Pressure study of structural properties and phonons in YBa2Cu3 O7

The pressure dependence of crystal structure and vibrational properties of YBa ₂ Cu ₃ O ₇ is investigated by first-principles calculations based on density functional theory. We have determined the optimized geometry for different unit cell volumes by relaxing the atoms to their force-free positions. The tendency of altered bond strength with pressure is consistent with experimental investigations and previous c-axis strain calculations. The pressure effect on the three A _1g phonon frequencies dominated by oxygen vibrations is in very good agreement with experimental investigations showing constant linear pressure coefficients d/dp over a wide range of pressure values.     

Dynamical patterns in clapping behavior.

A nonlinear dynamics framework that has been applied successfully to several laboratory idealizations of rhythmic behaviors was applied to a more naturally occurring behavior, clapping. Inertial loading of limbs and frequency of oscillation were manipulated. Displacement of relative phase from perfectly in phase and the variability of relative phase, both of which are used as indexes of coordination dynamics, increased with greater inertial imbalance between limbs. Increasing frequency exaggerated these effects. These hallmark properties of coupled oscillator dynamics appeared whether or not the hands contacted, albeit with the latter condition revealing a significant asymmetry in the dynamics. Results highlight the generality of the coupled oscillator regime in interlimb coordination as well as its appropriateness for characterizing behaviors that involve contact of limb surfaces and suggest one way in which perceptual information may tune the dynamical regime. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution

Directed evolution of the C25 farnesylgeranyl diphosphate synthase of Aeropyrum pernix (Fgs) was carried out by error-prone PCR with an in vivo color complementation screen utilizing carotenoid biosynthetic pathway enzymes. Screening yielded 12 evolved clones with C20 geranylgeranyl diphosphate synthase activity which were isolated and characterized in order to understand better the chain elongation mechanism of this enzyme. Analysis of these mutants revealed three different mechanisms of product chain length specificity. Two mutants (A64T and A64V) have a single mutation at the 8th amino acid upstream of a conserved first aspartate-rich motif (FARM), which is involved in the mechanism for chain elongation reaction of all prenyl diphosphate synthases. One mutant (A135T) carries a single mutation at the 7th amino acid upstream of another conserved region (141GQ142), which was recently found to be another important region controlling chain elongation of a type III C20 geranylgeranyl diphosphate synthase and Escherichia coli C15 farnesyl diphosphate synthase. Finally, one mutant carrying four mutations (V84I, H88R, I177 M and M191V) is of interest. Molecular modeling, site-directed mutagenesis and in vitro assays of this mutant suggest that product chain-length distribution can be also controlled by a structural change provoked by a cooperative interaction of amino acids.     

Impact of natural organic matter (NOM) on freshwater amphipods

Natural organic matter (NOM) isolated from the eutrophic Sanctuary Pond (Point Pelee National Park, Canada) has an adverse impact on amphipod species (Gammarus tigrinus and Chaetogammarus ischnus from Lake Müggelsee, Germany, and Eulimnogammarus cyaneus, from Lake Baikal, Russia). Increases in amphipod mortality, changes in peroxidase activity and increases of heat shock protein (hsp70) expression were observed upon exposure to NOM. The highest resistance to the adverse impact of NOM was observed with the endemic Baikalian amphipod E. cyaneus. However, the mechanisms behind this finding remains obscure. If differences in the sensitivity of the hsp70 antibody may be excluded, different modes of action may be postulated: because the adverse impact of NOM may be caused by reactive oxygen species (ROS) and the NOM itself, the observed differences may be due to the action of ROS alone (with E. cyaneus) and a combination of both adverse modes of action (European species).     

Three-dimensional segmentation and growth-rate estimation of small pulmonary nodules in helical CT images

Small pulmonary nodules are a common radiographic finding that presents an important diagnostic challenge in contemporary medicine. While pulmonary nodules are the major radiographic indicator of lung cancer, they may also be signs of a variety of benign conditions. Measurement of nodule growth rate over time has been shown to be the most promising tool in distinguishing malignant from nonmalignant pulmonary nodules. In this paper, we describe three-dimensional (3-D) methods for the segmentation, analysis, and characterization of small pulmonary nodules imaged using computed tomography (CT). Methods for the isotropic resampling of anisotropic CT data are discussed. 3-D intensity and morphology-based segmentation algorithms are discussed for several classes of nodules. New models and methods for volumetric growth characterization based on longitudinal CT studies are developed. The results of segmentation and growth characterization methods based on in vivo studies are described. The methods presented are promising in their ability to distinguish malignant from nonmalignant pulmonary nodules and represent the first such system in clinical use.     

Engineered articular cartilage: influence of the scaffold on cell phenotype and proliferation

Articular cartilage defects do not heal. Biodegradable scaffolds have been studied for cartilage engineering in order to implant autologous chondrocytes and help cartilage repair. We tested some new collagen matrices differing in collagen type, origin, structure and methods of extraction and purification, and compared the behavior of human chondrocytes cultured on them. Human chondrocytes were grown for three weeks on four different equine type I collagen matrices, one type I, III porcine collagen matrix and one porcine type II collagen matrix. After 21 days, samples were subjected to histochemical, immunohistochemical and histomorphometric analysis to study phenotype expression and cell adhesion. At 7, 14 and 21 days cell proliferation was studied by incorporation of [3H]-thymidine. Our data evidence that the collagen type influences cell morphology, adhesion and growth; indeed, cellularity and rate of proliferation were significantly higher and cells were rounder on the collagen II matrix than on either of the collagen I matrices. Among the collagen I matrices, we observed a great variability in terms of cell adhesion and proliferation. The present study allowed us to identify one type I collagen matrix and one type II collagen matrix that could be usefully employed as a scaffold for chondrocyte transplantation.     

POESIA: An ontological workflow approach for composing Web services in agriculture

This paper describes the POESIA approach to systematic composition of Web services. This pragmatic approach is strongly centered in the use of domain-specific multidimensional ontologies. Inspired by applications needs and founded on ontologies, workflows, and activity models, POESIA provides well-defined operations (aggregation, specialization, and instantiation) to support the composition of Web services. POESIA complements current proposals for Web services definition and composition by providing a higher degree of abstraction with verifiable consistency properties. We illustrate the POESIA approach using a concrete application scenario in agroenvironmental planning.Received: 15 December 2002, Accepted: 16 April 2003, Published online: 30 September 2003Edited by: V. AtluriRenato Fileto: fileto@ic.unicamp.br     

A Graph Abstract Machine Describing Event Structure Composition

Event structures, Game Semantics strategies and Linear Logic proof-nets arise in different domains (concurrency, semantics, proof-theory) but can all be described by means of directed acyclic graphs (dag's). They are all equipped with a specific notion of composition, interaction or normalization.We report on-going work, aiming to investigate the common dynamics which seems to underly these different structures.In this paper we focus on confusion free event structures on one side, and linear strategies [Jean-Yves Girard. Locus solum. Mathematical Structures in Computer Science, 11:301–506, 2001, C. Faggian and F. Maurel. Ludics nets, a game model of concurrent interaction. In Proc. of LICS'05 (Logic in Computer Science). IEEE Computer Society Press, 2005] on the other side. We introduce an abstract machine which is based on (and generalizes) strategies interaction; it processes labelled dag's, and provides a common presentation of the composition at work in these different settings.