Interval type-2 fuzzy modelling and stochastic search for real-world inventory management

Real-world systems present a variety of challenges to the modeller, not least of which is the problem of uncertainty inherent in their operation. In this research, an interval type-2 fuzzy model is applied to a real-world problem, the goal being to discover a suitable optimisation configuration to enable a search for an inventory plan using the model. To this end, a series of simulated annealing configurations and the interval type-2 fuzzy model were used to search for appropriate inventory plans for a large-scale real-world problem. A further set of tests were conducted in which the performance of the interval type-2 fuzzy model was compared with a corresponding type-1 fuzzy model. In these tests the results were inconclusive, though, as will be discussed there are many ways in which type-2 fuzzy logic can be exploited to demonstrate its advantages over a type-1 approach. To conclude, in this research we have shown that a combination of interval type-2 fuzzy logic and simulated annealing is a logical choice for inventory management modelling and inventory plan search, and propose that the benefits that a type-2 model offers, can make it preferable to a corresponding type-1 system

Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria

Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs) using a machine learning method inspired by the “Divide & Conquer” strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target genes and/or the promoter architectures resulting from the interaction of those binding sites with the RNA polymerase

Simulating trends of soil organic carbon in seven long-term experiments using the SOMM model of the humus types

Using the SOMM model of the humus types (Mor, Moder, Mull), simulations of SOM dynamics at seven long-term experiments were attempted as a part of a model evaluation exercise. The model comprises three compartments (undecomposed litter, partially humified litter, humus of mineral topsoil) and considers six processes of mineralization and humification as influenced by litter nitrogen and ash contents, soil C/N ratio, temperature and moisture. Results of simulations performed without any site-specific calibration mostly underestimate soil organic matter (SOM). Despite this lack of precision, general trends in SOM over time were often captured. Success of simulation was limited by difficulties in obtaining direct information about soil moisture regime, litter quantity and litter quality (nitrogen and ash content). Inadequacies in the model, such as no consideration of soil properties, may also account for some of the errors. Despite the limited success of the evaluation, it is encouraging that the model conceived for forested ecosystems, with additional development, may be applicable to non-forested systems. The exercise underlines the necessity of constant direct contact between modeller and data holder for a success of an evaluation.</p

Simulating trends of soil organic carbon in seven long-term experiments using the SOMM model of the humus types

Using the SOMM model of the humus types (Mor, Moder, Mull), simulations of SOM dynamics at seven long-term experiments were attempted as a part of a model evaluation exercise. The model comprises three compartments (undecomposed litter, partially humified litter, humus of mineral topsoil) and considers six processes of mineralization and humification as influenced by litter nitrogen and ash contents, soil C/N ratio, temperature and moisture. Results of simulations performed without any site-specific calibration mostly underestimate soil organic matter (SOM). Despite this lack of precision, general trends in SOM over time were often captured. Success of simulation was limited by difficulties in obtaining direct information about soil moisture regime, litter quantity and litter quality (nitrogen and ash content). Inadequacies in the model, such as no consideration of soil properties, may also account for some of the errors. Despite the limited success of the evaluation, it is encouraging that the model conceived for forested ecosystems, with additional development, may be applicable to non-forested systems. The exercise underlines the necessity of constant direct contact between modeller and data holder for a success of an evaluation.</p