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PubMed2001

Standardized terminological services enabling semantic interoperability between distributed and heterogeneous systems.

The interconnection of heterogeneous computer applications in medicine raises the issue of semantic interoperability, going beyond traditional approaches of terminological standardization in basically three aspects. First, the variety of medical vocabularies that currently coexist in different domains is a major barrier for the integration of autonomously developed applications. Fortunately, with the Unified Medical Language System (UMLS) there are machine-readable terminological sources that cover and integrate most of the existing medical vocabularies. Second, the exchanged data need to be processed by a machine for different purposes like patient data integration, access to literature and knowledge bases as well as clinical audit and research. Medical vocabularies provided as passive dictionaries are no longer sufficient. Software system developers should take advantage of terminological services for refining user queries, for mapping the user's terms to appropriate medical vocabularies etc. Third, the services should be accessible uniformly and transparently. In the CORBAmed initiative a proposal for a standardized interface for querying and accessing computerized medical terminology resources was created. Based on the mentioned principles the MUSTANG system (Medical UMLS based Terminology Server for Authoring, Navigating and Guiding the Retrieval to Heterogeneous Knowledge Sources) has been developed. It is implemented on a Windows NT platform using the ORACLE database management and development software. The terminological services are accessible via multiple interfaces. The MUSTANG-System and the experiences with using terminological services in practice are described. Opposed to other levels of standardization like syntactical message standards there is much more a hesitation in the use of standardized terminology.

Humans↗

PubMed2000

Quantification of posterior capsular opacification in digital images after cataract surgery.

PURPOSE: To describe a software program developed to provide an objective assessment of the amount of posterior capsular opacification (PCO) in high-resolution digital images of the posterior capsule after cataract surgery. METHODS: Images are analyzed by a set protocol of defining the area of the posterior capsule, removing the Purkinje light reflexes by intensity segmentation, contrast enhancement, filtering to enhance low-density PCO, and variance analysis using a co-occurrence matrix to assess texture. The accuracy of the system was tested for validity and repeatability. RESULTS: The software developed has been demonstrated to be an objective method of quantifying PCO. In validation tests, the image analysis-derived measure of PCO showed good agreement with clinically derived measures of PCO. Clinicians assessed PCO on a computer screen image and also under slit lamp examination (Pearson correlation coefficient for both methods >0.92). The entire acquisition and analysis system was demonstrated to have a confidence limit for 2 SDs of 9.8% for group data. CONCLUSIONS: This system is capable of producing an accurate and reproducible measure of PCO that is relevant to assessing techniques of PCO prevention.

Aged↗

PubMed1994

[A proposal for the use of tridimensional reconstruction in oncology to better assess tumor stage and response to therapy].

Besides radiation therapy, diagnostic imaging has always been considered the main medical application of three-dimensional (3D) reconstruction. On the contrary, our study focused mainly on the use of 3D reconstruction for both spatial characterization and morphometric evaluation of the reconstructed objects. We aimed at assisting physicians to solve clinical and therapeutic problems. In particular, in oncology, 3D reconstruction may allow the objective and accurate quantification of the volume of neoplastic lesions. Therefore, we decided to focus our attention on the spatial characterization and morphometric assessment of the examined neoplastic masses. Volumetric measurements based on 3D reconstruction may be of great value to assess volume changes after irradiation and/or chemotherapy of neoplastic lesions. This might also allow to compare, on the basis of such changes, the role of different treatment protocols on similar neoplastic lesions and, possibly, to lead to a new TNM staging system no longer based on 2D measurements but on volumes. To meet these clinical requirements, we developed a software system for accurate volume measurements. We believed 3D reconstruction to be suited to this purpose and therefore we implemented a software incorporating 3D reconstruction capabilities of abnormal anatomical structures from 2D images, the rotation of the volume of interest for better assessment of spatial relationships, and finally morphometric evaluation, for accurate volume measurements. Instead of calculating the volume of a neoplastic lesion by means of a 3D reconstruction algorithm considering voxels as indivisible (voxel-based approach), we implemented a surface rendering algorithm using a cell-based approach, because it allowed voxels to be represented as small volume units, which could be further divided by means of linear interpolation. Thus, great flexibility was possible in the determination of surfaces, together with a good approximation of the volume of the neoplastic lesions. To assess the reliability of the developed software system, we used a real phantom. Its known actual volume was compared with the one measured by our system and the difference, expressed as a percentage of the actual volume itself, was compared with the one obtained by using reconstruction algorithms with a voxel-based approach (1.4% vs 4.4%). The error produced by the latter is three times greater than the one produced by our algorithm. This is a major result for the physician: better approximation of the actual volume of a neoplastic lesion means better evaluation of the number of neoplastic cells in the lesion. This may be useful for the clinical management of the patient. In the paper, the first clinical applications of our algorithm are reported.

Algorithms↗

PubMed2005

InSNP: a tool for automated detection and visualization of SNPs and InDels.

Availability of high quality SNP data is a rate-limiting factor in understanding the impact of genetic variability on gene function and phenotype. Although global projects like HAPMAP generate large numbers of SNPs in an even spacing throughout the human genome, many variation studies have a more focused approach: in the follow-up of positional association findings, candidate gene studies, and functional genomics experiments, knowledge of all variations in a limited amount of sequence (e.g., a gene) is needed. This leads to a large number of resequencing experiments, for which there is a surprising lack of analysis software. We have thus developed specialized software (InSNP) for targeted mutation detection and compared its performance to Polyphred and Mutation Surveyor using 28 amplicons. Out of a total of 579 (InSNP), 644 (Polyphred), and 526 (Mutation Surveyor) SNP predictions, 39 SNPs were confirmed by human expert inspection, with five SNPs missed by Polyphred and one missed by InSNP using the default settings. For InDel detection, out of 70 (InSNP), 28 (Polyphred), and 693 (Mutation Surveyor) InDel predictions, two InDels were confirmed by human expert inspection, with one InDel missed by Polyphred. InSNP provides a user-friendly interface with better functionality for mutation detection than general-purpose sequence handling software. It provides similar SNP detection sensitivity and specificity as the public domain and commercial alternatives in the investigated dataset. We hope that InSNP lowers the barriers to the use of automated mutation detection software and aids in the improvement of the efficiency of such experiments. The Windows installer (setup) program and sample datasets are available at www.mucosa.de/insnp/.

Algorithms↗

PubMed1995

The development of ergonomics standards for software.

This paper introduces the background to the development of ergonomics standards for software, describes some of the issues that influence the standards that are developed, and provides a brief overview of the scope and current status of standards under development.

Journal Article↗

PubMed2006

Development and application of software tools for monitoring, assessment and reporting of data concerning the operation of urban wastewater treatment plants in Cyprus.

This work focuses on the development and application of appropriate software tools for recording, assessing and reporting data related to the operation of the Urban Wastewater Treatment Plants (UWTPs) in Cyprus. An appropriate Internet-Based Management System was designed, developed and installed at the premises of the UWTPs and of the Cypriot Competent Authority (Water Development Department - WDD) in order to coordinate and disseminate tasks and related information for monitoring the operation of UWTPs. In addition, a client Geographical Information System database was compiled to be used for obtaining and analyzing spatial information. The software tools are based on common procedures and state-of-the-art technology for the recording and transmission of data and information and they provide an integrated view related to the operation and the efficiency of wastewater treatment systems. Moreover, continuous control and systematic monitoring of the UWTPs by the operators as well as continuous and direct supervision of the UWTPs environmental performance is achieved by the personnel of the Competent Authority. Furthermore, direct and unobstructed provision of data to the Competent Authority of Cyprus is accomplished by the operators of the UWTPs, while the Competent Authority is supported to compose full and representative reports to the European Commission and other International Organizations. The developed tools enable the direct recording of data obtained through measurements and analyses, permit the comparison of data with existing legislation and provide an integrated picture of the operation of the wastewater treatment plants as well as the option to focus and assess each individual treatment stage.

Cities↗

PubMed2003

[Development of quantification analysis software for measuring regional cerebral blood flow by the modified split-dose method with (123)I-IMP before and after acetazolamide loading].

We developed a quantification analysis software program for measuring regional cerebral blood flow (rCBF) at rest and under acetazolamide (ACZ) stress by the modified split-dose (MSD) method with iodine-123 N-isopropyl-p-iodoamphetamine (IMP) and compared the rCBF values measured by the MSD method and by the split dose (123)I-IMP SPECT (SD) method requiring one continuous withdrawal of arterial blood. Since the MSD method allows the input of two arterial blood sampling parameter values, the background subtraction procedure for obtaining ACZ-induced images in the MSD method is not identical to the procedure in the SD method. With our software program for rCBF quantification, the resting rCBF values determined by the MSD method were closely correlated with the values measured by the SD method (r=0.94), and there was also a good correlation between the ACZ-induced rCBF values obtained by the MSD method and by the SD method (r=0.81). The increase in rCBF under ACZ stress was estimated to be approximately 26% by the SD method and 38% by the MSD method, suggesting that the MSD method tends to overestimate the increase in rCBF under ACZ stress in comparison with the SD method, but the variability of the rCBF values at rest and during ACZ stress analyzed by the MSD method was smaller than the variability with the SD method. Further clinical studies are required to validate our rCBF quantification analysis program for the MSD method.

Acetazolamide↗

PubMed2001

[Development and application of software in EDXRF spectrometer].

The present paper describes application softwares on file management system, multicomponent linear regression, rapid semi-quantitative analysis, analysis of coating thickness and multifunctional Lucas-tooth intensity correction, developed in EDXRF. Utilization of these software improves the analytical quality, management efficiency and development ability of scientific research.

Chromium↗

PubMed2002

Quantification of brain lesions using interactive automated software.

We developed an interactive program, Analysis of Brain Lesions (ABLe) so that researchers studying the effects of brain lesions on cognition could have a user-friendly tool that could quantitatively characterize such lesions. The program was prepared in Tcl/Tk and will run on any UNIX or PC LINUX platform with the MEDx medical imaging software package. The ABLe is almost completely automated and determines the brain lesion size as well as which cytoarchitectonic brain regions (Brodmann areas) are contained within the boundaries of the lesion. Lesion data from multiple subjects can be grouped together and the degree of lesion overlap displayed. All images are analyzed and displayed within standard Talairach coordinate space, and the precision of the match between the ABLe Brodmann area graphics and the subject/patient brain is easily confirmed. The program is the first easy-to-use software that contains these specific features and is available for interested researchers with a background in lesion analysis.

Adult↗

PubMed1998

[Evaluation of estimated blood concentration of propofol on wake-up using "ConGrase", a software to control the syringe pump for propofol infusion].

We developed a software to control a Graseby 3500 syringe pump for propofol infusion through the serial port of Apple Macintosh/Power-Macintosh computer. This software, "ConGrase", was developed with Metrowerks CodeWarrior Professional (CWP 1) and PowerPlant framework using C++. ConGrase communicates with the syringe pump at least every three seconds, and calculates the estimated blood concentration (EBC) of propofol based on the amount of propofol actually infused by applying either the Euler or Runge-Kutta method using the three-compartment pharmacokinetic model. The parameter sets reported by Gepts et al. are used. ConGrase was released at the 44 th Annual Meeting of the Japan Society of Anesthesiology, and is distributed freely. The mean and S.D. of the emergence EBC calculated by ConGrase were 1.22 micrograms.ml-1 and 0.16 microgram.ml-1, respectively. These values are almost the same as values already reported outside Japan. The necessary wake-up time can be calculated with this estimated concentration. With this system, anesthetists can control the EBC at the required level and avoid long delays before the patients wake up after anesthesia.

Adolescent↗

PubMed2003

[Development and its clinical application of an acid-base balance computer software].

OBJECTIVE: To develop acid-base balance computer software for estimating acid-base disturbance rapidly and accurately. METHODS: The data module was set up, based on Henderson-Hasselbalch (H-H) and compensation formula, and the program was written with Delphi 5.0. RESULTS: The right RESULTS was 100.0 percent in 118 cases of acid-base disturbance patients by the software, while those with the right RESULTS was 89.8 percent by hands (P<0.05). In 20 cases pure acid-base disturbance, 70 cases double acid-base disturbance and 28 cases with triple acid-base disturbance, it took only (9.0+/-0.6) seconds, (8.9+/-1.3) seconds and (9.1+/-1.6)seconds respectively, with software, while which were much less than those by hands ((20.4+/-16.8) seconds, (92.4+/-45.3) seconds and (128.6+/-66.4) seconds, respectively, P<0.001). CONCLUSION: This software has a terse interface, by which the acid-base disturbance was concluded exactly and quickly.

Acid-Base Equilibrium↗

PubMedDate not supplied

Medical imaging workstation: a software environment.

In a study to set up an experimental simple imaging workstation with facilities for image input, storage, presentation and manipulation, BAZIS developed a software package called FRACTALS (Filmless Radiology And Computerized Task Analysis Lab Software). The investment in the development of effective software for digital radiological workstations is of great importance in picture archiving and communication systems (PACS) research. General purpose workstations are becoming less expensive and more powerful. They are an important tool for performing radiological research and developing an adequate human interface. The software should provide the tools and flexibility for modifications that turn out to be required for interaction with the radiologists. The software package FRACTALS is presented in this paper and its applications and future developments are discussed.

Computer Systems↗

PubMed2001

Development and application of computer software for cell culture laboratory management.

Prototype computer software for a Cell Culture Laboratory Management System (CCLMS) has been developed to relieve cell culture specialists of the burden of manual recordkeeping. Conventional data archives in cell culture laboratories are prone to error and expensive to maintain. The reliance upon cell culture to provide models for biochemical and molecular biological research serves to magnify errors at great expense. The CCLMS prototype encapsulates a modular software application that manages the many aspects of cell culture laboratory recordkeeping. A transaction-based database stores detailed information on subcultures, freezes and thaws, prints waterproof labels for culture vessels, and provides for immediate historical trace-back of any cultured cell line. Linked database files store information specific to an individual culture flask while removing redundancy between similar groups of flasks. A frozen cell log maintains locations of all vials within any type of cryogenic storage unit, locates spaces for newly frozen cell lines, and generates alphabetical or numerical reports. Finally, modules for maintaining cell counts, user records, and culture vessel specifications to support a comprehensive automation process are incorporated within this software. The developed CCLMS prototype has been demonstrated to be an adaptable, reliable tool for improving training, efficiency, and historical rigor for two independent cell culture facilities.

Animals↗

PubMed2004

Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications.

A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.

Algorithms↗

PubMed2005

Measurements of the periocular facial area with Web-based software.

We developed a simple Web-based program to make measurements on displayed photographs between several ocular and periocular landmarks. The measurements were: (1) vertical distance between the margin of the upper and lower eyelids (palpebral aperture), (2) distance between the lower eyelid margin and the inferior corneal margin (palpebro-limbar distance); (3) interpupillary distance; (4) ocular proptosis. We measured the distances using the Web program and compared them with manual measurements on the subject's face. The measurements involved 102 eyes of 51 patients with a variety of ophthalmic conditions. There was good agreement between manual and computer measurements. For example, for manual measurements in 49 patients, we obtained interpupillary distances ranging from 45 to 69 mm (mean 61, SD 6), whereas for computer measurements we found values ranging from 42 to 49 mm (mean 59, SD 6). The mean of the differences between manual and computer measurements was -2.0 mm (SD 4.3) and the 95% limits of agreement were -6.5 to 10.5 mm. Thus, computer measurements tended to give a higher reading by between 0.8 and 3.2 mm (95% confidence interval for the difference). Web-based software may be used to perform measurements on two-dimensional pictures and the technique appears to be suitable for telemedical purposes.

Adolescent↗

PubMed1997

Physician- and counselor-tailored hybrid computer interfaces for cancer genetics risk analysis software.

During development of the Strang Breast Cancer Risk Evaluator, different computer interfaces were designed, implemented and tested for useability by physicians and genetics counselors during a counseling session. The current BCRE 2.3 implements a hybrid interface, combining modern GUI (graphical user interface) windows, buttons, and menus with a linear, sequence-of-operations chronological progression reminiscent of interfaces prior to the GUI revolution. Although such hybrids are considered by many interface specialists inappropriate to modern broad-spectrum computer applications, vertical market applications, including this one, can capitalize on such hybridization effectively. The hybrid interface provides multiple visual cues and directions to the user as to the next appropriate action, thereby allowing a physician or counselor to concentrate his/her attention on the patient, returning his/her gaze to the screen at sporadic and widely spaced moments. Hybrid interfaces combine specific interface elements--such as triple-scale checkboxes, text and design metaphors, "next step" helper icons, color-coded content, and color and graphically tailored on-screen reports (all of which constitute GUI elements)--with a strictly linear data accrual, approval, calculation, storage and reporting progression (which sequence constitutes a pre-GUI interface design). A first-generation design is presented: a hybrid combining the visual efficiency of GUI-improved interfaces with the practical efficiencies of stream-lined and linear progressions.

Computer Graphics↗

PubMed1996

National policies for technical change: where are the increasing returns to economic research?

Improvements over the past 30 years in statistical data, analysis, and related theory have strengthened the basis for science and technology policy by confirming the importance of technical change in national economic performance. But two important features of scientific and technological activities in the Organization for Economic Cooperation and Development countries are still not addressed adequately in mainstream economics: (i) the justification of public funding for basic research and (ii) persistent international differences in investment in research and development and related activities. In addition, one major gap is now emerging in our systems of empirical measurement-the development of software technology, especially in the service sector. There are therefore dangers of diminishing returns to the usefulness of economic research, which continues to rely completely on established theory and established statistical sources. Alternative propositions that deserve serious consideration are: (i) the economic usefulness of basic research is in the provision of (mainly tacit) skills rather than codified and applicable information; (ii) in developing and exploiting technological opportunities, institutional competencies are just as important as the incentive structures that they face; and (iii) software technology developed in traditional service sectors may now be a more important locus of technical change than software technology developed in "high-tech" manufacturing.

Employment↗

PubMed1997

Quantitative assessment of the presence of a single leg separation in Björk-Shiley convexoconcave prosthetic heart valves.

RATIONALE AND OBJECTIVES: The authors developed an analytic software package for the objective and reproducible assessment of a single leg separation (SLS) in the outlet strut of Björk-Shiley convexoconcave (BSCC) prosthetic heart valves. METHODS: The radiographic cinefilm recordings of 18 phantom valves (12 intact and 6 SLS) and of 43 patient valves were acquired. After digitization of regions of interest in a cineframe, several processing steps were carried out to obtain a one-dimensional corrected and averaged density profile along the central axis of each strut leg. To characterize the degree of possible separation, two quantitative measures were introduced: the normalized pit depth (NPD) and the depth-sigma ratio (DSR). The group of 43 patient studies was divided into a learning set (25 patients) and a test set (18 patients). RESULTS: All phantom valves with an SLS were detected (sensitivity, 100%) at a specificity of 100%. The threshold values for the NPD and the DSR to decide whether a fracture was present or not were 3.6 and 2.5, respectively. On the basis of the visual interpretations of the 25 patient studies (learning set) by an expert panel, it was concluded that none of the patients had an SLS. To achieve a 100% specificity by quantitative analysis, the threshold values for the NPD and the DSR were set at 5.8 and 2.5, respectively, for the patient data. Based on these threshold values, the analysis of patient data from the test set resulted in one false-negative detection and three false-positive detections. CONCLUSIONS: An analytic software package for the detection of an SLS was developed. Phantom data showed excellent sensitivity (100%) and specificity (100%). Further research and software development is needed to increase the sensitivity and specificity for patient data.

Adult↗