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At least 451 records · Page 25Linked to original sources
PubMed2006

IBZM tool: a fully automated expert system for the evaluation of IBZM SPECT studies.

PURPOSE: Visual reading of [(123)I]IBZM SPECT scans depends on the experience of the interpreter. Therefore, semi-quantification of striatal IBZM uptake is commonly considered mandatory. However, semi-quantification is time consuming and prone to error, particularly if the volumes of interest (VOIs) are positioned manually. Therefore, the present paper proposes a new software tool ("IBZM tool") for fully automated and standardised processing, evaluation and documentation of [(123)I]IBZM SPECT scans. METHODS: The IBZM tool is an easy-to-use SPM toolbox. It includes automated procedures for realignment and summation of multiple frames (motion correction), stereotactic normalisation, scaling, VOI analysis of striatum-to-reference ratio R, classification of R and standardised display. In order to evaluate the tool, which was developed at the University of Hamburg, the tool was transferred to the University of Hannover. There it was applied to 27 well-documented subjects: eight patients with multi-system atrophy (MSA), 12 patients with Parkinson's disease (PD) and seven controls. The IBZM tool was compared with manual VOI analysis. RESULTS: The sensitivity and specificity of the IBZM tool for the differentiation of the MSA subjects from the controls were 100% and 86%, respectively. The IBZM tool provided improved statistical power compared with manual VOI analysis. CONCLUSION: The IBZM tool is an expert system for the detection of reduced striatal D(2) availability on [(123)I]IBZM SPECT scans. The standardised documentation supports visual and semi-quantitative evaluation, and it is useful for presenting the findings to the referring physician. The IBZM tool has the potential for widespread use, since it appears to be fairly independent of the performance characteristics of the particular SPECT system used. The tool is available free of charge.

Adult↗
PubMed2004

Phylogenomic inference of protein molecular function: advances and challenges.

MOTIVATION: Protein families evolve a multiplicity of functions through gene duplication, speciation and other processes. As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. Phylogenomic analysis--combining phylogenetic tree construction, integration of experimental data and differentiation of orthologs and paralogs--has been proposed to address these errors and improve the accuracy of functional classification. The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution. RESULTS: Results of protein functional classification using phylogenomic analysis show fewer expected false positives overall than when pairwise methods of functional classification are employed. We present an overview of the motivations and fundamental principles of phylogenomic analysis, new methods developed for the key tasks, benchmark datasets for these tasks (when available) and suggest procedures to increase accuracy. We also discuss some of the methods used in the Celera Genomics high-throughput phylogenomic classification of the human genome. AVAILABILITY: Software tools from the Berkeley Phylogenomics Group are available at http://phylogenomics.berkeley.edu

Algorithms↗
PubMed2003

The use of Geographic Information System (GIS) in the frame of the contingency plan implemented during the 1999-2001 avian influenza (AI) epidemic in Italy.

A Geographic Information System (GIS) is a very powerful and flexible software tool for effective management of spatially referenced data (e.g., geodata). Coupling database and GIS technology provides the tools for a detailed analysis of spatial patterns and distributions in veterinary applications. A specific veterinary GIS (VetGIS) toolbox was developed to perform the calculation of indices such as Lorenz curve, GINI index, and a kernel-based animal density estimation. This software was employed for the analysis and management of avian influenza in Italy during the 1999-2000 epidemic.

Animals↗
PubMed2004

PET/CT image navigation and communication.

UNLABELLED: The advent of multimodality imaging scanners combining PET and CT has led to a new paradigm in image display and presentation that raises new challenges in workstation interpretation software, image navigation, and communication. The essence of multimodality imaging is the ability to overlay imaging information from different modalities in a visually compelling fashion. This is accomplished by combining functional and anatomic data into multidimensional views using color-encoding techniques that provide visual clues on the spatial distribution of image data. DISCUSSION: Combined PET/CT scanners provide spatially registered images from the two modalities acquired simultaneously in a single imaging session. Special reconstruction software and image display programs are required to rescale the native images from different spatial resolution into orthogonal or oblique reformatted planes in which data from PET images are color coded and superimposed on corresponding anatomic CT images. The color overlay technique allows the user to visually identify areas of high tracer activity and determine the underlying anatomic structure. Because of the multidimensional nature of the data, visualization requires interactive multidimensional navigation techniques that allow the viewer to move the visualization planes through three spatial directions and two additional dimensions. The fourth dimension is the continuum blend from PET to CT fusion, and the fifth is the dynamic range of the CT images that can be adjusted to display different tissue characteristics, such as bones, soft tissue, and lungs. Software tools currently available are often relatively complex, requiring the user to perform cumbersome maneuvers and time-consuming image manipulation to navigate through all dimensions and obtain adequate image settings and plane positioning for diagnostic interpretation of the image data. Moreover, the ability to convey these images to referring physicians is usually limited because of the lack of adequate viewing software. Distribution of results is usually performed instead through static "snapshots" of the fused images generated by the interpreting radiologist. The ability of the referring physician to navigate through the set of multimodality image data is thus limited. CONCLUSION: The wider adoption of multimodality PET/CT imaging techniques in routine clinical use will depend heavily on the development of more adequate image display and navigation tools that allow interpreting physicians to navigate easily and efficiently through multiple dimensions of data. Distribution of results to referring physicians and care providers also requires new tools for interactively reviewing the multimodality data, and current static images obtained from fused image data remain inadequate for proper visualization of the true content of images.

Algorithms↗
PubMed2025

GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life.

Evolutionary studies require extensive examination of genomic information across all domains of life. Despite the availability of a large number of genomes through GenBank, the effective visualization or comparison of the information they contain is challenging due to many reasons, including their size. We introduce genome-based retrieval and analysis parser, a comprehensive software tool to analyze genome files, and an online database housing an extensive collection of carefully curated, high-quality genome statistics for all the organisms available in the RefSeq database of National Center for Biotechnology Information. Users can either directly search, or select from precategorized groups, the organisms of their choice and retrieve data, and the output is generated as tables containing more than 200 columns of useful genomic information (base counts, GC content, Shannon entropy, codon usage, etc.) separately calculated for different genomic elements (e.g. coding sequences, introns, transfer RNA, ribosomal RNA, noncoding RNA, etc.). The data are independently displayed (if applicable) for each chromosomal, mitochondrial, plastid, or plasmid sequence. All the data can be visualized on the database or downloaded as comma-separated value or Excel files. The genome-based retrieval and analysis parser database is free to access without any registration and is publicly available at http://tacclab.org/gbrap/.

Software↗
PubMed2005

Integrating the Modelling of EN 1828 and Galen CCAM Ontologies with Protégé: towards a Knowledge Acquisition Tool for Surgical Procedures.

The presentation assess the usability of the ontology platform protégé integrated with the terminology reasoning tool RACER to represent different terminology systems as the CEN European standard EN 1828 which is a categorical structure and the extensive French coding system CCAM supported by a GALEN representation. We present the 2 systems and some results showing the easiness to test the consistence of the ontology or of instances of terminology systems.This type of software tool which is accessible as open source could support a convergent "reference terminology representation" approach. Based on a formal representation development and allowing diversity in linguistic expressiveness of end users this approach can associate shared knowledge acquisition in the public domain and competing systems, software developers and researchers.

Humans↗
PubMed2005

Can hand-held computers improve adherence to guidelines? A (Palm) Pilot study of family doctors in British Columbia.

OBJECTIVE: To examine whether Palm Prevention, a free software tool for Palm OS personal digital assistants (PDAs) that provides quick access to preventive guidelines in a patient-specific manner at the point of care, improved adherence to five preventive measures in primary care. DESIGN: Prospective intervention pilot study. SETTING: Vancouver, BC, and surrounding area. PARTICIPANTS: Eight general practitioners. INTERVENTIONS: Each physician used Palm Prevention for five preventive measures during routine preventive health visits with 10 patients (n = 80). Charts of consenting patients were reviewed for documentation of recommended maneuvers. MAIN OUTCOME MEASURES: Rates of adherence to five evidence-based guidelines selected from the Canadian and American task forces on preventive care and incorporated into Palm Prevention. RESULTS: Intervention and control physicians were similar in their familiarity with and use of PDAs, and they recruited similar patients for the study. Intervention and control groups had similar rates of screening for hypertension. Intervention improved adherence to the remaining four guidelines: cervical cancer screening increased 22% (only absolute increases are reported); hyperlipidemia screening increased 30%; colorectal cancer screening increased 27%; and prophylaxis with acetylsalicylic acid in high-risk patients increased 38%. Participants were surveyed after the study; all reported that they found the software helpful and would continue using Palm Prevention. Usage statistics showed that study participants used the tool outside the trial: users entered between 28 and 68 unique patients into the program during the 2-month intervention. CONCLUSION: This pilot study suggests PDAs are useful in improving preventive care and facilitating translation of knowledge into practice. This was particularly apparent with newer guidelines.

British Columbia↗
PubMed2004

CaspR: a web server for automated molecular replacement using homology modelling.

Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical residues, it has been found that screening for MR solutions with a large number of different homology models may still produce a suitable solution where the original template failed. Here we present the web tool CaspR, implementing such a strategy in an automated manner. On input of experimental diffraction data, of the corresponding target sequence and of one or several potential templates, CaspR executes an optimized molecular replacement procedure using a combination of well-established stand-alone software tools. The protocol of model building and screening begins with the generation of multiple structure-sequence alignments produced with T-COFFEE, followed by homology model building using MODELLER, molecular replacement with AMoRe and model refinement based on CNS. As a result, CaspR provides a progress report in the form of hierarchically organized summary sheets that describe the different stages of the computation with an increasing level of detail. For the 10 highest-scoring potential solutions, pre-refined structures are made available for download in PDB format. Results already obtained with CaspR and reported on the web server suggest that such a strategy significantly increases the fraction of protein structures which may be solved by MR. Moreover, even in situations where standard MR yields a solution, pre-refined homology models produced by CaspR significantly reduce the time-consuming refinement process. We expect this automated procedure to have a significant impact on the throughput of large-scale structural genomics projects. CaspR is freely available at http://igs-server.cnrs-mrs.fr/Caspr/.

Escherichia coli Proteins↗
PubMed2002

The potential of latent semantic analysis for machine grading of clinical case summaries.

OBJECTIVE: This paper introduces latent semantic analysis (LSA), a machine learning method for representing the meaning of words, sentences, and texts. LSA induces a high-dimensional semantic space from reading a very large amount of texts. The meaning of words and texts can be represented as vectors in this space and hence can be compared automatically and objectively. PSYCHOLOGICAL THEORY: A generative theory of the mental lexicon based on LSA is described. The word vectors LSA constructs are context free, and each word, irrespective of how many meanings or senses it has, is represented by a single vector. However, when a word is used in different contexts, context appropriate word senses emerge. CURRENT APPLICATIONS: Several applications of LSA to educational software are described, involving the ability of LSA to quickly compare the content of texts, such as an essay written by a student and a target essay. POTENTIAL MEDICAL APPLICATIONS: An LSA-based software tool is sketched for machine grading of clinical case summaries written by medical students.

Artificial Intelligence↗
PubMed2003

A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors.

Codon optimization enhances the efficiency of DNA expression vectors used in DNA vaccination and gene therapy by increasing protein expression. Additionally, certain nucleotide motifs have experimentally been shown to be immuno-stimulatory while certain others immuno-suppressive. In this paper, we present algorithms to locate a given set of immuno-modulatory motifs in the DNA expression vectors corresponding to a given amino acid sequence and maximize or minimize the number and the context of the immuno-modulatory motifs in the DNA expression vectors. The main contribution is to use multiple pattern matching algorithms to synthesize a DNA sequence for a given amino acid sequence and a graph theoretic approach for finding the longest weighted path in a directed graph that will maximize or minimize certain motifs. This is achieved using O(n(2)) time, where n is the length of the amino acid sequence. Based on this, we develop a software tool.

Algorithms↗
PubMed2006

Analysis and visualization of cell movement in the developing zebrafish brain.

Detailed reconstruction of the spatiotemporal history of embryonic cells is key to understanding tissue formation processes but is often complicated by the large number of cells involved, particularly so in vertebrates. Through a combination of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed the movement of mesencephalic and metencephalic cell populations in the early zebrafish embryo. To facilitate the analysis of our cell tracking data, we have created TracePilot, a software tool that allows interactive manipulation and visualization of tracking data. We demonstrate its utility by showing novel visualizations of cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot) is Java-based, available free of charge, and has a program structure that allows the incorporation of additional analysis tools.

Animals↗
PubMed1990

A computerized simulator for critical-care training: new technology for medical education.

A patient simulator has been developed for training, certification, modeling, and demonstrating problems in the management of critical-care patients. The Critical Care & Hemodynamic Monitoring Training System consists of a personal computer, software, and a replica of a human torso designed to enable students to practice critical-care medicine. The computer displays patient histories, laboratory results, treatment options, patient responses, and a real-time cardiac monitor. The torso apparatus is used to practice insertion of a hemodynamic monitoring catheter; the cardiac monitor displays catheter pressure readings as the catheter is advanced into the heart and also pulmonary artery and wedge position. Special screen calculators in the program may be used to determine hemodynamic, respiratory, ventilatory, and renal function indices. In contrast to previously described simulators and computer oriented instructional programs, this system contains no inherent data base. Instead, authors build a library of informative cases by using the hardware and software tools provided. Individual "modules" of patient information are authored, and these are transparently linked as a student undertakes management of a patient. Although this system is a technologic achievement, determination of its usefulness as an instructional tool or certification aid must come from broader use and controlled studies.

Clinical Competence↗
PubMed1997

Benchmark test cases for evaluation of computer-based methods for detection of setup errors: realistic digitally reconstructed electronic portal images with known setup errors.

PURPOSE: The purpose of this investigation was to develop methods and software for computing realistic digitally reconstructed electronic portal images with known setup errors for use as benchmark test cases for evaluation and intercomparison of computer-based methods for image matching and detecting setup errors in electronic portal images. METHODS AND MATERIALS: An existing software tool for computing digitally reconstructed radiographs was modified to compute simulated megavoltage images. An interface was added to allow the user to specify which setup parameter(s) will contain computer-induced random and systematic errors in a reference beam created during virtual simulation. Other software features include options for adding random and structured noise, Gaussian blurring to simulate geometric unsharpness, histogram matching with a "typical" electronic portal image, specifying individual preferences for the appearance of the "gold standard" image, and specifying the number of images generated. The visible male computed tomography data set from the National Library of Medicine was used as the planning image. RESULTS: Digitally reconstructed electronic portal images with known setup errors have been generated and used to evaluate our methods for automatic image matching and error detection. Any number of different sets of test cases can be generated to investigate setup errors involving selected setup parameters and anatomic volumes. This approach has proved to be invaluable for determination of error detection sensitivity under ideal (rigid body) conditions and for guiding further development of image matching and error detection methods. Example images have been successfully exported for similar use at other sites. CONCLUSIONS: Because absolute truth is known, digitally reconstructed electronic portal images with known setup errors are well suited for evaluation of computer-aided image matching and error detection methods. High-quality planning images, such as the visible human CT scans from the National Library of Medicine, are essential for producing realistic images. Sets of test cases with systematic and random errors in selected setup parameters and anatomic volumes are suitable for use as standard benchmarks by the radiotherapy community. In addition to serving as an aid to research and development, benchmark images may also be useful for evaluation of commercial systems and as part of a quality assurance program for clinical systems. Test cases and software are available upon request.

Computer Simulation↗
PubMed2006

Image processing software for 3D light microscopy.

Advances in microscopy now enable researchers to easily acquire multi-channel three-dimensional (3D) images and 3D time series (4D). However, processing, analyzing, and displaying this data can often be difficult and time- consuming. We discuss some of the software tools and techniques that are available to accomplish these tasks.

Animals↗
PubMed2003

[Electronic imaging with photo-realistic rendering for neuroanatomy teaching. Methods and preliminary results].

Advances in software, networking, and imaging technology provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge to the clinicians, researchers, educators, and students. Recent software tools initially produced for graphic imaging are now available in the medical graphic design field. The authors describe an original method they used to create electronic images of the central nervous system and its coverings with photo-realistic rendering. They present preliminary results and discuss the potential of this new technique as a teaching tool for neuroanatomy.

Computer-Assisted Instruction↗
PubMed1994

Dr. Browse, a digital image file format Browser.

The emerging widespread adoption of the Digital Imaging Communications in Medicine (DICOM) standard will increase the demand for radiologic image transfer between radiologic image acquisition, archive, display and printing devices. Unfortunately, there are and will continue to be many devices that do not and will not support this standard, especially older radiologic equipment and devices from nonradiologic vendors. Determining the image file format characteristics of images from such equipment is often difficult, and done on an ad hoc basis. We have developed a software tool that assists users in determining the image file format parameters of unknown radiologic images.

Analog-Digital Conversion↗
PubMed1996

Development and multi-institutional implementation of coding and transmission standards for health outcomes data.

Health care delivery institutions and providers, employers, and government agencies throughout the U.S. are sharing information and pooling resources in an attempt to produce reliable measurements of health outcomes. The rapid rate of growth in the collection and pooling of health outcomes data has prompted the need for standardization. The work of health care organizations and consortiums pooling data would be greatly facilitated by widely accepted standards for the coding and transmitting of outcomes data. Moreover, standards allow for the inter-operation of data capture products, data analysis tools, and data pooling services developed by a variety of different vendors. The Health Outcomes Institute (HOI) and Henry Ford Health System (HFHS) have developed and maintain a database of health outcomes questions which provides a mechanism for uniquely coding data elements. HFHS and the American Medical Group Association (AMGA) have created a software tool to facilitate the conversion and transmission of health outcomes data elements in an American Society for Testing and Materials (ASTM)/Health Level Seven (HL7) format, which incorporates HOI question standards.

Health Services Research↗
PubMed1999

Development of autonomous control in a closed microbial bioreactor.

Space-based life support systems which include ecological components will rely on sophisticated hardware and software to monitor and control key system parameters. Autonomous closed artificial ecosystems are useful for research in numerous fields. We are developing a bioreactor designed to study both microbe-environment interactions and autonomous control systems. Currently we are investigating N-cycling and N-mass balance in closed microbial systems. The design features of the system involve real-time monitoring of physical parameters (e.g. temperature, light), growth solution composition (e.g. pH, NOx, CO2), cell density and the status of important hardware components. Control of key system parameters is achieved by incorporation of artificial intelligence software tools that permit autonomous decision-making by the instrument. These developments provide a valuable research tool for terrestrial microbial ecology, as well as a testbed for implementation of artificial intelligence concepts. Autonomous instrumentation will be necessary for robust operation of space-based life support systems, and for use on robotic spacecraft. Sample data acquired from the system, important features of software components, and potential applications for terrestrial and space research will be presented.

Artificial Intelligence↗