Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map.

Few existing methods enable the visualization of relationships between regulatory genomic activities and genome organization as captured by Hi-C experimental data. Genome-wide Hi-C datasets are often displayed using "heatmap" matrices, but it is difficult to intuit from these heatmaps which biochemical activities are compartmentalized together. High-dimensional Hi-C data vectors can alternatively be projected onto three-dimensional space using dimensionality reduction techniques. The resulting three-dimensional structures can serve as scaffolds for projecting other forms of genomic information, thereby enabling the exploration of relationships between genome organization and various genome annotations. However, while three-dimensional models are contextually appropriate for chromatin interaction data, some analyses and visualizations may be more intuitively and conveniently performed in two-dimensional space. We present a novel approach to the visualization and analysis of chromatin organization based on the Self-Organizing Map (SOM). The SOM algorithm provides a two-dimensional manifold which adapts to represent the high dimensional chromatin interaction space. The resulting data structure can then be used to assess relationships between regulatory genomic activities and chromatin interactions. For example, given a set of genomic coordinates corresponding to a given biochemical activity, the degree to which this activity is segregated or compartmentalized in chromatin interaction space can be intuitively visualized on the 2D SOM grid and quantified using Lorenz curve analysis. We demonstrate our approach for exploratory analysis of genome compartmentalization in a high-resolution Hi-C dataset from the human GM12878 cell line. Our SOM-based approach provides an intuitive visualization of the large-scale structure of Hi-C data and serves as a platform for integrative analyses of the relationships between various genomic activities and genome organization.

An Empirical Evaluation of Force Feedback in Body-Powered Prostheses.

Myoelectric prostheses have many advantages over body-powered prostheses, yet the absence of sensory feedback in myoelectric devices is one reason body-powered devices are often preferred by amputees. While considerable progress has been made in the mechanical design and control of myoelectric prostheses, research on haptic feedback has not had a similar impact. In this study, we seek to develop a fundamental understanding of the utility of force feedback and vision in the functional operation of a body-powered upper-limb prosthesis. Using a custom body-powered prosthesis in which force feedback can be conditionally removed, we asked N=10 non-amputee participants to identify objects based on stiffness in four separate conditions with and without visual and/or force feedback. Results indicate that the combination of visual and force feedback allows for the best accuracy, followed by force feedback only, then visual feedback only. In addition, combining force feedback with visual feedback does not significantly affect identification timing compared to visual feedback alone. These findings suggest that consideration should be given to the development of force feedback displays for myoelectric prostheses that function like a Bowden cable, coupling the amputee's control input to the resulting feedback.