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Interactions 2 Reading Pdf Download
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Impact analysis has been defined as an activity of assessing the potential consequences of making a set of changes to software artifacts. Several approaches have been developed including performing impact analysis on a reflected model of class interactions analysis using class interactions prediction. One of the important elements in developing the reflected model is a consideration of any design pattern that the software employs. In this paper we propose a new class interactions prediction approach that includes a basic pattern analysis i.e., Boundary-Controller-Entity (BCE) pattern in its prediction process. To demonstrate the importance of the pattern consideration in the prediction process, a comparison between the new approach (with pattern consideration) and two selected current approaches (without pattern consideration) were conducted. The contributions of the paper are two-fold: (1) a new class interactions prediction approach; and (2) evaluation results show the new approach gives better accuracy of class interactions prediction than the selected current approaches.
(iii) Growth in a consortium induces a combination of known pairwise responses as well as novel higher-order responses in S. cerevisiae. To determine gene expression programs associated with higher-order interactions, we evaluated the DEGs of S. cerevisiae during growth within the three-species consortium. First, the extent to which the DEGs present during consortium growth could be predicted by the pairwise coculture DEGs was assessed by matching the genes in common between the pairwise and consortium conditions (Fig. 6A). Overall, 43% of the consortium DEGs were unique, i.e., expressed only during consortium growth and not under either pairwise condition, and 57% were present during pairwise coculture. Delving into this 57% of pairwise origin, 100% of the DEGs expressed during coculture with L. thermotolerans were expressed during consortium growth, and 73% of DEGs expressed during coculture with T. delbrueckii were expressed during consortium growth. This shows that pairwise ecological interactions are largely retained during consortium growth. The overall trend is that some prediction of interactions can be made from pairwise data; however, there indeed appears to be evidence for higher-order, or unpredictable, expression responses in S. cerevisiae.
Within this functional network there were also several clusters that consisted of majority higher-order interaction DEGs, which are notable as they may point to cellular responses that are indeed unique to higher-order interactions. This led us to perform functional enrichment and identify a network of the DEGs unique to the consortium growth condition in isolation (Fig. 6B and Fig. S6).
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