BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Anisotropic water diffusion in neural fibres such as nerve, white matter in spinal cord, or white matter in brain forms the basis for the utilization of diffusion tensor imaging (DTI) to track fibre pathways. The fact that water diffusion is sensitive to the underlying tissue microstructure provides a unique method of assessing the orientation and integrity of these neural fibres, which may be useful in assessing a number of neurological disorders. The purpose of this review is to characterize the relationship of nuclear magnetic resonance measurements of water diffusion and its anisotropy (i.e. directional dependence) with the underlying microstructure of neural fibres. The emphasis of the review will be on model neurological systems both in vitro and in vivo. A systematic discussion of the possible sources of anisotropy and their evaluation will be presented followed by an overview of various studies of restricted diffusion and compartmentation as they relate to anisotropy. Pertinent pathological models, developmental studies and theoretical analyses provide further insight into the basis of anisotropic diffusion and its potential utility in the nervous system.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/nbm.782

The basis of anisotropic water diffusion in the nervous system – a technical review

The state of the art of reconstruction of the axonal tracts in the central nervous system (CNS) using diffusion tensor imaging (DTI) is reviewed. This relatively new technique has generated much enthusiasm and high expectations because it presently is the only approach available to non-invasively study the three-dimensional architecture of white matter tracts. While there is no doubt that DTI fiber tracking is providing exciting new opportunities to study CNS anatomy, it is very important to understand its limitations. In this review we therefore assess the basic principles and the assumptions that need to be made for each step of the study, including both data acquisition and the elaborate fiber reconstruction algorithms. Special attention is paid to situations where complications may arise, and possible solutions are reviewed. Validation issues and potential future directions and improvements are also discussed.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/nbm.781

Fiber tracking: Principles and strategies - A technical review

Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analytical representation of only the solvent-accessible surface. There are a few programs that compute the analytical representation of the solvent-excluded surface, but they often have problems handling singular cases of self-intersecting surfaces and tend to fail on large molecules (more than 10,000 atoms). We describe here a program called MSMS, which is shown to be fast and reliable in computing molecular surfaces. It relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. The four algorithms composing MSMS are described and their complexity is analyzed. Special attention is given to the handling of self-intersecting parts of the solvent-excluded surface called singularities. The program has been compared with Connolly's program PQMS [M.L. Connolly (1993) Journal of Molecular Graphics, Vol. 11, pp. 139-141] on a set of 709 molecules taken from the Brookhaven Data Base. MSMS was able to compute topologically correct surfaces for each molecule in the set. Moreover, the actual time spent to compute surfaces is in agreement with the theoretical complexity of the program, which is shown to be O[n log(n)] for n atoms. On a Hewlett-Packard 9000/735 workstation, MSMS takes 0.73 s to produce a triangulated solvent-excluded surface for crambin (1 crn, 46 residues, 327 atoms, 4772 triangles), 4.6 s for thermolysin (3tln, 316 residues, 2437 atoms, 26462 triangles), and 104.53 s for glutamine synthetase (2gls, 5676 residues, 43632 atoms, 476665 triangles).

Reduced surface: An efficient way to compute molecular surfaces

Two- and three-dimensional (3D) white matter atlases were created on the basis of high-spatial-resolution diffusion tensor magnetic resonance (MR) imaging and 3D tract reconstruction. The 3D trajectories of 17 prominent white matter tracts could be reconstructed and depicted. Tracts were superimposed on coregistered anatomic MR images to parcel the white matter. These parcellation maps were then compared with coregistered diffusion tensor imaging color maps to assign visible structures. The results showed (a) which anatomic structures can be identified on diffusion tensor images and (b) where these anatomic units are located at each section level and orientation. The atlas may prove useful for educational and clinical purposes. © RSNA, 2003

Fiber tract-based atlas of human white matter anatomy.

( P ∂ ) ( ) 0 , | ( 0 0 ) 1 ( r r r r Ps r r r r s s P D t ∇ = ∂ , Initial Condition: − =δ ( ) 1 ( = + ∂ ∂ = = a s a s MP P D ρ ρ ρ • Define: Transport rate through interface 1 D Ma h = , M is the permeability coefficient The solution to the diffusion problem posed above, given rotational symmetry about the direction of the field gradient, is

http://www.secs.oakland.edu/~wzhou/research/ISMRM2009_amd_vol17_p263.pdf

An Analytical Model of Diffusion and Exchange of Water in White Matter from Diffusion-MRI and its Application in Measuring Axon Radii

We present a design schema for generating data visualizations using examples from art. With this approach a user: 1.) chooses a composition or detail from a favorite painting, 2.) generates a template by extracting characteristics or brushstrokes suitable for representing data variables, 3.) generates a pre-visualization of the data using a rendering framework [Sobel 2003] and, 4.) transfers the features from the painting using the Image Analogies, Texture-By-Numbers algorithm [Hertzmann et al. 2001].

Design-by-example: a schema for designing visualizations using examples from art

Visualization needs more visual design! (panel session)

/pdf/atlas-based-multi-direction-tractography-using-tensor-5gn5ex2e4y.pdf

Atlas­based multi­direction tractography using tensor registration and orientation statistics Abstract Submission No: 2281 Authors:

In this paper, we present a case study where we incorporate GOMS (Goals, Operators, Methods, and Selectors) [2] task analysis into the design process of a visual analysis tool. We performed GOMS analysis on an Electroencephalography (EEG) analyst's current data analysis strategy to identify important user tasks and unnecessary user actions in his current workflow. We then designed an EEG data visual analysis tool based on the GOMS analysis result. Evaluation results show that the tool we have developed, EEGVis, allows the user to analyze EEG data with reduced subjective cognitive load, faster speed and increased confidence in the analysis quality. The positive evaluation results suggest that our design process demonstrates an effective application of GOMS analysis to discover opportunities for designing better tools to support the user's visual analysis process.

/pdf/incorporating-goms-analysis-into-the-design-of-an-eeg-data-2qgd2tyla0.pdf

David H. Laidlaw

Papers

An Analytical Model of Diffusion and Exchange of Water in White Matter from Diffusion-MRI and its Application in Measuring Axon Radii

Design-by-example: a schema for designing visualizations using examples from art

Visualization needs more visual design! (panel session)

Atlasbased multidirection tractography using tensor registration and orientation statistics Abstract Submission No: 2281 Authors:

Incorporating GOMS analysis into the design of an EEG data visual analysis tool

David H. Laidlaw

Papers

An Analytical Model of Diffusion and Exchange of Water in White Matter from Diffusion-MRI and its Application in Measuring Axon Radii

Design-by-example: a schema for designing visualizations using examples from art

Visualization needs more visual design! (panel session)

Atlas­based multi­direction tractography using tensor registration and orientation statistics Abstract Submission No: 2281 Authors:

Incorporating GOMS analysis into the design of an EEG data visual analysis tool

Atlasbased multidirection tractography using tensor registration and orientation statistics Abstract Submission No: 2281 Authors: