Analytic Tableaux for Simple Type Theory and its First-Order Fragment

We study simple type theory with primitive equality (STT) and its first-order fragment EFO, which restricts equality and quantification to base types but retains lambda abstraction and higher-order variables. As deductive system we employ a cut-free tableau calculus. We consider completeness, compactness, and existence of countable models. We prove these properties for STT with respect to Henkin models and for EFO with respect to standard models. We also show that the tableau system yields a decision procedure for three EFO fragments

Morphological taphonomic transformations of fossil bones in continental environments, and repercussions of their chemical composition

The aim of this paper is to provide a summary of structural or surface modifications of vertebrate bone remains in continental palaeoenvironments that may have repercussions on their chemical composition. Both before and after burial, a different set of physical, chemical and biological agencies may produce modifications of the bone morphological structure and/or bone chemical composition. Several of these morphological modifications are diagnostic of particular agents, which otherwise may not be noticed or identified in a fossil association. In order to understand diagenesis, those events that occurred before final burial have to be considered, as they may strongly modify the bone morphological structure and influence post-burial changes

Bed-load Transport of Mixed-size Sediment: Fractional Transport Rates, Bed Forms, and the Development of a Coarse Bed-surface Layer

Fractional transport rates, bed surface texture, and bed configuration were measured after a mixed size sediment had reached an equilibrium transport state for seven different flow strengths in a recirculating laboratory flume. Fractional transport rates were also measured at the beginning of each run when the bed was well mixed and planar. The start-up observations allow us to describe the variation of fractional transport rates with bed shear stress for a constant bed surface texture and bed configuration. The start-up and equilibrium observations together allow, for the first time, an unambiguous description of the mutual adjustment among the transport, the bed configuration, and the bed surface, as the transport system moves toward equilibrium. We find that a substantial interaction exists among the transport, bed surface, and bed configuration. Bed forms and a coarse surface layer coexist over a range of bed shear stress. Under some flow conditions the size and shape of the bed forms are controlled by the presence of the coarse surface layer. At higher flows the coarse surface layer is eliminated by scour in the lee of the bed forms. If the bed surface is defined as that over which the bed forms move, a coherent relation between the bed surface texture and the transport grain size distribution may be defined. At equilibrium the transport rates of all fractions were not equally mobile, defined as identical transport and bed grain size distributions, although equal mobility was approached for runs in which the bed shear stress was more than twice that for initial motion of the mixture. Under some flow conditions the transport was observed to adjust away from equal mobility as the bed adjusted from a well-mixed start-up condition to an equilibrium state. Development of a partial static armor, wherein some individual grains become essentially immobile even though other grains in the same fraction remain in transport, is suggested to explain these adjustments between the transport and bed surface grain size distributions. Constraints on equilibrium mixed size sediment transport are defined. The special conditions for which equal mobility must hold and the relevance to natural conditions of flume results and the equal mobility concept are discussed

Functional Analysis of the Aspergillus nidulans Kinome

The filamentous fungi are an ecologically important group of organisms which also have important industrial applications but devastating effects as pathogens and agents of food spoilage. Protein kinases have been implicated in the regulation of virtually all biological processes but how they regulate filamentous fungal specific processes is not understood. The filamentous fungus Aspergillus nidulans has long been utilized as a powerful molecular genetic system and recent technical advances have made systematic approaches to study large gene sets possible. To enhance A. nidulans functional genomics we have created gene deletion constructs for 9851 genes representing 93.3% of the encoding genome. To illustrate the utility of these constructs, and advance the understanding of fungal kinases, we have systematically generated deletion strains for 128 A. nidulans kinases including expanded groups of 15 histidine kinases, 7 SRPK (serine-arginine protein kinases) kinases and an interesting group of 11 filamentous fungal specific kinases. We defined the terminal phenotype of 23 of the 25 essential kinases by heterokaryon rescue and identified phenotypes for 43 of the 103 non-essential kinases. Uncovered phenotypes ranged from almost no growth for a small number of essential kinases implicated in processes such as ribosomal biosynthesis, to conditional defects in response to cellular stresses. The data provide experimental evidence that previously uncharacterized kinases function in the septation initiation network, the cell wall integrity and the morphogenesis Orb6 kinase signaling pathways, as well as in pathways regulating vesicular trafficking, sexual development and secondary metabolism. Finally, we identify ChkC as a third effector kinase functioning in the cellular response to genotoxic stress. The identification of many previously unknown functions for kinases through the functional analysis of the A. nidulans kinome illustrates the utility of the A. nidulans gene deletion constructs

Theory of Concepts

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Accurate measurement of microsatellite length by disrupting its tandem repeat structure

Tandem repeats of simple sequence motifs, also known as microsatellites, are abundant in the genome. Because their repeat structure makes replication error-prone, variant microsatellite lengths are often generated during germline and other somatic expansions. As such, microsatellite length variations can serve as markers for cancer. However, accurate error-free measurement of microsatellite lengths is difficult with current methods precisely because of this high error rate during amplification. We have solved this problem by using partial mutagenesis to disrupt enough of the repeat structure of initial templates so that their sequence lengths replicate faithfully. In this work, we use bisulfite mutagenesis to convert a C to a U, later read as T. Compared to untreated templates, we achieve three orders of magnitude reduction in the error rate per round of replication. By requiring agreement from two independent first copies of an initial template, we reach error rates below one in a million. We apply this method to a thousand microsatellite loci from the human genome, revealing microsatellite length distributions not observable without mutagenesis