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At least 1,297 records · Page 72Linked to original sources
PubMedDate not supplied

Evaluating software for the clinical laboratory.

A set of guidelines to assist in structuring the software-evaluation process is presented. In recent years, laboratory professionals have increasingly assumed responsibility for the evaluation of software to be used in the laboratory for patient testing or administrative functions. This is a positive trend that brings user expertise to the selection of computer software but one that mandates the development of appropriate software evaluation procedures on the part of laboratory personnel. Software should be chosen that best conforms to the needs of the laboratory. Proper evaluation of available software is critical. Documentation should be reviewed, the software should be tested, capabilities must be compared with accrediting or licensing bodies' standards, and vendor support should be assessed. Development of a well-defined procedure for software evaluation will ensure selection of software that solves, not creates, problems.

Accreditation↗
PubMed2004

A model-based approach for automated in vitro cell tracking and chemotaxis analyses.

BACKGROUND: Chemotaxis may be studied in two main ways: 1) counting cells passing through an insert (e.g., using Boyden chambers), and 2) directly observing cell cultures (e.g., using Dunn chambers), both in response to stationary concentration gradients. This article promotes the use of Dunn chambers and in vitro cell-tracking, achieved by video microscopy coupled with automatic image analysis software, in order to extract quantitative and qualitative measurements characterizing the response of cells to a diffusible chemical agent. METHODS: Previously, we set up a videomicroscopy system coupled with image analysis software that was able to compute cell trajectories from in vitro cell cultures. In the present study, we are introducing a new software increasing the application field of this system to chemotaxis studies. This software is based on an adapted version of the active contour methodology, enabling each cell to be efficiently tracked for hours and resulting in detailed descriptions of individual cell trajectories. The major advantages of this method come from an improved robustness with respect to variability in cell morphologies between different cell lines and dynamical changes in cell shape during cell migration. Moreover, the software includes a very small number of parameters which do not require overly sensitive tuning. Finally, the running time of the software is very short, allowing improved possibilities in acquisition frequency and, consequently, improved descriptions of complex cell trajectories, i.e. trajectories including cell division and cell crossing. RESULTS: We validated this software on several artificial and real cell culture experiments in Dunn chambers also including comparisons with manual (human-controlled) analyses. CONCLUSIONS: We developed new software and data analysis tools for automated cell tracking which enable cell chemotaxis to be efficiently analyzed.

Cell Culture Techniques↗
PubMedDate not supplied

Preliminary results of 3D dose calculations with MCNP-4B code from a SPECT image.

Interface software was developed to generate the input file to run Monte Carlo MCNP-4B code from medical image in Interfile format version 3.3. The software was tested using a spherical phantom of tomography slides with known cumulated activity distribution in Interfile format generated with IMAGAMMA medical image processing system. The 3D dose calculation obtained with Monte Carlo MCNP-4B code was compared with the voxel S factor method. The results show a relative error between both methods less than 1 %.

Monte Carlo Method↗
PubMedDate not supplied

Development and application of a computerized workload measurement tool for nurse educators.

This paper describes the development and application of a computerized workload measurement tool for use in hospital nursing education departments. The tool was developed in response to a need to gather information to facilitate resource allocation within the nursing education department in times of severe fiscal constraint. Software was developed based on a commercially available spreadsheet to keep track of the time and nature of nursing educator activity as well as its location. Analysis of the results showed that most of the nurse educators' time was spent on educational activities. The workload measurement system provided useful information for both individual educators and for the department in assessing, planning and allocating resources for educators.

Education, Nursing, Continuing↗
PubMed2000

[A simple personal computer-based system for lung sound analysis].

Although lung sounds provide important information about the respiratory system, the analysis of lung sounds has not been widely used in clinical practice because of the complicated procedure involved. However, personal computer technology has made impressive strides in recent years. Today, practically all personal computer models on the market are equipped with the capacity for audio signal input and output. We developed a new computer system for lung sounds acquisition and analysis. The system hardware comprises only a personal computer and a microphone, and the software was developed for a widely used operating system (Windows 95). Our system can record, save, and replay lung sounds and analyze their time and frequency domains. To verify the accuracy of sound acquisition, we examined the frequency characteristics of the system as installed and utilized on 4 different machines. The characteristics were essentially flat throughout the 200-2,000 Hz spectrum within which almost all lung sounds were contained. We feel our system can serve as a simple and useful tool for lung sound analysis.

Humans↗
PubMed2003

An XML message broker framework for exchange and integration of microarray data.

MOTIVATION: Microarrays are an important research tool for the advancement of basic biological sciences. However this technology has yet to be integrated with clinical decision making. We have implemented an information framework based on the Microarray Gene Expression Markup Language (MAGE-ML) specification. We are using this framework to develop a test-bed integrated database application to identify genomic and imaging markers for diagnosis of breast cancer. RESULTS: We developed extensible software architecture for retrieving data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. The framework we developed will provide the necessary data integration to move microarray research from basic biological sciences to clinical applications. AVAILABILITY: Open source software will be available from SourceForge (http://sourceforge.net/projects/microsoap/).

Database Management Systems↗
PubMed1996

[Computerized anesthesia record. How far have we gone?].

There are more and more computerized anaesthetic records becoming available from various constructors. However, the setting up and operation of such a product depends on the development of concepts in computing. The second technological breakthrough, currently underway, is challenging principles which had seemed accepted up until now. The technical development concerns computer processing units, RAM or ROM. The development in software influences the operation of networks, multiple task and object programming. The graphic interface becomes the centre of this second revolution. All of these developments should be included in the proposed computerized anaesthetic records. Three factors determine the realisation of such a product: control of the data collecting process, the man-machine interface and the utilisation of storing data. The computerized anaesthetic record should be of open conception, allowing communication with all of the data bases and providing an interface with all the monitors and ventilators used in operating and recovery rooms. Now is the time to install the infrastructure network in operating and recovery rooms and to be thinking of acquiring the new generations of computerized anaesthetic records.

Anesthesiology↗
PubMedDate not supplied

[Diabetes mellitus educational software for health professionals: stages of design and development].

This research aimed at creating a software about Diabetes mellitus in order to stimulate the continuing education of health professionals as well as educative practices. The system was developed using Delphi application, through a data bank utilizing key-words and the Pascal language. The software includes key-words searching tools, improving the process of accessing the data bank.

Computer-Assisted Instruction↗
PubMed1998

An evolutionary solution to anesthesia automated record keeping.

In the course of five years the development of an automated anesthesia record keeper has evolved through nearly a dozen stages, each marked by new features and sophistication. Commodity PC hardware and software minimized development costs. Object oriented analysis, programming and design supported the process of change. In addition, we developed an evolutionary strategy that optimized motivation, risk management, and maximized return on investment. Besides providing record keeping services, the system supports educational and research activities and through a flexible plotting paradigm, supports each anesthesiologist's focus on physiological data during and after anesthesia.

Anesthesia↗
PubMed2001

Development of a space radiation Monte Carlo computer simulation based on the FLUKA and ROOT codes.

This NASA funded project is proceeding to develop a Monte Carlo-based computer simulation of the radiation environment in space. With actual funding only initially in place at the end of May 2000, the study is still in the early stage of development. The general tasks have been identified and personnel have been selected. The code to be assembled will be based upon two major existing software packages. The radiation transport simulation will be accomplished by updating the FLUKA Monte Carlo program, and the user interface will employ the ROOT software being developed at CERN. The end-product will be a Monte Carlo-based code which will complement the existing analytic codes such as BRYNTRN/HZETRN presently used by NASA to evaluate the effects of radiation shielding in space. The planned code will possess the ability to evaluate the radiation environment for spacecraft and habitats in Earth orbit, in interplanetary space, on the lunar surface, or on a planetary surface such as Mars. Furthermore, it will be useful in the design and analysis of experiments such as ACCESS (Advanced Cosmic-ray Composition Experiment for Space Station), which is an Office of Space Science payload currently under evaluation for deployment on the International Space Station (ISS). FLUKA will be significantly improved and tailored for use in simulating space radiation in four ways. First, the additional physics not presently within the code that is necessary to simulate the problems of interest, namely the heavy ion inelastic processes, will be incorporated. Second, the internal geometry package will be replaced with one that will substantially increase the calculation speed as well as simplify the data input task. Third, default incident flux packages that include all of the different space radiation sources of interest will be included. Finally, the user interface and internal data structure will be melded together with ROOT, the object-oriented data analysis infrastructure system. Beyond the benefits of 'objectivity', ROOT's incorporation will also provide a graphical user interface with powerful tools for input prior to the calculation, as well as for data analysis and visualization of the results.

Computer Simulation↗
PubMed2004

OsiriX: an open-source software for navigating in multidimensional DICOM images.

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

Computer Graphics↗
PubMed2005

The future of real-time cardiac magnetic resonance imaging.

Dynamic changes in cardiac structure and function are usually examined by real-time imaging techniques such as angiography or echocardiography. MRI has many advantages compared with these established cardiac imaging modalities. However, system hardware and software limitations have limited cardiac MRI to gated acquisitions that are lengthy and often result in failed acquisitions and examinations. Recently, MRI has evolved into a technique capable of imaging dynamic processes in real time. Improvements in hardware, pulse sequences, and image reconstruction algorithms have enabled real-time cardiac MRI with high spatial resolution, high temporal resolution, and various types of image contrast without requiring cardiac gating or breath-holding. This article provides an overview of current capability and highlights key technical and clinical advances. The future prospects of real-time cardiac MRI will depend on 1) the development of techniques that further improve signal to noise ratio, contrast, spatial resolution, and temporal resolution, without introducing artifacts; 2) the development of software infrastructure that facilitates rapid interactive examination; and 3) the development and validation of several new clinical assessments.

Computer Systems↗
PubMed1998

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.

Algorithms↗
PubMed2005

Development and evaluation of real competitive PCR for high-throughput quantitative applications.

Real competitive PCR (rcPCR) has been shown to have high sensitivity, reproducibility, and high-throughput potential. We describe further development and evaluation of this methodology as a tool for measuring nucleic acid abundance within a cell. Modifications to the original protocol allow analysis of gene expression levels using standard conditions regardless of mRNA abundance and assay type, thereby increasing throughput and ease of reaction setup while decreasing optimization time. In addition, we have developed a software package, TITAN, to automatically analyze the results. The details are relevant to researchers performing competitive PCR using any detection technique. The effectiveness of the described developments is demonstrated using 12 genes known to have differential expression in cell lines grown under normal and hypoxic conditions. Quantitative and qualitative comparisons to real-time PCR are presented. It is also demonstrated that the technique is capable of detecting submicroscopic chromosomal DNA deletions.

Breast Neoplasms↗
PubMed2000

Telepathology by the Internet.

A new concept for telemicroscopy has recently been introduced using the Internet and conventional web browser, with Java support for microscope remote control as well as image transfer and discussion (http://amba.charite.de/telemic/). The system has two major components: the telemicroscopy server, which is a computer with Internet access connected to the automatic microscope, and the telemicroscopy client, who remotely operates the microscope. This simplified telemicroscopy system allows any Internet user to become a consultant for telepathology without the acquisition of specialized hardware or software. For the inquirer seeking advice, however, this solution is still very expensive, since it requires a fully automated microscope. The present study describes a system that can be used for conventional microscopes. A video camera mounted on a microscope with a photo tube is connected to the frame grabber of a PC. Java-based telemicroscopy software transforms the computer into an Internet server, which automatically distributes new microscope images, after manual operations, to all connected clients. Any Internet user can access the web page of the server to become a telemicroscopy client. A Chat function allows for the online exchange of written text and a Discuss function enables the mouse button to display an arrow to all connected clients, which highlights distinct structures of the images. The system was optimized for simplicity, while presenting all features that are necessary to show and discuss difficult cases with any expert in the field who has Internet access. It offers new perspectives for telepathology and it is envisaged that many pathologists and scientists will use this facility to connect their personal microscopes to the Internet, forming a network for teleconsultation. To foster this development, the software described in this paper is being made freely available. Hopefully, this development will promote communication between pathologists and may thus increase the quality of diagnosis. Information on inquiry and installation of the software is available at the website mentioned above. Telemicroscopy sessions using the Telemic version for conventional microscopes can be scheduled by contacting the authors by e-mail (iver. petersen@charite.de).

Communication↗
PubMed1996

A data management software for the Sysmex NE 8000 haematology analyser.

The Sysmex NE 8000 (TOA-Japan) is a haematology analyser that performs blood cells count and leukocyte differential count. For facilitating the work of technical validation, we developed a software adapted to any IBM or compatible PC running under MS-DOS, to manage the analyser. Data are automatically collected via the RS-232 interface from the analyser or keyed in for the other techniques. The software deals with 64 different analyses entirely "user defined". Six technical alarms of the analyser are taken in account for red or white cells and platelets. An "electronic worksheet" presents the results or alarms with 10 patients to a page. This enables the lab technician to assess the coherence of the various data and to perform verifications or complementary tests if necessary. As an option, a blinking asterisk can signal any results out of predetermined range. By moving the cursor through the table, a test result can be deleted, modified or added. A function displays the patient previous files in a window because the data are recorded in long term archives at the end of the day. This long term recording allows a search of previous files to decide additional tests if the patient is unknown. If the patient is known, with additional tests previously performed, this procedure is time saving. A daily archive function classifies and prints the whole day's work in alphabetical order. A protocol of communication allows a connection to a mainframe computer Bayer-Technicon. This program and the user's manual are free of charge, available on request from J. P. Cambus.

Blood Cell Count↗
PubMed2002

Building an asynchronous web-based tool for machine learning classification.

Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.

Algorithms↗