An object-oriented taxonomy of medical data presentations.
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A variety of methods have been proposed for presenting medical data visually on computers. Discussion of and comparison among these methods have been hindered by a lack of consistent terminology. A taxonomy of medical data presentations based on object-oriented user interface principles is presented. Presentations are divided into five major classes-list, table, graph, icon, and generated text. These are subdivided into eight subclasses with simple inheritance and four subclasses with multiple inheritance. The various subclasses are reviewed and examples are provided. Issues critical to the development and evaluation of presentations are also discussed. (+info)
A three-dimensional model of the mouse at embryonic day 9.
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This paper describes a digital, three-dimensional model of the mouse embryo at E9. The model was made by reconstruction from images of serial histological sections digitally warped to remove distortions and has a resolution of approximately 9 microns. The model can be digitally resectioned in any plane to provide images which resemble conventional histological sections. The main tissues have been identified and delineated by digital painting so that the anatomical components can be visualized and manipulated in 3-D surface- and volume-rendered views. This provides a three-dimensional definition of anatomy that will provide a useful tool for interpreting and understanding spatial data in mouse embryos. The anatomy of the model is discussed where it provides landmarks for interpretation and navigation or where it is unexpected in light of existing descriptions of the E9 mouse embryo. The complete anatomy is not presented in this paper but will be available on CD-ROM. A detailed description of the technical aspects of the construction of the model is included in an appendix. The model is the first of a series that will form the basis for an atlas/database of mouse development. This reconstruction and its associated anatomy are available in a variety of data formats with some supporting software from http:@genex.hgu.mrc.ac.uk/. (+info)
Airway narrowing and internal structural constraints.
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A computer model has been developed to simulate the movement restriction in the lamina propria-submucosa (L-S) layer (sandwiched by the basement membrane and the muscle layer) in a cartilage-free airway due to constriction of the smooth muscle layer. It is assumed that the basement membrane is inextensible; therefore, in the two-dimensional simulation, the perimeter outlining the membrane is a constant whether the airway is constricted or dilated. The cross-sectional area of the L-S layer is also assumed to be constant during the simulated airway narrowing. Folding of the mucosal membrane in constricted airways is assumed to be a consequence of the L-S area conservation and also due to tethering between the basement membrane and the muscle layer. The number of tethers determines the number of folds. The simulation indicates that the pressure in the L-S layer resulting from movement restriction can be a major force opposing muscle contraction and that the maximum shortening of the muscle layer is inversely proportional to the number of tethers (or folds) and the L-S layer thickness. (+info)
The human visual system is optimised for processing the spatial information in natural visual images.
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A fundamental tenet of visual science is that the detailed properties of visual systems are not capricious accidents, but are closely matched by evolution and neonatal experience to the environments and lifestyles in which those visual systems must work. This has been shown most convincingly for fish and insects. For mammalian vision, however, this tenet is based more upon theoretical arguments than upon direct observations. Here, we describe experiments that require human observers to discriminate between pictures of slightly different faces or objects. These are produced by a morphing technique that allows small, quantifiable changes to be made in the stimulus images. The independent variable is designed to give increasing deviation from natural visual scenes, and is a measure of the Fourier composition of the image (its second-order statistics). Performance in these tests was best when the pictures had natural second-order spatial statistics, and degraded when the images were made less natural. Furthermore, performance can be explained with a simple model of contrast coding, based upon the properties of simple cells in the mammalian visual cortex. The findings thus provide direct empirical support for the notion that human spatial vision is optimised to the second-order statistics of the optical environment. (+info)
Heparan sulfate proteoglycans as extracellular docking molecules for matrilysin (matrix metalloproteinase 7).
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Many matrix metalloproteinases (MMPs) are tightly bound to tissues; matrilysin (MMP-7), although the smallest of the MMPs, is one of the most tightly bound. The most likely docking molecules for MMP-7 are heparan sulfate proteoglycans on or around epithelial cells and in the underlying basement membrane. This is established by extraction experiments and confocal microscopy. The enzyme is extracted from homogenates of postpartum rat uterus by heparin/heparan sulfate and by heparinase III treatment. The enzyme is colocalized with heparan sulfate in the apical region of uterine glandular epithelial cells and can be released by heparinase digestion. Heparan sulfate and MMP-7 are expressed at similar stages of the rat estrous cycle. The strength of heparin binding by recombinant rat proMMP-7 was examined by affinity chromatography, affinity coelectrophoresis, and homogeneous enzyme-based binding assay; the K(D) is 5-10 nM. Zymographic measurement of MMP-7 activity is greatly enhanced by heparin. Two putative heparin-binding peptides have been identified near the C- and N-terminal regions of proMMP-7; however, molecular modeling suggests a more extensive binding track or cradle crossing multiple peptide strands. Evidence is also found for the binding of MMP-2, -9, and -13. Binding of MMP-7 and other MMPs to heparan sulfate in the extracellular space could prevent loss of secreted enzyme, provide a reservoir of latent enzyme, and facilitate cellular sensing and regulation of enzyme levels. Binding to the cell surface could position the enzyme for directed proteolytic attack, for activation of or by other MMPs and for regulation of other cell surface proteins. Dislodging MMPs by treatment with compounds such as heparin might be beneficial in attenuating excessive tissue breakdown such as occurs in cancer metastasis, arthritis, and angiogenesis. (+info)
bioWidgets: data interaction components for genomics.
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MOTIVATION: The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. RESULTS: We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView. (+info)
Comparing response time, errors, and satisfaction between text-based and graphical user interfaces during nursing order tasks.
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Despite the general adoption of graphical users interfaces (GUIs) in health care, few empirical data document the impact of this move on system users. This study compares two distinctly different user interfaces, a legacy text-based interface and a prototype graphical interface, for differences in nurses' response time (RT), errors, and satisfaction when the interfaces are used in the performance of computerized nursing order tasks. In a medical center on the East Coast of the United States, 98 randomly selected male and female nurses completed 40 tasks using each interface. Nurses completed four different types of order tasks (create, activate, modify, and discontinue). Using a repeated-measures and Latin square design, the study was counterbalanced for tasks, interface types, and blocks of trials. Overall, nurses had significantly faster response times (P < 0.0001) and fewer errors (P < 0.0001) using the prototype GUI than the text-based interface. The GUI was also rated significantly higher for satisfaction than the text system, and the GUI was faster to leam (P < 0.0001). Therefore, the results indicated that the use of a prototype GUI for nursing orders significantly enhances user performance and satisfaction. Consideration should be given to redesigning older user interfaces to create more modern ones by using human factors principles and input from user-centered focus groups. Future work should examine prospective nursing interfaces for highly complex interactions in computer-based patient records, detail the severity of errors made on line, and explore designs to optimize interactions in life-critical systems. (+info)
The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.
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The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and as a by-product results in a 'morph movie'. We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an 'evolutionary morph'. Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of approximately 10 degrees and a maximum Calpha displacement of 17 A. Almost all involve at least one large torsion angle change of >140 degrees. The server is accessible at http://bioinfo.mbb.yale. edu/MolMovDB (+info)