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At least 181 records · Page 10Linked to original sources

PubMed2005

The CCPN data model for NMR spectroscopy: development of a software pipeline.

To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a "Data Model" that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research.

Computer Graphics↗

PubMed2000

Pk-fit: a pharmacokinetic/pharmacodynamic and statistical data analysis software.

This paper presents a new software, Pk-fit, to fit nonlinear models to kinetic and dynamic data. Directly connected to the spreadsheet, a statistical software component manager is available. In the data manager, Pk-fit includes the noncompartmental analysis module, the compartmental analysis module, the nonlinear kinetic process module, the drug absorption module, the pharmacodynamic data modeling module, the simultaneous fitting module, and the user-defined library module. In this paper, we present a detailed comparison of the kinetic analysis using Pk-fit and common software packages, PCNONLIN, MODFIT, MKMODEL, NONMEM, and SIPHAR, based on the textbook published by Gabrielsson in 1992, "Compilation of Analyzed Data Sets for Pharmacokinetic Software Evaluation." The comparison of Pk-fit with the reference softwares revealed that the parameters and their dispersion found with Pk-fit are consistent with the ones estimated with the other programs. In conclusion, Pk-fit constituted a valid tool for pharmacokinetic/pharmacodynamic data analysis.

Data Interpretation, Statistical↗

PubMed2000

Expression profile viewer (ExProView): a software tool for transcriptome analysis.

A software tool, Expression Profile Viewer (ExProView), for analysis of gene expression profiles derived from expressed sequence tags (ESTs) and SAGE (serial analysis of gene expression) is presented. The software visualizes a complete set of classified transcript data in a two-dimensional array of dots, a "virtual chip," in which each dot represents a known gene as characterized in the transcript databases Expressed Gene Anatomy Database or UniGene. The virtual chip display can be changed between representations of different conceptual systems for gene/protein classification and grouping. Four alternative projections are currently available: (i) cellular role, (ii) subcellular compartment, (iii) chromosome localization, and (iv) total UniGene display. However, the chip can be adapted to any other desired layout. By selecting dots, further information about the represented genes is obtained from the local database and WWW links. The software thus provides a visualization of global mRNA expression at the descriptive level and guides in the exploration of patterns of functional expression, while maintaining direct access to detailed information on each individual gene. To evaluate the software, public EST and SAGE gene expression data obtained from the Cancer Genome Anatomy Project at the National Center for Biotechnology Information were analyzed and visualized. A demonstration of the software is available at http://www.biochem.kth. se/exproview/.

Data Display↗

PubMed1998

Balancing needs, efficiency, and functionality in the provision of modeling software: a perspective of the NIH WinSAAM Project.

The development of new software or the refinement of existing software for new operating environments each calls for judicious balancing. On the one hand, we strive for simplicity, predictability, and operational protection as it is well recognized that software with these attributes will attract an audience of satisfied users. But, on the other hand, these attributes do not conjure a sense of power, efficiency, or flexibility, and these other properties are also appreciated by users, albeit a somewhat different group of users. The goal is to achieve a blend which isolates critical functionality, flexible control, and user support while meeting the needs of the broadest collection of serious users. In this chapter, we discuss the issues impacting the migration of SAAM to the Windows environment, the NIH WinSAAM Project, and we outline the steps taken to ensure its feasibility. In addition, we describe a new paradigm for software development and use which ensures the durability of the software for modeling.

Computer Simulation↗

PubMed1986

The current situation, aspects, and projects concerning nuclear medicine software in Europe.

Since the 1984 Congress of the Society of Nuclear Medicine-Europe in Helsinki, the "Task Group for European Nuclear Medicine Software Cooperation", which became the "Joint ENMS/SNME Nuclear Medicine Software Task Group" in London in 1985, has focused attention on establishing a new COST project (European Cooperation in the Field of Scientific and Technical Research) (COST 1981) in the field of nuclear medicine Software. On 20 March 1986, the mandate was finally approved officially by the COST Committee of Senior Officials in Brussels (see Editorial in this issue). The problems, content, and objectives of specific items and ideas regarding NM software that have been publicized at the European level are dealt with here. The reader actively interested in NM software is encouraged to participate in the COST framework and forum, in order to avoid duplication of effort and to utilize resources more efficiently by coordinating activities in nuclear medicine in Europe.

Artificial Intelligence↗

PubMed1995

Hologic QDR 2000 whole-body scans: a comparison of three combinations of scan modes and analysis software.

This study reports on the short-term in vivo precision and absolute measurements of three combinations of whole-body scan modes and analysis software using a Hologic QDR 2000 dual-energy X-ray densitometer. A group of 21 normal, healthy volunteers (11 male and 10 female) were scanned six times, receiving one pencil-beam and one array whole-body scan on three occasions approximately 1 week apart. The following combinations of scan modes and analysis software were used: pencil-beam scans analyzed with Hologic's standard whole-body software (PB scans); the same pencil-beam analyzed with Hologic's newer "enhanced" software (EPB scans); and array scans analyzed with the enhanced software (EA scans). Precision values (% coefficient of variation, %CV) were calculated for whole-body and regional bone mineral content (BMC), bone mineral density (BMD), fat mass, lean mass, %fat and total mass. In general, there was no significant difference among the three scan types with respect to short-term precision of BMD and only slight differences in the precision of BMC. Precision of BMC and BMD for all three scan types was excellent: < 1% CV for whole-body values, with most regional values in the 1%-2% range. Pencil-beam scans demonstrated significantly better soft tissue precision than did array scans. Precision errors for whole-body lean mass were: 0.9% (PB), 1.1% (EPB) and 1.9% (EA). Precision errors for whole-body fat mass were: 1.7% (PB), 2.4% (EPB) and 5.6% (EA). EPB precision errors were slightly higher than PB precision errors for lean, fat and %fat measurements of all regions except the head, although these differences were significant only for the fat and % fat of the arms and legs. In addition EPB precision values exhibited greater individual variability than PB precision values. Finally, absolute values of bone and soft tissue were compared among the three combinations of scan and analysis modes. BMC, BMD, fat mass, %fat and lean mass were significantly different between PB scans and either of the EPB or EA scans. Differences were as large as 20%-25% for certain regional fat and BMD measurements. Additional work may be needed to examine the relative accuracy of the scan mode/software combinations and to identify reasons for the differences in soft tissue precision with the array whole-body scan mode.

Absorptiometry, Photon↗

PubMed2004

Evaluation of a laser system for CT software simulation (EXOMIO) in patients with breast cancer.

PURPOSE: To develop a manually movable laser system connected to the CT table for alignment of the isocenter cross of irradiation fields on the patient's skin directly after CT software simulation. MATERIAL AND METHODS: The specially designed laser system was constructed in the authors' department, and the mean focusing accuracy of isocenter translations was analyzed using Alderson phantom measurements. The mean overall accuracy from setup to treatment of the whole procedure of CT software simulation was measured by the comparison of bone structures and mamma contour of the digitally reconstructed radiograph (DRR) with the verification film. The time taken for the different setup procedure steps was evaluated for 70 breast cancer patients who were treated using tangential fields. RESULTS: The mean focusing accuracy of the manually movable laser system after defined isocenter translation was measured as 0.8 +/- 0.5 mm, the mean patient movement on the CT table as 2.0 +/- 1 mm, and the mean positioning accuracy of the first treatment after patient positioning corresponding to the skin alignments as 3.9 +/- 1.5 mm. The time periods for the different steps of the CT software simulation were measured, and the total duration was found to be 35.8 +/- 3.3 min. CONCLUSION: In general, the main advantage of well-known CT software simulation when compared to conventional simulation is the relief of the real X-ray simulator which is feasible with fast planning software (EXOMIO) and the presented movable laser system.

Adult↗

PubMed2005

The effect of digital measurement software on photodynamic therapy.

BACKGROUND: To investigate the effect of refraction-corrected digital measurement software on photodynamic therapy (PDT) treatment spot size. METHODS: Experimental study using a calibrated Gullstrand-type model eye. The axial length of the model eye was set to different values, ranging from 20 to 31 mm, and the PDT treatment spot sizes obtained from refraction-corrected digital measurement software and manual measurement with a fixed-magnification factor, as well as four different indirect contact laser lenses, were calculated and compared for a treatment spot with a diameter of 4 mm. RESULTS: The maximum deviation from the treating laser spot was +39.6% under myopic and +17.4% under hyperopic conditions when the refraction-corrected digital measurement software was used. The maximum deviation was +14.2% under myopic and +13.3% under hyperopic conditions when the manual measurement with the fixed-magnification factor was used. CONCLUSIONS: The use of refraction-corrected digital measurement software produces a larger deviation from treating laser spot than the use of manual measurement with a fixed-magnification factor. Therefore, refraction-corrected digital measurement software might not be suitable for calculating the recommended PDT treatment spot size in eyes with high refractive errors.

Choroidal Neovascularization↗

PubMed2001

A new method and software for quantitative analysis of continuous intracranial pressure recordings.

OBJECTIVE: A computer software utilising a new method for quantitative analysis of intracranial pressure (ICP), was developed to provide a more accurate analysis of continuously recorded ICP. Intracranial pressure curves were analysed by the software to explore the relationship between mean ICP and the presence of ICP elevations. METHODS: The Sensometrics Pressure Analyser (version 1.2) software provides a quantitative analysis of the ICP curve, presenting the ICP recordings as a matrix of numbers of ICP elevations of different levels (e.g. 20 or 30 or 40 mmHg) and durations (e.g. 0.5, 5 or 10 minutes). The number of ICP elevations may be standardised by calculating the number of elevations during for instance a 10 hour period. The computer software was used to retrospectively analyse the ICP curves in our first consecutive 127 patients undergoing continuous 24 hours ICP monitoring during the two-year period from February 1997 to December 1998. The indications for ICP monitoring were suspected hydrocephalus, craniosynostosis or shunt failure. RESULTS: Analysis of the ICP curves revealed a rather weak relationship between mean ICP and the number of apparently abnormal ICP elevations (that is elevations of 20 mmHg or above). Abnormal ICP elevations were present in a relatively high proportion of cases with a normal mean ICP below 10 mmHg, or a borderline mean ICP between 10 and 15 mmHg. In addition, the ICP data of two cases are presented suggesting that mean ICP may be an inaccurate measure of ICP. CONCLUSIONS: The results of analysing ICP curves by means of this method and software reveal that calculation of ICP elevations of different levels and durations may represent a more accurate description of the ICP curve than calculation of mean ICP. The method may enhance the clinical application of ICP monitoring.

Adolescent↗

PubMed1994

Native American youths and cancer risk reduction. Effects of software intervention.

PURPOSE: Toward developing attractive and effective means to reduce cancer risks faced by Native American people, this study developed and tested interactive computer software to improve dietary choices and prevent tobacco use among Native American adolescents. METHODS: Based on a legend of the Seneca Nation, a cancer prevention lesson was developed and programmed for software. A sample of 368 Native American adolescents were divided randomly into intervention and control arms. Youths in both arms were pre-tested, youths in the intervention arm interacted with the software, and all youths were post-tested. Pre-test and post-test measures covered information and attitudes about cancer risks from dietary practices and tobacco use. RESULTS: Pre-test scores differed between the two arms on youths' age and on one outcome variable. Relative to their counterparts in the control arm, youths in the intervention arm increased their post-test scores on 8 of 12 outcome measurement variables. Process data gathered during intervention delivery indicated that nearly all youths were involved with the interactive software and lesson. CONCLUSION: Interactive computer software holds promise for delivering cancer risk reduction intervention aimed at modifying dietary habits and preventing tobacco use among Native American youth.

Adolescent↗

PubMed2004

Two-dimensional strain-a novel software for real-time quantitative echocardiographic assessment of myocardial function.

OBJECTIVES: We sought to assess the feasibility of 2-dimensional strain, a novel software for real-time quantitative echocardiographic assessment of myocardial function. METHODS: Conventional and a novel non-Doppler-based echocardiography technique for advanced wall-motion analysis were performed in 20 patients with myocardial infarction and 10 healthy volunteers from the apical views. Two-dimensional strain is on the basis of the estimation that a discrete set of tissue velocities are present per each of many small elements on the ultrasound image. This software permits real-time assessment of myocardial velocities, strain, and strain rate. These parameters were also compared with Doppler tissue imaging measurements in 10 additional patients. RESULTS: In all, 80.3% of infarct and 97.8% of normal segments could be adequately tracked by the software. Peak systolic strain, strain rate, and peak systolic myocardial velocities, calculated from the software, were significantly higher in the normal than in the infarct segments. In the 10 additional patients, velocities, strain, and strain rate obtained with the novel software were not significantly different from those obtained with Doppler tissue imaging. CONCLUSION: Two-dimensional strain can accomplish real-time wall-motion analysis, and has the potential to become a standard for real-time automatic echocardiographic assessment of cardiac function.

Adult↗

PubMed2004

Decreased use of iliac extensions and reduced graft junctions with software-assisted centerline measurements in selection of endograft components for endovascular aneurysm repair.

OBJECTIVE: The purpose of this study was to determine the impact of using computerized software-assisted centerline measurements for extensions and graft junctions during the selection of endograft components for modular aortic endografts in endovascular repair of abdominal aortic aneurysms. METHODS: From April 1998 to December 2002, 289 modular aortic endografts were implanted at our institution. These included 248 grafts (prior to 2002, group 1) with components selected on the basis of manual caliper measurements from combined contrast computed tomography (CT) and marker-catheter arteriography data, and 41 grafts (2002, group 2) with components selected with the use of computerized software that allowed for centerline measurements on 3-dimensional reconstructions based on CT data. These 2 groups were compared for the number and type of extensions required per case. Seventeen other relevant variables were analyzed for their potential influence on selection of endograft components. These variables included age, gender, maximum aneurysm size, level of distal fixation, length and diameter at the fixation points, endograft manufacturer (make), and configuration. The significance of the observed differences was analyzed with a multivariate regression model, adjusting for potentially confounding preoperative measures. RESULTS: Multivariate analysis demonstrated that the number of right iliac extensions, left iliac extensions, total extensions, and total graft junctions was significantly reduced by the use of computerized software-assisted centerline measurements (group 2) compared with caliper measurements (group 1), independent of all other 17 preoperative variables. Notably, the mean number of required right iliac extensions was double in group 1 versus group 2. CONCLUSIONS: Centerline software-assisted measurements can significantly reduce the need for iliac extensions and, concomitantly, the number of required endograft junctions. On average, twice as many extensions were required for right iliac fixation when the manual caliper measurements were used compared with software-assisted measurements. These findings are highly relevant to issues of total endograft cost and long-term endograft integrity and focus attention on the tools that may need to be considered standards of care rather than optional for selection of endograft components.

Adult↗

PubMed2002

Improving system quality through software evaluation.

The role of evaluation is examined with respect to quality of software in healthcare. Of particular note is the failure of the Therac-25 radiation therapy machine. This example provides evidence of several types of defect which could have been detected and corrected using appropriate evaluation procedures. The field of software engineering has developed metrics and guidelines to assist in software evaluation but this example indicates that software evaluation must be extended beyond the formally defined interfaces of the software to its real-life operating context.

Evaluation Studies as Topic↗

PubMed1996

Prism: a new approach to radiotherapy planning software.

PURPOSE: We describe the capabilities and performance of Prism, an innovative new radiotherapy planning system with unusual features and design. The design and implementation strategies are intended to assure high quality and clinical acceptability. The features include Artificial Intelligence tools and special support for multileaf collimator (MLC) systems. The design provides unusual flexibility of operation and ease of expansion. METHODS AND MATERIALS: We have implemented Prism, a three-dimensional (3D) radiotherapy treatment-planning system on standard commercial workstations with the widely available X window system. The design and implementation use ideas taken from recent software engineering research, for example, the use of behavioral entity-relationship modeling and the "Mediator Method" instead of ad-hoc programming. The Prism system includes the usual features of a 3D planning system, including Beam's Eye View and the ability to simulate any treatment geometry possible with any standard radiotherapy accelerator. It includes a rule-based expert system for automated generation of the planning target volume as defined in ICRU Report 50. In addition, it provides special support for planning treatments with a multileaf collimator (MLC). We also implemented a Radiotherapy Treatment Planning Tools Foundation for Prism, so that we are able to use software tools form other institutions without any source code modification. RESULTS: The Prism system has been in clinical operation at the University of Washington since July 1994 and has been installed at several other clinics. The system is run simultaneously by several users, each with their own workstation operating from a common networked database and software. In addition to the dosimetrists, the system is used by radiation oncologists to define tumor and target volumes and by radiation therapists to select treatment setups to load into a computer controlled accelerator. CONCLUSIONS: Experience with the installation and operation has shown the design to be effective as both a clinical and research tool. Integration of software tools has eased the development and significantly enhanced the clinical usability of the system. The design has been shown to be a sound basis for further innovation in radiation treatment planning software and for research in the treatment planning process.

Computer Communication Networks↗

PubMed2000

Clinical and practical requirements of online software for anesthesia documentation an experience report.

The aim of this paper is the presentation of a new version of the anesthesia documentation software, NarkoData, that has been used in routine clinical work in our department as part of an anesthesia information management system (AIMS) since 1995. The performance of this software is presented along with requirements for future development of such a system. The originally used version, NarkoData 3.0, is an online anesthesia documentation software established by the software company ProLogic GmbH. It was primarily developed as a disk-based system for the MacOS operating system (Apple Computer Inc.). Based on our routine experience with the system, a catalogue of requirements was developed that concentrated on improvement in the sequence of work, administration and data management. In 1996, the concepts developed in our department, in close co-operation with medical personnel and the software company, led to a considerable enlargement of the program functions and the subsequent release of a new version of NarkoData. Since 1997, more than 20 000 anesthesia procedures have been recorded annually with this new version at 115 decentralized work stations at our university hospital.

Anesthesiology↗

PubMed1997

Approaches for certification of electronic prescription software.

The proper management of drug treatment is essential, since adverse drug reactions are common reasons of hospitalisations. Expenditure on drug therapy has also been growing faster than any other aspect of health care in many countries. Savings and quality improvements in drug treatment could be achieved with computerised prescribing. In this paper, the architecture of an electronic prescription system is described in the light of software certification and registration. An electronic prescription system is an example of a system supporting shared care and therefore it should be person based, integrated, secure and confidential and data should be shared among health care institutions. The system architecture shares the idea of a virtual patient record and a smart card will be used as a key to prescription data located on the network. The certification and registration of medical software is a difficult and costly procedure. Ensuring the quality of software can be based on; certification of development process, voluntary evaluation, and post-market surveillance. Voluntary evaluation practice would be a precious tool for both the customers and software developers, and it would also be an invaluable source of information in terms of developing new software.

Certification↗

PubMed2000

Software sensors to monitor the dynamics of microbial communities: application to anaerobic digestion.

A mass balance based model has been derived to represent the dynamical behavior of the ecosystem contained in an anaerobic digester. The model considers two bacterial populations: acidogenic and methanogenic bacteria. It forms the basis for the design of a software sensor considering both a model of the biological system and on-line gaseous measurements. The software sensor computes the concentration of inorganic carbon and volatile fatty acids (VFA) in the digester. Another software sensor is dedicated to the estimation of the bacterial biomasses. The predictions of the software sensors for a real experiment are very close to the actual off-line measurements. The software sensors monitor the accumulation of VFA and thus very early detect a destabilization of the digester due to overloading. The presented methodology demonstrates the usefulness of advanced monitoring techniques for an improved understanding of the internal working of a biological system.

Bacteria, Anaerobic↗

PubMed2001

The effects of different image file formats and image-analysis software programs on dental radiometric digital evaluations.

OBJECTIVES: To determine if variations in radiodensity data are introduced by lossy Joint Photographic Experts Group (JPEG) compression and/or the use of three software programs. METHODS: An occlusal film with an aluminium step wedge was exposed, processed and digitized under standard conditions. Before the image was saved, the coordinates and the gray-scale value for each pixel in a 20 x 20 pixel area near the middle of the thickest step were recorded. These pixel coordinates and gray-scale values served as Truth 1. In addition, a digital simulated-radiographic image with assigned gray-scale values for each pixel was created and served as Truth 2. The digital data for the scanned radiograph and the simulated radiograph were saved as Tagged Image File Format (TIFF) and lossy JPEG files. Each file was opened with three software programs and the gray-scale values of homologous pixels were recorded. For these pixels in each image type, the mean gray-scale values and standard deviations were calculated. The pixel gray-scale values for each homologous pixel were also individually compared. RESULTS: When the TIFF images were opened with the three software programs, one program resulted in gray-scale values that were not concordant with truth. All JPEG images resulted in gray-scale values that were not concordant with truth. CONCLUSIONS: One software program added a column of 0s to data files. Lossy JPEG compression introduced potentially deleterious variations to radiodensity data, and at least two of the software programs performed JPEG image decompression differently.

Absorptiometry, Photon↗