The real estate factor: quantifying the impact of infarct location on stroke severity.
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BACKGROUND AND PURPOSE: The severity of the neurological deficit after ischemic stroke is moderately correlated with infarct volume. In the current study, we sought to quantify the impact of location on neurological deficit severity and to delineate this impact from that of volume. METHODS: We developed atlases consisting of location-weighted values indicating the relative importance in terms of neurological deficit severity for every voxel of the brain. These atlases were applied to 80 first-ever ischemic stroke patients to produce estimates of clinical deficit severity. Each patient had an MRI and National Institutes of Health Stroke Scale (NIHSS) examination just before or soon after hospital discharge. The correlation between the location-based deficit predictions and measured neurological deficit (NIHSS) scores were compared with the correlation obtained using volume alone to predict the neurological deficit. RESULTS: Volume-based estimates of neurological deficit severity were only moderately correlated with measured NIHSS scores (r=0.62). The combination of volume and location resulted in a significantly better correlation with clinical deficit severity (r=0.79, P=0.032). CONCLUSIONS: The atlas methodology is a feasible way of integrating infarct size and location to predict stroke severity. It can estimate stroke severity better than volume alone. (+info)
Design and implementation of a web-based, database-driven histology atlas: technology at work.
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At Vanderbilt University, the "Human Cell and Tissue Biology" course is a required lecture and laboratory course with 2 full-time instructors and 106 students. To address demands placed on faculty for individual attention, an interactive Web-based histology atlas was developed and implemented in January 2005. This atlas was specifically designed to complement the existing laboratory manual and to transform the manual into an interactive educational tool whereby students could view high-resolution images of histological specimens online. By utilizing a computer scripting language, interactive highlighting of histological structures was accomplished through the implementation of a simple mouse-rollover function. This computer-aided instruction software allows students to preview histological structures of interest prior to entering the laboratory, to have additional faculty-directed contact hours during laboratory, and to review material efficiently. The conversion of the originally developed static application into a database-driven tool streamlined the development and modification of the atlas while facilitating the creation of advanced features. Six weeks after launching this interactive atlas, Vanderbilt medical students logged 1,200 hr of use. Through the cooperative efforts of faculty and students, the interactive atlas evolved to meet the educational demands of medical students owing to the development and implementation of a database structure. The functionality and educational value of the interactive atlas in facilitating self-learning was ultimately measured by positive student feedback and use. (+info)
The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases.
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BACKGROUND: Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. RESULTS: We have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application. CONCLUSION: Anatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system. (+info)
A history of normal plates, tables and stages in vertebrate embryology.
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Developmental biology is today unimaginable without the normal stages that define standard divisions of development. This history of normal stages, and the related normal plates and normal tables, shows how these standards have shaped and been shaped by disciplinary change in vertebrate embryology. The article highlights the Normal Plates of the Development of the Vertebrates edited by the German anatomist Franz Keibel (16 volumes, 1897-1938). These were a major response to problems in the relations between ontogeny and phylogeny that amounted in practical terms to a crisis in staging embryos, not just between, but (for some) also within species. Keibel's design adapted a plate by Wilhelm His and tables by Albert Oppel in order to go beyond the already controversial comparative plates of the Darwinist propagandist Ernst Haeckel. The project responded to local pressures, including intense concern with individual variation, but recruited internationally and mapped an embryological empire. Though theoretically inconclusive, the plates became standard laboratory tools and forged a network within which the Institut International d'Embryologie (today the International Society of Developmental Biologists) was founded in 1911. After World War I, experimentalists, led by Ross Harrison and Viktor Hamburger, and human embryologists, especially George Streeter at the Carnegie Department of Embryology, transformed Keibel's complex, bulky tomes to suit their own contrasting demands. In developmental biology after World War II, normal stages-reduced to a few journal pages-helped domesticate model organisms. Staging systems had emerged from discussions that questioned the very possibility of assigning an embryo to a stage. The historical issues resonate today as developmental biologists work to improve and extend stage series, to make results from different laboratories easier to compare and to take individual variation into account. (+info)
The Bethesda Interobserver Reproducibility Study (BIRST): a web-based assessment of the Bethesda 2001 System for classifying cervical cytology.
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BACKGROUND: The Bethesda System (TBS) along with its companion atlas was updated in 2001 to improve standardization, clarity, and reproducibility of cervical cytology reporting. METHODS: The authors used a novel web-based format to compare assessments of 77 images demonstrating a range of classical and borderline cytologic changes by a self-selected group of United States cytotechnologists (n = 216) and pathologists (n = 185). RESULTS: Participants were highly experienced, with 71.2% of cytotechnologists and 53.0% of pathologists reporting >10 years of practice. The mean percentage of exact agreement with the panel was slightly though significantly higher for cytotechnologists (57.0%) compared with pathologists (53.4%), adjusted for experience (P = .004); cervical cytology percentage effort (P = .0005); or cervical accession volume (P = .0002). Compared with the TBS panel, exact agreement was achieved for 55.1% of image ratings compared with 82.3% agreement at the level of Negative vs non-Negative for images with a single-panel interpretation. Agreement with the panel was highest for images classified as Low-Grade Squamous Intraepithelial Lesion and lowest for Atypical Squamous Cells qualified as either of Undetermined Significance or Cannot Exclude a High-Grade Squamous Intraepithelial Lesion. Reviewers were less sensitive in identifying high-grade glandular lesions than they were in identifying high-grade squamous lesions at any threshold (P < .001). CONCLUSIONS: Morphologic appearances of images were more important determinants than participants' academic or professional degrees with regard to interobserver reproducibility in classifying cervical cytology images. Experienced cytotechnologists and pathologists performed similarly. Participants achieved higher sensitivity for identifying high-grade squamous lesions than they did for high-grade glandular lesions. These findings demonstrated that web-based studies may be useful in assessing interobserver agreement in classifying images. (+info)
Combining image features, case descriptions and UMLS concepts to improve retrieval of medical images.
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This paper evaluates a system, UBMedTIRS, for retrieval of medical images. The system uses a combination of image and text features as well as mapping of free text to UMLS concepts. UBMedTIRS combines three publicly available tools: a content-based image retrieval system (GIFT), a text retrieval system (SMART), and a tool for mapping free text to UMLS concepts (MetaMap). The system is evaluated using the ImageCLEFmed 2005 collection that contains approximately 50,000 medical images with associated text descriptions in English, French and German. Our experimental results indicate that the proposed approach yields significant improvements in retrieval performance. Our system performs 156% above the GIFT system and 42% above the text retrieval system. (+info)
Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles.
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Images (i.e., figures) are important experimental evidence that are typically reported in bioscience full-text articles. Biologists need to access images to validate research facts and to formulate or to test novel research hypotheses. We propose to build a biological question answering system that provides experimental evidences as answers in response to biological questions. As a first step, we develop natural language processing techniques to identify sentences that summarize image content. (+info)
Exploring the visual hallucinations of migraine aura: the tacit contribution of illustration.
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The visual aura of migraine is a subjective phenomenon, and what the migraineur experiences is necessarily inaccessible to others. Fortunately, however, the sufferer can occasionally reveal what is being seen by means of graphic representation, enabling an otherwise closed 'window' to be opened on the transiently dysfunctioning brain. This article explores the unique contribution that illustration has made to understanding mechanisms subserving the visual aura. The most revealing illustrations are those made by the very few scientists who have recorded and analysed the scotomas, and in particular the expanding fortification spectra, experienced during their migraine attacks. It is solely through illustrations such as these that the uniform nature of many of these hallucinations has been demonstrated. As a result, it follows that there is likely to be a similarly uniform repertoire of processes that generate the hallucinations in the occipital cortex. The precise form of the zigzags that comprise the fortification spectrum, their shimmering appearance, and in particular the speed of the peripheral spread, all of which are entirely dependent on graphic display for their elucidation, enable conclusions to be reached about a number of the underlying pathophysiological mechanisms, including the involvement of spreading cortical depression, that likely occur. Illustration has been pivotal too in revealing uncommon and sometimes curious, if not bizarre, visual hallucinations, the forms of which suggest that extrastriate and temporal lobe involvement contributes to migraine aura in some instances. Illustration can also be valuable in differential diagnosis, depicting other forms of visual hallucination which result from a variety of non-migrainous causes. Illustration, particularly when made during the attack, provides an unusual, little used but powerful tool which uniquely allows the sufferer's subjective visual experiences to inform objective analysis. In turn, this analysis leads to insights into some of the cerebral disturbances which subserve migraine aura. (+info)