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The only modifications we implemented included the use of 25,000 cells and optimization of the sonication step to yield a modal sheared chromatin size of ∼500 bp.
The network modifications we implemented suggest a distinctive set of metabolic conditions and requirements faced by M. tuberculosis during host infection compared with in vitro growth.
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The third modification we implement, in-gel ligation, is similar to but simpler than the tethering achieved using protein biotinylation in the tethered conformation capture (TCC) assay [ 13].
This reflects the modifications that we implemented in iNJ661v to reproduce the in vivo gene essentiality data in these parts of the metabolic network.
To apply a bias voltage to the sample, we implemented modifications to electrically isolate the microtome and the sample.
Following Rogers et al. (2011) brief suggestion on how their previous method could be extended to incorporate additional experimental information and metadata, we implemented modifications to the likelihood term.
Therefore, we implemented modifications to a previously reported 12-color immunophenotyping protocol 5 (Table 2 and Fig. 1) that allowed us to study these specific cell types of interest.
As another modification for biological applications, we implemented an option that allows improved separation of dense clusters according to their clustering coefficient (CC, the number of edges connecting the neighbors of the node divided by the maximum possible number of such edges).
Aside from these modifications to the reference panels, we implemented the admixture HMM as described in Pool et al. (2012).
We implemented this modification in WITNESS and explored its effect on fair (SSP = SSF = .6) and biased (SSP = .75; SSF = .5) simultaneous lineups, compared to showups.
The same gene combinations were used in a MP using PAUP v.4.0 [31] and also run through a local cluster in which we implemented a modification of the parsimony ratchet [32] following Carolan et al. [33].
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