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At least 577 records · Page 32Linked to original sources

PubMed1996

Lane tracking software for four-color fluorescence-based electrophoretic gel images.

Software to track sample lanes automatically in four-color, fluorescence-based, electrophoretic gel images has been developed for application in large-scale DNA sequencing projects. Lanes and lane boundaries are tracked by analyzing a first difference approximation to the gradient of a vertically integrated and processed "brightness" profile. Initially lanes are located in a region of the gel image selected for good horizontal lane spacing and signal strength. The software uses models of expected lane and interlane spacing and lateral lane behavior to maintain accurate tracking on imperfect gels. In areas where intensity-based tracking is difficult, interpixel column correlation is also used to locate and define lane features. Summary statistics and compressed-in-time images are generated for user evaluation of tracking performance. The software developed has been tested successfully on gel images with degradations including significant horizontal lane motion (curving) and image artifacts, and is now in full-scale use in our sequencing projects.

Algorithms↗

PubMed2006

Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species.

The domestication and improvement of fruit-bearing crops resulted in a large diversity of fruit form. To facilitate consistent terminology pertaining to shape, a controlled vocabulary focusing specifically on fruit shape traits was developed. Mathematical equations were established for the attributes so that objective, quantitative measurements of fruit shape could be conducted. The controlled vocabulary and equations were integrated into a newly developed software application, Tomato Analyzer, which conducts semiautomatic phenotypic measurements. To demonstrate the utility of Tomato Analyzer in the detection of shape variation, fruit from two F2 populations of tomato (Solanum spp.) were analyzed. Principal components analysis was used to identify the traits that best described shape variation within as well as between the two populations. The three principal components were analyzed as traits, and several significant quantitative trait loci (QTL) were identified in both populations. The usefulness and flexibility of the software was further demonstrated by analyzing the distal fruit end angle of fruit at various user-defined settings. Results of the QTL analyses indicated that significance levels of detected QTL were greatly improved by selecting the setting that maximized phenotypic variation in a given population. Tomato Analyzer was also applied to conduct phenotypic analyses of fruit from several other species, demonstrating that many of the algorithms developed for tomato could be readily applied to other plants. The controlled vocabulary, algorithms, and software application presented herein will provide plant scientists with novel tools to consistently, accurately, and efficiently describe two-dimensional fruit shapes.

Algorithms↗

PubMed1998

Integrated software for a macromolecular crystallography synchrotron beamline.

A package of software has been produced for the operation of the synchrotron beamline X12-C at the National Synchrotron Light Source at Brookhaven National Laboratory. Years of observing common user mistakes has enabled the production of software that reduces user errors significantly. Users of the beamline communicate with all the experimental apparatus, including both the data-collection equipment and the beamline components, including the monochromator, through an easy-to-use graphical user interface (GUI). Important features of the system are (1) its modularity, so that different underlying programs or different apparatus can be incorporated easily; (2) its ease of use, minimizing both user errors and training effort; and (3) that most of the experimental operations and parameters are logged automatically, again minimizing errors and facilitating more-or-less automatic reduction of the data. Features of the software are useful enough to have been incorporated into operations at other synchrotron beamlines.

Crystallography, X-Ray↗

PubMed1997

CT-based software for 3-D localization and reconstruction in stepping source brachytherapy.

This paper describes innovative software for catheter localization and three-dimensional (3-D) reconstruction in stepping source brachytherapy applications. Patient information is a set of computed tomography (CT) slices scanned during the implantation of brachytherapy catheters. Catheter geometry and patient anatomy are exported for use with dose calculation software modules. The errors produced by the system are also encouragingly low. Time saving was achieved, in terms of other traditional reconstruction techniques. Various automated procedures, 3-D graphics and a user-friendly GUI, have contributed to providing a powerful, comprehensive software tool, directly useable in the clinical practice.

Brachytherapy↗

PubMed2002

Hardware and software platform for real-time processing and visualization of echographic radiofrequency signals.

In this paper the architecture of a hardware and software platform, for ultrasonic investigation is presented. The platform, used in conjunction with an analog front-end hardware for driving the ultrasonic transducers of any commercial echograph, having the radiofrequency echo signal access, make it possible to dispose of a powerful echographic system for experimenting any processing technique, also in a clinical environment in which real-time operation mode is an essential prerequisite. The platform transforms any echograph into a test-system for evaluating the diagnostic effectiveness of new investigation techniques. A particular user interface was designed in order to allow a real-time and simultaneous visualization of the results produced in the different stages of the chosen processing procedure. This is aimed at obtaining a better optimization of the processing algorithm. The most important platform aspect, which also constitutes the basic differentiation with respect to similar systems, is the direct processing of the radiofrequency echo signal, which is essential for a complete analysis of the particular ultrasound-media interaction phenomenon. The platform completely integrates the architecture of a personal computer (PC) giving rise to several benefits, such as the quick technological evolution in the PC field and an extreme degree of programmability for different applications. The PC also constitutes the user interface, as a flexible and intuitive visualization support, and performs some software signal processing, by custom algorithms and commercial libraries. The realized close synergy between hardware and software allows the acquisition and real-time processing of the echographic radiofrequency (RF) signal with fast data representation.

Computer Graphics↗

PubMed1996

A computer software package to facilitate clinical audit of outpatient paediatric dentistry.

This paper reports the development and function of a computer program for clinical audit of outpatients in hospital paediatric dentistry in the United Kingdom. The project was one of several national audit projects supported by the Faculty of Dental Surgery, Royal College of Surgeons of England, and funded by the Department of Health. The software is designed to record data utilizing a nationally-agreed minimum set of codes for dental diagnosis, treatment and medical complications, together with patient demographic details pertaining to source of referral, age and sex of patient, and area of residence. A significant component of the software is a flexible report generator which allows data to be analysed using any combination of the above criteria. Audit of activity in hospital dentistry is desirable to enable comparisons to be made between groups of patients and treatments related to diagnosis. This provides the information necessary to enable improvements in clinical practice whilst also assisting the development of both local and national clinical guidelines. Use of this software package will enable such comparisons to be made not only within one hospital but also between different hospital and regions in the United Kingdom.

Ambulatory Care↗

PubMed1984

The importance of software programmable pacemakers: in vivo programming of a prototype device.

Recently, we have developed microcomputer-oriented pacemakers with true software flexibility. The first 25 devices implanted (DPG-1 type) exhibited an unexpected phenomenon caused by a microcomputer error. A safety mechanism switched off all special functions and automatically reset all parameters to standard settings. The problem was solved by noninvasive modification of the software. More than 200 units (TX-1 type), which are rate responsive pacemakers based on the QT principal, were implanted up to May 1984. These pacemakers were built using the same microelectronics as used in the DPG 1 pacemaker. Knowledge gained from clinical evaluation was directly applied not only to the patients receiving new implants but also to the preexisting implantees. This was done by software reprogramming in the implanted unit.

Arrhythmias, Cardiac↗

PubMed1993

Remote control software.

Any of these remote control packages will accomplish the task of controlling another PC from a distant machine. Since all of the programs are easy to use, perform the same functions, and provide excellent security, there is no one clear winner. If your aim is to control Windows programs remotely, then Carbon Copy for Windows is the fastest software. It falls short in running DOS based programs and has greater hardware requirements because it is a Windows application. Norton pcAnywhere is a reliable program that rivals Carbon Copy for Windows' speed, even when controlling a Windows program remotely. Its support for DOS is better. Close-Up is the easiest to install, will run DOS programs without problem, and can run Windows programs as well. Under Windows, DOS programs can be executed in a window or as a full screen application. However, its speed ratings when working in Windows have been among the slowest. Carbon Copy for the Mac brings most of the features of the Windows version of this program to the Macintosh environment. The software allows users to control remote Macintosh computers, and to perform file transfers in the background. It does not permit a PC to control a Mac or a Mac to control a PC. List prices for these programs are $179 to $199 for packages with host and remote software, but street prices range from approximately $100 to $120. A 9600 baud modem with data compression (yielding a net speed of about 14,400 bits/sec) and error correction costs approximately $200 to $300.(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Systems↗

PubMed2004

The effects of an interactive software application on the self-assessment ability of dental students.

A randomised controlled trial was designed to test an Internet-based interactive application as a stand-alone support for the development of self-assessment skills among second-year dental students at the Faculty of Dentistry, University of Malmö, Sweden. Fifty-two students were randomised into an experimental (n = 26) and a control group (n = 26). Both groups went through four identical learning cases in elementary clinical Periodontology during a period of 1 month. The experimental group received the cases with the interactive software, while the control group received them through a static web page. After the end of the learning phase, both groups were assessed blindly by two assessors during the interactive examination methodology. There was a moderate agreement between the two assessors, but both failed to find any significant differences between the two groups with regard to self-assessment skills and overall performance of the students. Students positively received the Internet support, but several attitude differences were observed between the two groups during the study. Time on task and competence with computers were positively correlated to assessment results for both groups. On the basis of these findings, it remains unclear if computer-based applications with automated feedback can constitute an effective remedial support for the improvement of self-assessment skills of students. In addition, for such applications to be successfully accepted, two factors are critical: students must have a clear perception of the benefits deriving from the use of the software and the use of the software should be integrated in the curriculum, replacing some of the existing workload.

Attitude to Computers↗

PubMed2001

Technical note: check software for use with trans-rectal ultrasound guided I-125 seed prostate implants.

In-house software has been developed to enable the dose distribution of a commercial treatment planning system to be verified prior to permanent trans-rectal ultrasound guided I-125 seed implantation of the prostate. Printouts enabling the required loading pattern to be communicated to other staff groups are also generated. This software can be obtained via the authors and the AAPM software exchange (URL: http://aapm.org/medphys/resources/software/index.htm).

Brachytherapy↗

PubMed2005

A method and software for segmentation of anatomic object ensembles by deformable m-reps.

Deformable shape models (DSMs) comprise a general approach that shows great promise for automatic image segmentation. Published studies by others and our own research results strongly suggest that segmentation of a normal or near-normal object from 3D medical images will be most successful when the DSM approach uses (1) knowledge of the geometry of not only the target anatomic object but also the ensemble of objects providing context for the target object and (2) knowledge of the image intensities to be expected relative to the geometry of the target and contextual objects. The segmentation will be most efficient when the deformation operates at multiple object-related scales and uses deformations that include not just local translations but the biologically important transformations of bending and twisting, i.e., local rotation, and local magnification. In computer vision an important class of DSM methods uses explicit geometric models in a Bayesian statistical framework to provide a priori information used in posterior optimization to match the DSM against a target image. In this approach a DSM of the object to be segmented is placed in the target image data and undergoes a series of rigid and nonrigid transformations that deform the model to closely match the target object. The deformation process is driven by optimizing an objective function that has terms for the geometric typicality and model-to-image match for each instance of the deformed model. The success of this approach depends strongly on the object representation, i.e., the structural details and parameter set for the DSM, which in turn determines the analytic form of the objective function. This paper describes a form of DSM called m-reps that has or allows these properties, and a method of segmentation consisting of large to small scale posterior optimization of m-reps. Segmentation by deformable m-reps, together with the appropriate data representations, visualizations, and user interface, has been implemented in software that accomplishes 3D segmentations in a few minutes. Software for building and training models has also been developed. The methods underlying this software and its abilities are the subject of this paper.

Algorithms↗

PubMed2003

Optimization of computer software settings improves accuracy of pulsed-field gel electrophoresis macrorestriction fragment pattern analysis.

Computer-assisted analysis of pulsed-field gel electrophoresis (PFGE) libraries can facilitate comparisons of fragment patterns present on multiple gels. We evaluated the ability of the Advanced Analysis (version 4.01) and Database (version 1.12) modules of the Phoretix gel analysis software package (Nonlinear USA, Inc., Durham, N.C.) to accurately match DNA fragment patterns. Two gels containing 38 lanes of SmaI-digested Enterococcus faecalis OG1RF DNA were analyzed to assess the impact of (i) varying the lane position of the standards, (ii) using gel plugs made at different times, and (iii) normalizing the fragment patterns by using molecular weight (MW) algorithms versus retardation factor (R(f)) algorithms. Two sets of PFGE libraries (one containing SmaI restriction patterns from 62 Enterococcus faecium isolates and the other containing SmaI restriction patterns of 89 Staphylococcus aureus isolates) were analyzed to assess the impact of varying the matching tolerance algorithm (designated as the vector box setting [VBS]) in the Phoretix software. Varying the lane position of standards on a gel and using gel plugs made on different days resulted in different VBSs, although it was not possible to judge whether those differences were statistically significant. Normalization of E. faecalis OG1RF fragment patterns by R(f) and MW methodology yielded no statistically significant differences in variability between the same fragment on different lanes. Suboptimal VBSs decreased the specificity with which related isolates were grouped together in dendrograms. The optimal VBS for analysis of PFGE fragment patterns from E. faecalis isolates differed from that for S. aureus isolates and sometimes was not that recommended by the manufacturer. Thus, computer-assisted analysis of PFGE patterns seemed to compensate for the intra- and intergel variation evaluated in the present study, and optimizing the software for the species to be tested was a critical preliminary step before further PFGE library analysis.

Algorithms↗

PubMed2006

Validation of VITEK 2 version 4.01 software for detection, identification, and classification of glycopeptide-resistant enterococci.

We evaluated the ability of the new VITEK 2 version 4.01 software to identify and detect glycopeptide-resistant enterococci compared to that of the reference broth microdilution method and to classify them into the vanA, vanB, vanC1, and vanC2 genotypes. Moreover, the accuracy of antimicrobial susceptibility testing with agents with improved potencies against glycopeptide-resistant enterococci was determined. A total of 121 enterococci were investigated. The new VITEK 2 software was able to identify 114 (94.2%) enterococcal strains correctly to the species level and to classify 119 (98.3%) enterococci correctly to the glycopeptide resistance genotype level. One Enterococcus casseliflavus strain and six Enterococcus faecium vanA strains with low-level resistance to vancomycin were identified with low discrimination, requiring additional tests. One of the vanA strains was misclassified as the vanB type, and one glycopeptide-susceptible E. facium wild type was misclassified as the vanA type. The overall essential agreements for antimicrobial susceptibility testing results were 94.2% for vancomycin, 95.9% for teicoplanin, 100% for quinupristin-dalfopristin and moxifloxacin, and 97.5% for linezolid. The rates of minor errors were 9% for teicoplanin and 5% for the other antibiotic agents. The identification and susceptibility data were produced within 4 h to 6 h 30 min and 8 h 15 min to 12 h 15 min. In conclusion, use of VITEK 2 version 4.01 software appears to be a reliable method for the identification and detection of glycopeptide-resistant enterococci as well as an improvement over the use of the former VITEK 2 database. However, a significant reduction in the detection time would be desirable.

Anti-Bacterial Agents↗

PubMed2000

Costs of smoking during pregnancy: development of the maternal and child health smoking attributable mortality, morbidity and economic costs (MCHSAMMEC) software.

The development and availability is described of new, user friendly software, the Maternal and Child Health Smoking Attributable Mortality, Morbidity and Economic Costs (MCHSAMMEC), that will allow states and other entities to estimate pregnancy related, smoking attributable costs for their population. The methodology underlying the MCHSAMMEC software, including calculations used in the prevalence based analysis of smoking attributable mortality and costs of infant neonatal care, are described, along with design and data management features and possible applications of the software for policy and program development at various levels of the health care system.

Adult↗

PubMed2002

The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.

Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe the SBW architecture and the current set of modules, as well as alternative implementation technologies.

Computational Biology↗

PubMed2006

Polyp detection with CT colonography: primary 3D endoluminal analysis versus primary 2D transverse analysis with computer-assisted reader software.

PURPOSE: To retrospectively compare primary three-dimensional (3D) endoluminal analysis with primary two-dimensional (2D) transverse analysis supplemented by computer-assisted reader (CAR) software for computed tomographic (CT) polyp detection and reader reporting times. MATERIALS AND METHODS: Ethical permission and patient consent were obtained from all donor institutions for use of CT colonography data sets. Twenty CT colonography data sets from 14 men (median age, 61 years; age range, 52-78 years) with 48 endoscopically proved polyps were selected. Polyp coordinates were documented in consensus by three unblinded radiologists to create a reference standard. Two radiologists read the data sets, which were randomized between primary 3D endoluminal views with 2D problem solving and 2D views supplemented by CAR software. Reading times and diagnostic confidence were documented. The CAR software highlighted possible polyps by superimposing circles on the 2D transverse images. Data sets were reread after 1 month by using the opposing analysis method. Detection rates were compared by using the McNemar test. Reporting times and diagnostic confidence were compared by using the paired t test and Mann-Whitney U test, respectively. RESULTS: Mean sensitivity values for polyps measuring 1-5, 6-9, and 10 mm or larger were 14%, 53%, and 83%, respectively, for 2D CAR analysis and 16%, 53%, and 67%, respectively, for primary 3D analysis. Overall sensitivity values were 41% for 2D CAR analysis and 39% for primary 3D analysis (P=.77). Reader 1 detected more polyps than reader 2, particularly when using the 3D fly-through method (P=.002). Mean reading times were significantly longer with the 3D method (P=.001). Mean false-positive findings were 1.5 for 2D analysis and 5.5 for 3D analysis. Reader confidence was not significantly different between analysis methods (P=.42). CONCLUSION: Two-dimensional CAR analysis is quicker and at least matches the sensitivity of primary 3D endoluminal analysis, with fewer false-positive findings.

Aged↗

PubMedDate not supplied

Informatics in radiology (infoRAD): free DICOM image viewing and processing software for the Macintosh computer: what's available and what it can do for you.

It is often necessary for radiologists to use digital images in presentations and conferences. Most imaging modalities produce images in the Digital Imaging and Communications in Medicine (DICOM) format. The image files tend to be large and thus cannot be directly imported into most presentation software, such as Microsoft PowerPoint; the large files also consume storage space. There are many free programs that allow viewing and processing of these files on a personal computer, including conversion to more common file formats such as the Joint Photographic Experts Group (JPEG) format. Free DICOM image viewing and processing software for computers running on the Microsoft Windows operating system has already been evaluated. However, many people use the Macintosh (Apple Computer) platform, and a number of programs are available for these users. The World Wide Web was searched for free DICOM image viewing or processing software that was designed for the Macintosh platform or is written in Java and is therefore platform independent. The features of these programs and their usability were evaluated. There are many free programs for the Macintosh platform that enable viewing and processing of DICOM images.

Microcomputers↗

PubMedDate not supplied

Linkage analyses in type I diabetes mellitus using CASPAR, a software and statistical program for conditional analysis of polygenic diseases.

We have developed software and statistical tools for linkage analysis of polygenic diseases. We use type I diabetes mellitus (insulin-dependent diabetes mellitus, IDDM) as our model system. Two susceptibility loci (IDDM1 on 6p21 and IDDM2 on 11p15) are well established, and recent genome searches suggest the existence of other susceptibility loci. We have implemented CASPAR, a software tool that makes it possible to test for linkage quickly and efficiently using multiple polymorphic DNA markers simultaneously in nuclear families consisting of two unaffected parents and a pair of affected siblings (ASP). We use a simulation-based method to determine whether lod scores from a collection of ASP tests are significant. We test our new software and statistical tools to assess linkage of IDDM5 and IDDM7 conditioned on analyses with 1 or 2 other unlinked type I diabetes susceptibility loci. The results from the CASPAR analysis suggest that conditioning of IDDM5 on IDDM1 and IDDM4, and of IDDM7 on IDDM1 and IDDM2 provides significant benefits for the genetic analysis of polygenic loci.

Alleles↗