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PubMedDate not supplied

E-Learning systems: promises and pitfalls.

OBJECTIVE: This review examines the use of e-learning systems in psychiatric education. METHOD: The authors review the Instructional System Design process, focusing on ADDIE (Analysis, Design, Development, Implementation, and Evaluation). The authors also report on two representative teaching projects, discussing the planning, work, and assessment required. RESULTS: The basic operations of these education software systems are relatively easy to learn. The real work is the project preparation which precedes software use and final implementation. CONCLUSIONS: Internet-based learning software is another tool in the educator's armamentarium. Educators must still utilize sound educational pedagogy to create effective learning instruments.

Education, Medical↗
PubMed2005

Mathematical modelling of migration: a suitable tool for the enforcement authorities?

A few years ago, it became accepted that the plastics industry could use migration modelling for compliance testing. When a calculation confirms that the migration of a compound from a plastic material or article is below the specific migration limit, this is considered sufficient documentation for compliance with legislation. In the case of non-compliance, the result needs to be verified experimentally. The European Commission recommends that the enforcement authorities use migration modelling as well to avoid long and expensive analysis. The aim of the present work was to investigate the practical possibilities of implementing migration-modelling software as a tool in official food control and possibly in improving the own-check programmes of Danish plastic-converting plants. Food inspectors from nine regional food control centres initially attended a training course in the use of a commercial modelling software package and were supported further during the project period of about 1 year. They visited 40 producers of final plastic materials and articles, but mainly due to a lack of elementary knowledge of the detailed composition of the materials only 16 full migration calculations were performed. A major reason was a lack of information from those in the raw material supply chain who considered their products protected by commercial confidentiality. In general, the food inspectors were in favour of using migration modelling for future control visits.

Commerce↗
PubMed2000

Windows software for cardiac electrophysiology studies and ablation monitoring.

A system for cardiac electrophysiology (EP) studies consisting of a Windows software package, a standard 120 MHz Pentium PC with a high-performance video card and a data acquisition card has been developed during this study. The system is capable of real time data acquisition and storage of 24 channels with simultaneous display of 1-16 arbitrarily chosen channels at a sampling rate of 500 Hz. It can be used clinically in electrophysiology studies and during catheter radio-frequency ablation treatment for monitoring the ablation and its effects. The built-in ablation monitoring capability enables combined EP study and ablation treatment, thus helping to reduce exposure times and the total time needed per patient. For clinical use the software includes versatile tools for data analysis and reduction. Our system has been developed in association with Department of Cardiology of Tampere University Hospital and has been in regular clinical use there.

Electrophysiology↗
PubMed2002

Neuroinformatics: the integration of shared databases and tools towards integrative neuroscience.

There is significant interest amongst neuroscientists in sharing neuroscience data and analytical tools. The exchange of neuroscience data and tools between groups affords the opportunity to differently re-analyze previously collected data, encourage new neuroscience interpretations and foster otherwise uninitiated collaborations, and provide a framework for the further development of theoretically based models of brain function. Data sharing will ultimately reduce experimental and analytical error. Many small Internet accessible database initiatives have been developed and specialized analytical software and modeling tools are distributed within different fields of neuroscience. However, in addition large-scale international collaborations are required which involve new mechanisms of coordination and funding. Provided sufficient government support is given to such international initiatives, sharing of neuroscience data and tools can play a pivotal role in human brain research and lead to innovations in neuroscience, informatics and treatment of brain disorders. These innovations will enable application of theoretical modeling techniques to enhance our understanding of the integrative aspects of neuroscience. This article, authored by a multinational working group on neuroinformatics established by the Organization for Economic Co-operation and Development (OECD), articulates some of the challenges and lessons learned to date in efforts to achieve international collaborative neuroscience.

Computational Biology↗
PubMed2005

Can't ID a difficult rash? Digital photos can help.

Using a software program with vivid illustrations can help your staff make difficult diagnoses of rashes. Some medical texts have no illustrations at all. Digital photos have much more clarity than traditional pictures. Encourage your staff to use diagnostic software as an educational tool. Use hypothetical cases. Train key individuals in use of software and have them train the rest of the staff.

Bioterrorism↗
PubMed1997

Application of photoshop-based image analysis to quantification of hormone receptor expression in breast cancer.

The benefit of quantifying estrogen receptor (ER) and progesterone receptor (PR) expression in breast cancer is well established. However, in routine breast cancer diagnosis, receptor expression is often quantified in arbitrary scores with high inter- and intraobserver variability. In this study we tested the validity of an image analysis system employing inexpensive, commercially available computer software on a personal computer. In a series of 28 invasive ductal breast cancers, immunohistochemical determinations of ER and PR were performed, along with biochemical analyses on fresh tumor homogenates, by the dextran-coated charcoal technique (DCC) and by enzyme immunoassay (EIA). From each immunohistochemical slide, three representative tumor fields (x20 objective) were captured and digitized with a Macintosh personal computer. Using the tools of Photoshop software, optical density plots of tumor cell nuclei were generated and, after background subtraction, were used as an index of immunostaining intensity. This immunostaining index showed a strong semilogarithmic correlation with biochemical receptor assessments of ER (DCC, r = 0.70, p < 0.001; EIA, r = 0.76, p < 0.001) and even better of PR (DCC, r = 0.86; p < 0.01; EIA, r = 0.80, p < 0.001). A strong linear correlation of ER and PR quantification was also seen between DCC and EIA techniques (ER, r = 0.62, p < 0.001; PR, r = 0.92, p < 0.001). This study demonstrates that a simple, inexpensive, commercially available software program can be accurately applied to the quantification of immunohistochemical hormone receptor studies.

Breast Neoplasms↗
PubMed2006

PhenoChipping of psychotic disorders: a novel approach for deconstructing and quantitating psychiatric phenotypes.

Psychiatric phenotypes as currently defined are primarily the result of clinical consensus criteria rather than empirical research. We propose, and present initial proof of principle for, a novel approach to characterizing psychiatric phenotypes. We have termed our approach PhenoChipping, by analogy with, and borrowing paradigms and tools from, gene expression microarray studies (GeneChipping). A massive parallel profiling of cognitive and affective state is done with a PhenoChip composed of a battery of existing and new quantitative psychiatric rating scales, as well as hand neuromotor measures. We present preliminary data from 104 subjects, 72 with psychotic disorders (bipolar disorder-41, schizophrenia-17, schizoaffective disorder-14), and 32 normal controls. Microarray data analysis software and visualization tools were used to investigate: 1. relationships between phenotypic items ("phenes"), including with objective motor measures, and 2. relationships between subjects. Our analyses revealed phenotypic overlap among, as well as phenotypic heterogeneity within, the three major psychotic disorders studied. This approach may be useful in helping us move beyond current diagnostic classifications, and suggests a combinatorial building-block (Lego-like) structure underlies psychiatric syndromes. The adaptation of microarray informatic tools for phenotypic analysis readily facilitates direct integration with gene expression profiling of lymphocytes in the same individuals, a strategy for molecular biomarker identification. Empirically derived clusterings of (endo)phenotypes and of patients will better serve genetic, pharmacological, and imaging research, as well as clinical practice.

Adult↗
PubMed1999

An approach for access differentiation design in medical distributed applications built on databases.

A formalized "top to bottom" design approach was described in [1] for distributed applications built on databases, which were considered as a medium between virtual and real user environments for a specific medical application. Merging different components within a unified distributed application posits new essential problems for software. Particularly protection tools, which are sufficient separately, become deficient during the integration due to specific additional links and relationships not considered formerly. E.g., it is impossible to protect a shared object in the virtual operating room using only DBMS protection tools, if the object is stored as a record in DB tables. The solution of the problem should be found only within the more general application framework. Appropriate tools are absent or unavailable. The present paper suggests a detailed outline of a design and testing toolset for access differentiation systems (ADS) in distributed medical applications which use databases. The appropriate formal model as well as tools for its mapping to a DMBS are suggested. Remote users connected via global networks are considered too.

Computer Communication Networks↗
PubMed2001

Artificial intelligence applications in the intensive care unit.

OBJECTIVE: To review the history and current applications of artificial intelligence in the intensive care unit. DATA SOURCES: The MEDLINE database, bibliographies of selected articles, and current texts on the subject. STUDY SELECTION: The studies that were selected for review used artificial intelligence tools for a variety of intensive care applications, including direct patient care and retrospective database analysis. DATA EXTRACTION: All literature relevant to the topic was reviewed. DATA SYNTHESIS: Although some of the earliest artificial intelligence (AI) applications were medically oriented, AI has not been widely accepted in medicine. Despite this, patient demographic, clinical, and billing data are increasingly available in an electronic format and therefore susceptible to analysis by intelligent software. Individual AI tools are specifically suited to different tasks, such as waveform analysis or device control. CONCLUSIONS: The intensive care environment is particularly suited to the implementation of AI tools because of the wealth of available data and the inherent opportunities for increased efficiency in inpatient care. A variety of new AI tools have become available in recent years that can function as intelligent assistants to clinicians, constantly monitoring electronic data streams for important trends, or adjusting the settings of bedside devices. The integration of these tools into the intensive care unit can be expected to reduce costs and improve patient outcomes.

Algorithms↗
PubMed2026

From complexity to clarity: Building dashboards for hit selection in high throughput screens.

High throughput screening produces large, complex datasets that are difficult to interrogate without programming expertise, making hit selection time-consuming and inflexible. While instrument software and commercial tools offer partial solutions, they often lack adaptability or require costly infrastructure. Interactive dashboards provide an effective alternative by enabling dynamic filtering and integrated visualization within a single interface. Here, we present simple R Markdown-based templates for creating customizable, modular dashboards for screen data analysis. Built using the flexdashboard and crosstalk R packages, and HTML widgets, these lightweight, easy-to-build HTML dashboards require no complex installation process or installation of licensed software. They support linked visualizations, threshold-based filtering (e.g., Z-score, p-value, fold change), and interactive data exploration and are shared as a standalone HTML file. This framework enables rapid, flexible hit selection across diverse high throughput screening applications and is designed for users with basic R experience.

High-Throughput Screening Assays↗
PubMed2000

A software data generator for radiographic imaging investigations.

A software data generation tool, intended to be used in radiographic applications, has been developed. The application integrates a phantom design module and an imaging simulator. Phantoms can be described as a set of either geometrical objects or voxels, or contours drawn on multiple tomographic slices. Radiographic projections of the phantoms are formed on the basis of a simulated irradiation process, with selectable imaging parameters. Comparison between actual projection images from a physical and a simulated phantom shows good correspondence. The application was used for digital tomosynthesis (DTS) investigations and has proven to be a useful tool in the study of tomographic noise. Further development is expected to expand the use of the application to more areas of radiological imaging research.

Algorithms↗
PubMed2004

OsiriX: an open-source software for navigating in multidimensional DICOM images.

A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

Computer Graphics↗
PubMedDate not supplied

A tool for designing digital test objects for module performance evaluation in medical digital imaging.

Currently, medical digital imaging systems are characterized by the introduction of additional modules such as digital display, image compression and image processing, as well as film printing and digitization. These additional modules require performance evaluation to ensure high image quality. A tool for designing computer-generated test objects applicable to performance evaluation of these modules is presented. The test objects can be directly used as digital images in the case of film printing, display, compression and image processing, or indirectly as images on film in the case of digitization. The performance evaluation approach is quality control protocol based. Digital test object design is user-driven according to specifications related to the requirements of the modules being tested. The available quality control parameters include input/output response curve, high contrast resolution, low contrast discrimination, noise, geometric distortion and field uniformity. The tool has been designed and implemented according to an object oriented approach in Visual C++ 5.0, and its user interface is based on the Microsoft Foundation Class Library version 4.2, which provides interface items such as windows, dialog boxes, lists, buttons, etc. The compatibility with DICOM 3.0 part 10 image formats specifications allows the integration of the tool in the existing software framework for medical digital imaging systems. The capability of the tool is demonstrated by direct use of the test objects in case of image processing, and indirect use of the test objects in case of film digitization.

Algorithms↗
PubMed1997

Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability.

MOTIVATION: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for site-directed mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR). RESULTS: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region. AVAILABILITY: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/+ ++matchbox_submit.html or sent by e-mail to matchbox/biq.fundp.ac.be (help available by just mailing help).

Algorithms↗
PubMedDate not supplied

MS-Express: data-extracting and -processing software for high-throughput experimentation with mass spectrometry.

High-throughput experiments (HTE) result in large amounts of raw data that have to be evaluated for sample classification. Especially mass spectrometry, a widely used detection method in catalytic HTE applications, produces enormous amounts of data. In the past few years, in catalysts research, several test rigs based on mass spectrometric detection have been independently reported by different groups. In a typical HTE, the catalysts are tested sequentially; the recording of the scans, however, occurs continuously. For this reason, the scans of interest have to be extracted from the raw data, and scans belonging to the same sample have to be averaged in a tedious procedure before further processing. In this publication, we present our custom-designed software MS-Express (mass spectrometry data-extracting and -processing software), an efficient tool for HTE MS data evaluation. MS-Express not only sorts the data, it also establishes statistical significance with the help of reference and blank data and provides concise information about abundance and intensity distributions of expected peaks. A special feature is that the program also reports unexpected MS signals, which potentially lead to unexpected discoveries.

Mass Spectrometry↗
PubMed2003

Informatics training in pathology residency programs: proposed learning objectives and skill sets for the new millennium.

CONTEXT: To be successful in tomorrow's health care environment, to make the most appropriate decisions for their laboratories, to optimize training and continuing medical education opportunities, and to advance pathology as a professional specialty, pathologists must possess basic informatics knowledge and proficiency. Traditional areas of anatomic and clinical pathology residency training employ learning objectives, knowledge expectations, and skill sets, but such items have not been as well developed or widely implemented for pathology informatics training. OBJECTIVE: We present a proposal that defines a standard and specific set of learning (knowledge) objectives and skill set (proficiency) expectations for resident training in pathology informatics. DESIGN: The proposal includes a comprehensive and detailed set of knowledge applications and proficiencies that will assist residency programs in developing basic pathology informatics training for residents. The content of the proposal is based on and compiled from existing successful pathology informatics training programs. Learning objectives include those related to general and enterprise computing as well as objectives related specifically to pathology informatics. Skill set expectations include the ability to use software that facilitates and adds value to the work of pathologists, including the use of a laboratory information system and of productivity software and other tools. Other topics include guidelines for evaluating residents' informatics competency, suggestions regarding curriculum structure and implementation, and recommendations for residents' computing infrastructure. CONCLUSION: This proposal provides a foundation for building effective and standard curricula for residency training in pathology informatics. These curricula will be able to meet increasing expectations and needs for pathologists to contribute to clinical information management.

Clinical Competence↗
PubMed2004

[Recommendations in the use of portal images].

Technical radiotherapy progress drive the practices towards increasingly more precise irradiations. The recent developments of the various imaging methods and specialized software made more controls possible. The fields of investigations relate to the quality assurance of the irradiation, the reproducibility of positioning, the movements evaluations and real time dosimetry. Radiotherapy finds, in the images exploitation, a strong potential in improving quality treatments, however it is conditioned by the implementation of ambitious programs, time consuming, but essential to grant the precision of virtual simulations and the daily practice. If all the existing technical devices and software offer higher tools than the current practices, the recommendations can be limited to the insurance of a sufficient precision and reproducibility of the whole treatments. It is thus fundamental to be able to filter the errors, the systematic deviations and to control the statistics of positioning and movements. Each radiotherapy department must apply an adapted program to each site and exploit the imaging chain to maintain its results.

Humans↗
PubMed2004

BIAS: Bioinformatics Integrated Application Software.

MOTIVATION: We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. AVAILABILITY: BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. CONTACT: hallett@mcb.mcgill.ca.

Computational Biology↗