Michigan State University

About: Michigan State University is a education organization based out in East Lansing, Michigan, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 60109 authors who have published 137074 publications receiving 5633022 citations. The organization is also known as: MSU & Michigan State.

A Review on Bilevel Optimization: From Classical to Evolutionary Approaches and Applications

Abstract: Bilevel optimization is defined as a mathematical program, where an optimization problem contains another optimization problem as a constraint. These problems have received significant attention from the mathematical programming community. Only limited work exists on bilevel problems using evolutionary computation techniques; however, recently there has been an increasing interest due to the proliferation of practical applications and the potential of evolutionary algorithms in tackling these problems. This paper provides a comprehensive review on bilevel optimization from the basic principles to solution strategies; both classical and evolutionary. A number of potential application problems are also discussed. To offer the readers insights on the prominent developments in the field of bilevel optimization, we have performed an automated text-analysis of an extended list of papers published on bilevel optimization to date. This paper should motivate evolutionary computation researchers to pay more attention to this practical yet challenging area.

Genetic control of multiple molecular forms of enzymes in plants: A review

Abstract: Progress in the field of biochemical genetics of diploid organisms has been considerable in the last decade. Much of this has been made possible by the introduction of improved electrophoretic procedures utilizing various gel matrices for separation of mixtures of proteins. Investigators of genetic control of protein synthesis have effectively used this tool to estimate the number of genes involved in the production of a protein or enzyme. These methods have already proved useful in providing information as to the number of polypeptide subunits that make up a protein molecule in studies with microorganisms (Levinthal et aL, 1962), animals (Markert, 1963), and plants (Scandalios, 1965a). In conjunction with the high-resolution \"zymogram\" method for displaying enzyme activity on gels (Hunter and Markert, 1957), the gel electrophoretic procedures have afforded the geneticist a means to study mutations which presumably alter the structure of enzymes, resulting in differential electrophoretic mobilities of the molecules, while their catalytic activity is retained. This is a new and promising dimension for studying gene action, since before the advent of these techniques similar studies were essentially confined to enzyme variation due to alterations in total catalytic activity. A large number of electrophoretic variants of enzymes have now been discovered (Shaw, 1965). With these findings came the knowledge that enzymes may exist in the same organism in more than one molecular form. Such multiple molecular forms of an enzyme in~ a single organism have been designated isozymes (Markert and Moller, 1959). Isozymes may differ in primary structure because they are encoded in different genes, either allelic or nonallelic. The primary structure may be further

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Abstract: Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Kinetic Explanation for Accumulation of Nitrite, Nitric Oxide, and Nitrous Oxide During Bacterial Denitrification

Abstract: The kinetics of denitrification and the causes of nitrite and nitrous oxide accumulation were examined in resting cell suspensions of three denitrifiers. An Alcaligenes species and a Pseudomonas fluorescens isolate characteristically accumulated nitrite when reducing nitrate; a Flavobacterium isolate did not. Nitrate did not inhibit nitrite reduction in cultures grown with tungstate to prevent formation of an active nitrate reductase; rather, accumulation of nitrite seemed to depend on the relative rates of nitrate and nitrite reduction. Each isolate rapidly reduced nitrous oxide even when nitrate or nitrite had been included in the incubation mixture. Nitrate also did not inhibit nitrous oxide reduction in Alcaligenes odorans, an organism incapable of nitrate reduction. Thus, added nitrate or nitrite does not always cause nitrous oxide accumulation, as has often been reported for denitrifying soils. All strains produced small amounts of nitric oxide during denitrification in a pattern suggesting that nitric oxide was also under kinetic control similar to that of nitrite and nitrous oxide. Apparent Km values for nitrate and nitrite reduction were 15 μM or less for each isolate. The Km value for nitrous oxide reduction by Flavobacterium sp. was 0.5 μM. Numerical solutions to a mathematical model of denitrification based on Michaelis-Menten kinetics showed that differences in reduction rates of the nitrogenous compounds were sufficient to account for the observed patterns of nitrite, nitric oxide, and nitrous oxide accumulation. Addition of oxygen inhibited gas production from 13NO3− by Alcaligenes sp. and P. fluorescens, but it did not reduce gas production by Flavobacterium sp. However, all three isolates produced higher ratios of nitrous oxide to dinitrogen as the oxygen tension increased. Inclusion of oxygen in the model as a nonspecific inhibitor of each step in denitrification resulted in decreased gas production but increased ratios of nitrous oxide to dinitrogen, as observed experimentally. The simplicity of this kinetic model of denitrification and its ability to unify disparate observations should make the model a useful guide in research on the physiology of denitrifier response to environmental effectors.

Two-stage dynamic signal detection: a theory of choice, decision time, and confidence.

Abstract: The 3 most often-used performance measures in the cognitive and decision sciences are choice, response or decision time, and confidence. We develop a random walk/diffusion theory-2-stage dynamic signal detection (2DSD) theory-that accounts for all 3 measures using a common underlying process. The model uses a drift diffusion process to account for choice and decision time. To estimate confidence, we assume that evidence continues to accumulate after the choice. Judges then interrupt the process to categorize the accumulated evidence into a confidence rating. The model explains all known interrelationships between the 3 indices of performance. Furthermore, the model also accounts for the distributions of each variable in both a perceptual and general knowledge task. The dynamic nature of the model also reveals the moderating effects of time pressure on the accuracy of choice and confidence. Finally, the model specifies the optimal solution for giving the fastest choice and confidence rating for a given level of choice and confidence accuracy. Judges are found to act in a manner consistent with the optimal solution when making confidence judgments.