Biomedical Visual Computing: Case Studies and Challenges

Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it's also fundamental to understanding models of complex phenomena.     

Effects of a single dose of N-Acetyl-5-methoxytryptamine (Melatonin) and resistance exercise on the growth hormone/IGF-1 axis in young males and females

Melatonin and resistance exercise alone have been shown to increase the levels of growth hormone (GH). The purpose of this study was to determine the effects of ingestion of a single dose of melatonin and heavy resistance exercise on serum GH, somatostatin (SST), and other hormones of the GH/insulin-like growth factor 1 (IGF-1) axis. Physically active males (n = 30) and females (n = 30) were randomly assigned to ingest either a melatonin supplement at 0.5 mg or 5.0 mg, or 1.0 mg of dextrose placebo. After a baseline blood sample, participants ingested the supplement and underwent blood sampling every 15 min for 60 min, at which point they underwent a single bout of resistance exercise with the leg press for 7 sets of 7 reps at 85% 1-RM. After exercise, participants provided additional blood samples every 15 min for a total of 120 min. Serum free GH, SST, IGF-1, IGFBP-1, and IGFBP-3 were determined with ELISA. Data were evaluated as the peak pre- and post-exercise values subtracted from baseline and the delta values analyzed with separate three-way ANOVA (p < 0.05). In males, when compared to placebo, 5.0 mg melatonin caused GH to increase (p = 0.017) and SST to decrease prior to exercise (p = 0.031), whereas both 0.5 and 5.0 mg melatonin were greater than placebo after exercise (p = 0.045) and less than placebo for SST. No significant differences occurred for IGF-1; however, males were shown to have higher levels of IGFBP-1 independent of supplementation (p = 0.004). The 5.0 mg melatonin dose resulted in higher IGFBP-3 in males (p = 0.017). In conclusion, for males 5.0 mg melatonin appears to increase serum GH while concomitantly lowering SST levels; however, when combined with resistance exercise both melatonin doses positively impacts GH levels in a manner not entirely dependent on SST.     

Flow distribution in spiral mandrel dies

An analysis of flow of a power law fluid in a spiral mandrel die is presented. The analysis is applied to study the effect of various die design parameters on the flow distribution at the end of the spiral mandrel section. Three variables that have a very strong effect on the flow distribution are the number of grooves, the initial clearance, and the groove helix angle. The distribution is improved by increasing the number of grooves, by using a non-zero initial clearance, and a relatively small helix angle. Two more variables that have a significant effect on the flow distribution are the taper angle and the initial groove depth. The optimum taper angle was found to be between 1 and 3 degrees. The distribution uniformity improves with the initial groove depth, while the pressure drop reduces at the same time.     

FOCUS ON ACCESS TO INSTITUTIONAL RESOURCES: A SYNTHESIS OF THE JISC FAIR PROGRAMME

The JISC-funded Focus of Access to Institutional Resources (FAIR) Programme ran from 2002-2005. The 14 projects within this programme investigated the cultural, organisational, legal and technical factors involved in providing places where institutional digital content, of which there is an increasing amount, could be stored and subsequently shared with others in the Higher and Further Education communities where appropriate. The primary technology to enable such sharing is the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH), a lightweight protocol based on sharing metadata about the digital content available. The technical issues were at times overshadowed by the cultural, organisational and legal issues that had to be addressed. The experience of the Programme as a whole provides a valuable insight to the issues at hand in sharing content and a good starting point for other institutions wishing to investigate this capability. A Synthesis of the Programme was commissioned in late 2004 to capture this experience, and all tangible outputs where produced. A website was produced providing a comprehensive listing of all project outputs and a printed brochure was published in late 2005 as an introduction to the Programme and its findings. This article summarises the findings of the FAIR Synthesis and provides a range of pointers to further information for subsequent investigation.     

An investigation of multiphase CFD modelling of a lateral sloshing tank

A near-resonant, sway-induced sloshing flow in a rectangular tank is used to compare a homogeneous and inhomogeneous multiphase approach for fluid density and viscosity in a commercial CFD code. Dimensional analysis of the relative motion between the phases suggests the application of an inhomogeneous multiphase model whereas previous published work has used the computationally cheaper homogeneous (or average property) approach. The comparison between the computational and experimental results shows that the homogeneous model tends to underestimate the experimental peak pressures by up to 50%. The inhomogeneous multiphase model gives good agreement with the experimental pressure data. Examination of the relative velocity at the fluid interface confirms that the inhomogeneous model is the appropriate model to use for the simulation of a violent sloshing flow.     

A comparison of the perceptual benefits of linear perspective and physically-based illumination for display of dense 3D streamtubes

Large datasets typically contain coarse features comprised of finer sub-features. Even if the shapes of the small structures are evident in a 3D display, the aggregate shapes they suggest may not be easily inferred. From previous studies in shape perception, the evidence has not been clear whether physically-based illumination confers any advantage over local illumination for understanding scenes that arise in visualization of large data sets that contain features at two distinct scales. In this paper we show that physically-based illumination can improve the perception for some static scenes of complex 3D geometry from flow fields. We perform human-subjects experiments to quantify the effect of physically-based illumination on participant performance for two tasks: selecting the closer of two streamtubes from a field of tubes, and identifying the shape of the domain of a flow field over different densities of tubes. We find that physically-based illumination influences participant performance as strongly as perspective projection, suggesting that physically-based illumination is indeed a strong cue to the layout of complex scenes. We also find that increasing the density of tubes for the shape identification task improved participant performance under physically-based illumination but not under the traditional hardware-accelerated illumination model.     

Graphical histories for visualization: supporting analysis, communication, and evaluation

Interactive history tools, ranging from basic undo and redo to branching timelines of user actions, facilitate iterative forms of interaction. In this paper, we investigate the design of history mechanisms for information visualization. We present a design space analysis of both architectural and interface issues, identifying design decisions and associated trade-offs. Based on this analysis, we contribute a design study of graphical history tools for Tableau, a database visualization system. These tools record and visualize interaction histories, support data analysis and communication of findings, and contribute novel mechanisms for presenting, managing, and exporting histories. Furthermore, we have analyzed aggregated collections of history sessions to evaluate Tableau usage. We describe additional tools for analyzing users’ history logs and how they have been applied to study usage patterns in Tableau.     

Interactive display of isosurfaces with global illumination

In many applications, volumetric data sets are examined by displaying isosurfaces, surfaces where the data, or some function of the data, takes on a given value. Interactive applications typically use local lighting models to render such surfaces. This work introduces a method to precompute or lazily compute global illumination to improve interactive isosurface renderings. The precompiled illumination resides in a separate volume and includes direct light, shadows, and intersections. Using this volume, interactive globally illuminated renderings of isosurfaces become feasible while still allowing dynamic manipulation of lighting, viewpoint and isovalue.     

Influence-based model decomposition for reasoning about spatially distributed physical systems

Many important science and engineering applications, such as regulating the temperature distribution over a semiconductor wafer and controlling the noise from a photocopy machine, require interpreting distributed data and designing decentralized controllers for spatially distributed systems. Developing effective computational techniques for representing and reasoning about these systems, which are usually modeled with partial differential equations (PDEs), is one of the major challenge problems for qualitative and spatial reasoning research.

This paper introduces a novel approach to decentralized control design, influence-based model decomposition, and applies it in the context of thermal regulation. Influence-based model decomposition uses a decentralized model, called an influence graph, as a key data abstraction representing influences of controls on distributed physical fields. It serves as the basis for novel algorithms for control placement and parameter design for distributed systems with large numbers of coupled variables. These algorithms exploit physical knowledge of locality, linear superposability, and continuity, encapsulated in influence graphs representing dependencies of field nodes on control nodes. The control placement design algorithms utilize influence graphs to decompose a problem domain so as to decouple the resulting regions. The decentralized control parameter optimization algorithms utilize influence graphs to efficiently evaluate thermal fields and to explicitly trade off computation, communication, and control quality. By leveraging the physical knowledge encapsulated in influence graphs, these control design algorithms are more efficient than standard techniques, and produce designs explainable in terms of problem structures.