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In the software algorithm, all modifications listed in UniMod are searched simultaneously with the tolerances specified as ±0.05 Da for peptides and MS/MS fragments (Shilov et al., 2007).
No protein modifications listed in either the ABRF Delta Mass database (www.abrf.org/index.cfm/dm.home) or the Unimod database (www.unimod.org) could give rise to the three observed species.
All modifications listed in this table are significant at a q-value of 0.05 and a complete list of all modifications with their mean counts and empirical p-values and q-values are in Additional File 1.
Any state σ of a discrete time Boolean network may be modified to be a steady state of the network through application of the rule modifications listed in Table 2 if no node is regulated by every undamaged node in the network and if the future state of every node depends only on the current state of other nodes.
The four modifications listed in the top two rows of Table 2 indicate a sufficient rule modification by adding x j as a new regulator for each of the four combinations of states of nodes x i and x j at time t.
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The 719 predicted positions of modification (listed in Additional file 1) from the seven species were mapped onto the universal alignment and then located on secondary structure maps of 16S and 23S rRNA (Figs. 1 and 2).
The remaining modifications listed on Table 2 involve x j in combination with existing regulators of x i.
Modifications listed are significant at a a-value of 0.05, with the full data listed in Additional File 1.
Modifications listed are significant at a q-value of 0.05, with the full data listed in Additional File 1.
Additionally, we will highlight the modifications that have been discovered in the last 5 years and have greatly added to the modifications listed above.
All the oligos used for genetic modifications are listed in Supplementary Table 1.
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