The mesh of each subject was resampled to obtain a node-to-node correspondence between subjects (Tucholka et al., 2012).
During this process Dowling obtained a node in her larynx and subsequently lost her voice for a time.
To construct a network for each stage, we weighted each node in the protein interaction network by their expression fold changes (absolute value, log2 scale) between consecutive groups and obtained a node-weighted protein interaction network for each stage.
This allows us to first fix a tolerable detection probability and then obtain a maximum node density from that.
The adjacency matrix encodes a network where a node (i.e. a gene) is connected to the previous and to the next one on the chromosome, so that for a circular chromosome we obtain a ring of nodes.
We started the experiment by building a 5-node Hadoop cluster before gradually increasing the nodes until we obtained a 19-node cluster.
After this duplication of reaction nodes, we obtain a directed network with 15 607 nodes and 43 938 edges, referred hereafter as the MetaCyc network.
However, since hop count of a pair of nodes cannot fully reflect the distance, it is difficult to obtain a good estimate for a node.
This information is exchanged with the neighboring nodes by broadcasting hello messages in order for a node to obtain a view of the load in the network in its 1-hop environment.
Localize patch: starting from the distance pairs matrix, a Multi-Dimensional Scaling (MDS-MAP) algorithm [32 34] is executed on the node to obtain a local map of the neighbor nodes.
Mean uncorrected pairwise distances between all samples on each branch of major bifurcating nodes were calculated with MEGA 4 [ 45] and divided by 0.015 (1.5%) to obtain a rough estimate of node age.
