Measuring Inconsistency in Declarative Process Specifications

We address the problem of measuring inconsistency in declarative process specifications, with an emphasis on linear temporal logic on fixed traces (LTLff). As we will show, existing inconsistency measures for classical logic cannot provide a meaningful assessment of inconsistency in LTL in general, as they cannot adequately handle the temporal operators. We therefore propose a novel paraconsistent semantics as a framework for inconsistency measurement. We then present two new inconsistency measures based on these semantics and show that they satisfy important desirable properties. We show how these measures can be applied to declarative process models and investigate the computational complexity of the introduced approach

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Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa

Wood formation is a complex developmental process governed by genetic and environmental stimuli. Populus and Eucalyptus are fast-growing, high-yielding tree genera that represent ecologically and economically important species suitable for generating significant lignocellulosic biomass. Comparative analysis of the developing xylem and leaf transcriptomes of Populus trichocarpa and Eucalyptus grandis together with phylogenetic analyses identified clusters of homologous genes preferentially expressed during xylem formation in both species. A conserved set of 336 single gene pairs showed highly similar xylem preferential expression patterns, as well as evidence of high functional constraint. Individual members of multigene orthologous clusters known to be involved in secondary cell wall biosynthesis also showed conserved xylem expression profiles. However, species-specific expression as well as opposite (xylem versus leaf) expression patterns observed for a subset of genes suggest subtle differences in the transcriptional regulation important for xylem development in each species. Using sequence similarity and gene expression status, we identified functional homologs likely to be involved in xylem developmental and biosynthetic processes in Populus and Eucalyptus. Our study suggests that, while genes involved in secondary cell wall biosynthesis show high levels of gene expression conservation, differential regulation of some xylem development genes may give rise to unique xylem properties.Genome Canada Large-Scale Applied Research Project (Project 168BIO) South African Department of Science and Technology (DST), Mondi and Sappi through the Forest Molecular Genetics (FMG) Programme, the Technology and Human Resources for Industry Programme (THRIP,UID 80118), and the National Research Foundation (NRF, UID 71255 and 86936) of South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-81372016-06-30hb201

A Comparative Study of the Arabidopsis thaliana Guard-Cell Transcriptome and Its Modulation by Sucrose

Microarray analysis was performed on RNA isolated from guard cells that were manually dissected from leaves of Arabidopsis. By pooling our data with those of two earlier studies on Arabidopsis guard cell protoplasts, we provide a robust view of the guard-cell transcriptome, which is rich in transcripts for transcription factors, signaling proteins, transporters, and carbohydrate-modifying enzymes. To test the hypothesis that photosynthesis-derived sugar signals guard cells to adjust stomatal opening, we determined the profile of genes expressed in guard cells from leaves that had been treated with sucrose. The results revealed that expression of 440 genes changed in guard cells in response to sucrose. Consistent with this hypothesis, these genes encoded cellular functions for photosynthesis and transport of sugars, water, amino acids, and ions. Plants of T-DNA insertion lines for 50 genes highly responsive to sucrose were examined for defects in guard cell function. Twelve genes not previously known to function in guard cells were shown to be important in leaf conductance, water-use efficiency, and/or stomate development. Of these, three are of particular interest, having shown effects in nearly every test of stomatal function without a change in stomatal density: TPS5 (At4g17770), a TRAF domain-containing protein (At1g65370), and a WD repeat–containing protein (At1g15440)