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.

We discovered that displaying experimentally captured kinematics data in an interactive three-dimensional setting provided an intuitive biological interpretation of biomechanical patterns. In particular, feedback from users who compared this environment with traditional two-dimensional graph methods showed that the advantage of seeing inherently 3D data in a virtual environment allowed them to better concentrate on data analyses. Subsequently, they were able to notice new motion patterns as well as differences and similarities in flight behavior at varying flight speeds.

Exploring dimensionality reduction of animal flight kinematics in an interactive virtual reality setting

We report the findings of a study designed to evaluate the effect of stereopsis and field of regard (FOR) in two different mixed reality (MR) simulation platforms: a head-mounted display (HMD) and a CAVE. We compared the performance of participants on two levels of stereopsis (mono and stereo) and two levels of FOR (90 degrees and 270 degrees) using a variety of scientific visualization tasks. Among the findings, we observed that not all the effects were consistent between the platforms. Stereo alone or in combination with higher FOR improved completion time on both platforms. However, adding stereo solely reduced the accuracy of the participants on the CAVE and improved on the HMD. Our findings extend prior knowledge on the contribution of visual fidelity components and suggests potential limits on MR simulation between platforms.

Effects of field of regard and stereoscopy and the validity of MR simulation for visual analysis of scientific data

We present and illustrate a new technique, Image Correlation Supersampling (ICS), for resampling volume data that are undersampled in one dimension. The resulting data satisfies the sampling theorem, and, therefore, many visualization algorithms that assume the theorem is satisfied can be applied to the data. Without the supersampling the visualization algorithms create artifacts due to aliasing. The assumptions made in developing the algorithm are often satisfied by data that is undersampled temporally. Through this supersampling we can completely characterize phenomena with measurements at a coarser temporal sampling rate than would otherwise be necessary. This can save acquisition time and storage space, permit the study of faster phenomena, and allow their study without introducing aliasing artifacts. The resampling technique relies on a priori knowledge of the measured phenomenon, and applies, in particular, to scalar concentration measurements of fluid flow. Because of the characteristics of fluid flow, an image deformation that takes each slice image to the next can be used to calculate intermediate slice images at arbitrarily fine spacing. We determine the deformation with an automatic, multi-resolution algorithm.

/pdf/de-aliasing-undersampled-volume-images-for-visualization-436g71rs0p.pdf

De-aliasing Undersampled Volume Images for Visualization

Table 1 provides descriptive statistics for the tractography and cognitive variables. Processing speed: There were trend level findings for step 1 (age, p = .079) and step 2 (TOIs, p = . 058). Age accounted for 28% of the variance in TMT-A performance (p =.079, trend). NTWL for the three TOIs accounted for an additional 41% of the variance (p = .101, trend for F change). Examination of standardized beta weights for the individual TOIs showed that NTWL in the right cingulum bundle was the strongest predictor (beta = − 585, p = .044 ; p > .05 for all other variables). Executive function: Step 1 was not significant (age, p = .46) and there was a trend level finding for step 2 (p = .08). Examination of standardized beta weights for the TOIs showed that NTWL in the interhemispheric fibers was the strongest predictor of TMT-B performance (beta = − .70, p = .01; p > .05 for all other variables). Conclusions

/pdf/p2-270-diffusion-tensor-imaging-tractography-correlation-1hnelprsv9.pdf

P2-270: Diffusion-tensor imaging tractography: Correlation with processing speed in aging

We present an intra-subject method for automated registration of wrist bones from computed to-mography (CT) volume images. The method makes possible the automated extraction of joint kinematicinformation from sets of volume images of wrists in different poses. The images may be acquired atrelatively low resolution, reducing the total acquisition time per human subject and general scan storagerequirements. The method is likely to be applicable to bones of other joints.Our registration method works on a sequence of CT images of the same wrist in two steps: in therst step, each CT volume is processed by a tissue classier that generates a localized distance eld.The distance eld approaches zero at bone boundaries. In the second step, the distance elds and ageometric bone model are used to track bone motion through the sequence of CT images. The distancevalue of each vertex in the geometric model is looked up in the corresponding distance eld. The boneposition and orientation are then automatically adjusted to minimize these distances. We infer a motion-governing bone hierarchy from the distance information. The derived hierarchy may have biologicalsignicance. We use the joint hierarchy to speed up the registration process.We validate the method on synthetic,

David H. Laidlaw

Papers

Exploring dimensionality reduction of animal flight kinematics in an interactive virtual reality setting

Effects of field of regard and stereoscopy and the validity of MR simulation for visual analysis of scientific data

De-aliasing Undersampled Volume Images for Visualization

P2-270: Diffusion-tensor imaging tractography: Correlation with processing speed in aging

Robust Automated Registration of Wrist Bones Using Tissue Classication and Distance Fields