SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
A flurry of software development, much of it web-based, offers alternatives for agencies to address PPS requirements, streamline operations, and improve agency performance. PPS changes everything--dramatically altering the home care community's financial incentives and focusing attention on technologies that will enable agencies to succeed in this new environment.
We have developed an automated, modular utility assessment software package called U-titer. The package implements the rating scale, category scaling, standard gamble, chronic and temporary time trade-off methods of assessing patient's preferences, and allows extensive tailoring of each method. In addition to calculating utilities, U-titer records information on the process experienced by the user. It can use information gathered in one module to coordinate another module. Our early experience suggests U-titer assessments are similar to traditional assessments. This software should facilitate both the study of patient's utilities and the study of the assessment methods and their implementation.
BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.
In this paper a simulation model is developed as a tool to describe the behavior of the inpatient admission system in a hospital. Due to difficulties involved in the self-development or vendor approach to model such a complex system, the author uses SIMAN software to develop a simulation model for the inpatient admission system. To most hospitals, advantages are gained in terms of reduced purchasing and maintenance cost, and ease of use, as this software can run on any personal computer.
This article identifies two areas of hospice care that may benefit the most from a point-of-care (POC) clinical documentation system: documentation for recertification and symptom/pain management. Applications as solutions for the hospice POC clinical documentation system need two documentation support tools: (1) knowledge-based external or internal reference data available to physicians or medical staff right at the bedside and (2) assisting medical staff in filling out electronic forms for clinical measurements by providing real-time prompts, clues, alerts, or other types of feedback, along with the common features such as pre-defined values in specific fields. Our study may encourage more software vendors to include clinical documentation support tools in their solutions.
Up to now, there has been no software model available that adequately addresses the growing importance of flexibility in using different information tools. Based on Java, Jini technology provides distributed and therefore robust software architecture. In case of an application crash, Jini is able to minimize the damage by adding functions that reverse the effects of the crash. Owing to increasing user mobility, it is necessary to be able to receive location-independent information. The growing use of powerful telecommunications suggests the application of 'wireless application protocol' (WAP) mobile telephones also for medical purposes. This paper presents the application of these new software trends (Jini and wireless application protocol).
Analysis software for medical image data tends to be expensive and usable only in a restricted environment. Therefore the aim of the current project was to implement a flexible framework for medical image processing and visualization which is portable among platforms and open to different data formats including DICOM 3.0. The software was designed as a set of tools which encapsulate specialized functionality. The tools are full stand alone applications, but they are also able to present a co-operating environment within which images and other information are communicated in real time. Currently, the emphasis is on quantitative analysis of PET data by kinetic modelling. However, general viewing capabilities are included, and the design is flexible enough that other types of processing can easily be integrated by simply plugging in Java classes. The software is successfully applied to PET data quantitation in clinical research studies and even patient studies. Portability was aimed at by encoding the programs in Java. Experience shows that the implementation of such a complex and computationally demanding Java application is feasible. Although there are major portability issues to consider, configurations can be found on which the software runs stably and at a speed comparable to C code if just-in-time compilation is available.
Teaching medical issues is increasingly demanding due to the permanent progress in medical sciences. Simultaneously, software applications are rapidly advancing with regard to their availability and easy use. Here a novel teaching program is presented for immunology, which is one of the fastest expanding topics in medical sciences. The requirements of media didactics were transferred to this e-learning tool for German students. After implementation, medical students evaluated the software and the different learning approaches showed acceptance. Altogether this novel software compares favourably to other English e-learning tools available in the Internet.
The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.
This article introduces an innovative collaboration between an orthopaedic surgeon's office and the hospital to assure complete and accurate admission information without duplication. With the use of point-of-care software, the assessment process was re-tooled. This change involved the patient/family assuming responsibility for completing paper and pencil in-depth history and systems review that was then used as part of the evaluation process and inputted into the database allowing for more effective outcomes assessment. In this re-tooling process, the concept of "sharing" information with the partnering hospital was explored. In collaborative discussions, the nursing admission assessment was targeted as a process where there was significant duplication. In fact, much of the information required on the 4-page form was already assessed and documented in the office setting. Consequently it was agreed that the majority of the inpatient nursing history/admission assessment form would be replaced with the assessment completed by the professional office staff. Because of incompatible software, the systems could not be linked but a printed copy of the form was sent to the hospital. Results measuring satisfaction, timesaving, and compliance with JCAHO documentation standards were part of the evaluation. Patients and clinicians were satisfied with the process. There was a significant timesaving for the in-patient RN which facilitated more direct contact with the patient and family.
OBJECTIVES: To compare simulated periodontal bone defect depth measured in digital radiographs with dedicated and non-dedicated software systems and to compare the depth measurements from each program with the measurements in dry mandibles. METHODS: Forty periodontal bone defects were created at the proximal area of the first premolar in dry pig mandibles. Measurements of the defects were performed with a periodontal probe in the dry mandible. Periapical digital radiographs of the defects were recorded using the Schick sensor in a standardized exposure setting. All images were read using a Schick dedicated software system (CDR DICOM for Windows v.3.5), and three commonly available non-dedicated software systems (Vix Win 2000 v.1.2; Adobe Photoshop 7.0 and Image Tool 3.0). The defects were measured three times in each image and a consensus was reached among three examiners using the four software systems. The difference between the radiographic measurements was analysed using analysis of variance (ANOVA) and by comparing the measurements from each software system with the dry mandibles measurements using Student's t-test. RESULTS: The mean values of the bone defects measured in the radiographs were 5.07 mm, 5.06 mm, 5.01 mm and 5.11 mm for CDR Digital Image and Communication in Medicine (DICOM) for Windows, Vix Win, Adobe Photoshop, and Image Tool, respectively, and 6.67 mm for the dry mandible. The means of the measurements performed in the four software systems were not significantly different, ANOVA (P = 0.958). A significant underestimation of defect depth was obtained when we compared the mean depths from each software system with the dry mandible measurements (t-test; P approximately equal to 0.000). CONCLUSIONS: The periodontal bone defect measurements in dedicated and in three non-dedicated software systems were not significantly different, but they all underestimated the measurements when compared with the measurements obtained in the dry mandibles.
The evaluation of the performance of clinical tests is a complex problem involving different steps and many statistical tools, not always structured in an organic and rational system. This paper presents a software which provides an organic system of statistical tools helping evaluation of clinical test performance. The program allows (a) the building and the organization of a working database, (b) the selection of the minimal set of tests with the maximum information content, (c) the search of the model best fitting the distribution of the test values, (d) the selection of optimal diagnostic cut-off value of the test for every positive/negative situation, (e) the evaluation of performance of the combinations of correlated and uncorrelated tests. The uncertainty associated with all the variables involved is evaluated. The program works in a MS-DOS environment with EGA or higher performing graphic card.
The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene-gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser.
Multimedia as a pedagogical tool has been widely adopted for improving the quality of teaching. This paper describes the construction of a teaching software package based on the characteristics of the "Genetics" course. It also discusses some particulars of multimedia teaching, the collection of teaching materials, the improvement of teaching effects, and the compilation of a multimedia textbook. How to enhance the quality of the teachers as well as the motivation of the students are also discussed.
Whole genome microarrays allow assessment of the profile of genes expressed under particular experimental conditions, including external stimuli such as pH or temperature, and internal changes brought about by deleting or over-expressing a gene. Such experiments produce large data sets, for which sophisticated analysis software is available. What is lacking are tools for analysing data sets from different experiments, in order to test and generate hypotheses about the links between regulatory networks. We describe here a method for presenting results from different experiments as a directed graph constructed using an automated graph drawing program xneato, enhanced by a logic program designed to cluster data and aid in the generation of hypotheses about possible gene interactions. A web-based front-end to the system has been constructed to explore and manipulate the graphical displays produced. Results of microarray experiments on Mycobacterium tuberculosis were used to develop and evaluate the visualization tool and initiate the development of an inference system for gene interactions based on such data. The GeneGraph project can be accessed at: zebrafish.doc.ic.ac.uk
We present a set of utilities and graphical user interface (GUI) tools for evaluating the quality of protein resonance assignments. The Assignment Validation Software (AVS) suite, together with new GUI features in the AutoAssign software package, provides a set of reports and graphs for validating protein resonance assignment data before its use in structure analysis and/or submission to the BioMagResBank (BMRB). Input includes a listing of resonance assignments and a summary of sequential connectivity data (i.e. triple resonance, NOE, or other data) used in deriving the assignments. These tools are useful for evaluating the accuracy of protein resonance assignments determined by either automated or manual methods.
Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.
An advanced numerical evaluation tool is proposed for calculating the magnetic flux density dispersed by high-voltage power lines. When compared to existing software packages based on the application of standardized methods, this tool turned out to be particularly suitable for making accurate evaluations on vast portions of the territory, especially when the contribution of numerous aerial and/or underground lines must be taken into account. The aspects of the tool of greatest interest are (1) the interaction with an electronic archive of power lines, from which all the information necessary for the calculation is obtained; (2) the use of three-dimensional models of both the power lines and the territory crossed by these; (3) the direct interfacing with electronic cartography; and finally (4) the use of a representation procedure for the results that is based on contour maps. The tool had proven to be very useful especially for Environmental Impact Assessment procedures relative to new power lines.