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At least 109 records · Page 6Linked to original sources
PubMed2003

Protein family annotation in a multiple alignment viewer.

SUMMARY: The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities. AVAILABILITY: The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com

Amino Acid Sequence↗
PubMed1992

Consistency between peer reviewers for a clinical specialty journal.

To analyze the consistency between independent peer reviewers in evaluating and ranking unsolicited articles, the authors used paired reviews of 422 unsolicited submissions to the Journal of Clinical Anesthesia from the end of 1988 through 1991. (The editors of this journal base their publication decisions, to a substantial degree, on congruence of their reviewers' recommendations). The reviewers were chosen for their interest in reviewing and areas of expertise. Their recommendations were ranged along a continuum of four categories: (1) accept outright, (2) accept with revision, (3) reject in present form (article could be revised and submitted again as a new submission), and (4) reject outright. The pairs of peer reviewers were consonant for 169 papers (40%), differed by one category for 168 papers (40%), differed by two categories for 73 papers (17%), and differed by three categories for 12 papers (3%). Thus, most articles' reviews were in consonance or close to it; articles reviewed by two members of the editorial board, however, were significantly less likely to be consonant (32%) than were those reviewed by two nonmembers (44%, chi-square, p = .027).

Anesthesiology↗
PubMed2005

Note regarding the word 'behavior' in glossaries of introductory textbooks, dictionaries, and encyclopedias devoted to psychology.

Glossaries of introductory textbooks in psychology, biology, and animal behavior were surveyed to find whether they induded the word 'behavior'. In addition to texts, encyclopedias and dictionaries devoted to the study of behavior were also surveyed. Of the 138 tests sampled across all three fields, only 38 (27%) included the term 'behavior' in their glossaries. Of the 15 encyclopedias and dictionaries surveyed, only 5 defined 'behavior'. To assess whether the term 'behavior' has disappeared from textbook glossaries or whether it has usually been absent, we sampled 23 introductory psychology texts written from 1886 to 1958. Only two texts contained glossaries, and the word 'behavior' was defined in both. An informal survey was conducted of students enrolled in introductory classes in psychology, biology, and animal behavior to provide data on the consistency of definitions. Students were asked to "define the word 'behavior'." Analysis indicated the definition was dependent upon the course. We suggest that future introductory textbook authors and editors of psychology-based dictionaries and encyclopedias include 'behavior' in their glossaries.

Adolescent↗
PubMed1999

A programmable rules engine to provide clinical decision support using HTML forms.

The authors have developed a simple method for specifying rules to be applied to information on HTML forms. This approach allows clinical experts, who lack the programming expertise needed to write CGI scripts, to construct and maintain domain-specific knowledge and ordering capabilities within WizOrder, the order-entry and decision support system used at Vanderbilt Hospital. The clinical knowledge base maintainers use HTML editors to create forms and spreadsheet programs for rule entry. A test environment has been developed which uses Netscape to display forms; the production environment displays forms using an embedded browser.

Artificial Intelligence↗
PubMed1995

Integration of a data dictionary and a clinical database in an expert system for acute abdominal pain.

Despite promising results, computer-aided diagnosis in acute abdominal pain is rarely used in the clinic. We therefore developed an expert system for acute abdominal pain to be used in clinical routine. The system is based on a new approach integrating a data dictionary, a clinical database and the knowledge base. A data dictionary editor has been developed (C++, WINDOWS, IBM-compatible PC) and a data dictionary for acute abdominal pain has been built up. The clinical database has been linked to a documentation program providing three modes of data entry. The documentation program has been evaluated extensively by clinicians. The integrated approach clearly separates clinical data from knowledge, but guarantees high consistency of data.

Abdominal Pain↗
PubMed2003

The design of distance-learning programmes and the role of content experts in their production.

This paper describes an effective and efficient approach to the production of distance-learning materials in which content experts, editors and instructional designers collaborate. The approach is based on the development of a clearly defined agreed educational strategy and the use of a template for the programme. This allows the content experts to assemble the first draft of the programme in an appropriate format, with further revisions being carried out by the educationists in collaboration with the content editor. A task-based approach was adopted in the programme and a two-column layout incorporating nine different types of educational enhancements was used. Useful educational strategies which should be considered in the development of the template for a distance learning programme can be categorized into the following three areas: (1). interactivity enhancements including questions posed, think points for reflection, and case scenarios linking theory to practice; (2). enrichment enhancements including illustrations, readings and quotes from experts; (3). action/practice enhancements highlighting the application of portfolio building--provides useful advice on topics covered as they relate to the AFRC examination, and encourages trainees to apply their knowledge. The use made of the enhancements varies in the different modules. This project was challenging and ambitious but our objectives were met with all 39 authors satisfactorily producing the 42 SELECT Units.

Critical Care↗
PubMed1989

Interactive graphic editor for analysis and enhancement of medical images.

We have developed an interactive graphic editor to define subregions within a volume of medical images arranged in serial sections. The editing methods include tracing and automatic growing of connected components defined by the gray level range. The editor performs a statistical analysis of the signal contained in each subvolume and is used in studies of magnetic resonance (MR) signal in medical images. The graphic editor is also used for creating 3D views from MR images based on the new volume-rendering algorithm. The editor transforms the volume of images by remapping their gray levels and by multiplanar cuts. The ability to suppress regions having the same signal intensity as the region of interest is important in generating an unobstructed view of the anatomical structures.

Brain↗
PubMed1998

[Development of a computer-assisted learning program for liver transplantation].

The German Society for Surgery recently decided to rename the "video library" as a "multimedia library", which will include also interactive, nonlinear computerised teachware in surgery. We report on the complex interaction of authors, editor, and the computer-based training laboratory, and the pitfalls with respect to data collection, structure, implementation, and technical aspects of the CD-ROM liver transplantation.

Computer-Assisted Instruction↗
PubMed1997

Writing and evaluating computer-based training programs.

Publishers are preparing for the hitech future and authors and editors need to also. Publishers know that book sales may be down in the future, while computer program sales are expected to increase. Most book publishers have added media divisions to position themselves for the future. Authors and editors can also shift from writing or editing books to developing computer-based training programs. This author tells you how to write, edit, or evaluate the new computer-based training programs.

Authorship↗
PubMed2004

RALEE--RNA ALignment editor in Emacs.

UNLABELLED: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS. AVAILABILITY: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples. CONTACT: sgj@sanger.ac.uk

Algorithms↗
PubMed2005

Developmental issues in school-based aggression prevention from a social-cognitive perspective.

Contemporary research on the development and prevention of aggressive behavior in childhood and adolescence emphasizes the importance of social-cognitive factors such as perceptual biases, problem-solving skills, and social-moral beliefs in the maintenance of aggression. Indeed, school-based social-cognitive intervention approaches have been identified as best practices by the Centers for Disease Control and Prevention. However, because child age is an important covariate of both intervention effectiveness and social-cognitive ability, school-based prevention program designers should keep in mind a number of issues identified through developmental research. In this paper, we review the social-cognitive model of aggressive behavior development as applied to prevention programming. We then discuss some of the ways in which the broader developmental research base can inform the design of aggression prevention programs. EDITORS' STRATEGIC IMPLICATIONS: Educational administrators and policy makers will find evidence in this review that school-based programs that employ a social-cognitive model represent a strategy that works for preventing violence. Prevention researchers will also benefit from the authors' insights regarding theoretical mediating processes and the importance of a developmental view.

Aggression↗
PubMed1989

A program for simulation of nerve equations with branching geometries.

A computer program has been developed for simulation of electrical activity in neurons with complex branching morphology, multiple channel types, and inhomogeneous channel distribution. The program is based around an interpreter and screen editor for flexible specification of nerve properties and analysis of simulation results. Efficient simulation of the nerve specification is accomplished with procedure calls to fast, compiled routines for integration of the nerve equations.

Cell Membrane↗
PubMed1984

Some electrical circuit properties of the organ of Corti. II. Analysis including reactive elements.

The simplified network model of the organ of Corti-hair cell complex that was studied in previous publications (Dallos, P. (1983): In: Hearing - Physiological Bases and Biophysics, pp. 32-37, editors: R. Klinke and R. Hartmann; Dallos, P. (1983): Hearing Res. 12, 89-119) is extended to include the capacitive reactances of hair cell 12, 89-119) is extended to include the capacitive reactances of hair cell membranes. With the assumption that the circuit is parametrically excited by resistance changes of the apical hair cell membrane, intracellular responses for outer (eO) and inner (eI) hair cells and the organ of Corti potential (eOC) are computed for the linear case. In order that frequency-dependent effects be primarily determined by the network properties of the system, the eO/eOC and eI/eOC ratios are considered. The amplitude and phase dependence of these computed functions is compared to corresponding experimental results from the third turn of the guinea pig's cochlea. The eO/eOC function is predicted to be a simple low-pass filter whose cutoff frequency (1250 Hz) is determined by the parallel resistance-capacitance circuit of the cell's baso-lateral membrane. This circuit prediction is in excellent agreement with the data. The eI/eOC function is again derived as a low-pass filter. The cutoff frequency is obtained as 472 Hz, which corresponds to an RC membrane time constant of 0.34 ms. Experimental data are widely divergent from this predicted pattern. In order to bring the theoretical and experimental results in agreement, two steps are necessary. First, a differentiation (i.e., multiplication by j omega) needs to be included in the input to inner hair cells to account for their velocity dependence [4,10]. Second, an underdamped complex pole, located above the cell's best frequency must be introduced. The velocity dependence and the resonance represented by the underdamped pole-pair indicate that the electrical response pattern of inner hair cells is more complex than that of outer hair cells.

Cell Membrane↗
PubMed1994

The genetic data environment an expandable GUI for multiple sequence analysis.

An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC workstations. There is no limitation to the number of external functions that can be linked to the interface. The length and number of sequences that can be handled are limited only by the size of virtual memory present on the workstation. The sequence data itself is used as the reference point from which analysis is done, and scalable graphic views are supported. It is suggested that future software development utilizing this expandable, user-defined menu system and the I/O linkage of external programs will allow biologists to easily integrate expertise from disparate fields into a single environment.

Algorithms↗
PubMed1998

A story of change.

In this introduction to Issues and Strategies for Reform in Medical Education: Lessons from Eight Medical Schools, the authors describe the overall objective of the supplement, which is to present the qualitative reflections of 12 faculty members at eight medical schools who worked to reform their schools' curricula as part of The Robert Wood Johnson Foundation's "Preparing Physicians for the Future: A Program in Medical Education." They outline the issues addressed in the reform efforts at all of the eight schools, including health promotion/disease prevention and ambulatory care, the editors' choice of a "vignette-based" format for the chapters, and the content of the three appendices that end the supplement. They conclude with a brief description of the lessons learned by all participants in the collaborative effort of producing this supplement on curriculum change.

Curriculum↗
PubMed2006

The diagnostic path, a useful visualisation tool in virtual microscopy.

BACKGROUND: The Virtual Microscopy based on completely digitalised histological slide. Concerning this digitalisation many new features in mircoscopy can be processed by the computer. New applications are possible or old, well known techniques of image analyses can be adapted for routine use. AIMS: A so called diagnostic path observes in the way of a professional sees through a histological virtual slide combined with the text information of the dictation process. This feature can be used for image retrieval, quality assurance or for educational purpose. MATERIALS AND METHODS: The diagnostic path implements a metadata structure of image information. It stores and processes the different images seen by a pathologist during his "slide viewing" and the obtained image sequence ("observation path"). Contemporary, the structural details of the pathology reports were analysed. The results were transferred into an XML structure. Based on this structure, a report editor and a search function were implemented. The report editor compiles the "diagnostic path", which is the connection from the image viewing sequence ("observation path") and the oral report sequence of the findings ("dictation path"). The time set ups of speech and image viewing serve for the link between the two sequences. The search tool uses the obtained diagnostic path. It allows the user to search for particular histological hallmarks in pathology reports and in the corresponding images. RESULTS: The new algorithm was tested on 50 pathology reports and 74 attached histological images. The creation of a new individual diagnostic path is automatically performed during the routine diagnostic process. The test prototype experienced an insignificant prolongation of the diagnosis procedure (oral case description and stated diagnosis by the pathologist) and a fast and reliable retrieval, especially useful for continuous education and quality control of case description and diagnostic work. DISCUSSION: The Digital Virtual Microscope has been designed to handle 1000 images per day in the daily routine work of a pathology institution. It implies the necessity of an automatic mechanism of image meta dating. The non - deterministic correlation between the oral statements (case report) and image information content guides the image meta dating. The presented software opens up new possibilities for a content oriented search in a virtual slide, and can successfully support medical education and diagnostic quality assurance.

Journal Article↗