The aim of our computational modeling is twofold. First, we seek to understand the relative contribution of cell proliferation, fate transition and respecification in mediating the pCLV3:HEC1-GR phenotype. We use the model to check which hypothetical scenarios are compatible with our experimental observations. Second, we aim to get insights into the hec1,2,3 phenotype which admits only limited ...

Definition of the counterfactual Dj . This all takes place at the level of hypothetical manipulations. The space may have a probability measure or just a measure. For some J (Z) = j, define Aj (z) = {z | J (z) = j}. For each element in the set, we “project” μD (z) onto the set. If we embed the set in L , this is clear. Otherwise, there may be other constructions (e.g., embed in space L and for ...

This paper presents a novel algorithm for identification and functional characterization of "key" genome features responsible for a particular biochemical process of interest. The central idea is that individual genome features are identified as "key" features if the discrimination accuracy between two classes of genomes with respect to a given biochemical process is sufficiently affected by th...

This observation comes from the fact that in standard ALP [ Kakas, et al., 1992 ] , hypotheses are restricted to atoms which are pre-speci ed as abducibles. However, distinction on the sentential form of hypotheses is not necessarily the point. In fact, the ALP framework is easily extended to include abducible rules [ Inoue and Sakama, 1994 ] . Namely, a set of hypothetical clauses are speci ed...

Earthworms affect nitrogen cycling directly through the consumption and assimilation of organic N and the turnover of N through excretion and mortality. Although earthworms can process large quantities of organic matter, organic-matter consumption by earthworms based on their nitrogen requirements has not been quanti®ed. Organic-matter consumption and the ef®ciency of nitrogen assimilation by e...

This paper describes the development of an approximate physical model that can be used for generating diierent types of protein crystallization behaviors or responses in varying physico-chemical environments. The modeling process involves three stages, two of which have been completed. The model developed in Stage I was over-simpliied and was aimed at providing the right computational avor of t...

Assigning functional information to hypothetical proteins in virus genomes is crucial for gaining insight into their proteomes. Human adenoviruses are medium sized viruses that cause a range of diseases. Their genomes possess proteins with uncharacterized function known as hypothetical proteins. Using a wide range of protein function prediction servers, functional information was obtained about...

Background: Stearoyl-CoA desaturase (SCD) is a key enzyme that converts saturated fatty acids (SFAs) to monounsaturated fatty acids (MUFAs) in fat biosynthesis. Despite being crucial for interpreting SCDs’ roles across species, the evolutionary relationship of SCD proteins across species has yet to be elucidated. This study aims to present this evolutionary relationship based on amino aci...

The SoxR protein of Escherichia coli responds to redox signals by activating the transcription of soxS, which encodes another transcription activator that directly stimulates oxidative stress genes. In contrast, Pseudomonas aeruginosa has an open reading frame (ORF) encoding a putative protein homologous to E. coli SoxR, but not to SoxS. Instead of a soxS homolog, ORFs encoding an unknown hypot...