Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Tchitchek, Nicolas; Eisfeld, Amie J; Tisoncik-Go, Jennifer; Josset, Laurence; Gralinski, Lisa E; Bécavin, Christophe; Tilton, Susan C; Webb-Robertson, Bobbie-Jo; Ferris, Martin T; Totura, Allison L; Li, Chengjun; Neumann, Gabriele; Metz, Thomas O; Smith, Richard D; Waters, Katrina M; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G

Multidimensional Scaling Reference Maps (MDS Ref Maps) and projections (MDS Projections) have been obtained using a modified version of the SVD-MDS method that we developed and used for this study. While the original SVD-MDS method presented in [29] projects a set of high dimensionality objects into a 2 or 3 dimensional metric space, the modified SVD-MDS method allows to project additional objects over a predefined MDS representation. The predefined MDS representation is named MDS Reference Map, and the overlaid MDS representations are named MDS Projections. The original SVD-MDS method performs the dimensional reduction of the objects by using a molecular dynamics approach, modeling objects by particles and pairwise distances between them by repulsion and attraction forces. The modified SVD-MDS method assigns an infinite mass to each object (i.e. particle) of the MDS Reference Map, resulting in a projection of the additional objects over the predefined representation. The Kruskal Stress criterion [28] shown in the representations quantifies the quality of the representations as a fraction of the information lost during the dimensionality reduction procedure.