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Sorted cells were selected through sequential gating (see online supplementary figure S3A) based on forward scatter (FSC), side scatter (SSC), trigger pulse width, to gate out doublets, DAPI to gate out dead cells and CD31/CD45 binding to exclude haematopoietic and endothelial cells.
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To determine the effect of peptides on chemokine binding and to exclude the contribution of chemokine internalization, we incubated cells at room temperature in the presence of 0.1% sodium azide.
The increased rigidity and exposure of both hydrophobic faces on the backbone more greatly constrain the surrounding water molecules and lead to a greater degree of disorganized binding interactions working to exclude this water and can lead to polymer precipitation [ 26, 27, 31].
Suppressors of cytokine signalling proteins are rapidly induced by activated STATs and act to block the cytokine signal either by direct inhibition of JAKs (SOCS-1), by binding to tyrosine phosphorylated receptor so as to exclude binding of other SH2 and PTB domain-containing signalling proteins such as STATs (CIS), or by both mechanisms (SOCS-3) (Ram and Waxman, 1999).
We also performed high salt washes of endosome preparations to exclude binding of OS-9 to the cytoplasmic side of the ER.
These primers were designed to exclude binding to any CpG dinucleotides to ensure amplification of both methylated and unmethylated sequences.
To exclude binding of uncoupled gold particles to tissue structures, control sections were incubated with a pure colloidal gold solution.
Primers were designed to exclude binding to any CpG dinucleotide to ensure amplification of both methylated and unmethylated forms of DNA.
The antibody libraries were in both cases pre-screened for binding to normal cells to exclude those antibodies reacting with common antigenes.
To exclude binding of the anti-SPH antibody to sphinganine, the trachea from WT or CF mice were removed, incubated in vitro with 10 μM sphinganine in 150 mM sodium acetate (pH 7.4) for 30 min, washed three times in 150 mM sodium acetate (pH 7.4), fixed for 36 h in 2% PFA (pH 7.3), and stained with the anti-SPH antibody.
Although no threshold was adopted for the ligand size, peptides were automatically excluded (because the unwanted ligand list also included all 20 amino acids), and a threshold of five residues in the binding site was chosen to exclude non-specific interactions.
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