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At least 109 records · Page 6Linked to original sources
PubMed1997

Automated planning target volume generation: an evaluation pitting a computer-based tool against human experts.

PURPOSE: Software tools are seeing increased use in three-dimensional treatment planning. However, the development of these tools frequently omits careful evaluation before placing them in clinical use. This study demonstrates the application of a rigorous evaluation methodology using blinded peer review to an automated software tool that produces ICRU-50 planning target volumes (PTVs). METHODS AND MATERIALS: Seven physicians from three different institutions involved in three-dimensional treatment planning participated in the evaluation. Four physicians drew partial PTVs on nine test cases, consisting of four nasopharynx and five lung primaries. Using the same information provided to the human experts, the computer tool generated PTVs for comparison. The remaining three physicians, designated evaluators, individually reviewed the PTVs for acceptability. To exclude bias, the evaluators were blinded to the source (human or computer) of the PTVs they reviewed. Their scorings of the PTVs were statistically examined to determine if the computer tool performed as well as the human experts. RESULTS: The computer tool was as successful as the human experts in generating PTVs. Failures were primarily attributable to insufficient margins around the clinical target volume and to encroachment upon critical structures. In a qualitative analysis, the human and computer experts displayed similar types and distributions of errors. CONCLUSIONS: Rigorous evaluation of computer-based radiotherapy tools requires comparison to current practice and can reveal areas for improvement before the tool enters clinical practice.

Expert Systems↗
PubMed1994

Software engineering tools.

We have looked at general descriptions and illustrations of several software development tools, such as tools for prototyping, developing DFDs, testing, and maintenance. Many others are available, and new ones are being developed. However, you have at least seen some examples of powerful CASE tools for systems development.

Data Display↗
PubMed1996

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://@www.sdsc.edu/CompSci/Biomed/ MEME.

Algorithms↗
PubMed2000

Visualization of multiple influences on ocellar flight control in giant honeybees with the data-mining tool Viscovery SOMine.

Viscovery SOMine is a software tool for advanced analysis and monitoring of numerical data sets. It was developed for professional use in business, industry, and science and to support dependency analysis, deviation detection, unsupervised clustering, nonlinear regression, data association, pattern recognition, and animated monitoring. Based on the concept of self-organizing maps (SOMs), it employs a robust variant of unsupervised neural networks--namely, Kohonen's Batch-SOM, which is further enhanced with a new scaling technique for speeding up the learning process. This tool provides a powerful means by which to analyze complex data sets without prior statistical knowledge. The data representation contained in the trained SOM is systematically converted to be used in a spectrum of visualization techniques, such as evaluating dependencies between components, investigating geometric properties of the data distribution, searching for clusters, or monitoring new data. We have used this software tool to analyze and visualize multiple influences of the ocellar system on free-flight behavior in giant honeybees. Occlusion of ocelli will affect orienting reactivities in relation to flight target, level of disturbance, and position of the bee in the flight chamber; it will induce phototaxis and make orienting imprecise and dependent on motivational settings. Ocelli permit the adjustment of orienting strategies to environmental demands by enforcing abilities such as centering or flight kinetics and by providing independent control of posture and flight course.

Animals↗
PubMed1994

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package.

The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for IIIGlc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043-10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A 'best first' approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in user-defined tolerances on the performance of the algorithm.

Algorithms↗
PubMed1999

The SPORT-NMR software: a tool for determining relaxation times in unresolved NMR spectra.

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning 1H and 13C T1rho measurement in a solid copolymer and 2H T1Z and T1Q measurement in a liquid crystal are shown and discussed.

Anisotropy↗
PubMed1998

SAAM II: Simulation, Analysis, and Modeling Software for tracer and pharmacokinetic studies.

Kinetic analysis and integrated systems modeling have contributed substantially to our understanding of the physiology and pathophysiology of metabolic systems and the distribution and clearance of drugs in humans and animals. In recent years, many researchers have become aware of the usefulness of these techniques in the experimental design. With this has come the recognition that the discipline of kinetic analysis requires its own expertise. The expertise can impact experimental design in many ways, from the collaborative and service activities in which individuals interact in formal ways to the development of software tools to aid in kinetic analysis. The purpose of this report is to describe one such software tool, Simulation, Analysis, and Modeling Software II (SAAM II). In the first part, we describe in general how the user can take advantage of the capabilities of the software system, and in the second part, we give three specific examples using multicompartmental models found in lipoprotein (apolipoprotein B [apoB] kinetics) and diabetes (glucose minimal model) research.

Algorithms↗
PubMed2002

A direct measure of facial similarity and its relation to human similarity perceptions.

Research is reported on a measure of facial similarity in which the similarity of 2 faces is defined as the Euclidean distance between them in a principal-component space. Five studies were conducted in which participants rated sets of facial images, and in which the measure was applied to 2 problems in the eyewitness literature. Comparisons of ratings with distances derived from the principal-component analysis suggest that the measure corresponds reasonably well to perceptions of facial similarity. In addition, the measure correlates strongly with empirical measures of lineup fairness and is related to eyewitness identification performance. Further potential applications include a software tool for constructing arrays of faces of varying similarity, and a software tool for reconstructing facial images from memory.

Adolescent↗
PubMed2002

ARROGANT: an application to manipulate large gene collections.

ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.

Base Sequence↗
PubMed2002

Trabecular microstructure and surface changes in the greater tuberosity in rotator cuff tears.

OBJECTIVE: When planning surgery in patients with rotator cuff tear, strength of bone at the tendon insertion and trabecular bone structure in the greater tuberosity are usually taken into consideration. We investigated radiographic changes in bone structure of the greater tuberosity in rotator cuff tears. DESIGN: Twenty-two human cadaveric shoulders from subjects ranging from 55 to 75 years of age were obtained. The integrity of the rotator cuff was examined by sonography to determine if it is intact without any tear, or torn partially or completely. The humeral head was sectioned in 3 mm thick coronal slab sections and microradiographed. After digitization of the microradiographs and imaging processing with in-house semi-automated image processing software tools developed using software interfaces on a Sun workstation, the trabecular histomorphometrical structural parameters and connectivity in the greater tuberosity were quantified. The degenerative changes on the surface of the greater tuberosity were interpreted blindly by 2 independent readers. RESULTS: Among the 22 shoulder specimens, the rotator cuff was found intact in 10 shoulders, partially in 7 and fully torn in 5. Statistically significant loss in apparent trabecular bone volume fraction, number of trabecular nodes, and number of trabecular branches, and a statistically significant increase in apparent trabecular separation and number of trabecular free ends were found in the greater tuberosity of the shoulders with tears. The loss was greater in association with full tear than in partial tear. Thickening of the cortical margin of the enthesis, irregularity of its surface, and calcification beyond the tidemark were observed in 2 (20%) shoulders with intact rotator cuff, in 6 (86%) shoulders with partial tear, and in 5 (100%) shoulders with full tear. CONCLUSIONS: Rotator cuff tears are associated with degenerative changes on the bone surface and with disuse osteopenia of the greater tuberosity. Aging, degenerative enthesopathy of the supraspinatus tendon, and rotator cuff tears appear closely related.

Aged↗
PubMed2000

PSG-EXPERT. An expert system for the diagnosis of sleep disorders.

This paper describes PSG-EXPERT, an expert system in the domain of sleep disorders exploring polysomnographic data. The developed software tool is addressed from two points of view: (1)--as an integrated environment for the development of diagnosis-oriented expert systems; (2)--as an auxiliary diagnosis tool in the particular domain of sleep disorders. Developed over a Windows platform, this software tool extends one of the most popular shells--CLIPS (C Language Integrated Production System) with the following features: backward chaining engine; graph-based explanation facilities; knowledge editor including a fuzzy fact editor and a rules editor, with facts-rules integrity checking; belief revision mechanism; built-in case generator and validation module. It therefore provides graphical support for knowledge acquisition, edition, explanation and validation. From an application domain point of view, PSG-Expert is an auxiliary diagnosis system for sleep disorders based on polysomnographic data, that aims at assisting the medical expert in his diagnosis task by providing automatic analysis of polysomnographic data, summarising the results of this analysis in terms of a report of major findings and possible diagnosis consistent with the polysomnographic data. Sleep disorders classification follows the International Classification of Sleep Disorders. Major features of the system include: browsing on patients data records; structured navigation on Sleep Disorders descriptions according to ASDA definitions; internet links to related pages; diagnosis consistent with polysomnographic data; graphical user-interface including graph-based explanatory facilities; uncertainty modelling and belief revision; production of reports; connection to remote databases.

Computer Systems↗
PubMed2003

A visual approach for the accurate determination of echocardiographic left ventricular ejection fraction by medical students.

BACKGROUND: Previously published reports show that there is significant intraobserver, interobserver, and interinstitutional variability in the determination of left ventricular (LV) ejection fraction (EF) by echocardiography. With the increased deployment of echocardiography (eg, handheld devices), there exists a need for developing a simple, intuitive approach for evaluating LVEF that allows a wider range of physicians to accurately and rapidly determine LVEF. OBJECTIVE: We sought to create a system for assessing LVEF that relies on recognition and matching of patterns, rather than on mathematic calculations and geometric assumptions. METHODS: A library of videoclips of cardiac function was compiled from 54 patients who spanned the spectrum of LVEF. LVEFs were calculated for these patients using standard echocardiographic methods, with further validation of a subsample using cardiac magnetic resonance imaging measurement of LVEF. The library of images was used to create a software tool for assessing LVEF on the basis of a "template-matching" approach. The software tool was then tested on medical students (N=13) to determine whether it enabled relatively untrained individuals to make accurate LVEF estimates. RESULTS: Using a template-matching approach for interpretation of echocardiograms, medical students were able to accurately estimate LVEF after only a limited introduction to echocardiography. Their LVEF estimates showed good correlation and agreement with gold standard (r = 0.88, standard square of the estimate = 6.0, limits of agreement = +12.0%, -15.6%). CONCLUSIONS: A new visual approach for assessing cardiac function using template matching can accurately estimate LVEF. With minimal training, medical students can make LVEF estimates that correlate well with gold standard. The application of this new approach includes allowing for the interpretation of LVEF from echocardiograms to be performed by a broader spectrum of physicians.

Adult↗
PubMed2000

Computer-aided ergonomics: a case study of incorporating ergonomics analyses into workplace design.

One of the primary goals of computer-aided ergonomics is to develop software tools that allow ergonomics information to be accessed at the earliest stages of design. This case study discusses a PC-based software program that allows a designer to quantify a worker's biomechanical risk for injury based on a proposed workplace design. The program couples an established software tool for biomechanical analysis, the Three-Dimensional Static Strength Prediction Program (3DSSPP), with a widely used computer-aided design software package, AutoCAD. The use of this "3DSSPP/AutoCAD interface" in the proactive analysis of an automotive assembly task is described and the results compared with an independent assessment using observations of workers performing the same task. Both studies yield similar conclusions, suggesting that proactive use of software such as the 3DSSPP/AutoCAD interface may be a valid tool in evaluating proposed workplace designs. In this context, issues in the analysis of workplace designs regarding the use of supporting ergonomic tools, assumptions, and posture selection are discussed.

Accidents, Occupational↗
PubMedDate not supplied

[Measurement technics].

Aim of the research has been the evaluation of an image processing technique suggested for measuring procedures in the field of dental materials and devices studies. An analysis of measurement systems and largest employment's equipments in the biotechnologies field has been performed. Particularly, digital and image processing technologies have been considered and, between them, an evaluation of "Image Tool" software, made by UTHSCSA and available freeware on Internet has been carried out. The "Image Tool" software showed to be easy in handling and reliable on this results. Since it is based on image processing, the measuring precision is related to subject to be evaluated dimensions and always in the 1/1000 tolerance. This software also allow the direct surfaces measuring and comparing. The process accuracy is at the same level of mechanical regulation's measuring instruments (calipers, micrometres, surface probes) but it is not comparable to the laser controlled equipments, like CAD-CAM systems, micrometres and surface explores, precision which are much more sophisticated and expensives.

Biotechnology↗
PubMed2002

Efficient multiple genome alignment.

MOTIVATION: To allow a direct comparison of the genomic DNA sequences of sufficiently similar organisms, there is an urgent need for software tools that can align more than two genomic sequences. RESULTS: We developed new algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. For example, it can align 85% percent of the complete genomes of six human adenoviruses (average length 35305 bp.) in 159 seconds. An alignment of 74% of the complete genomes of three of strains of E. coli (lengths: 5528445; 5498450; 4639221 approximately bp.) is produced in 30 minutes.

Algorithms↗
PubMed1987

Managing research data with self-documenting files.

Processing biomedical research data is frequently complex due to the evolutionary nature of experiments and the requisite modification of analysis software. For the past several years we have been evolving a set of software tools designed to improve our ability to respond to evolving experimental designs. These tools allow the investigator to easily manipulate the research data and specify desired data transformations at run time. Coupling of analysis software to research data files is dependent on data files that are commented in a manner similar to that used in programming languages. The resulting annotated data files are self-documenting, and their use facilitates visual interpretation of displayed data as well as automatic processing of subsets of data. Here we present a formal description of a self-documenting file and describe several software tools that facilitate processing of biomedical research data.

Electronic Data Processing↗
PubMed2003

Construction of patient-specific surface models from MR images: application to bioelectromagnetism.

Patient-specific geometric models are needed in many engineering problems. This work reports a novel software tool developed to construct individualized triangulated surface models from MR images. The program consists of three main parts: segmentation, triangulation and registration. The software tool was developed under the UNIX operating system. The application area demonstrated in this work is bioelectromagnetism but the program can be used as well in other engineering problems. The tool has been successfully applied in numerous cases, both for the thorax and the head.

Algorithms↗
PubMed2000

MuStaR and other software for locus-specific mutation databases.

As the human genome sequencing project nears completion, there has been a vast increase in the rate at which disease and nondisease associated variant sequences are being sought and detected. This has heightened the need for software with which to accumulate allelic variant (mutation) data, and with which to make the data accessible to the scientific community. Many ad hoc solutions have been developed by those interested in specific genes and diseases, and the creation of central databases which hold data for all genes has provided an alternative repository for some of the locus data. Despite this, few specialised software tools exist for researchers to create their own locus-specific allelic variant databases. This article describes methods available to potential curators, including software systems developed with the sole purpose of generating locus-specific mutation databases. In particular, the authors' own software, MuStaRtrade mark, is described. MuStaRtrade mark allows curators to maintain a database on a laptop computer if desired, while being able to export the data to an automatically generated Website which will run on any cgi compliant Web server. Searching the database and the submission of new mutations are made possible through fill-in Web forms. A number of other software tools which may be of use to curators are also described.

Chromosome Mapping↗