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To compare the ERs of different groups of SNPs, we did the analysis at two levels: for each individual environmental factor/category and for all environmental factors.
In model 1, we examined the crude association between each individual environmental exposure (measured as children's urinary arsenic, urinary cadmium, and urinary lead levels at age 5 years) and each outcome at age 5 years.
For each individual environmental DNA extract we ran three independent 30-μl PCR reactions with reaction mix consisting of 5 U of Pfu Turbo polymerase (Stratagene, La Jolla, CA, USA), 1× Pfu reaction buffer, 200 μm dNTPs (Pierce Nucelic Acid Technologies, Milwaukee, WI, USA), a 0.2 μM concentration of each primer in a volume of 100 μl, and 3-10 ngenomicic DNA as template.
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The ERs of eQTLs to intergenic SNPs were calculated for each of the 36 individual environmental factors and 6 environmental categories.
Linear regression was used to examine relationships between each individual or environmental characteristic and snack food consumption in separate models and also to examine relationships in a model including all of the characteristics simultaneously.
In addition to the genetic characteristics of each individual, the environmental circumstances affecting each person throughout their life are different.
Therefore, we conducted further analysis with the toluene exposure ratio, which was calculated as the quotient of each individual's environmental toluene concentration exposure divided by his measured urine hippuric acid concentration.
The coefficient of correlation for each individual gut environmental factor was calculated using the Spearman's rank correlation coefficient, and the correlative information was clustered individually by HCA to seek the covariation factor(s) that related to the induction of faecal IgA production (Fig. 4).
17 Additionally, the social cognitive theory states that there is an interaction between personal factors of the individual, environmental factors and human behaviour, where each influences the others.
The importance of individual environmental variables in explaining the distribution of each species modeled was determined by running jackknife tests within the Maxent interface [ 35].
Using MaxEnt 3.3.3 k [ 22, 79] we created response curves for these six ecological variables, performed jackknife tests to measure the importance of individual environmental variables in explaining the modelled distribution of each morphotype, and estimated potential niches per morphotype.
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