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Addition of IL-2+ IL-12+ IL-18 decreased the number of CD8+ T cells exhibiting these "exhausted" functional permutations.
To investigate this issue, we used Boolean gate analysis to study the different functional permutations displayed by CD8+ and CD4+ T cells under different stimulation conditions.
In general, addition of single cytokines failed to significantly change the functional permutations seen with ascites alone, although IL-2 had weak effects on several permutations (Supp. Fig. S3).
In the presence of 100% ascites fluid, the number of non-functional T cells increased, whereas the other functional permutations were reduced with the exception of mono-functional T cells expressing CCL4 (Fig. 4, second panel).
Two of the four functional permutations seen at baseline (specifically, monofunctional CD107a, and bi-functional CD107a and CCL4; Fig. 4) are also elevated in CD8+ T cells from HIV progressors compared to non-progressors, suggesting that these permutations may represent functionally exhausted T cells [19], [20].
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A total of four GO terms were found as significantly over-represented in the group of over-expressed genes by the application of a standard, un-weighted test for functional enrichment with the permutation correction (see Table 1).
After 10,000 random permutations for Arabidopsis functional categories to obtain null distribution for each protein-function FunScore, we gained 416 significant potential functions (p<0.05) for the 148 proteins, covering 26.7% of total 559 unknown core mitochondrial proteins (Data S7).
This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes.
This chapter focuses on the theory and practicalities of multiple-comparisons nonparametric randomization and permutation tests for functional neuroimaging experiments and this has been illustrated with worked examples.
Using the phenotype-based permutation on the functional gene set analysis (C2 collection, canonical pathways, chemical and genetic perturbations), two gene sets were found enriched in samples obtained from T2D subjects and one was enriched in samples from non-diabetic controls (Table S4).
This process eliminates noncoding sequences that interrupt coding regions in the germline genome, and joins over 225,000 remaining DNA segments, some of which require inversion or complex permutation to build functional genes.
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