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Among all the possible selection pathways, we observed improvements in both affinity and crossreactivity only when recombinant genetic libraries were screened in order from lowest to highest affinity chemokines (Fig. 2b, d).
Utilizing this set of pathways, we observed that hubs appeared in an increasing number of pathways (inset, Fig. 2A).
It seems likely that the differential expression of defense signaling pathways we observed in Bonny Best and H7996 is accompanied by expression of diverse additional plant genes that confer specific aspects of wilt susceptibility or tolerance.
In our previous computational study of apoptotic pathways, we observed a bistable behavior (selecting between cell death and survival) for degradation rates of Bax (μBax) lower than a threshold value (0.11 s−1), while monostable cell survival was predicted when μBax>0.11 s−1 (Figure 4A in Ref. [28]).
Generally, when we inhibited naïve CD8 T cell entry to LN, via the HEVs using CD62L antibody blockade, genetic deficiency of selectin ligands, or inhibition of chemokine receptor signaling via G-coupled receptor signaling pathways, we observed more naïve CD8 T cells in the blood, and we also observed more naïve CD8 T cells in non-lymphoid organs (Figure 6B).
The top three pathways we observed were paxillin signaling, granulocyte adhesion and diapedesis, and integrin signaling.
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Considering a network based on SorghumCyc hormone pathways and their neighbor pathways (pathways that contain overlapping DE genes with those found in the hormone-related pathways), we observe that few of the hormone pathways share overlapping DE genes.
Interestingly, while our transcription analyses were consistent with previous studies showing the downregulation of IRC7 by the nitrogen catabolite repression (NCR) pathway, we observed an increased concentration of 4MMP in response to DAP addition.
In our own study, which focused on the TLR pathway, we observed down-regulation of TNF-α, IL-12, and CCL2 and up-regulation of IL-10 and colony stimulating factors (CSF2 and CSF3) in tolerant cells [26].
After graded induction or inhibition of the TCR signaling pathway, we observed a graded expression of the NFAT-independent gene CD69 [26]; [27] (Fig. 5).
Matching together the biomarker molecules and genes included in the pathway, we observed some interesting genes that could be further investigated as putative biomarkers.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com