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PubMedDate not supplied

Application of pulse mixing method in software coincidence counting.

In recent years the software coincidence counting system, designed for absolute activity measurement, has been developed in the Czech Metrology Institute. In this system a true coincidence count rate is calculated from the records of time and amplitude data of individual pulses and may be determined by two different methods. The first one uses a coincidence resolving time, in a manner similar to a classical coincidence measurement. The second method applies the pulse mixing method formulae, so that it does not use the resolving time and the correction for accidental coincidences. Both methods have been tested on the same data from a 4pibeta (PC)-gamma coincidence measurement of 60Co sources. The difference between the results obtained from both calculation methods applied on the data from the same measurement did not exceed 0.015%. The details of both methods and the results of their comparison are presented.

Algorithms↗
PubMed2006

Experimental validation of coincidence summing corrections computed by the ETNA software.

The ETNA software has been developed to compute efficiency transfer and coincidence summing corrections. Different experiments are combined to test the validity of this last facility. Point sources with multi-gamma emitters are measured at several source-to-detector distances. Experimental correction factors are determined from the variation in the peaks' relative intensities versus the geometrical conditions. The ETNA code is used to compute the corrections due to coincidence summing for the same geometries. The calculated values are compared to the experimental ones.

Algorithms↗
PubMed2006

Software studies for germanium detectors data analysis.

Efficiency calibrations of multiple high-purity germanium (HPGe) detectors are being maintained at the National Institute of Standards and Technology (NIST). Four generally available software packages for HPGe detector gamma-ray spectrum analysis, including the one currently used at NIST, were tested on spectra collected from two HPGe detectors at different source-to-detector distances and using point sources and ampoules as calibration geometries. The resulting efficiency curves were inter-compared.

Algorithms↗
PubMed2005

Software and expert system for the management of chronic hepatitis B.

Whereas the doubling time of overall biomedical knowledge bases has been estimated at about 19 years, the body of indexed information related to HBV has doubled in the last 8 years; the one related to HBV and antivirals has doubled in the last 5 years and the one related to Interferon and contraindications has doubled in less than 48 months. In Hepatology, as well as in other fast changing areas of medicine, the demand that clinical decision should always be based on the best verified knowledge available, is becoming more and more difficult to comply with. The Italian network of competence for hepatic diseases (Liver Unit Networks Association or LUNA) was established in 2003 with the patronage of the Italian Ministry of Health, with the primary goal of promoting advanced clinical research and real-time information exchange among the participating centres, facilitating knowledge sharing and identification of best practices. The ICT infrastructure designed for this purpose includes four sets of online accessible software tools:

Chronic Disease↗
PubMed2002

Pise: software for building bioinformatics webs.

Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services.

Computational Biology↗
PubMed1994

Software-controlled testing for antidromic activation of single neurones.

This paper describes a technique which allows the determination of the shape of action potentials initiated spontaneously, orthodromically or antidromically, without the distorting effects on shape that may be produced by changes in latency of activation or by signal averaging techniques. Software-controlled stimulation allows precise control of parameters for antidromic collision testing. The method allows selective sampling of a single action potential from a rapidly discharging cell, from a population of similar cells or from a evoked action potential among spontaneous activity. It minimizes jitter in the antidromic peri-event histogram by presenting an antidromic stimulus at precise and reproducible delays following either a spontaneous or orthodromically evoked action potential.

Action Potentials↗
PubMed1997

Hopper: software for automating data tracking and flow in DNA sequencing.

MOTIVATION: Genome-scale DNA sequencing is a multistep process in which large numbers of small template clones are propagated, purified, sequenced and analyzed on acrylamide gels. A significant challenge to these projects is the scale at which the data handling must be done. Hence, large-scale sequencing facilities will benefit from tracking template DNA information (purification methods, reaction and electrophoresis conditions) in a systematic fashion. A lack of software tools that support automated sample entry, and automatic data storage, retrieval and analysis are a major hindrance to recording and using laboratory workflow information to monitor the overall quality of data production. RESULTS: The UNIX file system has been used to prototype automation of the flow of data from the ABI sequencer to a data repository. Data are automatically processed by a central Perl program, Hopper, which runs a series of programs that analyze data quality (read length estimate, fraction of indeterminate bases, and number of contaminating and repetitive sequences), assemble shotgun sequence data, and generates simple reports describing the results.

Database Management Systems↗
PubMed1988

PROSOFT: a general purpose software in protein chemistry.

Applesoft and 6502 Assembler software was designed to quickly perform operations commonly encountered in protein chemistry. It was not designed for a specific application but can be conveniently used to speed up the determination of protein primary structure.

Algorithms↗
PubMed1992

IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations.

'IBIS' is a set of computer programs concerned with the processing of electron micrographs, with particular emphasis on the requirements for structural analyses of biological macromolecules. The software is written in FORTRAN 77 and runs on Unix workstations. A description of the various functions and the implementation mode is given. Some examples illustrate the user interface.

Computer Systems↗
PubMed2003

GAAS: gene array analyzer software for management, analysis and visualization of gene expression data.

SUMMARY: GAAS, Gene Array Analyzer Software supports multi-user efficient management and suitable analyses of large amounts of gene expression data across replicated experiments. Its management framework handles input data generated by different technologies. A multi-user environment allows each user to store his/her own data visualization scheme, analysis parameters used, values and formats of the output data. The analysis engine performs: background and spot quality evaluation, data normalization, differential gene expression analyses in single and multiple replica experiments. Results of expression profiles can be interactively navigated through graphical interfaces and stored into output databases.

Algorithms↗
PubMed2003

ActionMap: A web-based software that automates loci assignments to framework maps.

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

Chromosome Mapping↗
PubMed2005

Development of a simple method to evaluate medical staff radiation dose and its application to a software system supporting PET facility operation.

In recent years, positron-emitting labelled radiopharmaceuticals have come to be used in conjunction with positron emission tomography (PET) in various clinical diagnoses. Radiation exposure of the medical staff is a key issue in the design of PET facilities intended to handle large numbers of persons for PET diagnosis. As a first step, the radiation dose to individuals who received radiopharmaceuticals was calculated using a mathematical phantom model and the EGS4 electromagnetic cascade Monte Carlo code and MCNP Monte Carlo code. Dose rate behind a lead shield was also calculated for various lead thicknesses. The radiation dose distribution around a syringe containing a positron emitter was calculated. The calculated dose distributions were fitted to polynomial equations. These calculations were evaluated against measurements. The second step was to evaluate medical staff dose at a specified time by superimposing dose distribution from each person who received radioisotopes taking into account radioactive decay. In this way, we developed software to support PET facility operation, namely, planning, prediction, control of medical staff dose and facility operation. This system was also designed to schedule daily radiopharmaceuticals production and to manage radioactive wastes by taking decay time into account.

Body Burden↗
PubMed2005

Large variations occur in bone density measurements of children when using different software.

BACKGROUND: Paediatric dual X-ray absorptiometry (DXA) studies present a number of technical problems. One of these is that the edge detection algorithms designed for the adult skeleton may fail for paediatric studies. Hologic provide alternative algorithms for low bone density studies. AIM: To assess low-density software for the analysis of paediatric DXA studies and to compare with the adult protocol. METHODS: Our centre has scanned 450 normal children as part of a normal range study. A subgroup of 103 children was selected using a random number generator. The group was distributed evenly between males and females and across the age range 5-17 years. Each individual underwent both a lumbar spine and a whole-body scan on a Hologic QDR-4500W DXA scanner. Both scans were analysed using the standard adult protocol and then re-analysed using the Hologic experimental paediatric protocol for whole body and the Hologic low-density protocol for lumbar spine. RESULTS: Both lumbar spine protocols showed an increase in bone mineral density with age; however, the low-density protocol always produced a lower bone mineral density result than the adult protocol. Bland-Altman analysis showed limits of agreement of 0.031-0.093 g x cm(-2) (male, 0.032-0.089 g x cm(-2); female, 0.031-0.096 g x cm(-2)). This represents a mean difference of 9%. Five results showed differences greater than the upper limit of agreement. All these cases were children under 11 years of age who had large areas of spine not identified as bone by the adult protocol. These children were all below the 30th percentile for the body mass index. The whole-body protocols showed similar increases in bone mineral density with age; however, the experimental paediatric protocol always produced a lower bone mineral density result than the adult protocol. Paired results showed limits of agreement of 0.0668-0.130 g x cm(-2) (male, 0.063-0.124 g x cm(-2); female, 0.073-0.134 g x cm(-2)). This represents a mean difference of 11%. Five results showed differences greater than the upper limit of agreement. CONCLUSIONS: For anteroposterior (AP) lumbar spine scans, the use of the paediatric algorithm in children under 11 years of age would prevent the largest failures in analysis. For whole-body scanning, the adult algorithm showed no major failures in children of 11 years or older. It is hoped that forthcoming improvements in whole-body density analysis will improve the results for those under 11 years of age. Normal range data should be generated for any new algorithm to allow proper interpretation of clinical studies.

Absorptiometry, Photon↗
PubMed2000

Design and evaluation of a software prototype for participatory planning of environmental adaptations.

A software prototype to support the planning process for adapting home and work environments for people with physical disabilities was designed and later evaluated. The prototype exploits low-cost three-dimensional (3-D) graphics products in the home computer market. The essential features of the prototype are: interactive rendering with optional hardware acceleration, interactive walk-throughs, direct manipulation tools for moving objects and measuring distances, and import of 3-D-objects from a library. A usability study was conducted, consisting of two test sessions (three weeks apart) and a final interview. The prototype was then tested and evaluated by representatives of future users: five occupational therapist students, and four persons with physical disability, with no previous experience of the prototype. Emphasis in the usability study was placed on the prototype's efficiency and learnability. We found that it is possible to realise a planning tool for environmental adaptations, both regarding usability and technical efficiency. The usability evaluation confirms our findings from previous case studies, regarding the relevance and positive attitude towards this kind of planning tool. Although the prototype was found to be satisfactorily efficient for the basic tasks, the paper presents several suggestions for improvement of future prototype versions.

Activities of Daily Living↗
PubMed2006

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

Computer Simulation↗
PubMed2005

Computer-aided disease prediction system: development of application software with SAS component language.

AIMS: The intricacy of predictive models associated with prognosis and risk classification of disease often discourages medical personnel who are interested in this field. The aim of this study was therefore to develop a computer-aided disease prediction model underpinning a step-by-step statistics-guided approach including five components: (1) data management; (2) exploratory analysis; (3) type of predictive model; (4) model verification; (5) interactive mode of disease prediction using SAS 8.02 Windows 2000 as a platform. METHODS: The application of this system was illustrated by using data from the Swedish Two-County Trial on breast cancer screening. The effects of tumour size, node status, and histological grade on breast cancer death using logistic regression model or survival models were predicted. A total of 20 questions were designed to exemplify the usefulness of each component. We also evaluated the system using a controlled randomized trial. Times to finish the above 20 questions were used as endpoint to evaluate the performance of the current system. User satisfaction with the current system such as easy to use, the efficiency of risk prediction, and the reduction of barrier to predictive model was also evaluated. RESULTS: The intervention group not only performed more efficiently than the control group but also satisfied with this application software. CONCLUSIONS: The MD-DP-SOS system characterized by menu-driven style, comprehensiveness, accuracy and adequacy assessment, and interactive mode of disease prediction is helpful for medical personnel who are involved in disease prediction.

Decision Support Techniques↗
PubMed2003

A 2-D diode array and analysis software for verification of intensity modulated radiation therapy delivery.

An analysis is made of a two-dimensional array of diodes that can be used for measuring dose generated in a plane by a radiation beam. This measuring device is the MapCHECK Model 1175 (Sun Nuclear, Melbourne, FL). This device has 445 N-type diodes in a 22 x 22 cm2 2-D array with variable spacing. The entire array of diodes is easily calibrated to allow for measurements in absolute dose. For IMRT quality assurance, each beam is measured individually with the beam central axis oriented perpendicular to the plane of diodes. Software is available to do the analytical comparison of measurements versus dose distributions calculated by a treatment planning system. Comparison criteria of percent difference and distance-to-agreement are defined by the operator. Data are presented that show the diode array has linear response when beam fluence changes by over 300-fold, which is typical of the level of modulation in intensity modulated radiation therapy, IMRT, beams. A linear dependence is also shown for a 100-fold change in monitors units delivered. Methods for how this device can be used in the clinic for quality assurance of IMRT fields are described. Measurements of typical IMRT beams that are modulated by compensators and MLCs are presented with comparisons to treatment planning system dose calculations. A time analysis is done for typical IMRT quality assurance measurements. The setup, calibration, and analysis time for the 2-D diode array are on the order of 20 min, depending on numbers of fields. This is significantly less time than required to do similar analysis with radiographic film. The 2-D diode array is ideal for per-plan quality assurance after an IMRT system is fully commissioned.

Algorithms↗