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PubMed2004

In silico physical mapping software for the Triticum aestivum genome.

The large size of the Triticum aestivum genome makes it unlikely that a complete genome sequence for wheat will be available in the near future. Exploiting the conserved genome organization between wheat and rice and existing genomic resources, we have constructed in silico physical mapping software for wheat, assigning a gross physical location(s) into chromosome bins to 22,626 representative wheat gene sequences. To validate the predictions from the software we compared the predicted locations of ten ESTs to their positions experimentally determined by SNP marker analysis. Six of the sequences were correctly positioned on the map including four that demonstrated a high level of colinearity with their orthologous rice genomic region. This tool will facilitate the development of molecular markers for regions of interest and the creation of map-based cloning strategies in areas demonstrating high levels of sequence conservation and organization between wheat and rice.

Computational Biology↗

PubMed2006

Segmentation of fascias, fat and muscle from magnetic resonance images in humans: the DISPIMAG software.

Segmentation of human limb MR images into muscle, fat and fascias remains a cumbersome task. We have developed a new software (DISPIMAG) that allows automatic and highly reproducible segmentation of lower-limb MR images. Based on a pixel intensity analysis, this software does not need any previous mathematical or statistical assumptions. It displays a histogram with two main signals corresponding to fat and muscle, and permits an accurate quantification of their relative spatial distribution. To allow a systematic discrimination between muscle and fat in any subject, fixed boundaries were first determined manually in a group of 24 patients. Secondly, an entirely automatic process using these boundaries was tested by three operators on four patients and compared to the manual approach, showing a high concordance.

Adipose Tissue↗

PubMed2005

Evaluation of the Quantitative Gated SPECT (QGS) software program in the presence of large perfusion defects.

OBJECTIVES: To evaluate the reproducibility and operator dependence for the quantitative regional left ventricular functional parameters (LVFP) assessed by Cedars-Sinai's Quantitative automated gated SPECT (QGS) software. METHODS: The QGS algorithm was reviewed in detail and potential operator dependencies were defined. Series of prototypes were selected, consisting of (a) normal perfusion, (b) perfusion defects in all perfusion regions, (c) perfusion studies of patients with angiographic confirmed normal coronary arteries, proximal (>or=70% stenoses) single and multiple vessel disease, and (d) spurious activity in close proximity. While defining and re-orienting the volume containing the left ventricle, the operator adjusted 8 variables/degrees of freedom (DF). The software was used without further operator interventions. Results were expressed as a coefficient of variation (COV). Separate COV were calculated per distinct DF. A segment was considered not robust when the COV did exceed 20% in a single DF, 15% in at least 2 DF, or 10% in at least 3 DF. RESULTS: Regional left ventricular EF and volumes showed excellent reproducibility. Normal perfusion and the vessel disease prototypes showed an excellent COV (for all re-orientation steps [33/prototype]) mostly below 5% for LVFP. However, regional wall motion and thickening became less reliable in the presence of large perfusion defects or artifacts. CONCLUSIONS: Quantitative estimates for regional left ventricular functional data show excellent reproducibility using automated gated SPECT. However, there may be substantial operator dependency in the presence of large defects or spurious activity in close proximity.

Algorithms↗

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↗

PubMed2005

Monitoring clinical performance: the role of software architecture.

Methods of assessing and monitoring the performance of clinicians have received a lot of publicity in recent years. We review the main methodologies concentrating on the distinction between monitoring individual performance and monitoring aggregated performance. We also highlight the importance and difficulties associated with incorporating and assessing risk factors into the process. We discuss how software architecture can be developed to implement these methodologies. We illustrate this development by a case study involving the creation of a software tool to produce funnel plots to analyse surgeon performance. We discuss how such tools are currently evaluated and propose that in future assessments of usability would benefit from an experimental study.

Computer Systems↗

PubMed1985

An interactive software for 81mKr pulmonary ventilation gating.

An interactive software to gate scintigraphic list-mode data collected from ventilation studies using a radioisotope of an inert gas (81mKr) has been developed. It allows the detection of end expiration and end inspiration phases in a time activity curve. It involves six phases: filtering of the curve; preselection of local extrema; validation of the preselection; choice of the parameters for the reconstruction; control of the selected cycles and display of parameters such as frequency, expiration time, breath amplitude; reconstruction of images representing the distribution of ventilation during a mean respiratory cycle. This software was tested on 116 data sets without a failure. The interactive definition and control of the selected times made the algorithm useful regardless of the count rate and the frequency. It could be adapted to gate other periodic or semiperiodic physiological phenomena.

Computers↗

PubMed1988

Software systems to control sensitivity studies of Monte Carlo simulation models.

Studies of the sensitivity of Monte Carlo models to changes in the values of their features involve repetitive simulations. Subsequent displays and analyses express variation in simulated outcomes as a function of change in location in multidimensional feature space and provide feedback via inputs for future simulations. A software system has been designed to control execution of the interacting programs required, reducing the need for human intervention. Assumptions about the goals and operation of the system as a whole are isolated within a program which executes component packages using interprogram control and communication mechanisms. The latter allow component programs to operate independently of the sources of data or the execution environment: they may be used separately, or in software systems, such as for sensitivity analysis of a Monte Carlo epidemic model. The methodology contributes to modularity at the level of executable programs and to the plausibility and efficiency of sensitivity studies.

Computer Simulation↗

PubMed1988

Analysis of chromium-51 release assay data using personal computer spreadsheet software.

The Chromium-51 release assay is a widely used technique to assess the lysis of labeled target cells in vitro. We have developed a simple technique to analyze data from Chromium-51 release assays using the widely available LOTUS 1-2-3 spreadsheet software. This package calculates percentage specific cytotoxicity and lytic units by linear regression. It uses all data points to compute the linear regression and can determine if there is a statistically significant difference between two lysis curves. The system is simple to use and easily modified, since its implementation requires neither knowledge of computer programming nor custom designed software. This package can help save considerable time when analyzing data from Chromium-51 release assays.

Chromium Radioisotopes↗

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↗

PubMedDate not supplied

Software control of sensing and stimulation for cardiac electrophysiological study.

A software-controlled cardiac stimulator for clinical investigations is described. The stimulator is programmed by the user at a keyboard, while current status and values of parameters are presented on a visual display screen. A menu of predefined cardiac electrophysiological tests is available for user selection. Validity checks on data keyed in by the user and internal checks on safe pacing limits are incorporated in case of malfunction or user error. The system consists of a separate relatively simple isolated sensing and stimulation unit which communicates, via a standard digital input output interface, with a controlling microcomputer. All timing and control functions are performed in software by the computer. The use of high-level FORTRAN as the main programming language provides the system with a high degree of adaptability.

Computers↗

PubMed1994

Predictive performance of two software packages (USC*PACK PC and Abbott PKS system) for the individualization of amikacin dosage in intensive care unit patients.

Many dosing methods (nomogram, pharmacokinetic methods, Bayesian methods) can be used for the individualization of amikacin dosing. Among these methods, it is now well known that the Bayesian method provides a rapid and accurate means for individualizing dosage requirements for patients with diverse pharmacokinetic profiles. However, one problem has not been fully resolved. Should we use population-based parameters reflecting the patient population being monitored or should we used general population parameters? The aim of this study was to answer this question using two widely used software programs (USC*PACK PC and Abbott PKS system) and two different population parameters sets. Predictive performance of these methods was assessed with respect to the prediction of amikacin serum concentrations in intensive care unit (ICU) patients. Our results show that the differences between predicted and measured concentrations were unbiased when the population parameters used were adequate. Precision values were comparable with previously reported values. The predictive performance of the two tested software programs are very comparable in ICU patients. In addition, we demonstrated that performance can be enhanced when using population-based parameters which reflect the patient population being monitored. It is therefore advisable for each user to properly characterize each particular patient population.

Adolescent↗

PubMed1992

SPACAR: a software subroutine package for simulation of the behavior of biomechanical systems.

Direct dynamics computer simulation is gaining importance as a research tool in the biomechanical study of complex human movements. Therefore, the need for general-purpose software packages with which the equations of motion can be derived automatically and solved numerically is growing. In this paper such a method is described: SPACAR. The method is compared to well-known commercially available software packages. On the basis of the results obtained on a test problem simulated with both SPACAR and DADS, it is concluded that both methods are accurate; DADS is much faster. The user-friendliness of SPACAR is less than that of DADS. However, SPACAR has two major advantages. First is the basic deformability of all elements, which allows handling of all kinds of problems within a unified framework; second is the full availability of the source code, which allows the experienced user to broaden the scope of possibilities to any extent.

Biomechanical Phenomena↗

PubMed1985

A software package for the microcomputer control and analysis of research on schedule-induced polydipsia.

This manuscript describes a software package called POLY which offers a range of routines designed to allow the user to set up, run and analyze data for research on schedule-induced polydipsia. The three major routines described are SETUP, RUN and ANALYSIS. The routines are flexible and give the user efficient control over the parameters of the research and the collection and analysis of the data. Although designed for research on schedule-induced polydipsia, the software can be used for other research purposes, requiring only changes in the support hardware.

Animals↗

PubMed1993

BASIC-language software for simultaneous monitoring of blood glucose level and neuronal firing frequency.

We have designed software for an Apple II GS microcomputer allowing simultaneous on-line monitoring of blood glucose level and neuronal firing frequency in experimental rats. Blood glucose level in the carotid blood was continuously measured by a glucose analyzer and digitized through an A/D board. The firing rate of a brain neuron, recorded by a classical technique, was counted by a versatile interface adapter. Both parameters are graphically displayed on the screen. They can also be exported to another computer for off-line analysis. This software is adaptable to other experimental applications in electrophysiology, involving the monitoring of glycemia or other biological parameters.

Animals↗

PubMed1990

Applications of the EVE software for visual modeling.

EVE, the Early Vision Emulation software, is a system for the stimulation of early visual processing. EVE has the ability to carry out the operations of a wide variety of models of spatial vision, motion detection and processing, and spatial sampling. We introduce the EVE software and illustrate some of its applications for models of pattern detection, pattern discrimination, and motion detection.

Humans↗

PubMed1988

Concurrent clinical review: using microcomputer-based DRG-software.

Since the introduction of the Prospective Payment System based on Diagnosis Related Groups (DRGs) in the U.S.A., important information technologies are arising. We discuss how Professional Review Organizations, (PROS) are forcing a better control of appropriateness and quality of medical care. Hospitals should have the internal capabilities to perform, at least, the same reviews as performed by the PROs. Concurrent Clinical Review Systems based on DRGs are a special type of information technology that take place during and even before patient hospitalization, therefore allowing an 'on line' monitoring information. Low-cost microcomputers are playing a major role in the popularization of this technology. 'Clinical Review System' is a microcomputer-based software that renders easy and feasible and otherwise complex task. An effort should be made in order to adapt the philosophy underlying this or other similar software to the European needs.

Computers↗

PubMed1989

Development of personal computer software for a visual electrophysiology laboratory.

This paper describes the software developed by the authors in order to introduce the flexibility and computing power of a modern personal computer in an existing visual electrophysiology laboratory. The basic problems that a programmer must solve in order to implement the main tasks requested are discussed. Such problems include signal acquisition, signal averaging, artifact rejection, time domain analysis, frequency domain analysis and data management. The software developed following our guidelines makes it possible for a personal computer equipped with a commercial analog-to-digital converter to interface directly with the physiologic amplifiers and visual stimulators commonly used either for classical electroretinography or for pattern and focal electroretinography.

Electroretinography↗

PubMed1991

A software for the elaboration of job histories.

This article presents a software designed to help the occupational physician elaborate, print and automatically interrogate the job histories of workers. The need for the surveillance of professional risks throughout careers is the basic assumption on which this software is based and it runs on a PC.

Forms and Records Control↗