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PubMed2003

Software objects in distributed flow measurements.

Increasing complexity of the contemporary industrial measurement systems is a common characteristic. Partitioning of the measurement process into software components that can be realized as separate objects facilitates the development of the measurement system. Using a client/server approach, the measurement system components become shareable and accessible across the network. The components can be deployed anywhere on the network and shared by a considerable number of applications. The paper describes a realization of the flow measurement system with distributed software components, i.e., measurement procedures, which include the concurrent calculation of the measurement results and the corresponding uncertainties.

Computer Communication Networks↗

PubMed1987

Microcomputer system for data acquisition and software handling in chromatography.

A complete, powerful yet simple and inexpensive microcomputer system for chromatography is described. It consists of an electronic interface card and an exploiting software, both controlled by an independent microcomputer. The interface includes all necessary circuits for digitizing the chromatographic signal and for controlling the actuators and the sensors connected with the chromatograph. The software, clock-interrupted, allows simultaneous data acquisition, mathematical treatment, connected plotting, and printing, and drives injection valves and gradient elution pumps. This system is both suitable for high-speed capillary gas chromatography and for high-performance liquid chromatography.

Chromatography↗

PubMed2000

Use of optimization software to determine rugged analysis conditions in high-performance liquid chromatography.

The ruggedness evaluation of an analytical method is now generally required for further validation. By considering ruggedness at an early stage of method development, major disappointments and amount of work could be avoided. This work shows that the optimization software OSIRIS can be helpful for the chromatographer during a method development, as it takes into account the method ruggedness. The ruggedness of the analysis conditions is then evaluated all along the selectivity optimization procedure. This optimization software belongs to the interpretive methods that consist of predicting the optimum conditions by modeling first the solute retention over the parameter space using a minimum number of preliminary runs. The choice of a response function is studied. This response function must be able to take into account several individual criteria: analysis time, minimal resolution and ruggedness of each parameter. Some optimum separations, determined using a ruggedness criteria or not, are given and compared in terms of long term repeatability.

Chromatography, High Pressure Liquid↗

PubMed2001

A hybrid artificial neural network as a software sensor for optimal control of a wastewater treatment process.

For control and automation of biological treatment processes, lack of reliable on-line sensors to measure water quality parameters is one of the most important problems to overcome. Many parameters cannot be measured directly with on-line sensors. The accuracy of existing hardware sensors is also not sufficient and maintenance problems such as electrode fouling often cause trouble. This paper deals with the development of software sensor techniques that estimate the target water quality parameter from other parameters using the correlation between water quality parameters. We focus our attention on the preprocessing of noisy data and the selection of the best model feasible to the situation. Problems of existing approaches are also discussed. We propose a hybrid neural network as a software sensor inferring wastewater quality parameter. Multivariate regression, artificial neural networks (ANN), and a hybrid technique that combines principal component analysis as a preprocessing stage are applied to data from industrial wastewater processes. The hybrid ANN technique shows an enhancement of prediction capability and reduces the overfitting problem of neural networks. The result shows that the hybrid ANN technique can be used to extract information from noisy data and to describe the nonlinearity of complex wastewater treatment processes.

Automation↗

PubMed2006

TM4 microarray software suite.

Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open-source tools for data management and reporting, image analysis, normalization and pipeline control, and data mining and visualization. An integrated MIAME-compliant MySQL database is included. This chapter describes each component of the suite and includes a sample analysis walk-through.

Algorithms↗

PubMed2006

High-content screening: emerging hardware and software technologies.

The field of high-content screening has flourished since 2000 with advancements in automated fluorescence microscopy technologies, fluorescent labeling techniques, and sophisticated image analysis software. Through the use of these technologies, researchers can now monitor cellular and molecular events in individual cells in vitro following drug treatment or RNAi and rapidly screen compound and siRNA libraries. This chapter discusses current and next-generation hardware and software features and capabilities.

Animals↗

PubMed1992

DUE software highlights therapeutic issues.

Drug use evaluation (DUE) or drug use review (DUR) for the ambulatory care setting is creating many opportunities to improve the pharmaceutical care provided by pharmacists. This study documents one year of peer-review interventions based on a retrospective drug utilization review software system (Qualisure, Q-A, Inc.) that screens patient profiles for a high likelihood of drug therapy problems. Letters are written to physicians and pharmacists providing care to these patients. The software identifies frequent opportunities for selecting therapeutic class alternatives to prescribed agents. Antibiotics, antihistamines, nonsteroidal anti-inflammatory drugs, and antidepressants were the classes for which therapeutic class alternatives were most often recommended.

Drug Prescriptions↗

PubMed1998

A novel and innovative quantitative kinetic software for virological colorimetric assays.

This study addresses the limited range of quantification with colorimetric assays (ELISA) starting from the analysis of color production in a reference external curve. An automatic ELISA management software, designated Quanti-Kin Detection System (QKDS) is described, which retains the sensitivity of the end-point reading and extends the dynamic range up to five logarithms with mathematical interpretation of color production. The QKDS software is a generic system suitable for different types of ELISA with substrate incubation at room temperature, does not require dedicated instruments, performs accurate quantification (including assay quality control) and has a user friendly interface. Specific applications were developed for three types of analytes: antibodies, viral antigens and nucleic acids. Data are presented on three representative QKDS applications to HIV antibodies, p24 antigen and proviral DNA kits. The precision of quantification is strictly correlated with the precision of the kit; however, for almost all samples with known analyte amount, the error percentage was below 10%, only for two cases in quantification of HIV proviral DNA the error percentage was around 25%. The necessity for a wide quantification range has been demonstrated by measuring clinical samples, which showed a distribution in all possible quantification ranges for all kits.

Animals↗

PubMed2001

The Virtual Cell: a software environment for computational cell biology.

The newly emerging field of computational cell biology requires software tools that address the needs of a broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging in the area of gene expression. Although some of these established modeling approaches can be adapted to address problems of interest to cell biologists, relatively few software development efforts have been directed at the field as a whole. The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers. It serves to aid the construction of cell biological models and the generation of simulations from them. The system enables the formulation of both compartmental and spatial models, the latter with either idealized or experimentally derived geometries of one, two or three dimensions.

Biology↗

PubMed2001

HEpiMA: software for the identification of heterogeneity in meta-analysis.

Meta-analysis is a quantitative method available to epidemiologists, psychologists, social scientists and others who wish to produce a summary measure of the effect of exposure on disease, based on results from published studies along with a summary measure of uncertainty. The magnitude of the effect vary from study to study because of differences in the features of these studies (design, population, control of confounding variables etc.). From the various studies an estimator is formed by pooling the results found in each study in one summary measure. This summary (or pooled) measure is meaningful only if the magnitude of heterogeneity between study effects is small and can be explained by sampling variation. In this paper, we present HEpiMA, a new comprehensive and user-friendly software program for epidemiologic meta-analysis. HEpiMA has new features that are not available in other programs. The program carries out a complete study of heterogeneity of study effects with 11 hypothesis test results. In addition to model-based methods, the program also implements bootstrap methodology. New useful estimators of heterogeneity, Ri and CV(B), developed by the authors are given in the output. In addition to these unique features, the major advantage of this software is the option for direct entry of adjusted relative risk estimates of individual studies, the most common form of presentation of results in the epidemiologic literature. This program may also be useful for meta-analysts of clinical trials, in which the relative risk is the parameter of interest as it also allows the entry of crude data under the form of 2x2 tables.

Epidemiologic Methods↗

PubMed2003

Model validation software for classification models using repeated partitioning: MVREP.

The process of assessing the prediction ability of a computational model is called model validation. For models predicting a categorical response, the prediction ability is usually quantified by prediction measures such as sensitivity, specificity, and accuracy. This paper presents a software Model Validation using Repeated Partitioning (MVREP) that implements a computer-intensive, nonparametric approach to model validation, which we call the re-partitioning method. MVREP, developed using the SAS Macro language, repeats the process of randomly partitioning a dataset and subsequently performing standard model validation procedures, such as cross-validation, a large number of times and generates the empirical sampling distributions of prediction measures. The means of the sampling distributions serve as the point estimates of prediction measures of the model. The variances of the sampling distributions provide a direct assessment of variability for the point estimates of prediction measures. An example is presented using a mouse developmental toxicity chemical dataset to illustrate how the software can be used for the assessment of structure-activity relationships models.

Animals↗

PubMed2003

Software to compute and conduct sequential Bayesian phase I or II dose-ranging clinical trials with stopping rules.

The aim of dose-ranging phase I (resp. phase II) clinical trials is to rapidly identify the maximum tolerated dose (MTD) (resp., minimal effective dose (MED)) of a new drug or combination. For the conduct and analysis of such trials, Bayesian approaches such as the Continual Reassessment Method (CRM) have been proposed, based on a sequential design and analysis up to a completed fixed sample size. To optimize sample sizes, Zohar and Chevret have proposed stopping rules (Stat. Med. 20 (2001) 2827), the computation of which is not provided by available softwares. We present in this paper a user-friendly software for the design and analysis of these Bayesian Phase I (resp. phase II) dose-ranging Clinical Trials (BPCT). It allows to carry out the CRM with stopping rules or not, from the planning of the trial, with choice of model parameterization based on its operating characteristics, up to the sequential conduct and analysis of the trial, with estimation at stopping of the MTD (resp. MED) of the new drug or combination.

Bayes Theorem↗

PubMed1998

The Multi Unit Activity analyzer: a Windows based hardware-software system for low cost, high speed analog to digital data conversion, data acquisition and window discrimination.

The Multi Unit Activity analyzer is a hardware-software package for multi-purpose, two-channel data acquisition, with a computer dependent maximal digitizing frequency selectable from 1 to 27,000 s(-1) on both channels simultaneously. The hardware is connected to an IBM compatible PC through one of the serial ports (standard RS 232 interface). Software was developed to view digitized signals and record or read them on or from the harddisk. The program can also perform amplitude based window discrimination on the raw signal, on-line or during replay. The system is used for recording and analyzing multi unit activity from neuronal tissue in our electrophysiology lab but it can be applied in a variety of other settings. Basic programming routines are available that allow customized data acquisition.

Analog-Digital Conversion↗

PubMed2000

Windows software for cardiac electrophysiology studies and ablation monitoring.

A system for cardiac electrophysiology (EP) studies consisting of a Windows software package, a standard 120 MHz Pentium PC with a high-performance video card and a data acquisition card has been developed during this study. The system is capable of real time data acquisition and storage of 24 channels with simultaneous display of 1-16 arbitrarily chosen channels at a sampling rate of 500 Hz. It can be used clinically in electrophysiology studies and during catheter radio-frequency ablation treatment for monitoring the ablation and its effects. The built-in ablation monitoring capability enables combined EP study and ablation treatment, thus helping to reduce exposure times and the total time needed per patient. For clinical use the software includes versatile tools for data analysis and reduction. Our system has been developed in association with Department of Cardiology of Tampere University Hospital and has been in regular clinical use there.

Electrophysiology↗

PubMed1998

Trigeminal neuropathy: improved imaging with a dental computed tomography software program.

PURPOSE: This study evaluated the use of images obtained by a dental computed tomography (CT) software program in the diagnosis and treatment of trigeminal neuropathy associated with jaw abnormality. PATIENTS AND METHODS: Twelve patients with jaw abnormality associated with trigeminal neuropathy as the presenting symptom were studied by plain film radiography (PFR) and by a dental CT software program (DS) that displays multiple panoramic and cross-sectional views of the mandible and maxilla. The two modalities were compared for delineation of the integrity of mandibular foramen, mandibular canal, mental foramen, incisive foramen, and incisive canal. Also, displacement of the neurovascular bundle was evaluated and scored. RESULTS: The DS was superior to PFR in showing the bony integrity of the foramina and canals in the jaws, as well as the degree of displacement of the neurovascular bundle. CONCLUSION: DS should be the study of choice for evaluating trigeminal neuropathy associated with abnormalities of the jaws.

Adult↗

PubMed2000

QED v 1.0: a software package for quantitative electron diffraction data treatment.

A new software package for quantitative electron diffraction data treatment of unknown structures is described. No "a priori" information is required by the package which is able to perform in successive steps the 2-D indexing of digitised diffraction patterns, the extraction of the intensity of the collected reflections and the 3-D indexing of all recorded patterns, giving as results the lattice parameters of the investigated structure and a series of data files (one for each diffraction pattern) containing the measured intensities and the relative e.s.d.s of the 3-D indexed reflections. The software package is mainly conceived for the treatment of diffraction patterns taken with a Gatan CCD Slow-Scan Camera, but it can also deal with generic digitised plates. The program is designed to extract intensity data suitable for structure solution techniques in electron crystallography. The integration routine is optimised for a correct background evaluation, a necessary condition to deal with weak spots of irregular shape and an intensity just above the background.

Algorithms↗

PubMed1989

A user-oriented software for cytological image analysis. Application to automatic DNA content measurement of thyroid cells.

More and more physicians and researchers in biology and image processing and analysis are using and developing methods which involve image analysing systems: image analysis permits replacement of qualitative subjective evaluation of cytological and histological specimens by quantitative methods. The purpose of our work was to provide a software which would fulfil constraints set by different users. This software is based on the following features: an automated cytology oriented architecture, a standard user interface and a selectable user mode. The system has been used to build a protocol for DNA content measurement on thyroid cells.

DNA, Neoplasm↗

PubMed2000

Use of the software 'Poser4' in reconstruction of accident and crime scenes.

The reconstruction of accident and crime scenes demands the full attention of the forensic working physician. Description by words is often difficult and liable to be misunderstood. Reconstruction in the original places of events are expensive and in some cases impossible. Computer graphics and animations give the possibility to construct the original course of events. Poser4 is a software package to perform these reconstructions in an easy and vivid way. We investigated the possibilities of reconstructing an accident with this software.

Accidents↗