Data Definition Ontology for clinical data integration and querying.

This paper describes an approach to build a Data Definition Ontology (DDO) in the context of full domain ontology integration with datasets in order to share and query clinical heterogeneous data repositories. We have adapted an existing semantic web tool (D2RQ) to implement a process that automatically generates the DDO from a database information model, thanks to reverse engineering and schema mapping approaches. This study has been performed in the context of the DebugIT European project (Detecting and Eliminating Bacteria UsinG Information Technology) that aims to control and monitor the bacterial growth via a semantic interoperability platform (IP). The evaluation of the process is based, first, on the accuracy of the produced DDO for different samples of database storage and second, by checking the congruency between the DDO and the D2RQ database mapping file.

Color-encoded distance visualization of cranial nerve-vessel contacts.

PURPOSE: Visualization of pathological contact between cranial nerves and vascular structures at the surface of the brainstem is important for diagnosis and treatment of neurovascular compression (NVC) syndromes. We developed a method for improved visualization of this abnormality. METHODS: Distance fields were computed using preoperative MRI scans of individuals with NVC syndromes to support the topological representation of brainstem surface structures with quantitative information. Polygonal models of arteries, cranial nerves and the brainstem were generated using segmented T2 weighted MR data. After color-coding the polygonal models with the respective distances, enhanced color visualization of vessel-nerve locations with possible contacts was achieved. RESULTS: The proposed method was implemented and applied to surgical planning in a dozen cases of NVC syndrome. Two selected cases were chosen to demonstrate the feasibility and subjective improvement provided by our visualization technique. Expert neurosurgeons found the improvement valuable and useful for these cases. CONCLUSION: Color-encoded distance information significantly improves the perceptibility of potential nerve-vessel contacts. This method contributes to a better understanding of the complex anatomical situation at the surface of the brainstem and assists in planning of surgery.

Hybrid visualization for white matter tracts using triangle strips and point sprites.

Diffusion tensor imaging is of high value in neurosurgery, providing information about the location of white matter tracts in the human brain. For their reconstruction, streamline techniques commonly referred to as fiber tracking model the underlying fiber structures and have therefore gained interest. To meet the requirements of surgical planning and to overcome the visual limitations of line representations, a new real-time visualization approach of high visual quality is introduced. For this purpose, textured triangle strips and point sprites are combined in a hybrid strategy employing GPU programming. The triangle strips follow the fiber streamlines and are textured to obtain a tube-like appearance. A vertex program is used to orient the triangle strips towards the camera. In order to avoid triangle flipping in case of fiber segments where the viewing and segment direction are parallel, a correct visual representation is achieved in these areas by chains of point sprites. As a result, a high quality visualization similar to tubes is provided allowing for interactive multimodal inspection. Overall, the presented approach is faster than existing techniques of similar visualization quality and at the same time allows for real-time rendering of dense bundles encompassing a high number of fibers, which is of high importance for diagnosis and surgical planning.

Fast and accurate connectivity analysis between functional regions based on DT-MRI.

Diffusion tensor and functional MRI data provide insight into function and structure of the human brain. However, connectivity analysis between functional areas is still a challenge when using traditional fiber tracking techniques. For this reason, alternative approaches incorporating the entire tensor information have emerged. Based on previous research employing pathfinding for connectivity analysis, we present a novel search grid and an improved cost function which essentially contributes to more precise paths. Additionally, implementation aspects are considered making connectivity analysis very efficient which is crucial for surgery planning. In comparison to other algorithms, the presented technique is by far faster while providing connections of comparable quality. The clinical relevance is demonstrated by reconstructed connections between motor and sensory speech areas in patients with lesions located in between.

Sonographic investigations of the gastrointestinal tract of granivorous birds.

This article describes the sonographic examination of the normal gastrointestinal tract of granivorous birds. Preliminary tests with dead birds were performed to get an idea of the sonographic echotexture of the avian gastrointestinal tract. Later, clinically healthy seedeaters of different weights were examined sonographically. As equipment a convex microcurved scanner with a particularly small coupling surface and an adjustable frequency from 5.5-7.5 MHz was used. For the investigation of the gastrointestinal tract, six sonographic approaches are described. After a starving time of 18 hours in the granivorous birds and water input, the best sonographic image quality could be obtained. Using this method, the crop, ventriculus, intestines, and cloaca could be demonstrated sonographically; whereas, it was not possible to visualize the normal proventriculus in granivorous birds. In contrast to mammals, the different layers of the wall of the gastrointestinal tract could not be visualized with the equipment used. Motility of individual parts of the gastrointestinal tract (GI tract), however, could be well demonstrated.

The Feeding Ecology of Five Sympatric Finch Species.

Within habitats the overlap of food-size utilization of five sympatric finch species is almost 100% despite considerable differences in culmen lengths. It is suggested that the differences in bill size reflect differences in the proportion of large seeds in the set of habitats in which each species feeds and does not function to reduce competition within habitats. Although seed production was sufficient to maintain the finch populations through winter, the finches did eat at least 40% of the available seeds. Of the five finch species commonly present at least three seem to be limited by their winter food supply. The diversity of finches in the yield was not significantly correlated with either food abundance or food diversity.