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PubMed1991

CANEST: a microcomputer program for estimating cancer in a cohort.

Certain diseases and symptoms carry an overrepresentation of cancer. To be able to measure the strength of such an association it is necessary to be able to predict cancer development in the group being observed. A computer program for computers running under the MS DOS operating system has been developed for this purpose. The program is written in the CLIPPER programming language. The estimates are based on incidence and prevalence data from the Swedish Cancer Registry for the years 1958 to 1986. The program also computes confidence intervals based on the Poisson distribution. The results can be printed out or exported to other programs for further analysis.

Cohort Studies↗

PubMed1989

A microcomputer data base system for maternal serum alpha fetoprotein screening programmed in BASIC.

A computer program was developed for the IBM PC computer to be used for maternal serum alpha fetoprotein screening (MSAFP). This program, written in BASIC, 1) maintains a data base for patients tested, 2) allows input and storage of MSAFP results, 3) calculates the gestational age dependent result in multiple of the median (MOM), 4) makes an individualized interpretation of the result based on maternal age, weight and diabetes, 5) makes an appropriate recommendation for subsequent action based on the result, and 6) prints a report containing the above information. In addition, the program will print a daily log of patients tested, provides a follow-up sheet to assist in tracking abnormal results to term, converts the data files into files which can be easily intergrated into more powerful data base programs, and generates a monthly statement for billing purposes. The program can be easily modified by someone with minimal training in the BASIC programming language.

Female↗

PubMed1992

On the assessment of bioequivalence in a two-period cross-over design.

The results obtained with Meineke and De Mey's algorithm for posterior probability distributions in the nonparametric evaluation of two-period cross-over bioequivalence studies are critically discussed. Suggestions for improvement of their program NEWPARM are given. It is shown that this program in its present form cannot handle the results from bioequivalence studies in which more than 15 subjects participated. For larger study sizes, conversion to a more powerful programming language capable of handling large three-dimensional arrays, is mandatory. An alternative algorithm, allowing large sample sizes to be analysed nonparametrically without program conversion, is offered. A general bioequivalence program written by the author, into which this alternative algorithm is implemented, has been in use by a number of pharmaceutical companies and drug regulatory agencies since February 1990; its most recent update is Version 3.7 (BIOEQV37.EXE) of October 1990.

Algorithms↗

PubMed1991

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

Algorithms↗

PubMed1988

Low back pain: development and five-year prospective application of a computerized quality-based diagnostic and treatment protocol.

A standardized protocol for low back pain was developed and computerized so that it could be used as a concurrent monitoring system for large patient populations. The software incorporated a relational database management system (RDBMS) and C language, a flexible, general-purpose programming language that is fast and portable. The protocol was then applied to a uniform group of industrial patients for 5 years. The results demonstrated that a quality-based protocol could be successfully computerized and applied to a large group of patients as a concurrent monitoring system. Quality care was insured by adherence to the computerized protocol. Associated economic results showed decreases in actual number of accidents each year (from 98/year prior to the study to 42/year in the last study year), in lost work days (from 3640/year before the study to 2118/year in the last year), and in costs (savings averaged $430,000/year). The goal of this study was to provide quality medicine; the economic benefits were a bonus. The monitoring system differed from those of the past in that it was driven by the basic medical information taken from the history, physical examination, and radiograph findings. The monitoring physicians were unbiased because they were not allowed to become involved in the patient's ongoing care. There was no rebound phenomenon (an initial drop in cases followed by a gradual return to the prestudy level); this was attributed to the constant monitoring of each case from beginning to end. These results led to the following conclusions: (a) Computerization of a standardized medical approach for low back pain is practical.(ABSTRACT TRUNCATED AT 250 WORDS)

Back Pain↗

PubMed1991

A computational study of convoluted back projection algorithm.

Image reconstruction by computerized tomography is a complex mathematical process. This paper describes the practical implementation of a tomographic reconstruction algorithm on different types of computers (micro to mainframe) and in different programming languages (BASIC to OCCAM) and performance studies were made.

Algorithms↗

PubMed1990

Calculating haemodynamic parameters and interpreting arterial blood gas samples using a pocket computer.

The pocket computer, being both cheaper and more powerful, has brought computing within the realm of many intensive care nurses. The problem, however, is one of a lack of dedicated software that is able to perform clinical tasks or calculations; thus making the nurse's work easier. The aim of this article, therefore, is to present two programs for a popular pocket computer that will not only introduce the nurse to simple BASIC programming language, but will also provide useful bedside information.

Blood Gas Analysis↗

PubMed1985

Nonlinear regression on a microcomputer: which program?

Eleven published programs for performing nonlinear regression using a microcomputer have been reviewed. They have been assessed according to many criteria, especially: application, program language, algorithm used, method for calculating partial differentials, facility for weighting, desirable input and output features, robustness during execution, memory requirements, accessability, ease of implementation and evaluation and testing. No one program contains all the desirable characteristics discussed, but guidance is given as to which might be the most suitable for a particular purpose or for a given microcomputer system.

Algorithms↗

PubMed1985

Signal averaging by microcomputer using a program written in a high-level language.

A program, written in the language Pascal, is described for signal averaging with a microcomputer. The program instructs the computer to acquire data from two channels on-line. For up to 3 channels of extracellular or intracellular recording analysed simultaneously, it was found not to be necessary to employ machine code or an assembler to provide adequate temporal resolution.

Action Potentials↗

PubMed1990

A computer program to aid in the preparation of reagent solutions.

A computer program for calculating required amounts of reagents for making up chemical solutions is presented. The program also maintains a custom list of available reagents. Use of the interactive mode guides the novice in entering the required information. The program is written in the BASIC programming language for IBM compatible microcomputers. It is available without cost from the author.

Indicators and Reagents↗

PubMed1989

Precise water vapor pressure value calculations.

Precise values for water vapor pressure in saturated systems may be computed using the Goff-Gratch equation. This equation has been adapted for convenient use on microcomputers. A Microsoft BASIC listing of the programming version of the equation is presented. This BASIC version may be easily translated into other high level programming languages and thus is suitable for use on many computer systems for routine laboratory computations.

Manometry↗

PubMed1989

(PLOT79): a comprehensive portable Fortran scientific line graphics system, as applied to biomedical research.

Scientific results are often most succinctly presented in graphical form. We describe a system for computer-generated scientific line graphics known as (PLOT79), named to commemorate the SIGGRAPH CORE graphics standard proposal of 1979. (PLOT79) is a widely used and actively evolving graphics system, written primarily in SFTRAN3, a structured procedural computer language which can be translated readily into Fortran. The package embodies concepts of sound software engineering, having been designed from the outset to be portable, maintainable and hardware-independent; much of the effort required to implement the system was directed toward the development of software engineering tools to ensure these goals. A modular design strategy has allowed a wide variety of graphics output devices to be supported. (PLOT79) has been installed under numerous operating systems, and software tools provided by UNIX have allowed particularly efficient installation and use of the system. Access to (PLOT79) is available through three avenues: (1) linking (PLOT79) routines with a user-written high-level program; (2) use of pre-written high-level applications programs which perform certain frequently-required tasks such as the plotting of simple two or three-dimensional data; or (3) the use of an interactive graphics command parser known as slides. (PLOT79) has proven popular among workers in the physical sciences and engineering both for its easy availability, openness (all source code is provided), and powerful capability. The system presents an equally important (though lesser known) resource for biomedical research, as demonstrated by examples from ongoing biomedical research projects. It also provides a focus for discussion of the practical limitations inherent in existing graphics standards and programming languages.

Computer Graphics↗

PubMed1990

The technical aspects of computers.

This chapter is concerned with the technical aspects of computers. It is therefore concerned with how computers came about in the way they did, and who were the people who pioneered their development--what they were like in the early years, what they are like now, and what are likely to be the future developments. The emphasis is always on giving information to the readers so that they may know what questions to ask of the experts and, equally important, which experts to spend time with. In consequence of this last statement it becomes necessary to present a panorama showing the range of computers both size-wise and cost-wise; such scenario will therefore cover the vista from large main-frames (which must inevitably be needed in District Health Authorities and District General Hospitals) to the desk-top personal computers which all clinicians of the future will find essential. Because readers will be experiencing the impact and, hopefully, the benefits of the computer at the lower end of the size and price scale, considerable space has been devoted to explaining the various items (disc drives, monitors, printers) that pervade the microcomputer scene. New terminology must be introduced to readers if they are to discuss intelligently their computer needs to the providers of such facilities. Just as an automobile is no use without oil, petrol, water and a competent user, so the computer hardware needs computer software and a competent user. The chapter therefore continued with some considerable space being devoted to software (operating systems, programming languages, utilities and expert systems) so that the user will have clear guidance as to which path to follow in order to become a competent user of the present and future technology. Because of the rapid advances in data storage, in networking and in computer programs, the clinicians of tomorrow will have vast sources of information at their disposal. This latter will include not only patient records, but also drug data-sheets, textbooks, journals and research reports. Finally, lack of space has prevented some topics receiving more than a cursory mention. This is known but, like real life, one has to make judgements as to the relative importance of the topics and include those which come out top. It is hoped that the readers will not be too disappointed: if they absorb all that is here they will be very knowledgeable indeed.

Computer Peripherals↗

PubMed1992

Simple SAS macros for the calculation of exact binomial and Poisson confidence limits.

Statistical analysis using confidence intervals is now a preferred approach in the medical literature, and confidence limits for binomial proportions and Poisson counts are commonly required. Normal approximations of varying accuracy are often used in such situations and it is not generally realised that non-iterative exact solutions are available. This paper shows that the exact binomial and Poisson confidence limits can be expressed very simply in terms of the inverse beta and inverse gamma distributions, and describes two macros in the SAS programming language to perform the computations. The exact solutions are compared with some approximations and further applications of the techniques are described.

Binomial Distribution↗

PubMed1992

Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison.

A platform program that performs biological sequence comparison provides a case study to compare the relative advantages of a machine-independent approach to parallel computation versus a machine-specific approach. The program consists of two routines: (i) PSCANLIB, which compares a single biological sequence against a database of sequences, and (ii) PCOMPLIB, which compares a database of sequences against another database of sequences, or against itself. The program was first parallelized to run on the Intel Hypercube parallel computer using native Hypercube commands to coordinate the parallel computation. The parallelization logic of the program was then translated into a machine-independent parallel programming language, Linda. These two approaches to parallelization are contrasted in terms of: (i) the expressive power of the logic that coordinates the parallel computation, (ii) the portability of the machine-independent version to other parallel machines and (iii) the relative efficiency of the two versions of the program. In the benchmark tests reported, the benefits of the machine-independent approach were achieved with only a modest sacrifice in efficiency.

Algorithms↗

PubMed1992

A PC program for performing multigroup longitudinal comparisons using the Potthoff-Roy analysis and orthogonal polynomials.

A PC-program performing the Potthoff-Roy (PR) multigroup (G-sample) analysis of longtidinal data is described and illustrated. This program and the underlying statistical model are useful in the comparison of several longitudinal samples. Applications include the study of growth, development, adaptation, aging, and treatment effects (in short, any phenomenon in which the passage of time is important) for which serial data are available. Specifically, this method fits polynomials to the average growth curves in the samples, and tests hypotheses concerning the curves themselves and the individual coefficients of the polynomials. The program features the utilization of orthogonal polynomial regression coefficients (OPRCs) and is written in GAUSS, a relatively inexpensive yet comprehensive matrix programming language. It is documented that using OPRCs to comprise the within-individual or time design matrix has several advantages over the more usual choice of the successive-powers-of-t form of this matrix and an example of one important such advantage is provided. GAUSS was employed to make the program readily-accessible (i.e., executable code) to biomedical investigators. The GAUSS compiler is not required to run this program. Information regarding the availability of the program is provided in the Appendix.

Child↗

PubMed1986

Distribution of ventilation and perfusion: a teaching model.

Models can be used as teaching tools to study complex phenomena. This model uses simplifications of blood gas subroutines to provide fast execution of the effect of the distribution of ventilation and blood flow in the lung on arterial blood gases. Assumptions are made that introduce only small errors but that avoid the use of iterations which would slow down execution. The use of Turbo-Pascal as the programming language allows for not only speed in development and execution but also portability to a variety of computers including CP/M systems and IBM-PCs.

Carbon Dioxide↗

PubMed1992

Dynamic arrays for fast, efficient, data manipulation during image analysis: a new software tool for exploratory data analysis.

Memory reallocation is used to construct a run-time data structure for fast/efficient storage of information during collection and analysis. The data structure presented uses dynamic memory but does not require the use of pointers to link nodes of information together. It allows for simple and efficient access to data via array indexing rather than through the use of lists or tree structures and it provides flexibility for competing storage requirements that are determined dynamically. The data structure is developed in the C programming language and a suite of ANSI standard C subroutines that make up a run-time data structure management system is provided.

Abstracting and Indexing↗