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To explore whether allele frequencies of the EuroAIMs differed significantly among the Spanish samples, we treated each individual EuroAIM marker as a candidate locus for association in a mock study where Canary Islanders were taken as "cases" and Iberians were considered "controls".
Furthermore, to neutralize the soluble fraction of endotoxin associated with the PM samples, we treated added Polymyxin B (PMB), an antibiotic that specifically binds LPS and prevents its binding to TLR4 receptors on the macrophages.
To evaluate the effectiveness of catalase in destroying H2O2 in samples, we treated some samples from the mixed standard (pH 3.2) + H2O2 control experiment (10 mL) with 20 μL of a 1% catalase solution.
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Because the iControl has more than 3000 samples, we treat it as a background population for our TCGA analysis and use it as a control group (that is also used in AGS).
Since each of the PXN mutations was non-repeating, i.e., found only in a single patient sample, we treated all of the samples with mutations as a group (MT, n = 7) and compared them to a set of 60 wild-type PXN samples (WT, n = 60).
The root of M2b in our tree differs in two positions to the earlier definition of Sun et al. [ 7] i.e. transition at np 182 is present in all of our M2b samples so we treated this as basal mutation and lack of this in one sample of Sun et al. [ 7] could be better explained by reversion event, second our all M2b samples has poly 'A' at np 16180 16182 and twelve 'C's thereafter.
The replication analysis was performed using the Geuvadis DNA-seq samples where we treated each Geuvadis population separately in a meta-analysis.
According to the AQS ambient pollutant manual (U.S. EPA 2004), daily observations can be estimated in terms of the arithmetic mean of hourly observations only if the number of these observations is greater than 18 (i.e., ≥ 75% of intended samples); otherwise, we treated them as missing data.
X-ray diffraction analysis (XRD) was used to ensure no feldspar remained in the samples; if feldspar was detected, we treated the samples again with hydrofluoric acid until all feldspar had been removed.
Based on this information, and our sample of Araliaceae, we treated this fossil as the first fossil evidence for the most inclusive clade that excludes Aralia and Panax.
Thus, we treated samples with EMA and then carried out an initial round of PCR of a long stretch of DNA (16S gene, 1514 bp).
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