Each sample was measured in triplicate on the three different assay dates and had a variability of less than 10%.
Using the JMP statistical package [ 44], we carried out nested ANOVAs for single assay dates, with killing treatment and selection line(within killing treatment) as explanatory variables.
Overall, host population density in infected assay tubes was lower than that in the uninfected controls (MANOVA: F1,64 = 5.61, p = 0.0209), with an average reduction of 20 25% during the last 3 assay dates (day 9, 11, 13).
The application of UC particles in homogeneous assay dates back to the work by Mitchell and Morgan in 2007, and subsequently by Kuningas and co-workers who utilized the streptavidin conjugated UC particles as donors and biotinylated phycobiliprotein (biotin-BPE) as the acceptor.
An early (pre-surgical) assay date would indicate its role in triggering an initial diagnostic biopsy procedure, while a late assay date could indicate post-treatment recurrent disease.
The intermittently low breath pH values we observed were not correlated with subject, study day, or assay date, and resampling of banked samples suggested that they could not be attributed to random laboratory error.
Furthermore, information on sampling conditions such as those considered here (in addition, whenever relevant, to batch number, assay date, and information on any deviation from the planned protocol) should be collected for all study subjects so that their possible impact can be characterized and if required corrected for.
The model included the fixed effects for genotype (AA or AB), assay date (the AATI batch effect of samples run together on the same day with 4 levels), alternate transcript abundance (the GBP5 alternate-splicing transcripts: wild-type, +5 bps, and retained intron), and a random effect of animal to account for common effects of individuals across days and shared effects on alternate transcripts.
These read counts were then analyzed using the same model as described above for the AATI data to determine if differential splicing of the three alternatively spliced transcripts was observed in the RNA-seq data, with the exception that assay date was not necessary in the model.
iii) Latency time: For each assay date, we calculated the proportion of infectious individuals (i.e., that produced infectious forms) in a population; this proportion reflects the timing of the onset of the production of infectious forms and thus latency time.
For those in vitro assays included in ToxCast Phase I, the associated information, including contractor/collaborator, assay type, date stamp, assays/endpoints and references (publications and websites), are also provided in the EPA ToxCast website.
