Recurrence quantification analysis of turbulent fluctuations in the plasma edge of Tokamak Chauffage Alfveacuten Breacutesilien tokamak

Recurrences are close returns of a given state in a time series, and can be used to identify different dynamical regimes and other related phenomena, being particularly suited for analyzing experimental data. In this work, we use recurrence quantification analysis to investigate dynamical patterns in scalar data series obtained from measurements of floating potential and ion saturation current at the plasma edge of the Tokamak Chauffage Alfveacuten Breacutesilien [R. M. O. Galva approximate to o , Plasma Phys. Controlled Fusion 43, 1181 (2001)]. We consider plasma discharges with and without the application of radial electric bias, and also with two different regimes of current ramp. Our results indicate that biasing improves confinement through destroying highly recurrent regions within the plasma column that enhance particle and heat transport.

Automatic Network Fingerprinting through Single-Node Motifs

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs-a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks.

N-(4-chlorophenyl)maleimide

In the title compound, C10H6ClNO2, the dihedral angle between the benzene and maleimide rings is 47.54 (9)degrees. Molecules form centrosymmetric dimers through C-H center dot center dot center dot O hydrogen bonds, resulting in rings of graph- set motif R2 2(8) and chains in the [100] direction. Molecules are also linked by C-H center dot center dot center dot Cl hydrogen bonds along [001]. In this same direction, molecules are connected to other neighbouring molecules by C-H center dot center dot center dot O hydrogen bonds, forming edge- fused R-4(4)(24) rings.

1-(2-Furoyl)-3-(o-tolyl)thiourea

The title compound, C13H12N2O2S, was synthesized from furoyl isothiocyanate and o-toluidine in dry acetone. The thiourea group is in the thioamide form. The central thiourea fragment makes dihedral angles of 2.6 (1) and 22.4 (1)degrees with the ketofuran group and the benzene ring, respectively. The molecular structure is stabilized by N-H...O hydrogen bonds. In the crystal structure, centrosymmetrically related molecules are linked by a pair of N-H...S hydrogen bonds to form a dimer with an R-2(2)(6) ring motif.

Theoretical investigation of atomic and electronic structures of Ga(2)O(3)(ZnO)(6)

Transparent conducting oxides (TCO) are widely used in technological applications ranging from photovoltaics to thin-film transparent field-effect transistors. In this work we report a first-principles investigation, based on density-functional theory, of the atomic and electronic properties of Ga(2)O(3)(ZnO)(6) (GZO(6)), which is a promising candidate to be used as host oxide for wide band gap TCO applications. We identify a low-energy configuration for the coherent distribution of the Ga and Zn atoms in the cation positions within the experimentally reported orthorhombic GZO(6) structure. Four Ga atoms are located in four-fold sites, while the remaining 12 Ga atoms in the unit cell form four shared Ga agglomerates (a motif of four atoms). The Zn atoms are distributed in the remaining cation sites with effective coordination numbers from 3.90 to 4.50. Furthermore, we identify the natural formation of twin-boundaries in GZO(6), which can explain the zigzag modulations observed experimentally by high-resolution transmission electron microscopy in GZO(n) (n=9). Due to the intrinsic twin-boundary formation, polarity inversion in the ZnO tetrahedrons is present which is facilitated by the formation of the Ga agglomerates. Our analysis shows that the formation of fourfold Ga sites and Ga agglomerates are stabilized by the electronic octet rule, while the distribution of Ga atoms and the formation of the twin-boundary help alleviate excess strain. Finally we identify that the electronic properties of GZO(6) are essentially determined by the electronic properties of ZnO, i.e., there are slight changes in the band gap and optical absorption properties.

Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Functional microarray analysis suggests repressed cell-cell signaling and cell survival-related modules inhibit progression of head and neck squamous cell carcinoma

Background: Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+) and recurrent head and neck squamous cell carcinoma (HNSCC) may increase our understanding of the complex biology of this disease. Methods: Tumor samples were obtained from untreated HNSCC patients undergoing surgery. Patients were classified according to pathologic lymph node status (positive or negative) or tumor recurrence (recurrent or non-recurrent tumor) after treatment (surgery with neck dissection followed by radiotherapy). Using microarray gene expression, we screened tumor samples according to modules comprised by genes in the same pathway or functional category. Results: The most frequent alterations were the repression of modules in negative lymph node (N0) and in non-recurrent tumors rather than induction of modules in N+ or in recurrent tumors. N0 tumors showed repression of modules that contain cell survival genes and in non-recurrent tumors cell-cell signaling and extracellular region modules were repressed. Conclusions: The repression of modules that contain cell survival genes in N0 tumors reinforces the important role that apoptosis plays in the regulation of metastasis. In addition, because tumor samples used here were not microdissected, tumor gene expression data are represented together with the stroma, which may reveal signaling between the microenvironment and tumor cells. For instance, in non-recurrent tumors, extracellular region module was repressed, indicating that the stroma and tumor cells may have fewer interactions, which disable metastasis development. Finally, the genes highlighted in our analysis can be implicated in more than one pathway or characteristic, suggesting that therapeutic approaches to prevent tumor progression should target more than one gene or pathway, specially apoptosis and interactions between tumor cells and the stroma.

Molluscicidal and ovicidal activities of plant extracts of the Piperaceae on Biomphalaria glabrata (Say, 1818)

Schistosomiasis is a tropical disease caused by Schistosoma and occurs in 54 countries, mainly in South America, the Caribbean region, Africa and the eastern Mediterranean. Currently, 5 to 6 million Brazilian people are infected and 30,000 are under infection risk. Typical of poor regions, this disease is associated with the lack of basic sanitation and very frequently to the use of contaminated water in agriculture, housework and leisure. One of the most efficient methods of controlling the disease is application of molluscicides to eliminate or to reduce the population of the intermediate host snail Biomphalaria glabrata. Studies on molluscicidal activity of plant extracts have been stimulated by issues such as environmental preservation, high cost and recurrent resistance of snails to synthetic molluscicides. The aim of this study was to determine the molluscicide action of extracts from Piperaceae species on adult and embryonic stages of B. glabrata. Fifteen extracts from 13 Piperaceae species were obtained from stems, leaves and roots. Toxicity of extracts was evaluated against snails at two different concentrations (500 and 100 ppm) and those causing 100% mortality at 100 ppm concentration were selected to obtain the LC(90) (lethal concentration of 90% mortality). Piper aduncum, P. crassinervium, P. cuyabanum, P. diospyrifolium and P. hostmannianum gave 100% mortality of adult snails at concentrations ranging from 10 to 60 ppm. These extracts were also assayed on embryonic stages of B. glabrata and those from P. cuyabanum and P. hostmannianum showed 100% ovicidal action at 20 ppm.

The role of exon shuffling in shaping protein-protein interaction networks

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains), self-interacting (able to interact with another copy of themselves) and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions: Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Morpholin-4-ium morpholine-4-carbodithioate

The title compound, C(4)H(10)NO(+)center dot C(5)H(8)NOS(2)(-), is built up of a morpholinium cation and a dithiocarbamate anion. In the crystal, two structurally independent formula units are linked via N-H center dot center dot center dot S hydrogen bonds, forming an inversion dimer, with graph-set motif R(4)(4)(12).

Stratigraphy of near-valley head quaternary deposits and evidence of climate-driven slope-channel processes in southern Brazilian highlands

During the past 40 years colluvial and alluvial deposits have been used in Brazil as good indicators of regional landscape sensitivity to Quaternary environmental changes. In spite of the low resolution of most of the continental sedimentary record, geomorphology and sedimentology may favor palaeoenvironmental interpretation when supported by independent proxy data. This paper presents results obtained from pedostratigraphic sequences, in near-valley head sites of southern Brazilian highlands, based on geomorphologic. sedimentologic, micromorphologic, isotopic and palynologic data. Results point to environmental changes, with ages that coincide with Marine Isotopic Stages (MIS) 5b; 3; 2 and 1. During the late Pleistocene, although under temperatures and precipitation lower than today, the local record points to relatively wet local environments, where shallow soil-water saturated zones contributed to erosion and sedimentation during periods of climatic change, as during the transition between MIS 2 and MIS 1. Late Pleistocene events with ages that coincide with the Northern Hemisphere Younger Dryas are also depicted. During the mid Holocene, slope-wash deposits suggest a climate drier than today, probably under the influence of seasonally contrasted precipitation regimes. The predominance of overland flow-related sedimentary deposits suggests an excess of precipitation over evaporation that influenced local palaeohydrology. This environmental condition seems to be recurrent and explains how slope morphology had influenced pedogenesis and sedimentation in the study area. Due to relative sensitiveness, resilience and short source-to-sink sedimentary pathways, near-valley head sites deserve further attention in Quaternary studies in the humid tropics. (c) 2008 Elsevier B.A. All rights reserved.

Postural control during prolonged standing in persons with chronic low back pain

Prolonged standing has been associated with the onset of low back pain symptoms in working populations. So far, it is unknown how individuals with chronic low back pain (CLBP) behave during prolonged unconstrained standing (PS). The aim of the present study was to analyze the control of posture by subjects with CLBP during PS in comparison to matched healthy adults. The center of pressure (COP) position of 12 CLBP subjects and 12 matched healthy controls was recorded in prolonged standing (30 min) and quiet stance tasks (60 s) on a force plate. The number and amplitude of COP patterns, the root mean square (RMS), speed, and frequency of COP sway were analyzed. Statistical analyses showed that CLBP subjects produced less Postural changes in the antero-posterior direction with decreased postural sway during the prolonged standing task in comparison to the healthy group. Only CLBP subjects were influenced by the prolonged standing task, as demonstrated by their increased COP RMS, COP speed and COP frequency in the quiet standing trial after the prolonged standing task in comparison to the pre-PS trial. The present study provides additional evidence that individuals with CLBP might have altered sensory-motor function. Their inability to generate responses similar to those of healthy subjects during prolonged standing may contribute to CLBP persistence or an increase risk of recurrent back pain episodes. Moreover, quantification of postural changes during prolonged standing could be useful to identify CLBP subjects prone to postural control deficits. (C) 2008 Elsevier B.V. All rights reserved.

Genetic potential of a maize population from Southern Brazil for the modified convergent-divergent selection scheme

Maize (Zea mays L.) is a very important cereal to world-wide economy which is also true for Brazil, particularly in the South region. Grain yield and plant height have been chosen as important criteria by breeders and farmers from Santa Catarina State (SC), Brazil. The objective of this work was to estimate genetic-statistic parameters associated with genetic gain for grain yield and plant height, in the first cycle of convergent-divergent half-sib selection in a maize population (MPA1) cultivated by farmers within the municipality of Anchieta (SC). Three experiments were carried out in different small farms at Anchieta using low external agronomic inputs; each experiment represented independent samples of half-sib families, which were evaluated in randomized complete blocks with three replications per location. Significant differences among half-sib families were observed for both variables in all experiments. The expected responses to truncated selection of the 25% better families in each experiment were 5.1, 5.8 and 5.2% for reducing plant height and 3.9, 5.7 and 5.0% for increasing grain yield, respectively. The magnitudes of genetic-statistic parameters estimated evidenced that the composite population MPA1 exhibits enough genetic variability to be used in cyclical process of recurrent selection. There were evidences that the genetic structure of the base population MPA1, as indicated by its genetic variability, may lead to expressive changes in the traits under selection, even under low selection pressure.

Genetic variability in S(1) families from different maize populations.

Genetic variability in S(1) families from different maize populations. The objectives of the present work were directed towards the study of genetic: variablilty In seven maize populations with a broad genetic base, as a guide for population improvement. The field evaluation was conducted in completely randomized blocks, at one location (Anhembi, Sao Paulo state) with different groups, of S(1) families Obtained from seven populations (GO-D: dent type, GO-F: flint type, GO-L: long car, GO-G: thick Car; and composites G3, G4 and GO-S). Estimates were obtained for genetic variance (progeny mean basis), phenotypic variance of families means, and coefficient of heritability (broad sense) for progeny means. Estimates of heritability were high for Car weight (0,89 to 0.94), car length (0.77 to 0.88) and car diameter (0.77 to 0.92); and lower for plant height (0.58 to 0.80) and Car height (0.54 to 0.84), thus showing the high Potential of the populations for recurrent selection based oil S, families. Ear yield in the base populations used as controls varied front 11,200 kg ha(-1) (GO-D) to 12,800 kg ha(-1) (G3). The means of S(1) families varied from 6,070 kg ha(-1) (GO-F) to 7,380 kg ha(-1) (G4); the Inbreeding depression in S(1) Families varied front 37.5% (G4) to 48.0% (G3) relative to the non-inbred population.

A lipocalin sequence signature modulates cell survival

Lipocalins are beta-barrel proteins, which share three conserved motifs in their amino acid sequence. In this study, we identified by a peptide mapping approach, a seven-amino acid sequence related to one of these motifs (motif 2) that modulates cell survival. A synthetic peptide based on an insect lipocalin displayed cytoprotective activity in serum-deprived endothelial cells and leucocytes. This activity was dependent on nitric oxide synthase. This sequence was found within several lipocalins, including apolipoprotein D, retinol binding protein, lipocalin-type prostaglandin D synthase, and many unknown proteins, suggesting that it is a sequence signature and a lipocalin conserved property. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.