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At least 433 records · Page 24Linked to original sources

[Design and implementation of aphasia rehabilitation software based on speech recognition].

A new software therapy instrument is proposed for the rehabilitation of aphasia caused by cerebral disorder, which is different from general drug therapy or physical therapy and is, based on modern speech and biofeedback principles. Aphasia rehabilitation software package on the therapy instrument were designed and implement. The features of the software and its future application were discussed.

Aphasia↗

The component-based architecture of the HELIOS medical software engineering environment.

The constitution of highly integrated health information networks and the growth of multimedia technologies raise new challenges for the development of medical applications. We describe in this paper the general architecture of the HELIOS medical software engineering environment devoted to the development and maintenance of multimedia distributed medical applications. HELIOS is made of a set of software components, federated by a communication channel called the HELIOS Unification Bus. The HELIOS kernel includes three main components, the Analysis-Design and Environment, the Object Information System and the Interface Manager. HELIOS services consist in a collection of toolkits providing the necessary facilities to medical application developers. They include Image Related services, a Natural Language Processor, a Decision Support System and Connection services. The project gives special attention to both object-oriented approaches and software re-usability that are considered crucial steps towards the development of more reliable, coherent and integrated applications.

Computer Communication Networks↗

Maximizing the utilization and impact of medical educational software by designing for local area network (LAN) implementation.

The design, development and implementation of medical education software often occurs without sufficient consideration of the potential benefits that can be realized by making the software network aware. These benefits can be considerable and can greatly enhance the utilization and potential impact of the software. This article details how multiple aspects of the IMMEX problem solving project have benefited from taking maximum advantage of LAN resources.

California↗

Using software agents to maintain autonomous patient registries for clinical research.

A software agent is an application that can function in an autonomous and intelligent fashion. We have used mobile software agents to maintain clinicians' patient research databases (patient registries). Agents were used to acquire data from the clinician and place it into the registries, copy data from hospital databases into the registries, and report data from the registries. The agents were programmed with the intelligence to navigate through complex network security, interact with legacy systems, and protect themselves from various forms of failure at multiple levels. To maximize the separation between our system and the hospital information infrastructure we often used Java, a platform-independent language, to program and distribute our software agents. By using mobile agents, we were able to distribute the computing time required by these applications to underutilized host machines upon which the registries could be maintained.

Databases as Topic↗

Does pornography-blocking software block access to health information on the Internet?

CONTEXT: The Internet has become an important tool for finding health information, especially among adolescents. Many computers have software designed to block access to Internet pornography. Because pornography-blocking software cannot perfectly discriminate between pornographic and nonpornographic Web sites, such products may block access to health information sites, particularly those related to sexuality. OBJECTIVE: To quantify the extent to which pornography-blocking software used in schools and libraries limits access to health information Web sites. DESIGN AND SETTING: In a simulation of adolescent Internet searching, we compiled search results from 24 health information searches (n = 3206) and 6 pornography searches (n = 781). We then classified the content of each site as either health information (n = 2467), pornography (n = 516), or other (n = 1004). We also compiled a list of top teen health information sites (n = 586). We then tested 6 blocking products commonly used in schools and libraries and 1 blocking product used on home computers, each at 2 or 3 levels of blocking restrictiveness. MAIN OUTCOME MEASURE: Rates of health information and pornography blocking. RESULTS: At the least restrictive blocking setting, configured to block only pornography, the products blocked a mean of only 1.4% of health information sites. The differences between blocking products was small (range, 0.6%-2.3%). However, about 10% of health sites found using some search terms related to sexuality (eg, safe sex, condoms) and homosexuality (eg, gay) were blocked. The mean pornography blocking rate was 87% (range, 84%-90%). At moderate settings, the mean blocking rate was 5% for health information and 90% for pornography. At the most restrictive settings, health information blocking increased substantially (24%), but pornography blocking was only slightly higher (91%). CONCLUSIONS: Blocking settings have a greater impact than choice of blocking product on frequency of health information blocking. At their least restrictive settings, overblocking of general health information poses a relatively minor impediment. However, searches on some terms related to sexuality led to substantially more health information blocking. More restrictive blocking configurations blocked pornography only slightly more, but substantially increased blocking of health information sites.

Access to Information↗

Product review: lucis image processing software.

Lucis is a software program that allows the manipulation of images through the process of selective contrast pattern emphasis. Using an image-processing algorithm called Differential Hysteresis Processing (DHP), Lucis extracts and highlights patterns based on variations in image intensity (luminance). The result is that details can be seen that would otherwise be hidden in deep shadow or excessive brightness. The software is contained on a single floppy disk, is easy to install on a PC, simple to use, and runs on Windows 95, Windows 98, and Windows NT operating systems. The cost is $8,500 for a license, but is estimated to save a great deal of money in photographic materials, time, and labor that would have otherwise been spent in the darkroom. Superb images are easily obtained from unstained (no lead or uranium) sections, and stored image files sent to laser printers are of publication quality. The software can be used not only for all types of microscopy, including color fluorescence light microscopy, biological and materials science electron microscopy (TEM and SEM), but will be beneficial in medicine, such as X-ray films (pending approval by the FDA), and in the arts.

Algorithms↗

SAmBA: an interactive software for optimizing the design of biological macromolecules crystallization experiments.

SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr.

Algorithms↗

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.

Algorithms↗

Quadrat analysis software for the detection of spatial or temporal clustering.

A software program is presented which automates the quadrat analysis procedure for detecting spatial or temporal clustering outlined by Boots and Getis. The software essentially compares observed values within areal or temporal sampling units to those values that would have been obtained were the values distributed randomly. A chi-square test of significance is used to assess whether the values are dispersed in a non-random pattern and a t-test is used to assess whether the values are dispersed in a non-regular pattern. The software requires DOS 3.3 or higher and reads dBase-compatible data files.

Chi-Square Distribution↗

Database and software for the analysis of mutations at the lacI gene in both transgenic rodents and bacteria.

The use of transgenic rodents for the study of genetic toxicology has increased dramatically in the past several years. A great deal of the recent work has employed the lacI locus in transgenic mice. In addition to the transgenic data, a substantial amount of information exists regarding mutation of the lacI gene in bacteria. In an effort to centralize the information regarding mutations in the lacI gene in both rodents and bacteria, we have created a computerized database that contains information about DNA sequence alterations on about 500 mutations in transgenic rodents and 8,000 mutations in bacteria. We have also produced a software package for the analysis of the lacI database. Routines have been developed for the analysis of single base substitutions, including programs to (i) determine if two mutational spectra are different; (ii) determine if mutations show a DNA strand bias; (iii) determine the frequency of transitions and transversions; (iv) display the number and kind of mutations observed at each base in the coding region; (v) perform nearest neighbor analysis; and (vi) display mutable amino acids in the lacI protein. The software runs only on IBM-compatible machines running Microsoft Windows. The software and lacI database are freely available via the internet (http:/(/)sunsite.unc.edu/dnam/mainpage.++ +html).

Amino Acids↗

A brief review on software developments for group sequential and adaptive designs.

In this paper the currently available software we know for group sequential and adaptive designs is briefly reviewed. Stand-alone packages as well as modules within software packages or programming languages exist. New software developments for adaptive designs enable the user to perform data dependent design adaptations while controlling the Type I error rate.

Biometry↗

Quantitative densitometry of proteins stained with coomassie blue using a Hewlett Packard scanjet scanner and Scanplot software.

In the present study we evaluated the performance of a software/scanner system that employed the Hewlett Packard (HP) ScanJet Plus and Scanplot Software for densitometric quantification of protein loads stained with Coomassie Brilliant Blue following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Gels with bovine serum albumin (BSA) standards, ranging from 0.125 to 10 micrograms, were scanned using reflectance densitometry with 127 microns step size in both the x and y directions and a resolution of 200 dots per inch. Densitometric volume was calculated for each protein band from scanner output in the tagged image file format (TIFF) by a customized software package, Scanplot V. 4.05 (Cunningham Engineering). Protein loads between 0.125 and 10.0 micrograms vs. volume were fit by a second-order regression: Volume = -0.58 x protein load2 + 16.82 x protein load + 7.87 (r = 0.991, p < 0.01). The same gels were scanned and quantified using a transmittance laser densitometer; densitometric volumes measured by both systems were highly correlated (r2 = 0.981, p < 0.01). Additional gels of BSA, smooth muscle myosin heavy chain (myosin), and actin displayed linear relationships between protein loads up to 4.0 micrograms and densitometric volume reflecting unique dye binding properties. We conclude that accurate and reproducible quantitative densitometry of SDS-PAGE can be performed using the HP ScanJet Plus scanner and Scanplot software.

Actins↗

Software package for the management of sequencing projects using lacI transgenic animals.

The bacterial lacI gene has been used for many years as a mutational target for the study of the mechanisms of mutation. A wealth of information has been collected for many mutagenic treatments and in strains with diverse DNA repair backgrounds. Recently this gene has been used in the construction of a transgenic mouse, named Big Blue, and a transgenic rat, as well as a rat cell line. The lacI gene in these animals and cells can conveniently be recovered and analyzed in bacteria. This makes it possible to study mutagenic potential of chemical compounds in vivo using a mammal. Tissue, strain, and gender specificity can be addressed. In addition, mutations recovered from tumour tissues or from animals with specific genetic backgrounds can be analyzed conveniently. The mammalian systems can produce large numbers of mutants that require computer assistance to manage the samples and the resulting DNA sequence data. Accordingly, a computer software system was developed. The system maintains an inventory of bacteriophage lambda lacI mutants and allows entry of mutant sequences while performing accuracy checks on the data. The software features several options for displaying lists of mutants. The system can perform several analyses, including mutant class compilations, mutational spectra comparisons, and clonal expansions analysis. An extensive database obtained from the bacterial lacI system is included with the software and can be analyzed along with mutants derived from transgenic animals.

Algorithms↗

The UMD-LDLR database: additions to the software and 490 new entries to the database.

Mutations in the LDL receptor gene (LDLR) cause familial hypercholesterolemia (FH), one of the most frequent hereditary dominant disorders. The protein defect was identified in 1973, the gene was localized by in situ hybridization in 1985, and since, a growing number of mutations have been reported. The UMD-LDLR database is customized software that has been developed to list all mutations, and also to provide means to analyze them at the nucleotide and protein levels. The database has been recently modified to fulfill the recommendations of the Nomenclature Working Group for human gene mutations. However, in the current version, both the nomenclature and usual LDLR gene mutation names are reported since the latter are more commonly used. The software has also been modified to accommodate the splicing mutations and alleles that carry two nucleotide variations. The current version of UMD-LDLR contains 840 entries, of which 490 are new entries. Point mutations account for 90% of all mutations in the LDLR gene; the remaining are mostly major rearrangements, due to the presence of Alu sequences. Three new routines have been implemented in the software, thus giving users access to 13 sorting tools. In addition to the database, a Web site containing information about polymorphisms, major rearrangements, and promoter mutations is available. Both are accessible to the scientific community (www.umd.necker.fr) and should help groups working on LDLR to check their mutations and identify new ones, and greatly facilitate the understanding of functional classes/genotype relationships and of genotype/phenotype correlations.

Databases, Genetic↗

A software system for interventional magnetic resonance image-guided prostate brachytherapy.

OBJECTIVE: Current prostatic brachytherapy implant procedures use ultrasound imaging for geometric guidance during surgery, with pre-surgical planning based on ultrasound images and post-surgical dosimetry based on computed tomography (CT). This procedure suffers from the poor soft-tissue contrast of ultrasound and CT and problems inherent in the repositioning of the patient at surgery. We have designed and implemented an integrated real-time imaging and treatment-planning software system that combines the superior soft-tissue contrast of magnetic resonance (MR) images with the real-time acquisition of those images for localization, verification, and dosimetric purposes. The system permits the surgeon and patient to complete all phases of treatment in one setting. MATERIALS AND METHODS: We utilize an intra-operative MR unit that permits real-time imaging and stereotactic localization during a surgical procedure. Our software system integrates with the unit and features (i) a calibration schema to calibrate the prostatic surgical implant template within the unit, (ii) full volumetric data acquisition of the prostate, (iii) interactive three-dimensional (3D) treatment planning with volumetric dose evaluation, and (iv) geometric and dosimetric feedback during the surgical procedure. We utilize a software architecture that uses mediators between the abstract data types, or objects. These mediators communicate state changes in individual objects (e.g., a change in a catheter position) to other objects (e.g., a dose-volume histogram) that depend on these changes. A consistent 3D representation of the treatment volumes allows interactive reconstruction of the volumes on arbitrary MR image sections and real-time dose computations. RESULTS: We have successfully implemented the system clinically and have treated 143 patients (as of August 2000). The system supports four clinical phases. The first consists of calibrating the implant template with respect to the patient's anatomy and the MR unit. The second consists of acquiring a complete volumetric MR data set of the prostatic volume. The third consists of delineating the treatment volume (often a sub-volume of the prostate) and the dose-limiting critical volumes. These volumes are used in determining the surgical treatment plan based on catheter and seed placement in the prostate and a dosimetric evaluation of all volumes. The final phase consists of implanting the catheters with the radioactive seeds, where each catheter is imaged and compared to the planned position of the catheter, thus allowing a direct comparison, and possible adjustment, of the implanted versus planned catheter position. CONCLUSIONS: The system is highly interactive, and has great flexibility in its design, maintainability, and clinical practice. The system provides an efficient model to support the surgical procedure. The system significantly improves the diagnostic information provided to the clinician and the treatment planner and the geometric accuracy of the surgical procedure compared to ultrasound procedures. The system allows excellent critical structure sparing, both through interactive placement of the catheters with high geometric accuracy and through the definition of the actual sub-prostatic volumes possible with MR.

Brachytherapy↗

Using technical innovations in clinical practice: the Drinker's Check-Up software program.

Interest in assessing and treating a variety of psychological conditions with software programs is increasing rapidly. This article reviews a software program for problem drinkers entitled the Drinker's Check-Up (DCU) and illustrates its use with three patients. The DCU is based on the principles of brief motivational interventions and can be used as a stand-alone intervention by therapists without expertise in substance abuse or as a prelude to alcohol treatment services. It is the first software program to provide integrated assessment, feedback, and assistance with decision making for individuals experiencing problems with alcohol. Preliminary data from an ongoing clinical trial of the DCU as a stand-alone intervention indicate that it is an effective intervention for a wide range of problem drinkers.

Adult↗

Computer assisted data collection for stereology: rationale and description of point counting stereology (PCS) software.

The paper describes microcomputer software for point counting stereology. Stereology includes a collection of statistical methods that quantify the images of light and transmission electron microscopy. The methods use test grids placed over images to collect raw data, which includes counts of points, intersections, transections, and profiles. In turn, the counts are included in stereological equations that give estimates of compartmental volumes, surfaces, lengths, or numbers. These parameters describe the composition of a structure in three-dimensional space. The PCS (point counting stereology) System Software III serves as a data collection, storage, and management tool. Users set up point counting protocols without programming, enter data by pressing predefined function (MS-DOS) or alphabetic keys (UNIX), store data in files, select files for analysis, and calculate results as stereological densities. The latest version of the PCS software includes a new user interface and is designed as a research "front end" that can feed data either into the calculation tools of a stereology tutorial (Bolender, 1992, this issue) or into the analysis routines of quantitative morphology databases (Bolender and Bluhm, 1992).

Animals↗

Software for counting cells and estimating structural volumes with the optical disector and fractionator.

We describe MS-DOS software for the optical volume fractionator (OVF), a stereological method combining the principles of the optical disector (Gundersen et al.: Acta Pathol. Microbiol. Immunol. Scand., 96:857-881, 1988) and fractionator (Gundersen: J. Microsc., 143:3-45, 1986). The OVF program estimates the volume of a fixed and embedded structure, the numerical density of cells, and the total number of cells in a structure. The hardware requirements include a PC computer (386 or 486 with VGA graphics) and a conventional light microscope fitted with a rotating stage, extension tube, and length gauge. The software includes an introduction, tutorial, simulator, laboratory tool kit, and report generator. The tool kit improves the efficiency of gathering stereological data with light microscopy and offers a convenient link between the data of light and electron microscopy. A novel algorithm, based on fractionator sampling, gives the volume of a fixed and embedded structure from the same set of sections used for cell counting. A laboratory example illustrates the operation of the software.

Algorithms↗