry procedures could be performed with direct operational commands of the system as well as with preprogrammed command files, and final results of searches were printed out with a line printer. The major advantages of the present system described in this report include: (1) the relatively easy and rapid creation of the database, (2) ease of modification of the database structures even after the system design is finished, (3) operational commands in combination with conditional operator(s) are flexible and powerful enough to allow the end user to retrieve data based on various kinds of criteria, (4) a high-level programming language provided by the R:base automates a series of database procedures with relative ease, (5) relational capabilities of the database management system can enhance the possibility of reconstruction of a new data file from a single or several preexisting data files, and (6) the system can be realized at reasonable cost.

Cardiac Catheterization↗
PubMed1995

Annotating PDB files with scene information.

We have implemented extensions to the Brookhaven Protein Data Bank (PDB) file format for incorporating scene information such as viewing parameters, additional molecular information (e.g., van der Waals radii and atom colors), and user-defined graphics. These extensions were made in conformance with the PDB standard and provide sufficient information to render the scene in various styles such as space-filling images and ribbon diagrams. For the past 5 years these extensions have been used in the MidasPlus molecular modeling system and have proved both powerful and sufficient for generating complex molecular images. We propose that the extensions to the PDB presented here be adopted by the molecular modeling community for incorporation into visualization programs.

Computer Graphics↗
PubMed2001

Conversion of capillary electrophoresis microchip genotyping data for analysis with Genetic Profiler software.

The collection and conversion of 4-color fluorescent genotyping data from capillary array electrophoresis microchip devices and its conversion to a format easily and rapidly analyzed by Genetic Profiler genotyping software is presented. Microchip fluorescence intensity data are acquired and stored as 4-color tab-delimited text. These files are converted to electrophoretic signal data (ESD) files using a utility program (TEXT-to-ESD) written in C. TEXT-to-ESD generates an ESD file by converting text data to binary data and then appending a 632-byte ESD-file trailer. Up to 96 ESD files are then assembled into a run folder and imported into Genetic Profiler, where data are reduced to 4-color electropherograms and analyzed. In this manner, DNA fragment sizing data acquired with our high-speed electrophoretic microchip devices can be rapidly analyzed using robust commercial software. Additionally, the conversion program allows sizing of data with Genetic Profiler that have been preprocessed using other third-party software, such as BaseFinder.

Alleles↗
PubMed1990

[Proposal for a data collection system for colposcopy services].

A computerized system for colpocytologic data collection and filing, is presented. A descriptive and easy to elaborate recording of anamnestical data and examination findings is achieved using two correlated files. Step by step filing is obtained by multichoice scheme which progressively appears on the screen.

Colposcopy↗
PubMed1998

Iditis: protein structure database.

The validation, enrichment and organization of the data stored in PDB files is essential for those data to be used accurately and efficiently for modelling, experimental design and the determination of molecular interactions. The Iditis protein structure database has been designed to allow the widest possible range of queries to be performed across all available protein structures. The Iditis database is the most comprehensive protein structure resource currently available, and contains over 500 fields of information describing all publicly deposited protein structures. A custom-written database engine and graphical user interface provide a natural and simple environment for the construction of searches for complex sequence- and structure-based motifs. Extensions and specialized interfaces allow the data generated by the database to used in conjunction with a wide range of applications.

Database Management Systems↗
PubMed2004

Anatomic and functional long-term results of canal wall-down mastoidectomy.

The objective of this study was to evaluate, over the long-term, the anatomic and functional outcome of canal wall-down mastoidectomy performed for chronic otitis media with cholesteatoma and chronic otomastoiditis resistant to all conservative treatment. The study was made through a retrospective review of 338 cases of consecutive primary canal wall-down mastoidectomies performed between 1974 and 1998. Included were 259 cases with sufficient data. In all cases, functional reconstruction was performed at the same time as the mastoidectomy. Demographic and clinical data were collected from each file. From the clinical data, the surgical techniques, complications, the number of follow-up visits necessary to ensure cavity cleanliness, details of care provided over the period 1 to 24 years (mean, 7 years) after the operation, and audiometric data from admission and from the latest postoperative follow-up were retained. Canal wall-down mastoidectomies were followed up an average of 10 times during the first 6 months after operation, twice a year over the 6-year period following surgery, and less than twice a year beyond the 6-year period. Care was dispensed for meatal stenosis, scars, infections, polyps, and beads of cholesteatoma. Surgical revisions were performed because of residual or recurrent cholesteatoma in 6.1% of the cases, because of perforation of the tympanic membrane in 7.3% of the cases, and to improve hearing in 12.2% of the cases. At the last consultation, 1 to 24 years after surgery, cavities were found to be dry and self-cleaning in 95% of the cases, and still humid, with otorrhea, in 5% of the cases. Over the long-term, the hearing threshold remained unchanged in 41.3% of the cases. It was improved after surgery by 10 to 19 dB in 15.4% of the cases, by 20 to 29 dB in 11.5% of the cases, and by more than 29 dB in 3.8% of the cases. The hearing threshold was thus improved or at least remained unchanged in 72.0% of cases. Hearing losses occurred in 28% of the cases: by 10 to 19 dB in 11.9%, by 20 to 29 dB in 6.5%, and by more than 29 dB in 9.2% of the cases. A sensorineural hearing loss of more than 60 dB at all frequencies occurred immediately after the operation in 2 cases (0.7%). There was 1 case of facial paralysis (0.3%). Four patients (1.5%) complained of persistent vertigo. Canal wall-down mastoidectomy is an adequate treatment for chronic otitis with cholesteatoma or chronic otomastoiditis. The anatomic and functional results are satisfactory, and the rate of complications is acceptably low. A tympanoplasty can be performed simultaneously. Thus, for the large majority of patients, only a single intervention is required; however, a small minority can benefit from a revision tympanoplasty. In order to obtain these results, both the patient and the surgeon should engage in a long-term follow-up.

Adolescent↗
PubMed1982

Trends in Tennessee Medicaid acute care: use and expenditures, 1974-1978.

Because person-level data are not currently available at the Federal level, many questions regarding the use and expenditures of Medicaid services remain unanswered. This article demonstrates the capability of State Medicaid Management Information Systems (MMIS) to provide data that can address a variety of Medicaid program issues at both the State and Federal levels. Using data from the Tennessee Medicaid files, we analyze MMIS data to demonstrate the utility of person level statistics and to indicate methodologies useful for future analytic efforts, particularly in constructing utilization rates for policy and program management activities. While total Tennessee Medicaid enrollment is declining, the number of disabled enrollees and the proportion of aged enrollees are increasing. Tennessee Medicaid average covered lengths of stay exhibit a downward trend, but covered days of care rates are increasing due to higher admission rates. Medicaid payments per enrollee increased drastically, primarily due to increases in average payments per day and, to a lesser extent, increased utilization. Medicaid utilization and expenditures are highly skewed toward aged and disabled enrollees and toward those with less than six consecutive quarters of enrollment. Similarly, whites exhibit a disproportionate use of inpatient services. Analyses of diagnostic case-mix indicate stable patterns of both AFDC and disabled enrollees over time. Differences in case-mix and length of stay between the two eligibility groups are consistent with the respective characteristics of these populations.

Adolescent↗
PubMed1986

A method for reconstructing patterns of somatosensory cerebral cortical activity.

An interactive graphics package was developed in order to acquire, display, and manipulate images of cerebral cortical autoradiographic data. The primary purpose for development of the system was to reconstruct accurate 2-dimensional maps of the functional activity within the somatosensory cerebral cortex. A Datacube Q-bus graphics module (QVG/QAF-123) was interfaced with the Micro PDP-11/23 to accept a standard RS170 video input signal, and autoradiographs of serial sections (each 20 microns thick) of a cerebral cortex were digitized individually to 768 X 512 X 8 bit resolution. Input look-up tables were used to standardize the autoradiographic data. Boundaries of the somatosensory cortex were entered (with a Summagraphics MM 1201 digitizer), and the image data was stored on disk file (a method of data compression was devised). A method for segmenting the image data for many (sequential) sections was developed that provided arrays from which the maps were generated. Thresholding, histogram equalization, edge detection and edge enhancement, and filters in both the spatial and frequency domains were employed to process the images of the maps. Plots of optical density values along any axis of the maps and gray level histograms of any map region could also be generated. Maps made by the described method are much higher in resolution than those produced by traditional (manual) methods, and permit analysis of the reconstructions in both the frequency and spatial domains.

Animals↗