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At least 1,369 records · Page 76Linked to original sources
PubMed1992

A new computer program for detailed off-line analysis of swimming navigation in the Morris water maze.

The program TRACK-ANALYZER runs on AT-compatible microcomputers and performs off-line analysis of data recorded from Morris water-maze experiments by means of a video tracking system or digitizing tablet. Raw data must be available on disk as ASCII-files listing position coordinates sampled at a constant frequency. Automatic recognition and correction of artifacts and missing data is a key feature of the program, as well as the option to combine commands to user-defined macros. TRACK-ANALYZER offers maximal flexibility regarding experimental schedule, maze geometry and recording parameters and may also be used to analyze open-field activity. In addition to calculating basic parameters of the swim path, such as path length and time, the program counts crossings and hits of goal platform and four virtual reference annuli, calculates search times in five different maze fields, determines directionality, tortuosity and turning preferences of swimming behavior and allows the viewing of any number of trials simultaneously on screen. ASCII-formated data output may easily be exported to commercial statistics and graphics software.

Animals↗
PubMedDate not supplied

RECPAM: a computer program for recursive partition and amalgamation for censored survival data and other situations frequently occurring in biostatistics. I. Methods and program features.

The methodology of recursive partition and amalgamation in biostatistics is presented and a FORTRAN program for its implementation, RECPAM, is described. RECPAM can be used to obtain classifications of patients according to several criteria commonly occurring in clinical biostatistics: an example is prognostic classification based on survival data. Classes are defined by simple statements, expressed in clinical terms, about predictor variables (e.g. prognostic factors). Special features of RECPAM are: the possibility of implementing a variety of classification criteria, the integration of recursive partition and amalgamation, and the availability of several strategies for constructing classification trees. A simple example to illustrate input and output features is given. The scope and flexibility of RECPAM will be illustrated in greater detail in a subsequent paper.

Algorithms↗
PubMed1992

NHPPREG: a computer program for the analysis of nonhomogeneous Poisson process data with covariates.

A program written in C is described which finds maximum likelihood estimates of regression coefficients and other relevant parameters for a point process with covariates. The data are assumed to come from a Poisson point process and may be modelled, at the user's choice, either totally parametrically or semi-parametrically. Furthermore, extra Poisson variation may be introduced, in both the parametric and semi-parametric approach, by the device of random effects. The work closely follows the theory developed by Lawless (1987).

Humans↗
PubMed1996

MIXOR: a computer program for mixed-effects ordinal regression analysis.

MIXOR provides maximum marginal likelihood estimates for mixed-effects ordinal probit, logistic, and complementary log-log regression models. These models can be used for analysis of dichotomous and ordinal outcomes from either a clustered or longitudinal design. For clustered data, the mixed-effects model assumes that data within clusters are dependent. The degree of dependency is jointly estimated with the usual model parameters, thus adjusting for dependence resulting from clustering of the data. Similarly, for longitudinal data, the mixed-effects approach can allow for individual-varying intercepts and slopes across time, and can estimate the degree to which these time-related effects vary in the population of individuals. MIXOR uses marginal maximum likelihood estimation, utilizing a Fisher-scoring solution. For the scoring solution, the Cholesky factor of the random-effects variance-covariance matrix is estimated, along with the effects of model covariates. Examples illustrating usage and features of MIXOR are provided.

Antipsychotic Agents↗
PubMed1996

MIXREG: a computer program for mixed-effects regression analysis with autocorrelated errors.

MIXREG is a program that provides estimates for a mixed-effects regression model (MRM) for normally-distributed response data including autocorrelated errors. This model can be used for analysis of unbalanced longitudinal data, where individuals may be measured at a different number of timepoints, or even at different timepoints. Autocorrelated errors of a general form or following an AR(1), MA(1), or ARMA(1,1) form are allowable. This model can also be used for analysis of clustered data, where the mixed-effects model assumes data within clusters are dependent. The degree of dependency is estimated jointly with estimates of the usual model parameters, thus adjusting for clustering. MIXREG uses maximum marginal likelihood estimation, utilizing both the EM algorithm and a Fisher-scoring solution. For the scoring solution, the covariance matrix of the random effects is expressed in its Gaussian decomposition, and the diagonal matrix reparameterized using the exponential transformation. Estimation of the individual random effects is accomplished using an empirical Bayes approach. Examples illustrating usage and features of MIXREG are provided.

Adolescent↗
PubMed1995

An interactive computer program for determining areas bounded by drug concentration curves using lagrange interpolation.

The LAGRAN method of Rocci and Jusko for determining the area of plasma concentration curves has been implemented in a user-friendly form. Drug concentration versus time data may be entered using the keyboard or imported in the form of simple text files from spreadsheets or other software. The MSDOS program allows prompt graphic observation of the data. The effect of selecting different fitting modes for each segment of the curve may be viewed interactively using this graphic display. Pharmacokinetic parameters that are provided by the program include mean residence time, variance of the residence time, plasma clearance, and steady-state volume of distribution.

Dose-Response Relationship, Drug↗
PubMed2005

frailtypack: a computer program for the analysis of correlated failure time data using penalized likelihood estimation.

Correlated survival outcomes occur quite frequently in the biomedical research. Available software is limited, particularly if we wish to obtain smoothed estimate of the baseline hazard function in the context of random effects model for correlated data. The main objective of this paper is to describe an R package called frailtypack that can be used for estimating the parameters in a shared gamma frailty model with possibly right-censored, left-truncated stratified survival data using penalized likelihood estimation. Time-dependent structure for the explanatory variables and/or extension of the Cox regression model to recurrent events are also allowed. This program can also be used simply to obtain directly a smooth estimate of the baseline hazard function. To illustrate the program we used two data sets, one with clustered survival times, the other one with recurrent events, i.e., the rehospitalizations of patients diagnosed with colorectal cancer. We show how to fit the model with recurrent events and time-dependent covariates using Andersen-Gill approach.

Cluster Analysis↗
PubMed2005

How many patients in atrial fibrillation admitted to an acute medical unit will benefit from oral anticoagulation? Application of the results of the major randomized controlled trials to 141 consecutive, unselected, elderly patients using a decision support computer program.

BACKGROUND: Although several randomized, control trials (RTC) suggest that oral anticoagulation (OAC) benefits patients with atrial fibrillation (AF), this might not be true for hospitalized patients with co-morbid conditions. If the results of the RTCs are valid, then how many patients in AF admitted to an acute medical unit will benefit from OAC? METHODS: An RCT-based decision analysis model calculated the quality-adjusted life expectancy (QALE) gain from OAC for 141 unselected consecutive patients over 65 years of age with AF admitted to an acute medical unit. RESULTS: If treated with aspirin, all 141 patients were predicted to gain QALE compared with placebo. If the quality of life adjustment (QoLA) on OAC was the same as placebo, then 104 patients were predicted to benefit from OAC compared with aspirin, while 63 patients were predicted to benefit at a QoLA of 0.99 (overall benefit 0.13+/-0.15 QALYs, range 0.01-0.88 QALYs). These 63 patients were more likely to have had a stroke, diabetes, hypertension, heart failure or heart attack, and less likely to have impaired renal function than those predicted not to benefit. The 78 patients predicted not to benefit from OAC included 11 younger patients without heart failure, hypertension, diabetes or cerebrovascular disease; the remaining 67 patients, however, were older, more likely to have heart failure and/or renal impairment and were at high risk of both stroke and bleeding. CONCLUSION: An RCT-based decision analysis model suggests that more than half the patients in AF admitted to a small rural hospital with acute medical conditions are unlikely to benefit from OAC, while all will benefit from aspirin.

Journal Article↗
PubMed2004

Development and evaluation of digital subtraction radiography computer program.

OBJECTIVE: We developed a new program for digital subtraction radiography (DSR) having useful functions to get the DSR image more accurately and efficiently. The purpose of this study was to evaluate the accuracy of the DSR image acquired using the new program as compared with the ready-made program. STUDY DESIGN: Four observers performed the DSR process using our program and the ready-made program for digital intraoral radiographs taken from incisor, premolar, and molar regions. The statistical difference was evaluated between the programs, between the observers, and between the regions. RESULTS: The DSR image using our program was superior to that with the ready-made program in all the observers and all the radiographed regions. Also, there was the statistical difference among the observers, especially in our program. CONCLUSION: The DSR image using the new program was very accurate compared with ready-made program, so the program was useful to get an accurate DSR image.

Humans↗
PubMed1992

Improved indication and followup in transurethral resection of the prostate using the computer program CLIM: a prospective study.

Analysis of preoperative and postoperative detrusor pressure-flow measurements with the aid of the IBM compatible software package CLIM in 29 patients who underwent transurethral prostatic resection indicated that CLIM supplies reliable obstruction parameters that are recommended for preoperative assessment and postoperative followup, and that approximately a third of the patients who present with prostatism are nonobstructed, suggesting that the indication for transurethral resection of the prostate is over assessed.

Adult↗
PubMed1997

Computer programs to analyze brain electrical activity during copulatory pelvic thrusting in male rats.

Two microcomputer programs have been developed to simultaneously record and analyze the brain electrical activity: multiple unit activity (MUA) and electroencephalogram (EEG), and the accelerometric signals generated in relation to the pelvic thrusting that performs the male rat during the copulatory responses of mount, intromission, and ejaculation. CAPTUMUL is a program allowing the on line capture of the different signals and the further off line delimitation of the brain signals occurring in exact temporal relation with the accelerometric record of motor responses. The ANAMUA program allows the off line analysis of the neuronal firing rate in MUA records at different discrimination levels according to the amplitude of the neuronal spikes, and compare these data in various behavioral situations. The use of these programs provides a way of correlating in time the changes of brain electrical activity occurring in animals in free-movement with the brief motor events of copulation as well as with other behaviors (i.e., genital grooming, sniffing, running, walking). Advantages of this software include the recording of sequential events, a better and rapid handling of data and a reliable method to analyze the MUA with different discrimination levels according to the amplitude of the neuronal spikes.

Animals↗
PubMed1998

The GPRIME package: computer programs for identifying the best regions of aligned genes to target in nucleic acid hybridisation-based diagnostic tests, and their use with plant viruses.

The GPRIME (Group PRIMEr design) programs examine aligned sets of gene sequences to discover homologous regions to be targeted in diagnostic tests. The core program moves a 'window' over the aligned sequences and calculates, at each window position, a 'redundancy value', namely the number of sequences that would represent all permutations of the variable sequence positions within that window. Regions with minimal redundancy values may then be targeted in diagnostic tests based on oligonucleotide hybridisation. The likely specificity of tests targeting such regions can be assessed by searching the international databases with those regions using FASTA. The GPRIME programs, which include programs for designing primers to distinguish between two sub-sets of a group of aligned sequences, can be obtained from http://life.anu.edu.au/software.html. We have used GPRIME to design redundant primers for RT-PCR tests to detect all potexviruses and tobamoviruses, and then used these, together with a previously reported pair of primers for the Potyviridae, to screen some Australian orchid collections. Two orchid viruses previously reported from Australia were found; cymbidium mosaic potexvirus was common, but odontoglossum ringspot tobamovirus was not. In addition the recently described ceratobium mosaic potyvirus was found to be common, and three other novel potyviruses were also found.

DNA Primers↗
PubMed1998

Application of a computer program for genetic typing of classical swine fever virus isolates from Germany.

The commercial software program HLA SequiTyper (Amersham Pharmacia Biotech), designed originally for human leukocyte antigen typing, was adapted for rapid typing of classical swine fever (CSF) virus isolates. The program compares new sequence data with those stored in a database file and calculates the most probable assignment. For generating the CSF virus sequence database, 150 bp of the 5' nontranslated genomic region (5'-NTR) from 88 German classical swine fever virus isolates from outbreaks between 1984 and 1997 were solid-phase sequenced directly after RT-PCR amplification. Sequence alignments showed that they all belonged to the previously defined genetic group 2. Within this group, six different subgroups could be distinguished, and were designated according to the geographic location where they are either still endemic or where they appeared most commonly. The advantage of using the HLA SequiTyper program is that it reads directly the sequence files as generated by the ALF sequencer (Amersham Pharmacia Biotech), making any manipulations unnecessary. In addition, a constant quality control of the raw sequence data can be achieved, as more than one sequence from the same isolate can be evaluated at once. Using this approach, new CSF isolates can be typed within 2 days.

Animals↗
PubMed2004

Computer programs to facilitate the estimation of time-dependent drug effects on ion channels.

The programs I-VOC and I-ROC have been designed to facilitate the analysis of drug effects on currents through ion channels in the cell membrane, measured by means of voltage-clamp. They are written in Igor Pro (WaveMetrics) and read exported files or raw data files generated by the Pulse (HEKA Electronic) or pClamp (Axon Instruments) programs. With I-VOC, the sweeps of current through voltage-operated ion channels can be quantified within six time ranges, and current run-down can be corrected for after the currents are fitted during the control period. Linear leak current can be subtracted even when the P/n method is not used. The results are plotted and tabulated. With I-ROC, an analogous program, receptor-operated currents can be quantified, the peak current or rate of desensitization can be fitted and run-down corrected for. Chart-like data can be converted to a sweep-like format. Several procedures are incorporated for rapid graphical data presentation. These programs accelerate and improve the estimation of drug effects on ion channels.

Animals↗