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At least 1,459 records · Page 81Linked to original sources
PubMed2005

Advection-dispersion modelling tools: what about numerical dispersion?

In general the transport of dissolved substances and fine suspended particles is governed by the one-dimensional advection-dispersion equation. In order to model the transport of dissolved substances and fine suspended particles, the advection-dispersion equation is incorporated into commonly used urban drainage modelling tools such as InfoWorks CS (Wallingford Software, United Kingdom) and MOUSE (DHI Software, Denmark). Two examples show the use of InfoWorks CS and MOUSE using standard model settings. Modelling results using tracer experiments show that numerical model parameters need to be altered in order to calibrate the model. Using tracer experiments as a model calibration tool, it is shown that a non-negligible amount of dispersion is generated by InfoWorks CS and MOUSE and that it is in fact the numerical dispersion that is calibrated.

Calibration↗
PubMedDate not supplied

Object-oriented design of medical imaging software.

A special software package for interactive display and manipulation of medical images was developed at the University Hospital of Geneva, as part of a hospital wide Picture Archiving and Communication System (PACS). This software package, called Osiris, was especially designed to be easily usable and adaptable to the needs of noncomputer-oriented physicians. The Osiris software has been developed to allow the visualization of medical images obtained from any imaging modality. It provides generic manipulation tools, processing tools, and analysis tools more specific to clinical applications. This software, based on an object-oriented paradigm, is portable and extensible. Osiris is available on two different operating systems: the Unix X-11/OSF-Motif based workstations, and the Macintosh family.

Computer Communication Networks↗
PubMed2004

A shockwave approach for web-based clinical motion analysis.

Advances in Internet connectivity and personal multimedia computing have created opportunities for integrating simple motion analysis into clinical practice. The Macromedia Shockwave environment provides tools for creating media-rich software that runs within a Web browser. For this project, clinical motion analysis software was created using Shockwave that can load digital video clips of a client's motion, step/shuttle/play through the clip, superimpose a grid over the video image, measure relative joint angles, scale to a linear factor, measure distances, and measure average velocities. After installing the Shockwave and Quicktime video plug-ins, the Motion Analysis Tools-Shockwave program runs directly from a Web page hyperlink. Program testing involved comparing angle measurements, linear distances, stride length, and walking speed among six video clips. The first three clips were of a transtibial prosthesis being carried through the field of view (640 x 480, 320 x 240, 320 x 240 enlarged to 640 x 480). The second set of three clips was of a metal square carried through the field of view. Average root mean square errors were 2.0 degrees for angle measures and 1.2 cm for length measures. Stride length standard deviation was 4.6 cm (mean length = 212.1 cm). Average walking speed standard deviation was 0.015 m/s (mean speed = 1.15 m/s). The test results were consistent with video motion analysis results and within an acceptable range for clinical design-making. This Web-based motion analysis approach provides a useful tool for ubiquitous, quantitative, clinical gait analysis.

Decision Support Techniques↗
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↗
PubMed2003

Binding site characteristics in structure-based virtual screening: evaluation of current docking tools.

Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets (cyclooxygenase-2, estrogen receptor, p38 MAP kinase, gyrase B, thrombin, gelatinase A, neuraminidase) in order to assess their accuracy in virtual screening. Sets of known inhibitors were added to and ranked relative to a random library of drug-like compounds. Performance was compared in terms of enrichment factors and CPU time consumption. Results and specific features of the two new tools are discussed and compared to previously published results using FlexX (Tripos, Inc.) as a docking engine. In addition, general criteria for the selection of docking algorithms and scoring functions based on binding-site characteristics of specific protein targets are proposed. Figure Enrichment factors obtained with FlexX, Glide and FRED docking engines in combination with different scoring functions for seven selected targets with highly variable binding sites

Algorithms↗
PubMed2004

Using the Mplus computer program to estimate models for continuous and categorical data from twins.

Historically, the focus of behavior genetic research was to obtain estimates of the sources of familial resemblance for a single phenotype. Current research strategies have moved beyond heritability estimates to the search for physiological and behavioral mechanisms by which genetic risk is translated into individual differences in behavior and disease liability. Such research questions often require multivariate designs and complex analytic models, including the analysis of continuous and categorical dependent variables within the same model. Recent advances in computer software for categorical data analysis have increased the tools available for researchers in behavior genetics. This paper describes how to use the Mplus software program (Muthén and Muthén, 1998, 2002) for the analysis of data obtained from twins. Example analyses include two- and five-group twin models for univariate and bivariate continuous and categorical variables. Data on alcoholism and age at first drink drawn from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders are used to illustrate how Mplus can be used to analyze multiple-category variables, recode and transform variables, select subgroups for analysis, handle subjects with incomplete data, include constraints to ensure non-negative loadings, include model covariates, model sex differences, and test alternative hypotheses about mediation of genetic risk by measured variables.

Adolescent↗
PubMed2005

Talairach-based parcellation of neonatal brain magnetic resonance imaging data: validation of a new approach.

BACKGROUND AND PURPOSE: Talairach-based parcellation (TP) of human brain magnetic resonance imaging (MRI) data has been used increasingly in clinical research to make regional measurements of brain structures in vivo. Recently, TP has been applied to pediatric research to elucidate the changes in regional brain volumes related to several neurological disorders. However, all freely available tools have been designed to parcellate adult brain MRI data. Parcellation of neonatal MRI data is very challenging owing to the lack of strong signal contrast, variability in signal intensity within tissues, and the small size and thus difficulty in identifying small structures used as landmarks for TP. Hence the authors designed and validated a new interactive tool to parcellate brain MRI data from newborns and young infants. METHODS: The authors' tool was developed as part of a postprocessing pipeline, which includes registration of multichannel MR images, segmentation, and parcellation of the segmented data. The tool employs user-friendly interactive software to visualize and assign the anatomic landmarks required for parcellation, after which the planes and parcels are generated automatically by the algorithm. The authors then performed 3 sets of validation experiments to test the precision and reliability of their tool. RESULTS: Validation experiments of intra-and interrater reliability on data obtained from newborn and 1-year-old children showed a very high sensitivity of >95% and specificity >99.9%. The authors also showed that rotating and reformatting the original MRI data results in a statistically significant difference in parcel volumes, demonstrating the importance of using a tool such as theirs that does not require realignment of the data prior to parcellation. CONCLUSIONS: To the authors' knowledge, the presented approach is the first TP method that has been developed and validated specifically for neonatal brain MRI data. Their approach would also be valuable for the analysis of brain MRI data from older children and adults.

Brain↗
PubMed1993

Non-invasive assessment of cardiovascular mechanics using a new, user-friendly software application.

Currently, in most non-invasive imaging laboratories, echocardiographic tracings are interpreted by "eyeballing" M-mode and 2-dimensional echocardiographic recordings. This subjective method of data analysis severely hampers the possibility of serial assessment of physiological interventions on cardiovascular disease states. Moreover, acquisition of important cardiovascular physiological data usually requires recordings of instantaneous aortic pressure and flow data that, until recently, could only be acquired invasively in the cardiac catheterization laboratory. Recently, our laboratory has developed and validated new "non-invasive" methods for the acquisition of aortic pressure and flow using calibrated subclavian pulse tracings and continuous wave aortic Doppler, respectively. With these limitations and new developments in mind, we developed new software that enables simultaneous non-invasive acquisition of left ventricular (LV) chamber geometry and aortic pressure and flow data. This new, user-friendly software in conjunction with other non-invasive tools allows non-invasive quantification of multiple cardiovascular physiological parameters. More importantly, the new software enables objective and serial assessment of multiple pharmacological interventions on various patients' disease states.

Aged↗
PubMed2004

Modeling energy savings from urban shade trees: an assessment of the CITYgreen energy conservation module.

CITYgreen software has become a commonly used tool to quantify the benefits of urban shade trees. Despite its frequent use, little research has been conducted to validate results of the CITYgreen energy conservation module. The first objective of this study is to perform a familiar application of CITYgreen software to predict the potential energy savings contribution of existing tree canopies in residential neighborhoods during peak cooling summer months. Unlike previous studies utilizing CITYgreen, this study also seeks to assess the software's performance by comparing model results (i.e., predicted energy savings) with actual savings (i.e., savings derived directly from energy consumption data provided by the electric utility provider). Homeowners in an older neighborhood with established trees were found to use less energy for air-conditioning than homeowners in a recently developed site. Results from the assessment of model performance indicated that CITYgreen more accurately estimated the energy savings in the highly vegetated, older neighborhood.

Cities↗
PubMed2005

ProGenGrid: a grid-enabled platform for bioinformatics.

In this paper we describe the ProGenGrid (Proteomics and Genomics Grid) system, developed at the CACT/ISUFI of the University of Lecce which aims at providing a virtual laboratory where e-scientists can simulate biological experiments, composing existing analysis and visualization tools, monitoring their execution, storing the intermediate and final output and finally, if needed, saving the model of the experiment for updating or reproducing it. The tools that we are considering are software components wrapped as Web Services and composed through a workflow. Since bioinformatics applications need to use high performance machines or a high number of workstations to reduce the computational time, we are exploiting a Grid infrastructure for interconnecting wide-spread tools and hardware resources. As an example, we are considering some algorithms and tools needed for drug design, providing them as services, through easy to use interfaces such as the Web and Web service interfaces built using the open source gSOAP Toolkit, whereas as Grid middleware we are using the Globus Toolkit 3.2, exploiting some protocols such as GSI and GridFTP.

Computational Biology↗
PubMed2000

Mapping XML documents into databases: a Data-Driven Framework for bioinformatic data interchange.

The Data-Driven Framework (DDF) described here addresses two major problems for healthcare Electronic Data Interchange, data formats and software development costs. The use of a standard XML Document Type Definition (DTD) allows robust representation in any application area and leverages industry-standard tools and development directions. The DDF allows reduced software development and maintenance costs since all data-entry and database tools are generated from the DTD. The DTD can change and the tools can be regenerated. The case-study below uses the DDF for reporting cell assays to determine the roles of factors influencing cellular gene expression and regulation.

Computer Communication Networks↗
PubMedDate not supplied

Serum proteomic features for detection of endometrial cancer.

To find new potential biomarkers for detection of endometrial cancer (EC), 70 serum samples including 40 from EC patients and 30 from normal healthy females were detected by surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF-MS) using WCX2 (weak cation exchange) protein chip. Mass spectra were then assessed with three powerful data-mining tools: a tree classifier, Biomarker Wizard software, and Biomarker Patterns System. The diagnostic pattern combined with 13 potential biomarkers could differentiate EC patients from healthy persons, with a specificity of 100%, sensitivity of 92.5%, and total coincidence of 95.7%. The combination of surface-enhanced laser desorption-ionization with bioinformatics tools could help find new biomarkers and establish with high sensitivity and specificity for the detection of EC.

Adult↗
PubMed2001

LISA: an intranet-based flexible database for protein crystallography project management.

The increase in the number of projects carried out in protein crystallography laboratories has emphasized the need for effective management of project information and data. To meet this need, a flexible web-accessible database for protein crystallography project management (LISA) has been developed using the open-source software MySQL and PHP4. The database contains information about all aspects of structure-determination projects, including primer and plasmid sequences, protein expression, purification and crystallization results, structure coordinate files and resultant publications. The database web pages include links to relevant servers and contain, in addition, tools for processing stored information. The software package is freely available.

Crystallography↗
PubMed2003

Experiences with a generator tool for building clinical application modules.

OBJECTIVES: To elaborate main system characteristics and relevant deployment experiences for the health information system (HIS) Orbis/OpenMed, which is in widespread use in Germany, Austria, and Switzerland. METHODS: In a deployment phase of 3 years in a 1.200 bed university hospital, where the system underwent significant improvements, the system's functionality and its software design have been analyzed in detail. We focus on an integrated CASE tool for generating embedded clinical applications and for incremental system evolution. We present a participatory and iterative software engineering process developed for efficient utilization of such a tool. RESULTS: The system's functionality is comparable to other commercial products' functionality; its components are embedded in a vendor-specific application framework, and standard interfaces are being used for connecting subsystems. The integrated generator tool is a remarkable feature; it became a key factor of our project. Tool generated applications are workflow enabled and embedded into the overall data base schema. Rapid prototyping and iterative refinement are supported, so application modules can be adapted to the users' work practice. CONCLUSIONS: We consider tools supporting an iterative and participatory software engineering process highly relevant for health information system architects. The potential of a system to continuously evolve and to be effectively adapted to changing needs may be more important than sophisticated but hard-coded HIS functionality. More work will focus on HIS software design and on software engineering. Methods and tools are needed for quick and robust adaptation of systems to health care processes and changing requirements.

Computer Systems↗
PubMed1996

Digital subtraction angiography for arteriovenous malformations in stereotactic radiosurgery.

Images coming from digital subtraction angiography (DSA) are affected by a perspective distortion due to the use of image intensifiers. As a result, DSA cannot be used for the accurate definition of stereotactic coordinates. A correction method has been developed to enable the use of DSA for the radiosurgery of arteriovnous malformations. A software program and a special phantom tool were employed. The phantom is made by a computer-controlled drilling machine which makes holes in a Plexiglas plate. It has 865 calibration steel spheres with coordinates determined with a precision of 0.01 mm. A calibration image is acquired by a personal computer, and the software calculates the transformation algorithm to superimpose the image on the known positions of the phantom. This algorithm is saved and then recalled to transform the diagnostic images.

Angiography, Digital Subtraction↗
PubMed1996

Finding genes by computer: the state of the art.

Discovering new genes, and their functions, can be aided not only by special purpose gene (and coding region) finding software, but also by searches in key databases, and by programs for finding particular sites relevant to gene expression, such as promoters and splice sites. No one software package includes all the necessary tools. I describe here the main kinds of tools; their working principles, strengths and limitations; and how combined evidence from multiple tools can aid in optimum gene identification.

Amino Acid Sequence↗
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↗