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Nexus file for phylogenetic analysis. (ZIP 7 kb)

Additional file 3: Table S2. Summary of the Illumina sequencing data.

A, Western blot showing AMY3 transfected HEK293 cells demonstrate a marked increase in level of expression of CTR and RAMP3 proteins compared to wild-type (WT) HEK cells. B, in BV2 cells, RAMP3 protein expression shows a marked decreased after RAMP3 siRNA transfection compared to the control non-transfected cells. (JPEG 1495 kb)

Gene Ontology (GO) process category enrichments for the NQP and prion prediction data sets from human (the same sets that are analyzed in Tables 1, 2, 3 and 4). These are derived using the website GOrilla [52]. (TXT 3 kb)

Cox models are commonly used in the analysis of time to event data. One advantage of Cox models is the ability to include time-varying covariates, often a binary covariate that codes for the occurrence of an event that affects an individual subject. A common assumption in this case is that the effect of the event on the outcome of interest is constant and permanent for each subject. In this paper we propose a modification to the Cox model to allow the influence of an event to exponentially decay over time. Methods for generating data using the inverse cumulative density function for the proposed model are developed. Likelihood ratio tests and AIC are investigated as methods for comparing the proposed model to the commonly used permanent exposure model. A more general model proposed by Cox and Oakes [1] is also discussed. A simulation study is performed and three different data sets are presented as examples.

Complete set of 739 unique cyclodipeptide synthases identified in a global analysis of publicly available prokaryotic genomes. (XLSX 144Â kb)

Additional file 4: Figure S2. Evolutionary trajectories and apparent selection of all mutation hotspots identified by population sequencing. Mutations arose either in the MATα (left) or MATa (right) as indicated immediately to the left of each mutation. On the vertical axis are the names of the mutations, giving the closest gene, coordinates with respect to that gene and the nature of the nucleotide substitution. On the horizontal axis are each of the six evolutionary time points (UV, R1, R2, R3, R4, R5) and the mean allele frequency change (M). Frequencies of the mutant alleles are represented by shades of green. Mean allele frequency changes are represented in shades of red (M 1, increasing frequency). Mutations linked by connectors and marked with an asterisk indicate pairs with significantly similar initial frequency (binomial test, p > 0.05).

In this video we observe the double-wing featured shown in figure 5 of the manuscript. The transmission of the waveguide increases for a liquid's RI of 1.602 matching the glass's. while on the other side, with a liquid of 1.604 matching the effective RI of the guided mode we observe a decrease in the transmission.

Previously described Ď Neoblast markers are not specific to the Ď -class. Plots were made using an online single cell RNAseq resource published by [40] ( http://radiant.wi.mit.edu/app/ ). Legend of neoblast classes in top right. (PNG 245 kb)

Radiodonts, stem-group euarthropods that evolved during the Cambrian explosion, were among the largest and most diversified lower palaeozoic predators. These animals were widespread geographically, occupying a variety of ecological niches, from benthic foragers to nektonic suspension feeders and apex predators. Here, we describe the largest Cambrian hurdiid radiodont known so far, Titanokorys gainesi, gen. et sp. nov., from the Burgess Shale (Marble Canyon, Kootenay National Park, British Columbia). Estimated to reach half-a-meter in length, this new species bears a very large ovoid-shaped central carapace with distinct short posterolateral processes and an anterior spine. Geometric morphometric analyses highlight the high diversity of carapace shapes in hurdiids and show that Titanokorys bridges a morphological gap between forms with long and short carapaces. Carapace shape, however, is prone to homoplasy and shows no consistent relationship with trophic ecology, as demonstrated by new data, including a reappraisal of the poorly known Pahvantia. Despite distinct carapaces, Titanokorys shares similar rake-like appendages for sediment-sifting with Cambroraster, a smaller but much more abundant sympatric hurdiid from the Burgess Shale. The co-occurrence of these two species on the same bedding planes highlights the potential competition for benthic resources and the high diversity of large predators sustained by Cambrian communities.