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Results from each of these constrained tree searches were saved individually and subsequently joined into a single hypothesis file to perform the topology tests according to the Treefinder manual [ 55].
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According to this hypothesis, filing for bankruptcy in Spain is very costly for both small firms and their creditors.
Its high expression in expanding cells strengthens this hypothesis (Additional file 3F).
However, a phylogeny that includes more homologs does not support this hypothesis (Additional file 3).
Inferred gene trees were visualized to study their concordance to the working species tree hypothesis (Additional file 1).
However, the relationships between these domains in a phylogenetic tree of all PDZ domains don't agree with this hypothesis (Additional File 3).
38% of the decisions were based on published data, 30% on personal communications, and 29% on biological hypothesis (Additional file 2: Table S2).
We investigated whether variation in distinct HSCT donor groups (that is, donors matched to recipients with no complications, and those matched to mild aGVHD) caused the reduced performance, but could not substantiate this hypothesis (Additional file 6).
We also considered the possibility that ARGONAUTE binding could preferentially stabilize the subset of mRNA degradation products with 5' U or A terminal nucleotides, but did not find evidence supporting this hypothesis (Additional file 8).
Our preliminary analysis of the transcriptome of Rasless MEFs that recovered their proliferative ability after silencing of Rb via the introduction of specific shRNA constructs [ 19] appears to support this hypothesis (Additional file 7: Figure S2).
The results showed that the GFP output of the isolated AND gate was approximately 7 times stronger than that of the half adder's AND gate, thus confirming our hypothesis (Additional file 1: Figure S8).
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