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For the initial experiment, a Brute-Force matcher is used to compare the ORB descriptors.
Alternatively, mixtures of transformants were cultured in liquid media identical to those used for the initial experiment, processed using ds-Linear PCR and the resulting double-stranded DNA products were then resolved on Agarose gels.
For the initial experiment, we used a subset of 250 abstracts that had already been curated for genes in PubMed because at that time we did not have access to an automatic gene annotation tool.
The amplitude of the decrease of kinase levels is larger than for the initial experiment and much bigger from SW480 than from Hs68 lysates: 50 kinases with levels reduced more than 75% in SW480 versus 10 in Hs68 (respectively 63%and25%5% of all decreased kinases), likely due to a more efficient geldanamycin treatment (see Figure 2b).
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We used E. coli for some of the initial experiments because Shigella belongs to the E. coli species, and its Lipid A (a 1,4′-bis-phosphorylated diglucosamine backbone to which variable lengths and numbers of acyl chains are covalently linked that anchors LPS to the outer membrane of Gram-negative bacteria) is identical to that of Shigella (Lindberg et al, 1991).
Pairwise raw agreement (% of responses in common) and Cohen's Kappa for each pair of Turkers appears in Table 7. > Following the completion of this second experiment, we compared the concept relation accuracy for the Turker judgments for both the initial experiment and the current experiment, as shown in Table 4.
Table 4 shows the concept relation accuracy for the Turker judgments (corresponding to Quadrant 4 from Table 2) for both the initial experiment (Expt 1) and the current experiment (Expt 2).
For the initial experiments, we randomly select one PAP from room 2010 and another from room 2011; the detailed specification of selected p APs is given in the Table 1.
For the initial experiments to rule out mechanical or electrical artifacts, recordings lasted 1 s and were spaced randomly between 1 and 3 minutes.
Mice 8 12 weeks of age were infected intraperitoneally with a sublethal dose of 100 PFU of CB3 in Dulbecco's Modified Eagle Medium (DMEM) for the initial experiments.
The standard deviations for the initial experiments, as shown in the three curves of Figure 2B, are 0.0750, 0.1209 and 0.1580 for the low, medium and high luminance cases respectively.
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