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Because the gray pumice and lava block samples were charged with microlites in the matrix, we did not use micro-FTIR.

To test the significance of the gene ranking enrichment result for each weighting score matrix, we did 100 random permutations for the q-value enrichment.

Although collagen is a major component of the bone matrix, we did not observe significant cell attachment with collagen-coated scaffolds (data not shown).

In the PGs, another component of the extracellular matrix, we did not find any abnormalities either in the morphology or in the distribution.

While we used the IFN-γ and IL-4 PCR data in our predictor matrix, we did not impute missing values for these variables given the large number of missing data for each (102 for each of IFN-γ and IL-4).

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(2) For the coupling matrix, we do not assume that outer coupling configuration matrix is symmetric or irreducible, which is different from coupling in [8, 16].

Since the chondrocytes are fixed in the matrix we do not consider cell motility.

In the construction of the SCC matrices, we did not apply any pre-filtering step to exclude low-variance probe-sets; however, we applied a stringent threshold (corrected P ) to call a SCC value significant, thus reducing the number of False Positive co-regulatory interactions.

Thus in our initial approach to data analysis (generating Matrix 1) we did not define events, but utilized endpoints only.

A detailed sensitivity analysis is not feasible because the model is expensive to simulate (particularly for the long time frames of Figure 9, for example), the number of parameters is large and would require calculation of 46x46 Fischer Information matrix (or cross-correlation matrix), and we do not have standard error estimates for all of the data used to identify the model.

To prove this DNA fragments were indeed nuclear matrix dependent fragments we did the PCR based assay, which showed that 10 out of 15 putative S/MARs where actually associated with the nuclear matrix of Giardia.

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