SEARCH · PubMed Health

Results for “Software”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources

PubMed2006

Comparison of fMRI coregistration results between human experts and software solutions in patients and healthy subjects.

Functional magnetic resonance imaging (fMRI) performed by echo-planar imaging (EPI) is often highly distorted, and it is therefore necessary to coregister the functional to undistorted anatomical images, especially for clinical applications. This pilot study provides an evaluation of human and automatic coregistration results in the human motor cortex of normal and pathological brains. Ten healthy right-handed subjects and ten right-handed patients performed simple right hand movements during fMRI. A reference point chosen at a characteristic anatomical location within the fMRI sensorimotor activations was transferred to the high resolution anatomical MRI images by three human fMRI experts and by three automatic coregistration programs. The 3D distance between the median localizations of experts and programs was calculated and compared between patients and healthy subjects. Results show that fMRI localization on anatomical images was better with the experts than software in 70% of the cases and that software performance was worse for patients than healthy subjects (unpaired t-test: P = 0.040). With 45.6 mm the maximum disagreement between experts and software was quite large. The inter-rater consistency was better for the fMRI experts compared to the coregistration programs (ANOVA: P = 0.003). We conclude that results of automatic coregistration should be evaluated carefully, especially in case of clinical application.

Adolescent↗

PubMed2006

Computer-assisted learning in medicine. How to create a novel software for immunology.

Teaching medical issues is increasingly demanding due to the permanent progress in medical sciences. Simultaneously, software applications are rapidly advancing with regard to their availability and easy use. Here a novel teaching program is presented for immunology, which is one of the fastest expanding topics in medical sciences. The requirements of media didactics were transferred to this e-learning tool for German students. After implementation, medical students evaluated the software and the different learning approaches showed acceptance. Altogether this novel software compares favourably to other English e-learning tools available in the Internet.

Allergy and Immunology↗

PubMed2005

Validation of new clinical quantitative analysis software applicable in spine orthopaedic studies.

The objective of this study was to evaluate an X-ray films analysis software, i.e. to estimate the reliability and validity of clinical measurements by means of this software. The authors first performed tests of precision and reproducibility of measures. The precision for dynamic modules was estimated at +/-2 degrees for the lumbar analysis and +/-3 degrees for the cervical one. Mean reproducibility coefficients calculated for postural modules are about 4 degrees for the angular parameters and 3 mm for the linear ones. We also evaluated clinical applicability of the software through its validity. Reference values calculated on a population of healthy subjects showed agreement with the literature. Then, when analysing postural X-ray films of severe scoliotic patients, we found that inter-observer reproducibility coefficients show a lower reliability of measurements; the main cause seems to be the low visibility of anatomic landmarks due to the quality of X-ray films and to the degree of deformity. This study allowed to better estimate the reliability and the usefulness of this tool, allowing for multicentric studies and exchanges.

Cervical Vertebrae↗

PubMed2005

Comparative evaluation of two two-dimensional gel electrophoresis image analysis software applications using synovial fluids from patients with joint disease.

The proteomic composition of synovial fluid (SF) may hold clues to understanding the molecular basis of arthritis. However, the highly viscous nature and proteomic complexity of SF present a challenge when analyzing results obtained by two-dimensional gel electrophoresis (2D-GE). Several software applications are available for analyzing 2D-GE images. Despite inherent strengths and weaknesses, no comparison between these applications has been reported using SF or any human fluid specimens. We evaluated two common software packages--PDQuest and Progenesis Workstation--for spot detection, matching, and quantitation of 2D-GE images of SF from four patients with arthritic disease. Initially, whole 2D-gel images were analyzed for spot detection, which suggested that PDQuest is more consistent than Progenesis; however, PDQuest appeared to require more user intervention than Progenesis. Subsequently, two small areas (spots well resolved and spots not well resolved) were selected from each gel image, which were analyzed by the software for spot detection, matching, volume, and resolution. These analyses suggest that both tools can quantify well-resolved spots relatively consistently when compared with manual spot detection (the "gold standard"). The "3D viewer" option offered by both tools enables correct spot identification and matching. The strengths and weaknesses of these computer tools can provide guidance in the choice of a particular workstation for identifying biomarkers of arthritis.

Adult↗

PubMed2005

Evaluation of new software for angiographic determination of right ventricular volumes.

OBJECTIVES: The scope of the study was to evaluate a recent software for angiographic volume determination as compared to cardiovascular magnetic resonance imaging. BACKGROUND: A new right ventricular analysis software closes a diagnostic gap in quantitative angiography. Cardiovascular magnetic resonance imaging short axis multi slice summation is a validated reference standard. METHODS: Right ventricular angiograms were acquired in frontal and lateral projection in 15 pediatric and 17 adult patients. Additional angiograms were acquired in RAO30 degrees /LAO60 degrees projections in 10 adult patients. The tested models comprised area length with different regressions, multi-slice with different regressions, Boak, and pyramid method. Original regressions were used to calculate angiographic right ventricular volume. Right ventricular reference volumes were determined by multi-slice summation from cardiac magnetic resonance short-axis images. RESULTS: Mean inter-observer difference was -1 ml (95% confidence: -35-34 ml) and mean intra-observer difference was 0 ml (95% confidence: -22-22 ml). There was no significant difference (4 ml, 95% confidence: -22-30 ml) between geometric calibration and calibration by a sphere. The area length and multi-slice models demonstrated the best agreement with the cardiac magnetic resonance reference. Performance was best for the Onnasch Lange models. CONCLUSION: The evaluated software provides acceptably accurate volume estimates for the majority of ventricles. In a few cases larger errors may occur, however. The area length and multi-slice models preferably with Onnasch Lange regressions may be recommended. Inter- and intra-observer agreement were excellent. Geometric calibration using data from DICOM header files may be used.

Adolescent↗

PubMed1995

Molecular fragments associated with non-genotoxic carcinogens, as detected using a software program based on graph theory: their usefulness to predict carcinogenicity.

We assembled 390 chemicals with a structure non-alerting to DNA-reactivity (145 carcinogens and 245 non-carcinogens) for which rodent carcinogenicity data were available. These non-alerting chemicals were defined by the absence in their molecules of DNA-reactive (directly or after metabolic activation) alerting structures, as described by Ashby and coworkers (Mutat. Res., 204 (1988) 17-115; Mutat. Res., 223 (1989) 73-103; Mutat. Res., 257 (1991) 209-227; Mutat. Res., 286 (1993) 3-74). Using our software program based on graph theory we analyzed the compounds in order to estimate the program's ability to predict nonalerting carcinogens. Our software fragmented the structural formula of the chemicals into all possible fragments of contiguous atoms with size between 2 and 8 (non-hydrogen) atoms and learned about statistically significant fragments from a training set of chemicals. These fragments were used to predict carcinogenicity or lack thereof in a verification set of compounds. For 390 runs of the software program we used (n - 1) of the chemicals as a training set, to predict the excluded chemical at each run (as a test set). Using two different probability thresholds to select significant fragments (P = 0.05 and P = 0.125 1-tailed according to binomial distribution), we performed two analyses: in the better one (P = 0.05) 19% of the molecules tested lacked significant fragments, for the remaining 81% the observed level of accuracy of the prediction was 66.0% against an expected level of accuracy of 51.7%. The difference was highly significant (P < 0.0001). We also examined the more significant activating fragments (biophores) and discussed at length both their biological plausibility and the working hypothesis that additional alerting structures for carcinogenicity (not only those related to genotoxicity) can be detected using this type of SAR approach. This new class of alerting structures could identify subfamilies of congeneric analogs active through mechanisms of receptor mediated carcinogenesis.

Carcinogens↗

PubMed1993

Using an integrated software package for clinical data analysis on a microcomputer.

An integrated software package was used effectively for entering, organizing and analyzing clinical research data on a microcomputer. Both the database and the spreadsheet components of the package were used in the process. The database component enabled a form to be created for entering the data. The spreadsheet component was used in the organization and analysis of data. Macros were written within the spreadsheet environment for the statistical analysis of data. The purpose of this paper is to illustrate how an integrated software like Symphony could offer features beyond simply the use of a spreadsheet for the analysis of research data. Also highlighted are the other useful features of the integrated software that are not directly related to data analysis.

Adolescent↗

PubMed1995

A graphics-based software system to develop and analyze models of musculoskeletal structures.

We have created a graphics-based software system that enables users to develop and analyze musculoskeletal models without programming. To define a model using this system one specifies the surfaces of the bones, the kinematics of the joints and the lines of action and force-generating parameters of the muscles. Once a model is defined, the function of each muscle can be analyzed by computing its length, moment arms, force and joint moments. The software has been implemented on a computer graphics workstation so that users can view the model from any perspective and graphically manipulate the joint kinematics and musculoskeletal geometry. Models can also be animated to visualize the results of motion analysis experiments. Since the software can be used to study models of many different musculoskeletal structures, it can enhance the productivity of investigators working on diverse problems in biomechanics.

Algorithms↗

PubMed1985

Software that detects and analyzes bioelectrical events by assessing the fit of modeled subintervals.

A software system is described which has been used to identify, average, and otherwise analyse different kinds of electrophysiological events. Spontaneous miniature end-plate potentials were identified by assessing the fit of subintervals within suspected event-containing intervals to flexibly defined model subevents. It was thus practical to apply complex, explicit, and stable criteria in the estimation of the frequency and mean time course of these spontaneous events. This software also mediated the objective rejection of noise-contaminated elements from samples of either evoked or spontaneous potentials. Average event time courses were comprised of a series of estimates of the standard deviations as well as the means. Each analysis generated thousands of individual event amplitudes which were used to improve estimates of quantal release and response parameters. This software allowed more complete analysis of tape-recorded experiments which conserved test compounds and animals, and enabled the observation of simultaneous and equal degrees of action upon spontaneous and evoked potentials, which suggested that a common mechanism was involved.

Animals↗

PubMed1996

Maxsim, software for the analysis of multiple axonal arbors and their simulated activation.

In order to analyze the structural organization of complex axonal arbors reconstructed from histological serial sections, and to investigate the functional implications of their geometrical properties, we developed software providing the following facilities: (1) direct importation of data files generated by a commercially available 3-D light-microscopic reconstruction system, including routine procedures for identification and correction of data acquisition errors; (2) real-time 3-D rotations of the arbors in the stack of serial sections; (3) multiple interactive display modes; (4) possibility of modifying diameter and/or connectivity of different branches; (5) simulation of the invasion of the arbor by a single action potential initiated at any chosen point, and visualization of spatio-temporal profiles of activation; (6) extraction of quantitative data converted to standard file formats compatible with available mathematical software. All these tools can be applied to single or multiple axons, individually or simultaneously. The software, called Maxsim, is a highly flexible C-written program running on graphical workstations using the UNIX operating system and X-Window environment.

Animals↗

PubMed1994

Software for the analysis of mutations at the human hprt gene.

Mutations at the human hypoxanthine-guanine phosphoribosyl transferase gene (hprt) are currently of great interest because mutations at this locus are being used as a biomonitor of human mutagenic exposure. Not only can somatic hprt mutants arising in vivo in humans be recovered and sequenced, but there is also a considerable body of information about the in vitro mutational spectra of different carcinogens at this locus. Previously, we reported the creation of a computerized database containing DNA-sequence information on human hprt mutants (Cariello et al. (1992) Environ. Mol. Mutagen., 20, 81-83). In the present manuscript, software for the analysis of mutations in the hprt database is described. Numerous routines have been developed for the analysis of single-base substitutions, including programs to (i) determine if two mutational spectra are different, (ii) display the number of mutations and mutable sites in each exon, (iii) determine if mutations show a DNA-strand bias, (iv) determine the frequency of transitions and transversions, (v) display the number and kind of mutations observed at each base in the coding region, (vi) perform nearest-neighbor analysis and (vii) display mutable amino acids in the hprt protein. The software runs only on IBM-compatible machines with MS-DOS. The software and hprt database is freely available via the INTERNET using remote file-transfer protocol. These programs simplify the analysis of the rapidly increasing information about hprt mutation. The programs permit the facile comparison between in vitro and in vivo data, as well as the identification of mutational patterns that may be of importance to experimenters using hprt as a biomonitor and and of importance to researchers studying mechanisms of mutation.

Amino Acids↗

PubMed1992

Enhancing bioprocess operability with generic software sensors.

This paper discusses the concept of generic model-based software sensors with particular reference to bioprocess application. The industrial need for software sensing is considered and two industrial bioprocess systems are used in order to highlight the operability problems which warrant their development. Alternative philosophies for formulation are considered and the relative merits of the methodologies discussed. In particular, two different procedures are presented--an adaptive linear model based method, and a method based upon artificial neural networks. The performances of these alternative approaches are studied by their application to two industrial demonstrator processes. The results serve to highlight the operability improvements that can be gained through software sensor development.

Biosensing Techniques↗

PubMedDate not supplied

AIDA's fourth-generation software functionality.

Aspects characterizing typical, office-like environments are described and common procedures are extracted. These are used to derive the requirements of fourth-generation software packages. Typical fourth-generation software packages are discussed, and a presentation is given of a fourth-generation software package called AIDA, including all its functional aspects.

Database Management Systems↗

PubMed1992

APIS: a software for model identification, simulation and dosage regimen calculations in clinical and experimental pharmacokinetics.

APIS is a software package based on mathematical modelling which provides a reliable approach in optimizing drug therapy. It was designed to assist clinicians in interpreting blood drug levels so that drug therapy may be better and more cost-effective. It is a methodological approach to describe, predict and control the kinetic behaviour of a drug. This software incorporates the principle of Bayesian procedures, i.e. one can use all available patient information (population) to determine patient-specific parameter estimates. These estimates can then be used to design an optimal and individualized drug regimen. APIS is an attractive and useful tool for clinical and experimental pharmacokinetics. APIS may be used on any IBM compatible computer using the Microsoft-Windows environment. The software is menu driven to provide a very user-friendly tool for analysing pharmacokinetic data and for designing dosage regimens.

Amikacin↗

PubMed1993

MoG: molecular graphics software for the Commodore Amiga.

As recently described by Garavelli, the Commodore Amiga 3000 computer is "nearly ideal" for desktop molecular modeling. The chief drawback to date, has been the lack of suitable software. This paper describes a new desktop molecular modeling package, MoG, which is suitable for both research and educational use. The speed of the Amiga 3000 means that MoG competes very favorably with software on IBM-PC machines, and its graphics capabilities allow excellent space-filling representations. The availability of cheap software-compatible home-computer versions of the Amiga places interactive molecular graphics within the reach of many senior high-school students, undergraduates and graduate students.

Antibodies↗

PubMed1992

Biostatistical manual (BIOSTAT) for potency control and for evaluation of effectiveness of the WHO-EPI vaccines: software for personal computers.

In accordance with WHO requirements, a specialized software has been developed for personal computers to analyse the potency data of the EPI vaccines and to evaluate the effectiveness of the vaccination. The software has three parts and allows users to create files from control data (BIOSTAT), to check the function of the software and statistical formulae (BIOSDEMO), and to understand the logic and structure of the data processing system and the statistical models (BIOSDOC).

Evaluation Studies as Topic↗

PubMed1996

A methodology for solving physiologically based pharmacokinetic models without the use of simulation softwares.

The objective of the present study was to develop and validate a methodology for solving physiologically based pharmacokinetic (PBPK) models without the use of simulation software. The approach involves keying the parameter values and model equations into Microsoft Excel spreadsheets, and conducting simulations by solving the model equations according to Euler's method of numerical integration. This approach was applied to simulate the pharmacokinetics of styrene in rats exposed to 80 and 600 ppm for 6 h. The simulation results were plotted along with experimental data using the regular graphic features available in Excel, and validated by comparing them with simulation results obtained using a commercially available software (Advanced Continuous Simulation Language, ACSL). The simulations obtained with ACSL and Excel, in general, differed by <1%. The methodology developed in the present study should help informed individuals understand and solve PBPK models, without having to use "black-box' kind of computer programs and simulation softwares.

Algorithms↗

PubMed1990

A fully automated chromatographic peak detection and treatment software for multi-user multi-task computers.

A fully automated method is presented for the detection and integration of chromatographic peak software in which the only parameter to define is the data acquisition frequency; this has to be chosen high enough to minimize some Nyquist frequency problems. Programmed in C language, the software is used on a Unix like system (Xenix) to emphasize its automaticity. The performance of the system in liquid chromatography has been studied in respect of noise frequency and intensity. It is shown that the classical signal-to-noise ratio is obsolete for definition of the detection limit since frequency analysis allows some signal filtration; these limitations are described. An example is given of simulation with Gaussian peaks convoluted with noise characterized by its intensity and frequency distribution. The validity of the software is demonstrated for some HPLC separations.

Autoanalysis↗