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Search Results: 1 - 10 of 20181 matches for " Alexander Knapp "
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Palatability of Selected Alpine Plant Litters for the Decomposer Lumbricus rubellus (Lumbricidae)
Alexander Rief, Brigitte A. Knapp, Julia Seeber
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045345
Abstract: On alpine pastureland the decline in large-bodied earthworm numbers and biomass after abandonment of management might be the result of a shift from highly palatable grass litter to poorly digestible leaf litter of dwarf shrubs. To test this hypothesis, we analysed nitrogen, phosphorous and total phenolic contents of fresh and aged litter of eight commonly occuring alpine plant species and compared consumption rates of these food sources in a controlled feeding experiment with Lumbricus rubellus (Lumbricidae). Furthermore, we analysed the microbial community structure of aged litter materials to check for a relationship between the microbial characteristics of the different plant litter types and the food choice of earthworms. Plant litters differed significantly in their chemical composition, earthworms, however, showed no preference for any litter species, but generally rejected fresh litter material. Microbial community structures of the litter types were significantly different, but we could find no evidence for selective feeding of L. rubellus. We conclude that L. rubellus is a widespread, adaptable ubiquist, which is able to feed on a variety of food sources differing in quality and palatability, as long as they have been exposed to wheathering.
Truly On-The-Fly LTL Model Checking
Moritz Hammer,Alexander Knapp,Stephan Merz
Computer Science , 2005,
Abstract: We propose a novel algorithm for automata-based LTL model checking that interleaves the construction of the generalized B\"{u}chi automaton for the negation of the formula and the emptiness check. Our algorithm first converts the LTL formula into a linear weak alternating automaton; configurations of the alternating automaton correspond to the locations of a generalized B\"{u}chi automaton, and a variant of Tarjan's algorithm is used to decide the existence of an accepting run of the product of the transition system and the automaton. Because we avoid an explicit construction of the B\"{u}chi automaton, our approach can yield significant improvements in runtime and memory, for large LTL formulas. The algorithm has been implemented within the SPIN model checker, and we present experimental results for some benchmark examples.
An Institutional Framework for Heterogeneous Formal Development in UML
Alexander Knapp,Till Mossakowski,Markus Roggenbach
Computer Science , 2014,
Abstract: We present a framework for formal software development with UML. In contrast to previous approaches that equip UML with a formal semantics, we follow an institution based heterogeneous approach. This can express suitable formal semantics of the different UML diagram types directly, without the need to map everything to one specific formalism (let it be first-order logic or graph grammars). We show how different aspects of the formal development process can be coherently formalised, ranging from requirements over design and Hoare-style conditions on code to the implementation itself. The framework can be used to verify consistency of different UML diagrams both horizontally (e.g., consistency among various requirements) as well as vertically (e.g., correctness of design or implementation w.r.t. the requirements).
Splitting methods for time integration of trajectories in combined electric and magnetic fields
Christian Knapp,Alexander Kendl,Antti Koskela,Alexander Ostermann
Physics , 2015,
Abstract: The equations of motion of a single particle subject to an arbitrary electric and a static magnetic field form a Poisson system. We present a second-order time integration method which preserves well the Poisson structure and compare it to commonly used algorithms, such as the Boris scheme. All the methods are represented in a general framework of splitting methods. We use the so-called $\phi$ functions, which give efficient ways for both analyzing and implementing the algorithms. Numerical experiments show an excellent long term stability for the new method considered.
An Institution for Simple UML State Machines
Alexander Knapp,Till Mossakowski,Markus Roggenbach,Martin Glauer
Computer Science , 2014,
Abstract: We present an institution for UML state machines without hierarchical states. The interaction with UML class diagrams is handled via institutions for guards and actions, which provide dynamic components of states (such as valuations of attributes) but abstract away from details of class diagrams. We also study a notion of interleaving product, which captures the interaction of several state machines. The interleaving product construction is the basis for a semantics of composite structure diagrams, which can be used to specify the interaction of state machines. This work is part of a larger effort to build a framework for formal software development with UML, based on a heterogeneous approach using institutions.
Sex and the Single Cell. II. There Is a Time and Place for Sex
Carmen C. Robinett,Alexander G. Vaughan,Jon-Michael Knapp,Bruce S. Baker
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000365
Abstract: The Drosophila melanogaster sex hierarchy controls sexual differentiation of somatic cells via the activities of the terminal genes in the hierarchy, doublesex (dsx) and fruitless (fru). We have targeted an insertion of GAL4 into the dsx gene, allowing us to visualize dsx-expressing cells in both sexes. Developmentally and as adults, we find that both XX and XY individuals are fine mosaics of cells and tissues that express dsx and/or fruitless (fruM), and hence have the potential to sexually differentiate, and those that don't. Evolutionary considerations suggest such a mosaic expression of sexuality is likely to be a property of other animal species having two sexes. These results have also led to a major revision of our view of how sex-specific functions are regulated by the sex hierarchy in flies. Rather than there being a single regulatory event that governs the activities of all downstream sex determination regulatory genes—turning on Sex lethal (Sxl) RNA splicing activity in females while leaving it turned off in males—there are, in addition, elaborate temporal and spatial transcriptional controls on the expression of the terminal regulatory genes, dsx and fru. Thus tissue-specific aspects of sexual development are jointly specified by post-transcriptional control by Sxl and by the transcriptional controls of dsx and fru expression.
Sex and the Single Cell. II. There Is a Time and Place for Sex
Carmen C. Robinett,Alexander G. Vaughan,Jon-Michael Knapp,Bruce S. Baker
PLOS Biology , 2010, DOI: 10.1371/journal.pbio.1000365
Abstract: The Drosophila melanogaster sex hierarchy controls sexual differentiation of somatic cells via the activities of the terminal genes in the hierarchy, doublesex (dsx) and fruitless (fru). We have targeted an insertion of GAL4 into the dsx gene, allowing us to visualize dsx-expressing cells in both sexes. Developmentally and as adults, we find that both XX and XY individuals are fine mosaics of cells and tissues that express dsx and/or fruitless (fruM), and hence have the potential to sexually differentiate, and those that don't. Evolutionary considerations suggest such a mosaic expression of sexuality is likely to be a property of other animal species having two sexes. These results have also led to a major revision of our view of how sex-specific functions are regulated by the sex hierarchy in flies. Rather than there being a single regulatory event that governs the activities of all downstream sex determination regulatory genes—turning on Sex lethal (Sxl) RNA splicing activity in females while leaving it turned off in males—there are, in addition, elaborate temporal and spatial transcriptional controls on the expression of the terminal regulatory genes, dsx and fru. Thus tissue-specific aspects of sexual development are jointly specified by post-transcriptional control by Sxl and by the transcriptional controls of dsx and fru expression.
Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and Structure
Clorinda Lori, Antonella Lantella, Alessandra Pasquo, Leila T. Alexander, Stefan Knapp, Roberta Chiaraluce, Valerio Consalvi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064824
Abstract: Pim-1 kinase, a serine/threonine protein kinase encoded by the pim proto-oncogene, is involved in several signalling pathways such as the regulation of cell cycle progression and apoptosis. Many cancer types show high expression levels of Pim kinases and particularly Pim-1 has been linked to the initiation and progression of the malignant phenotype. In several cancer tissues somatic Pim-1 mutants have been identified. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of Pim-1 kinase. We expressed and purified some of the mutants of Pim-1 kinase that are expressed in cancer tissues and reported in the single nucleotide polymorphisms database. The point mutations in the variants significantly affect the conformation of the native state of Pim-1. All the mutants, expressed as soluble recombinant proteins, show a decreased thermal and thermodynamic stability and a lower activation energy values for kinase activity. The decreased stability accompanied by an increased flexibility suggests that Pim-1 variants may be involved in a wider network of protein interactions. All mutants bound ATP and ATP mimetic inhibitors with comparable IC50 values suggesting that the studied Pim-1 kinase mutants can be efficiently targeted with inhibitors developed for the wild type protein.
Toll-Like Receptor 4 Engagement Drives Differentiation of Human and Murine Dendritic Cells from a Pro- into an Anti-Inflammatory Mode
Romana Luger, Sneha Valookaran, Natalie Knapp, Caterina Vizzardelli, Alexander M. Dohnal, Thomas Felzmann
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0054879
Abstract: The dendritic cell (DC) coordinates innate and adaptive immunity to fight infections and cancer. Our observations reveal that DCs exposed to the microbial danger signal lipopolysaccharide (LPS) in the presence of interferon-γ (IFN-γ) acquire a continuously changing activation/maturation phenotype. The DCs’ initial mode of action is pro-inflammatory via up-regulation among others of the signaling molecule interleukin (IL) 12, which polarizes IFN-γ secreting type 1 helper T-cells (Th1). Within 24 hours the same DC switches from the pro- into an anti-inflammatory phenotype. This is mediated by autocrine IL-10 release and secretion of soluble IL-2 receptor alpha (sIL-2RA) molecules. T-cells, when contacted with DCs during their anti-inflammatory phase loose their proliferative capacity and develop regulatory T-cell (Treg) -like anti-inflammatory functions indicated by IL-10 secretion and elevated FoxP3 levels. Studying the kinetics of IL-12 and IL-10 expression from LPS/IFN-γ activated myeloid DCs on a single cell level confirmed these observations. When T-cells are separated from DCs within 24 hours, they are spared from the anti-inflammatory DC activity. We conclude that, in addition to differentiation of DCs into distinct subsets, the observed sequential functional phases of DC differentiation permit the fine-tuning of an immune response. A better understanding of time-kinetic DC features is required for optimally exploiting the therapeutic capacity of DCs in cancer immune therapy.
Rarity, Species Richness, and the Threat of Extinction—Are Plants the Same as Animals?
Sandra Knapp
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001067
Abstract: Assessment of conservation status is done both for areas or habitats and for species (or taxa). IUCN Red List categories have been the principal method of categorising species in terms of extinction risk, and have been shown to be robust and helpful in the groups for which they have been developed. A recent study highlights properties associated with extinction risk in flowering plants, focusing on the species-rich hot spot of the Cape region of South Africa, and concludes that merely following methods derived from studies of vertebrates may not provide the best estimates of extinction risk for plants. Biology, geography, and history all are important factors in risk, and the study poses many questions about how we categorise and assess species for conservation priorities.
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