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Sample records for analysis reveals complexity

  1. Differential network analysis reveals evolutionary complexity in secondary metabolism of Rauvolfia serpentina over Catharanthus roseus

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    Shivalika Pathania

    2016-08-01

    Full Text Available Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Towards these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These mechanisms may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of Rauvolfia serpentina, and key genes that contribute towards diversification of specific metabolites.

  2. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus.

    Science.gov (United States)

    Pathania, Shivalika; Bagler, Ganesh; Ahuja, Paramvir S

    2016-01-01

    Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.

  3. Conjunctival lymphangioma in a 4-year-old girl revealed tuberous sclerosis complex

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    Freiberg, Florentina Joyce

    2016-09-01

    Full Text Available Background: To present a case of conjunctival lymphangioma in a girl with tuberous sclerosis complex.Methods/results: A 4-year-old girl presented with a relapsing cystic lesion of the bulbar conjunctiva in the right eye with string-of-pearl-like dilation of lymphatic vessels and right-sided facial swelling with mild pain. Best-corrected vision was not impaired. Examination of the skin revealed three hypomelanotic macules and a lumbal Shagreen patch. Magnetic resonance imaging (MRI findings displayed minimal enhancement of buccal fat on the right side. Cranial and orbital MRI showed signal enhancement in the right cortical and subcortical areas. Genetic analysis revealed a heterozygous deletion encompassing exon 1 and 2 of the gene (tuberous sclerosis complex 1 gene, confirming the diagnosis of tuberous sclerosis complex.Conclusion: In conjunctival lymphangioma, tuberous sclerosis complex should be considered as the primary disease.

  4. Combining complexity measures of EEG data: multiplying measures reveal previously hidden information.

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    Burns, Thomas; Rajan, Ramesh

    2015-01-01

    Many studies have noted significant differences among human electroencephalograph (EEG) results when participants or patients are exposed to different stimuli, undertaking different tasks, or being affected by conditions such as epilepsy or Alzheimer's disease. Such studies often use only one or two measures of complexity and do not regularly justify their choice of measure beyond the fact that it has been used in previous studies. If more measures were added to such studies, however, more complete information might be found about these reported differences. Such information might be useful in confirming the existence or extent of such differences, or in understanding their physiological bases. In this study we analysed publically-available EEG data using a range of complexity measures to determine how well the measures correlated with one another. The complexity measures did not all significantly correlate, suggesting that different measures were measuring unique features of the EEG signals and thus revealing information which other measures were unable to detect. Therefore, the results from this analysis suggests that combinations of complexity measures reveal unique information which is in addition to the information captured by other measures of complexity in EEG data. For this reason, researchers using individual complexity measures for EEG data should consider using combinations of measures to more completely account for any differences they observe and to ensure the robustness of any relationships identified.

  5. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

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    Karin Voordeckers

    2015-11-01

    Full Text Available Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts.

  6. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

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    Masakazu Kohda

    2016-01-01

    Full Text Available Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4 as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3 and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21 as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

  7. Phylogenetic diversity and genotypical complexity of H9N2 influenza A viruses revealed by genomic sequence analysis.

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    Guoying Dong

    Full Text Available H9N2 influenza A viruses have become established worldwide in terrestrial poultry and wild birds, and are occasionally transmitted to mammals including humans and pigs. To comprehensively elucidate the genetic and evolutionary characteristics of H9N2 influenza viruses, we performed a large-scale sequence analysis of 571 viral genomes from the NCBI Influenza Virus Resource Database, representing the spectrum of H9N2 influenza viruses isolated from 1966 to 2009. Our study provides a panoramic framework for better understanding the genesis and evolution of H9N2 influenza viruses, and for describing the history of H9N2 viruses circulating in diverse hosts. Panorama phylogenetic analysis of the eight viral gene segments revealed the complexity and diversity of H9N2 influenza viruses. The 571 H9N2 viral genomes were classified into 74 separate lineages, which had marked host and geographical differences in phylogeny. Panorama genotypical analysis also revealed that H9N2 viruses include at least 98 genotypes, which were further divided according to their HA lineages into seven series (A-G. Phylogenetic analysis of the internal genes showed that H9N2 viruses are closely related to H3, H4, H5, H7, H10, and H14 subtype influenza viruses. Our results indicate that H9N2 viruses have undergone extensive reassortments to generate multiple reassortants and genotypes, suggesting that the continued circulation of multiple genotypical H9N2 viruses throughout the world in diverse hosts has the potential to cause future influenza outbreaks in poultry and epidemics in humans. We propose a nomenclature system for identifying and unifying all lineages and genotypes of H9N2 influenza viruses in order to facilitate international communication on the evolution, ecology and epidemiology of H9N2 influenza viruses.

  8. Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

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    Jaiswal Dinesh Kumar

    2012-10-01

    Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

  9. Fractal analysis reveals reduced complexity of retinal vessels in CADASIL.

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    Michele Cavallari

    2011-04-01

    Full Text Available The Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL affects mainly small cerebral arteries and leads to disability and dementia. The relationship between clinical expression of the disease and progression of the microvessel pathology is, however, uncertain as we lack tools for imaging brain vessels in vivo. Ophthalmoscopy is regarded as a window into the cerebral microcirculation. In this study we carried out an ophthalmoscopic examination in subjects with CADASIL. Specifically, we performed fractal analysis of digital retinal photographs. Data are expressed as mean fractal dimension (mean-D, a parameter that reflects complexity of the retinal vessel branching. Ten subjects with genetically confirmed diagnosis of CADASIL and 10 sex and age-matched control subjects were enrolled. Fractal analysis of retinal digital images was performed by means of a computer-based program, and the data expressed as mean-D. Brain MRI lesion volume in FLAIR and T1-weighted images was assessed using MIPAV software. Paired t-test was used to disclose differences in mean-D between CADASIL and control groups. Spearman rank analysis was performed to evaluate potential associations between mean-D values and both disease duration and disease severity, the latter expressed as brain MRI lesion volumes, in the subjects with CADASIL. The results showed that mean-D value of patients (1.42±0.05; mean±SD was lower than control (1.50±0.04; p = 0.002. Mean-D did not correlate with disease duration nor with MRI lesion volumes of the subjects with CADASIL. The findings suggest that fractal analysis is a sensitive tool to assess changes of retinal vessel branching, likely reflecting early brain microvessel alterations, in CADASIL patients.

  10. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

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    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  11. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  12. DNA Barcode Analysis of Thrips (Thysanoptera) Diversity in Pakistan Reveals Cryptic Species Complexes.

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    Iftikhar, Romana; Ashfaq, Muhammad; Rasool, Akhtar; Hebert, Paul D N

    2016-01-01

    Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode) region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN) system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27%) at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%). BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci), and one predatory thrips (Aeolothrips intermedius) showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

  13. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

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    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  14. Proteomic analysis of HIV-1 Nef cellular binding partners reveals a role for exocyst complex proteins in mediating enhancement of intercellular nanotube formation

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    Mukerji Joya

    2012-06-01

    Full Text Available Abstract Background HIV-1 Nef protein contributes to pathogenesis via multiple functions that include enhancement of viral replication and infectivity, alteration of intracellular trafficking, and modulation of cellular signaling pathways. Nef stimulates formation of tunneling nanotubes and virological synapses, and is transferred to bystander cells via these intercellular contacts and secreted microvesicles. Nef associates with and activates Pak2, a kinase that regulates T-cell signaling and actin cytoskeleton dynamics, but how Nef promotes nanotube formation is unknown. Results To identify Nef binding partners involved in Pak2-association dependent Nef functions, we employed tandem mass spectrometry analysis of Nef immunocomplexes from Jurkat cells expressing wild-type Nef or Nef mutants defective for the ability to associate with Pak2 (F85L, F89H, H191F and A72P, A75P in NL4-3. We report that wild-type, but not mutant Nef, was associated with 5 components of the exocyst complex (EXOC1, EXOC2, EXOC3, EXOC4, and EXOC6, an octameric complex that tethers vesicles at the plasma membrane, regulates polarized exocytosis, and recruits membranes and proteins required for nanotube formation. Additionally, Pak2 kinase was associated exclusively with wild-type Nef. Association of EXOC1, EXOC2, EXOC3, and EXOC4 with wild-type, but not mutant Nef, was verified by co-immunoprecipitation assays in Jurkat cells. Furthermore, shRNA-mediated depletion of EXOC2 in Jurkat cells abrogated Nef-mediated enhancement of nanotube formation. Using bioinformatic tools, we visualized protein interaction networks that reveal functional linkages between Nef, the exocyst complex, and the cellular endocytic and exocytic trafficking machinery. Conclusions Exocyst complex proteins are likely a key effector of Nef-mediated enhancement of nanotube formation, and possibly microvesicle secretion. Linkages revealed between Nef and the exocyst complex suggest a new paradigm of

  15. Complex analysis

    CERN Document Server

    Freitag, Eberhard

    2005-01-01

    The guiding principle of this presentation of ``Classical Complex Analysis'' is to proceed as quickly as possible to the central results while using a small number of notions and concepts from other fields. Thus the prerequisites for understanding this book are minimal; only elementary facts of calculus and algebra are required. The first four chapters cover the essential core of complex analysis: - differentiation in C (including elementary facts about conformal mappings) - integration in C (including complex line integrals, Cauchy's Integral Theorem, and the Integral Formulas) - sequences and series of analytic functions, (isolated) singularities, Laurent series, calculus of residues - construction of analytic functions: the gamma function, Weierstrass' Factorization Theorem, Mittag-Leffler Partial Fraction Decomposition, and -as a particular highlight- the Riemann Mapping Theorem, which characterizes the simply connected domains in C. Further topics included are: - the theory of elliptic functions based on...

  16. Comparative interactomics: analysis of arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants.

    Science.gov (United States)

    Paul, Anna-Lisa; Liu, Li; McClung, Scott; Laughner, Beth; Chen, Sixue; Ferl, Robert J

    2009-04-01

    As a first step in the broad characterization of plant 14-3-3 multiprotein complexes in vivo, stringent and specific antibody affinity purification was used to capture 14-3-3s together with their interacting proteins from extracts of Arabidopsis cell suspension cultures. Approximately 120 proteins were identified as potential in vivo 14-3-3 interacting proteins by mass spectrometry of the recovered complexes. Comparison of the proteins in this data set with the 14-3-3 interacting proteins from a similar study in human embryonic kidney cell cultures revealed eight interacting proteins that likely represent reasonably abundant, fundamental 14-3-3 interaction complexes that are highly conserved across all eukaryotes. The Arabidopsis 14-3-3 interaction data set was also compared to a yeast in vivo 14-3-3 interaction data set. Four 14-3-3 interacting proteins are conserved in yeast, humans, and Arabidopsis. Comparisons of the data sets based on biochemical function revealed many additional similarities in the human and Arabidopsis data sets that represent conserved functional interactions, while also leaving many proteins uniquely identified in either Arabidopsis or human cells. In particular, the Arabidopsis interaction data set is enriched for proteins involved in metabolism.

  17. Gene Coexpression Analysis Reveals Complex Metabolism of the Monoterpene Alcohol Linalool in Arabidopsis Flowers[W][OPEN

    Science.gov (United States)

    Ginglinger, Jean-François; Boachon, Benoit; Höfer, René; Paetz, Christian; Köllner, Tobias G.; Miesch, Laurence; Lugan, Raphael; Baltenweck, Raymonde; Mutterer, Jérôme; Ullmann, Pascaline; Beran, Franziska; Claudel, Patricia; Verstappen, Francel; Fischer, Marc J.C.; Karst, Francis; Bouwmeester, Harro; Miesch, Michel; Schneider, Bernd; Gershenzon, Jonathan; Ehlting, Jürgen; Werck-Reichhart, Danièle

    2013-01-01

    The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus predicted to be involved in monoterpenoid metabolism. We show that all four selected genes, the two terpene synthases (TPS10 and TPS14) and the two cytochrome P450s (CYP71B31 and CYP76C3), are simultaneously expressed at anthesis, mainly in upper anther filaments and in petals. Upon transient expression in Nicotiana benthamiana, the TPS enzymes colocalize in vesicular structures associated with the plastid surface, whereas the P450 proteins were detected in the endoplasmic reticulum. Whether they were expressed in Saccharomyces cerevisiae or in N. benthamiana, the TPS enzymes formed two different enantiomers of linalool: (−)-(R)-linalool for TPS10 and (+)-(S)-linalool for TPS14. Both P450 enzymes metabolize the two linalool enantiomers to form different but overlapping sets of hydroxylated or epoxidized products. These oxygenated products are not emitted into the floral headspace, but accumulate in floral tissues as further converted or conjugated metabolites. This work reveals complex linalool metabolism in Arabidopsis flowers, the ecological role of which remains to be determined. PMID:24285789

  18. Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

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    Paul De Barro

    Full Text Available BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010. Only two species proposed in Dinsdale et al. (2010 departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED and Middle East - Asia Minor 1 (MEAM1, showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of

  19. Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2).

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    Harel, Elad; Engel, Gregory S

    2012-01-17

    Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2.

  20. Revitalizing Complex Analysis: A Transition-to-Proof Course Centered on Complex Topics

    Science.gov (United States)

    Sachs, Robert

    2017-01-01

    A new transition course centered on complex topics would help in revitalizing complex analysis in two ways: first, provide early exposure to complex functions, sparking greater interest in the complex analysis course; second, create extra time in the complex analysis course by eliminating the "complex precalculus" part of the course. In…

  1. COMBINED DELAY AND GRAPH EMBEDDING OF EPILEPTIC DISCHARGES IN EEG REVEALS COMPLEX AND RECURRENT NONLINEAR DYNAMICS.

    Science.gov (United States)

    Erem, B; Hyde, D E; Peters, J M; Duffy, F H; Brooks, D H; Warfield, S K

    2015-04-01

    The dynamical structure of the brain's electrical signals contains valuable information about its physiology. Here we combine techniques for nonlinear dynamical analysis and manifold identification to reveal complex and recurrent dynamics in interictal epileptiform discharges (IEDs). Our results suggest that recurrent IEDs exhibit some consistent dynamics, which may only last briefly, and so individual IED dynamics may need to be considered in order to understand their genesis. This could potentially serve to constrain the dynamics of the inverse source localization problem.

  2. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina

    2013-02-11

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina; Malara, Natalia Maria; Trunzo, Valentina; Perozziello, Gerardo; Neužil, Pavel; Francardi, Marco; Roveda, Laura; Renne, Maria; Prati, Ubaldo; Mollace, Vincenzo; Manz, Andreas; Di Fabrizio, Enzo M.

    2013-01-01

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction's strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Complex (Nonstandard) Six-Layer Polytypes of Lizardite Revealed from Oblique-Texture Electron Diffraction Patterns

    International Nuclear Information System (INIS)

    Zhukhlistov, A.P.; Zinchuk, N.N.; Kotel'nikov, D.D.

    2004-01-01

    Association of simple (1T and 3R) and two complex (nonstandard) orthogonal polytypes of the serpentine mineral lizardite from the Catoca kimberlite pipe (West Africa) association is revealed from oblique-texture electron diffraction patterns. A six-layer polytype with an ordered superposition of equally oriented layers (notation 3 2 3 2 3 4 3 4 3 6 3 6 or ++ - -00) belonging to the structural group A and a three-layer (336 or I,I,II) or a six-layer (336366 or I,I,II,I,II,II) polytype with alternating oppositely oriented layers and semi-disordered structure are identified using polytype analysis

  5. Cumulative trauma and symptom complexity in children: a path analysis.

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    Hodges, Monica; Godbout, Natacha; Briere, John; Lanktree, Cheryl; Gilbert, Alicia; Kletzka, Nicole Taylor

    2013-11-01

    Multiple trauma exposures during childhood are associated with a range of psychological symptoms later in life. In this study, we examined whether the total number of different types of trauma experienced by children (cumulative trauma) is associated with the complexity of their subsequent symptomatology, where complexity is defined as the number of different symptom clusters simultaneously elevated into the clinical range. Children's symptoms in six different trauma-related areas (e.g., depression, anger, posttraumatic stress) were reported both by child clients and their caretakers in a clinical sample of 318 children. Path analysis revealed that accumulated exposure to multiple different trauma types predicts symptom complexity as reported by both children and their caretakers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    OpenAIRE

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the exis...

  7. Transmitter receptors reveal segregation of the arcopallium/amygdala complex in pigeons (Columba livia).

    Science.gov (United States)

    Herold, Christina; Paulitschek, Christina; Palomero-Gallagher, Nicola; Güntürkün, Onur; Zilles, Karl

    2018-02-15

    At the beginning of the 20th century it was suggested that a complex group of nuclei in the avian posterior ventral telencephalon is comparable to the mammalian amygdala. Subsequent findings, however, revealed that most of these structures share premotor characteristics, while some indeed constitute the avian amygdala. These developments resulted in 2004 in a change of nomenclature of these nuclei, which from then on were named arcopallial or amygdala nuclei and referred to as the arcopallium/amygdala complex. The structural basis for the similarities between avian and mammalian arcopallial and amygdala subregions is poorly understood. Therefore, we analyzed binding site densities for glutamatergic AMPA, NMDA and kainate, GABAergic GABA A , muscarinic M 1 , M 2 and nicotinic acetylcholine (nACh; α 4 β 2 subtype), noradrenergic α 1 and α 2 , serotonergic 5-HT 1A and dopaminergic D 1/5 receptors using quantitative in vitro receptor autoradiography combined with a detailed analysis of the cyto- and myelo-architecture. Our approach supports a segregation of the pigeon's arcopallium/amygdala complex into the following subregions: the arcopallium anterius (AA), the arcopallium ventrale (AV), the arcopallium dorsale (AD), the arcopallium intermedium (AI), the arcopallium mediale (AM), the arcopallium posterius (AP), the nucleus posterioris amygdalopallii pars basalis (PoAb) and pars compacta (PoAc), the nucleus taeniae amgygdalae (TnA) and the area subpallialis amygdalae (SpA). Some of these subregions showed further subnuclei and each region of the arcopallium/amygdala complex are characterized by a distinct multi-receptor density expression. Here we provide a new detailed map of the pigeon's arcopallium/amygdala complex and compare the receptor architecture of the subregions to their possible mammalian counterparts. © 2017 Wiley Periodicals, Inc.

  8. Interpreting Popov criteria in Lure´ systems with complex scaling stability analysis

    Science.gov (United States)

    Zhou, J.

    2018-06-01

    The paper presents a novel frequency-domain interpretation of Popov criteria for absolute stability in Lure´ systems by means of what we call complex scaling stability analysis. The complex scaling technique is developed for exponential/asymptotic stability in LTI feedback systems, which dispenses open-loop poles distribution, contour/locus orientation and prior frequency sweeping. Exploiting the technique for alternatively revealing positive realness of transfer functions, re-interpreting Popov criteria is explicated. More specifically, the suggested frequency-domain stability conditions are conformable both in scalar and multivariable cases, and can be implemented either graphically with locus plotting or numerically without; in particular, the latter is suitable as a design tool with auxiliary parameter freedom. The interpretation also reveals further frequency-domain facts about Lure´ systems. Numerical examples are included to illustrate the main results.

  9. Proteomic analysis of human norepinephrine transporter complexes reveals associations with protein phosphatase 2A anchoring subunit and 14-3-3 proteins

    International Nuclear Information System (INIS)

    Sung, Uhna; Jennings, Jennifer L.; Link, Andrew J.; Blakely, Randy D.

    2005-01-01

    The norepinephrine transporter (NET) terminates noradrenergic signals by clearing released NE at synapses. NET regulation by receptors and intracellular signaling pathways is supported by a growing list of associated proteins including syntaxin1A, protein phosphatase 2A (PP2A) catalytic subunit (PP2A-C), PICK1, and Hic-5. In the present study, we sought evidence for additional partnerships by mass spectrometry-based analysis of proteins co-immunoprecipitated with human NET (hNET) stably expressed in a mouse noradrenergic neuroblastoma cell line. Our initial proteomic analyses reveal multiple peptides derived from hNET, peptides arising from the mouse PP2A anchoring subunit (PP2A-Ar) and peptides derived from 14-3-3 proteins. We verified physical association of NET with PP2A-Ar via co-immunoprecipitation studies using mouse vas deferens extracts and with 14-3-3 via a fusion pull-down approach, implicating specifically the hNET NH 2 -terminus for interactions. The transporter complexes described likely support mechanisms regulating transporter activity, localization, and trafficking

  10. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits

    NARCIS (Netherlands)

    Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick; Kristiansson, Kati; Mattsson, Hannele; Nõukas, Margit; Sapkota, Yadav; Schick, Ursula; Porcu, Eleonora; Rüeger, Sina; McDaid, Aaron F; Porteous, David; Winkler, Thomas W; Salvi, Erika; Shrine, Nick; Liu, Xueping; Ang, Wei Q; Zhang, Weihua; Feitosa, Mary F; Venturini, Cristina; van der Most, Peter J; Rosengren, Anders; Wood, Andrew R; Beaumont, Robin N; Jones, Samuel E; Ruth, Katherine S; Yaghootkar, Hanieh; Tyrrell, Jessica; Havulinna, Aki S; Boers, Harmen; Mägi, Reedik; Kriebel, Jennifer; Müller-Nurasyid, Martina; Perola, Markus; Nieminen, Markku; Lokki, Marja-Liisa; Kähönen, Mika; Viikari, Jorma S; Geller, Frank; Lahti, Jari; Palotie, Aarno; Koponen, Päivikki; Lundqvist, Annamari; Rissanen, Harri; Bottinger, Erwin P; Afaq, Saima; Wojczynski, Mary K; Lenzini, Petra; Nolte, Ilja M; Sparsø, Thomas; Schupf, Nicole; Christensen, Kaare; Perls, Thomas T; Newman, Anne B; Werge, Thomas; Snieder, Harold; Spector, Timothy D; Chambers, John C; Koskinen, Seppo; Melbye, Mads; Raitakari, Olli T; Lehtimäki, Terho; Tobin, Martin D; Wain, Louise V; Sinisalo, Juha; Peters, Annette; Meitinger, Thomas; Martin, Nicholas G; Wray, Naomi R; Montgomery, Grant W; Medland, Sarah E; Swertz, Morris A; Vartiainen, Erkki; Borodulin, Katja; Männistö, Satu; Murray, Anna; Bochud, Murielle; Jacquemont, Sébastien; Rivadeneira, Fernando; Hansen, Thomas F; Oldehinkel, Albertine J; Mangino, Massimo; Province, Michael A; Deloukas, Panos; Kooner, Jaspal S; Freathy, Rachel M; Pennell, Craig; Feenstra, Bjarke; Strachan, David P; Lettre, Guillaume; Hirschhorn, Joel; Cusi, Daniele; Heid, Iris M; Hayward, Caroline; Männik, Katrin; Beckmann, Jacques S; Loos, Ruth J F; Nyholt, Dale R; Metspalu, Andres; Eriksson, Johan G; Weedon, Michael N; Salomaa, Veikko; Franke, Lude; Reymond, Alexandre; Frayling, Timothy M; Kutalik, Zoltán

    2017-01-01

    There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at

  11. Proteomic analysis of the crayfish gastrolith chitinous extracellular matrix reveals putative protein complexes and a central role for GAP 65.

    Science.gov (United States)

    Glazer, Lilah; Roth, Ziv; Weil, Simy; Aflalo, Eliahu D; Khalaila, Isam; Sagi, Amir

    2015-10-14

    Chitin is a major component of arthropod cuticles, where it forms a three-dimensional network that constitutes the scaffold upon which cuticles form. The chitin fibers that form this network are closely associated with specific structural proteins, while the cuticular matrix contains many additional structural, enzymatic and other proteins. We study the crayfish gastrolith as a simple model for the assembly of calcified cuticular structures, with particular focus on the proteins involved in this process. The present study integrates a gastrolith-forming epithelium transcriptomic library with data from mass spectrometry analysis of proteins extracted from the gastrolith matrix to obtain a near-complete picture of gastrolith protein content. Using native protein separation we identified 24 matrix proteins, of which 14 are novel. Further analysis led to discovery of three putative protein complexes, all containing GAP 65 the most abundant gastrolith structural protein. Using immunological methods we further studied the role of GAP 65 in the gastrolith matrix and forming epithelium, as well as in the newly identified protein complexes. We propose that gastrolith matrix construction is a sequential process in which protein complexes are dynamically assembled and disassembled around GAP 65, thus changing their functional properties to perform each step in the construction process. The scientific interest on which this study is based arises from three main features of gastroliths: (1) Gastroliths possess partial analogy to cuticles both in structural and molecular properties, and may be regarded, with the appropriate reservations (see Introduction), as simple models for cuticle assembly. At the same time, gastroliths are terminally assembled during a well-defined period, which can be controlled in the laboratory, making them significantly easier to study than cuticles. (2) Gastroliths, like the crayfish exoskeleton, contain stable amorphous calcium carbonate (ACC) rather

  12. EXPLORATORY DATA ANALYSIS AND MULTIVARIATE STRATEGIES FOR REVEALING MULTIVARIATE STRUCTURES IN CLIMATE DATA

    Directory of Open Access Journals (Sweden)

    2016-12-01

    Full Text Available This paper is on data analysis strategy in a complex, multidimensional, and dynamic domain. The focus is on the use of data mining techniques to explore the importance of multivariate structures; using climate variables which influences climate change. Techniques involved in data mining exercise vary according to the data structures. The multivariate analysis strategy considered here involved choosing an appropriate tool to analyze a process. Factor analysis is introduced into data mining technique in order to reveal the influencing impacts of factors involved as well as solving for multicolinearity effect among the variables. The temporal nature and multidimensionality of the target variables is revealed in the model using multidimensional regression estimates. The strategy of integrating the method of several statistical techniques, using climate variables in Nigeria was employed. R2 of 0.518 was obtained from the ordinary least square regression analysis carried out and the test was not significant at 5% level of significance. However, factor analysis regression strategy gave a good fit with R2 of 0.811 and the test was significant at 5% level of significance. Based on this study, model building should go beyond the usual confirmatory data analysis (CDA, rather it should be complemented with exploratory data analysis (EDA in order to achieve a desired result.

  13. Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex

    DEFF Research Database (Denmark)

    Laursen, Nick Stub; Andersen, Kasper Røjkjær; Braren, Ingke

    2011-01-01

    with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only...

  14. An introduction to complex analysis and geometry

    CERN Document Server

    D'Angelo, John P

    2010-01-01

    An Introduction to Complex Analysis and Geometry provides the reader with a deep appreciation of complex analysis and how this subject fits into mathematics. The book developed from courses given in the Campus Honors Program at the University of Illinois Urbana-Champaign. These courses aimed to share with students the way many mathematics and physics problems magically simplify when viewed from the perspective of complex analysis. The book begins at an elementary level but also contains advanced material. The first four chapters provide an introduction to complex analysis with many elementary

  15. Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle.

    Science.gov (United States)

    Mateescu, Raluca G; Garrick, Dorian J; Reecy, James M

    2017-01-01

    Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory could be more efficient in dissecting the genetic architecture of complex traits. Phenotypic measures of 23 traits reflecting carcass characteristics, components of meat quality, along with mineral and peptide concentrations were used along with Illumina 54k bovine SNP genotypes to derive an annotated gene network associated with meat quality in 2,110 Angus beef cattle. The efficient mixed model association (EMMAX) approach in combination with a genomic relationship matrix was used to directly estimate the associations between 54k SNP genotypes and each of the 23 component traits. Genomic correlated regions were identified by partial correlations which were further used along with an information theory algorithm to derive gene network clusters. Correlated SNP across 23 component traits were subjected to network scoring and visualization software to identify significant SNP. Significant pathways implicated in the meat quality complex through GO term enrichment analysis included angiogenesis, inflammation, transmembrane transporter activity, and receptor activity. These results suggest that network analysis using partial correlations and annotation of significant SNP can reveal the genetic architecture of complex traits and provide novel information regarding biological mechanisms

  16. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

    Energy Technology Data Exchange (ETDEWEB)

    Prochnik, Simon E.; Umen, James; Nedelcu, Aurora; Hallmann, Armin; Miller, Stephen M.; Nishii, Ichiro; Ferris, Patrick; Kuo, Alan; Mitros, Therese; Fritz-Laylin, Lillian K.; Hellsten, Uffe; Chapman, Jarrod; Simakov, Oleg; Rensing, Stefan A.; Terry, Astrid; Pangilinan, Jasmyn; Kapitonov, Vladimir; Jurka, Jerzy; Salamov, Asaf; Shapiro, Harris; Schmutz, Jeremy; Grimwood, Jane; Lindquist, Erika; Lucas, Susan; Grigoriev, Igor V.; Schmitt, Rudiger; Kirk, David; Rokhsar, Daniel S.

    2010-07-01

    Analysis of the Volvox carteri genome reveals that this green alga's increased organismal complexity and multicellularity are associated with modifications in protein families shared with its unicellular ancestor, and not with large-scale innovations in protein coding capacity. The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are uniquely suited for investigating the evolution of multicellularity and development. We sequenced the 138 Mb genome of V. carteri and compared its {approx}14,500 predicted proteins to those of its unicellular relative, Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials, and few species-specific protein-coding gene predictions. Interestingly, volvocine algal-specific proteins are enriched in Volvox, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.

  17. Harmonic and complex analysis in several variables

    CERN Document Server

    Krantz, Steven G

    2017-01-01

    Authored by a ranking authority in harmonic analysis of several complex variables, this book embodies a state-of-the-art entrée at the intersection of two important fields of research: complex analysis and harmonic analysis. Written with the graduate student in mind, it is assumed that the reader has familiarity with the basics of complex analysis of one and several complex variables as well as with real and functional analysis. The monograph is largely self-contained and develops the harmonic analysis of several complex variables from the first principles. The text includes copious examples, explanations, an exhaustive bibliography for further reading, and figures that illustrate the geometric nature of the subject. Each chapter ends with an exercise set. Additionally, each chapter begins with a prologue, introducing the reader to the subject matter that follows; capsules presented in each section give perspective and a spirited launch to the segment; preludes help put ideas into context. Mathematicians and...

  18. Transcriptome, carbohydrate, and phytohormone analysis of Petunia hybrida reveals a complex disturbance of plant functional integrity under mild chilling stress

    Science.gov (United States)

    Bauerfeind, Martin Andreas; Winkelmann, Traud; Franken, Philipp; Druege, Uwe

    2015-01-01

    Cultivation of chilling-tolerant ornamental crops at lower temperature could reduce the energy demands of heated greenhouses. To provide a better understanding of how sub-optimal temperatures (12°C vs. 16°C) affect growth of the sensitive Petunia hybrida cultivar ‘SweetSunshine Williams’, the transcriptome, carbohydrate metabolism, and phytohormone homeostasis were monitored in aerial plant parts over 4 weeks by use of a microarray, enzymatic assays and GC-MS/MS. The data revealed three consecutive phases of chilling response. The first days were marked by a strong accumulation of sugars, particularly in source leaves, preferential up-regulation of genes in the same tissue and down-regulation of several genes in the shoot apex, especially those involved in the abiotic stress response. The midterm phase featured a partial normalization of carbohydrate levels and gene expression. After 3 weeks of chilling exposure, a new stabilized balance was established. Reduced hexose levels in the shoot apex, reduced ratios of sugar levels between the apex and source leaves and a higher apical sucrose/hexose ratio, associated with decreased activity and expression of cell wall invertase, indicate that prolonged chilling induced sugar accumulation in source leaves at the expense of reduced sugar transport to and reduced sucrose utilization in the shoot. This was associated with reduced levels of indole-3-acetic acid and abscisic acid in the apex and high numbers of differentially, particularly up-regulated genes, especially in the source leaves, including those regulating histones, ethylene action, transcription factors, and a jasmonate-ZIM-domain protein. Transcripts of one Jumonji C domain containing protein and one expansin accumulated in source leaves throughout the chilling period. The results reveal a dynamic and complex disturbance of plant function in response to mild chilling, opening new perspectives for the comparative analysis of differently tolerant cultivars

  19. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  20. Advances in real and complex analysis with applications

    CERN Document Server

    Cho, Yeol; Agarwal, Praveen; Area, Iván

    2017-01-01

    This book discusses a variety of topics in mathematics and engineering as well as their applications, clearly explaining the mathematical concepts in the simplest possible way and illustrating them with a number of solved examples. The topics include real and complex analysis, special functions and analytic number theory, q-series, Ramanujan’s mathematics, fractional calculus, Clifford and harmonic analysis, graph theory, complex analysis, complex dynamical systems, complex function spaces and operator theory, geometric analysis of complex manifolds, geometric function theory, Riemannian surfaces, Teichmüller spaces and Kleinian groups, engineering applications of complex analytic methods, nonlinear analysis, inequality theory, potential theory, partial differential equations, numerical analysis , fixed-point theory, variational inequality, equilibrium problems, optimization problems, stability of functional equations, and mathematical physics.  It includes papers presented at the 24th International Confe...

  1. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

    OpenAIRE

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

    2012-01-01

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed...

  2. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2014-02-01

    Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

  3. Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; Campbell, Elizabeth A.

    2017-07-13

    The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.

  4. Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly

    Science.gov (United States)

    Cottee, Matthew A; Muschalik, Nadine; Wong, Yao Liang; Johnson, Christopher M; Johnson, Steven; Andreeva, Antonina; Oegema, Karen; Lea, Susan M; Raff, Jordan W; van Breugel, Mark

    2013-01-01

    Centrioles organise centrosomes and template cilia and flagella. Several centriole and centrosome proteins have been linked to microcephaly (MCPH), a neuro-developmental disease associated with small brain size. CPAP (MCPH6) and STIL (MCPH7) are required for centriole assembly, but it is unclear how mutations in them lead to microcephaly. We show that the TCP domain of CPAP constitutes a novel proline recognition domain that forms a 1:1 complex with a short, highly conserved target motif in STIL. Crystal structures of this complex reveal an unusual, all-β structure adopted by the TCP domain and explain how a microcephaly mutation in CPAP compromises complex formation. Through point mutations, we demonstrate that complex formation is essential for centriole duplication in vivo. Our studies provide the first structural insight into how the malfunction of centriole proteins results in human disease and also reveal that the CPAP–STIL interaction constitutes a conserved key step in centriole biogenesis. DOI: http://dx.doi.org/10.7554/eLife.01071.001 PMID:24052813

  5. Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

    Science.gov (United States)

    Mavhunga, Elizabeth

    2018-04-01

    Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

  6. Cooperativity of complex salt bridges

    OpenAIRE

    Gvritishvili, Anzor G.; Gribenko, Alexey V.; Makhatadze, George I.

    2008-01-01

    The energetic contribution of complex salt bridges, in which one charged residue (anchor residue) forms salt bridges with two or more residues simultaneously, has been suggested to have importance for protein stability. Detailed analysis of the net energetics of complex salt bridge formation using double- and triple-mutant cycle analysis revealed conflicting results. In two cases, it was shown that complex salt bridge formation is cooperative, i.e., the net strength of the complex salt bridge...

  7. Bio-Signal Complexity Analysis in Epileptic Seizure Monitoring: A Topic Review

    Directory of Open Access Journals (Sweden)

    Zhenning Mei

    2018-05-01

    Full Text Available Complexity science has provided new perspectives and opportunities for understanding a variety of complex natural or social phenomena, including brain dysfunctions like epilepsy. By delving into the complexity in electrophysiological signals and neuroimaging, new insights have emerged. These discoveries have revealed that complexity is a fundamental aspect of physiological processes. The inherent nonlinearity and non-stationarity of physiological processes limits the methods based on simpler underlying assumptions to point out the pathway to a more comprehensive understanding of their behavior and relation with certain diseases. The perspective of complexity may benefit both the research and clinical practice through providing novel data analytics tools devoted for the understanding of and the intervention about epilepsies. This review aims to provide a sketchy overview of the methods derived from different disciplines lucubrating to the complexity of bio-signals in the field of epilepsy monitoring. Although the complexity of bio-signals is still not fully understood, bundles of new insights have been already obtained. Despite the promising results about epileptic seizure detection and prediction through offline analysis, we are still lacking robust, tried-and-true real-time applications. Multidisciplinary collaborations and more high-quality data accessible to the whole community are needed for reproducible research and the development of such applications.

  8. Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

    International Nuclear Information System (INIS)

    Gunn, Shelly; Gorre, Mercedes; Mohammed, Mansoor; Yeh, I-Tien; Lytvak, Irina; Tirtorahardjo, Budi; Dzidic, Natasha; Zadeh, Soheila; Kim, Jaeweon; McCaskill, Chris; Lim, Lony

    2010-01-01

    HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to 'ratio skewing' caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two

  9. Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks

    Directory of Open Access Journals (Sweden)

    Toni Vallès-Català

    2016-03-01

    Full Text Available In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs, a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.

  10. Communication Analysis of Information Complexes.

    Science.gov (United States)

    Malik, M. F.

    Communication analysis is a tool for perceptual assessment of existing or projected information complexes, i.e., an established reality perceived by one or many humans. An information complex could be of a physical nature, such as a building, landscape, city street; or of a pure informational nature, such as a film, television program,…

  11. Nonlinear analysis of gas-water/oil-water two-phase flow in complex networks

    CERN Document Server

    Gao, Zhong-Ke; Wang, Wen-Xu

    2014-01-01

    Understanding the dynamics of multi-phase flows has been a challenge in the fields of nonlinear dynamics and fluid mechanics. This chapter reviews our work on two-phase flow dynamics in combination with complex network theory. We systematically carried out gas-water/oil-water two-phase flow experiments for measuring the time series of flow signals which is studied in terms of the mapping from time series to complex networks. Three network mapping methods were proposed for the analysis and identification of flow patterns, i.e. Flow Pattern Complex Network (FPCN), Fluid Dynamic Complex Network (FDCN) and Fluid Structure Complex Network (FSCN). Through detecting the community structure of FPCN based on K-means clustering, distinct flow patterns can be successfully distinguished and identified. A number of FDCN’s under different flow conditions were constructed in order to reveal the dynamical characteristics of two-phase flows. The FDCNs exhibit universal power-law degree distributions. The power-law exponent ...

  12. Analysis of chromosome rearrangements on the basis of synaptonemal complexes in the offspring of mice exposed to γ-rays

    International Nuclear Information System (INIS)

    Kalikinskaya, E.I.; Bogdanov, Yu.F.; Kolomiets, O.L.; Shevchenko, V.A.

    1986-01-01

    Electron-microscopic analysis of synaptonemic complexes (SC), spread on the hypophase surface, was conducted to investigate chromosome rearrangements in sterile and semisterile F 1 malemause offsprings, exposed to 5 Gy γ-rays Paralelly Chromosome rearrangement account in diakinesis-metaphase 1 was conducted using light microscope, in the same animals. During SC analysis in pachytene chromosome rearrangements were found in 63% of spermatocytes. Under chromosome analysis in diakinesis-metaphase 1 in the same animals chromosome rearrangements were found only in 32% of cells. SC analysis allows one to reveal chromosome rearrangements, which can not be revealed in diakinesis-metaphase 1

  13. Complex analysis conformal inequalities and the Bieberbach conjecture

    CERN Document Server

    Kythe, Prem K

    2015-01-01

    Complex Analysis: Conformal Inequalities and the Bieberbach Conjecture discusses the mathematical analysis created around the Bieberbach conjecture, which is responsible for the development of many beautiful aspects of complex analysis, especially in the geometric-function theory of univalent functions. Assuming basic knowledge of complex analysis and differential equations, the book is suitable for graduate students engaged in analytical research on the topics and researchers working on related areas of complex analysis in one or more complex variables. The author first reviews the theory of analytic functions, univalent functions, and conformal mapping before covering various theorems related to the area principle and discussing Löwner theory. He then presents Schiffer’s variation method, the bounds for the fourth and higher-order coefficients, various subclasses of univalent functions, generalized convexity and the class of a-convex functions, and numerical estimates of the coefficient problem. The boo...

  14. Common cause failure analysis methodology for complex systems

    International Nuclear Information System (INIS)

    Wagner, D.P.; Cate, C.L.; Fussell, J.B.

    1977-01-01

    Common cause failure analysis, also called common mode failure analysis, is an integral part of a complex system reliability analysis. This paper extends existing methods of computer aided common cause failure analysis by allowing analysis of the complex systems often encountered in practice. The methods presented here aid in identifying potential common cause failures and also address quantitative common cause failure analysis

  15. 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

    Directory of Open Access Journals (Sweden)

    Gustafsson Lars

    2010-12-01

    Full Text Available Abstract Background Because of their functional significance, the Major Histocompatibility Complex (MHC class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective

  16. Joint cross-correlation analysis reveals complex, time-dependent functional relationship between cortical neurons and arm electromyograms

    Science.gov (United States)

    Zhuang, Katie Z.; Lebedev, Mikhail A.

    2014-01-01

    Correlation between cortical activity and electromyographic (EMG) activity of limb muscles has long been a subject of neurophysiological studies, especially in terms of corticospinal connectivity. Interest in this issue has recently increased due to the development of brain-machine interfaces with output signals that mimic muscle force. For this study, three monkeys were implanted with multielectrode arrays in multiple cortical areas. One monkey performed self-timed touch pad presses, whereas the other two executed arm reaching movements. We analyzed the dynamic relationship between cortical neuronal activity and arm EMGs using a joint cross-correlation (JCC) analysis that evaluated trial-by-trial correlation as a function of time intervals within a trial. JCCs revealed transient correlations between the EMGs of multiple muscles and neural activity in motor, premotor and somatosensory cortical areas. Matching results were obtained using spike-triggered averages corrected by subtracting trial-shuffled data. Compared with spike-triggered averages, JCCs more readily revealed dynamic changes in cortico-EMG correlations. JCCs showed that correlation peaks often sharpened around movement times and broadened during delay intervals. Furthermore, JCC patterns were directionally selective for the arm-reaching task. We propose that such highly dynamic, task-dependent and distributed relationships between cortical activity and EMGs should be taken into consideration for future brain-machine interfaces that generate EMG-like signals. PMID:25210153

  17. From real to complex analysis

    CERN Document Server

    Dyer, R H

    2014-01-01

    The purpose of this book is to provide an integrated course in real and complex analysis for those who have already taken a preliminary course in real analysis. It particularly emphasises the interplay between analysis and topology. Beginning with the theory of the Riemann integral (and its improper extension) on the real line, the fundamentals of metric spaces are then developed, with special attention being paid to connectedness, simple connectedness and various forms of homotopy. The final chapter develops the theory of complex analysis, in which emphasis is placed on the argument, the winding number, and a general (homology) version of Cauchy's theorem which is proved using the approach due to Dixon. Special features are the inclusion of proofs of Montel's theorem, the Riemann mapping theorem and the Jordan curve theorem that arise naturally from the earlier development. Extensive exercises are included in each of the chapters, detailed solutions of the majority of which are given at the end. From Real to...

  18. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

    DEFF Research Database (Denmark)

    Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

    2015-01-01

    species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

  19. Analysis and control of complex dynamical systems robust bifurcation, dynamic attractors, and network complexity

    CERN Document Server

    Imura, Jun-ichi; Ueta, Tetsushi

    2015-01-01

    This book is the first to report on theoretical breakthroughs on control of complex dynamical systems developed by collaborative researchers in the two fields of dynamical systems theory and control theory. As well, its basic point of view is of three kinds of complexity: bifurcation phenomena subject to model uncertainty, complex behavior including periodic/quasi-periodic orbits as well as chaotic orbits, and network complexity emerging from dynamical interactions between subsystems. Analysis and Control of Complex Dynamical Systems offers a valuable resource for mathematicians, physicists, and biophysicists, as well as for researchers in nonlinear science and control engineering, allowing them to develop a better fundamental understanding of the analysis and control synthesis of such complex systems.

  20. Connected magma plumbing system between Cerro Negro and El Hoyo Complex, Nicaragua revealed by gravity survey

    Science.gov (United States)

    MacQueen, Patricia; Zurek, Jeffrey; Williams-Jones, Glyn

    2016-11-01

    Cerro Negro, near León, Nicaragua is a young, relatively small basaltic cinder cone volcano that has been unusually active during its short lifespan. Multiple explosive eruptions have deposited significant amounts of ash on León and the surrounding rural communities. While a number of studies investigate the geochemistry and stress regime of the volcano, subsurface structures have only been studied by diffuse soil gas surveys. These studies have raised several questions as to the proper classification of Cerro Negro and its relation to neighboring volcanic features. To address these questions, we collected 119 gravity measurements around Cerro Negro volcano in an attempt to delineate deep structures at the volcano. The resulting complete Bouguer anomaly map revealed local positive gravity anomalies (wavelength 0.5 to 2 km, magnitude +4 mGal) and regional positive (10 km wavelength, magnitudes +10 and +8 mGal) and negative (12 and 6 km wavelength, magnitudes -18 and -13 mGal) Bouguer anomalies. Further analysis of these gravity data through inversion has revealed both local and regional density anomalies that we interpret as intrusive complexes at Cerro Negro and in the Nicaraguan Volcanic Arc. The local density anomalies at Cerro Negro have a density of 2700 kg m-3 (basalt) and are located between -250 and -2000 m above sea level. The distribution of recovered density anomalies suggests that eruptions at Cerro Negro may be tapping an interconnected magma plumbing system beneath El Hoyo, Cerro La Mula, and Cerro Negro, and more than seven other proximal volcanic features, implying that Cerro Negro should be considered the newest cone of a Cerro Negro-El Hoyo volcanic complex.

  1. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Directory of Open Access Journals (Sweden)

    Aamena Alshamsi

    Full Text Available Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  2. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Science.gov (United States)

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2015-01-01

    Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  3. System-wide analysis reveals a complex network of tumor-fibroblast interactions involved in tumorigenicity.

    Directory of Open Access Journals (Sweden)

    Megha Rajaram

    Full Text Available Many fibroblast-secreted proteins promote tumorigenicity, and several factors secreted by cancer cells have in turn been proposed to induce these proteins. It is not clear whether there are single dominant pathways underlying these interactions or whether they involve multiple pathways acting in parallel. Here, we identified 42 fibroblast-secreted factors induced by breast cancer cells using comparative genomic analysis. To determine what fraction was active in promoting tumorigenicity, we chose five representative fibroblast-secreted factors for in vivo analysis. We found that the majority (three out of five played equally major roles in promoting tumorigenicity, and intriguingly, each one had distinct effects on the tumor microenvironment. Specifically, fibroblast-secreted amphiregulin promoted breast cancer cell survival, whereas the chemokine CCL7 stimulated tumor cell proliferation while CCL2 promoted innate immune cell infiltration and angiogenesis. The other two factors tested had minor (CCL8 or minimally (STC1 significant effects on the ability of fibroblasts to promote tumor growth. The importance of parallel interactions between fibroblasts and cancer cells was tested by simultaneously targeting fibroblast-secreted amphiregulin and the CCL7 receptor on cancer cells, and this was significantly more efficacious than blocking either pathway alone. We further explored the concept of parallel interactions by testing the extent to which induction of critical fibroblast-secreted proteins could be achieved by single, previously identified, factors produced by breast cancer cells. We found that although single factors could induce a subset of genes, even combinations of factors failed to induce the full repertoire of functionally important fibroblast-secreted proteins. Together, these results delineate a complex network of tumor-fibroblast interactions that act in parallel to promote tumorigenicity and suggest that effective anti

  4. Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex.

    Science.gov (United States)

    Brankovics, Balázs; van Dam, Peter; Rep, Martijn; de Hoog, G Sybren; J van der Lee, Theo A; Waalwijk, Cees; van Diepeningen, Anne D

    2017-09-18

    The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

  5. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

    Science.gov (United States)

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

    2012-10-09

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

  6. Transcriptomic analysis of human retinal detachment reveals both inflammatory response and photoreceptor death.

    Directory of Open Access Journals (Sweden)

    Marie-Noëlle Delyfer

    Full Text Available BACKGROUND: Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. METHODOLOGY/PRINCIPAL FINDINGS: Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. CONCLUSIONS/SIGNIFICANCE: This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery.

  7. Using value-based analysis to influence outcomes in complex surgical systems.

    Science.gov (United States)

    Kirkpatrick, John R; Marks, Stanley; Slane, Michele; Kim, Donald; Cohen, Lance; Cortelli, Michael; Plate, Juan; Perryman, Richard; Zapas, John

    2015-04-01

    Value-based analysis (VBA) is a management strategy used to determine changes in value (quality/cost) when a usual practice (UP) is replaced by a best practice (BP). Previously validated in clinical initiatives, its usefulness in complex systems is unknown. To answer this question, we used VBA to correct deficiencies in cardiac surgery at Memorial Healthcare System. Cardiac surgery is a complex surgical system that lends itself to VBA because outcomes metrics provided by the Society of Thoracic Surgeons provide an estimate of quality; cost is available from Centers for Medicare and Medicaid Services and other contemporary sources; the UP can be determined; and the best practice can be established. Analysis of the UP at Memorial Healthcare System revealed considerable deficiencies in selection of patients for surgery; the surgery itself, including choice of procedure and outcomes; after care; follow-up; and control of expenditures. To correct these deficiencies, each UP was replaced with a BP. Changes included replacement of most of the cardiac surgeons; conversion to an employed physician model; restructuring of a heart surgery unit; recruitment of cardiac anesthesiologists; introduction of an interactive educational program; eliminating unsafe practices; and reducing cost. There was a significant (p value (quality/cost) in a complex surgical system. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  8. Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex

    DEFF Research Database (Denmark)

    Laursen, Nick Stub; Andersen, Kasper Røjkjær; Braren, Ingke

    2011-01-01

    with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only...... slightly affects the C5-CVF interface, explaining the IgA dependence for SSL7-mediated inhibition of C5 cleavage. CVF functions as a relatively rigid binding scaffold inducing a conformational change in C5, which positions its cleavage site in proximity to the serine protease Bb. A general model...

  9. Functional complexity of the axonal growth cone: a proteomic analysis.

    Directory of Open Access Journals (Sweden)

    Adriana Estrada-Bernal

    Full Text Available The growth cone, the tip of the emerging neurite, plays a crucial role in establishing the wiring of the developing nervous system. We performed an extensive proteomic analysis of axonal growth cones isolated from the brains of fetal Sprague-Dawley rats. Approximately 2000 proteins were identified at ≥ 99% confidence level. Using informatics, including functional annotation cluster and KEGG pathway analysis, we found great diversity of proteins involved in axonal pathfinding, cytoskeletal remodeling, vesicular traffic and carbohydrate metabolism, as expected. We also found a large and complex array of proteins involved in translation, protein folding, posttranslational processing, and proteasome/ubiquitination-dependent degradation. Immunofluorescence studies performed on hippocampal neurons in culture confirmed the presence in the axonal growth cone of proteins representative of these processes. These analyses also provide evidence for rough endoplasmic reticulum and reveal a reticular structure equipped with Golgi-like functions in the axonal growth cone. Furthermore, Western blot revealed the growth cone enrichment, relative to fetal brain homogenate, of some of the proteins involved in protein synthesis, folding and catabolism. Our study provides a resource for further research and amplifies the relatively recently developed concept that the axonal growth cone is equipped with proteins capable of performing a highly diverse range of functions.

  10. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yu, E-mail: yuzhang@xmu.edu.c [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Shao Jun [Shanghai EENT Hospital of Fudan University, Shanghai (China); Krausert, Christopher R. [Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States); Zhang Sai [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Jiang, Jack J. [Shanghai EENT Hospital of Fudan University, Shanghai (China); Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States)

    2011-01-15

    Research highlights: Low-dimensional human glottal area data. Evidence of chaos in human laryngeal activity from high-speed digital imaging. Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic analysis is capable of

  11. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    International Nuclear Information System (INIS)

    Zhang Yu; Shao Jun; Krausert, Christopher R.; Zhang Sai; Jiang, Jack J.

    2011-01-01

    Research highlights: → Low-dimensional human glottal area data. → Evidence of chaos in human laryngeal activity from high-speed digital imaging. → Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. → Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic

  12. Visualization and Analysis of Complex Covert Networks

    DEFF Research Database (Denmark)

    Memon, Bisharat

    systems that are covert and hence inherently complex. My Ph.D. is positioned within the wider framework of CrimeFighter project. The framework envisions a number of key knowledge management processes that are involved in the workflow, and the toolbox provides supporting tools to assist human end......This report discusses and summarize the results of my work so far in relation to my Ph.D. project entitled "Visualization and Analysis of Complex Covert Networks". The focus of my research is primarily on development of methods and supporting tools for visualization and analysis of networked......-users (intelligence analysts) in harvesting, filtering, storing, managing, structuring, mining, analyzing, interpreting, and visualizing data about offensive networks. The methods and tools proposed and discussed in this work can also be applied to analysis of more generic complex networks....

  13. Distinguishing PTSD, Complex PTSD, and Borderline Personality Disorder: A latent class analysis

    Directory of Open Access Journals (Sweden)

    Marylène Cloitre

    2014-09-01

    Full Text Available Background: There has been debate regarding whether Complex Posttraumatic Stress Disorder (Complex PTSD is distinct from Borderline Personality Disorder (BPD when the latter is comorbid with PTSD. Objective: To determine whether the patterns of symptoms endorsed by women seeking treatment for childhood abuse form classes that are consistent with diagnostic criteria for PTSD, Complex PTSD, and BPD. Method: A latent class analysis (LCA was conducted on an archival dataset of 280 women with histories of childhood abuse assessed for enrollment in a clinical trial for PTSD. Results: The LCA revealed four distinct classes of individuals: a Low Symptom class characterized by low endorsements on all symptoms; a PTSD class characterized by elevated symptoms of PTSD but low endorsement of symptoms that define the Complex PTSD and BPD diagnoses; a Complex PTSD class characterized by elevated symptoms of PTSD and self-organization symptoms that defined the Complex PTSD diagnosis but low on the symptoms of BPD; and a BPD class characterized by symptoms of BPD. Four BPD symptoms were found to greatly increase the odds of being in the BPD compared to the Complex PTSD class: frantic efforts to avoid abandonment, unstable sense of self, unstable and intense interpersonal relationships, and impulsiveness. Conclusions: Findings supported the construct validity of Complex PTSD as distinguishable from BPD. Key symptoms that distinguished between the disorders were identified, which may aid in differential diagnosis and treatment planning.

  14. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  15. Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

    Directory of Open Access Journals (Sweden)

    Jie Qiu

    Full Text Available Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou and a wild line (Lanxi 1 collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1 no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2 besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3 high heterozygous rates (0.19-0.49 were observed in several semi-wild lines; and (4 over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

  16. Phosphoproteome analysis of functional mitochondria isolated from resting human muscle reveals extensive phosphorylation of inner membrane protein complexes and enzymes

    DEFF Research Database (Denmark)

    Zhao, Xiaolu; Leon, Ileana R; Bak, Steffen

    2011-01-01

    . In skeletal muscle, mitochondrial dysfunction is linked to insulin resistance in humans with obesity and type 2 diabetes. We performed a phosphoproteomic study of functional mitochondria isolated from human muscle biopsies with the aim to obtain a comprehensive overview of mitochondrial phosphoproteins...... in insulin resistance. We also assigned phosphorylation sites in mitochondrial proteins involved in amino acid degradation, importers and transporters, calcium homeostasis, and apoptosis. Bioinformatics analysis of kinase motifs revealed that many of these mitochondrial phosphoproteins are substrates....... Future comparative phosphoproteome analysis of mitochondria from healthy and diseased individuals will provide insights into the role of abnormal phosphorylation in pathologies, such as type 2 diabetes....

  17. Complex analysis a modern first course in function theory

    CERN Document Server

    Muir, Jerry R

    2015-01-01

    A thorough introduction to the theory of complex functions emphasizing the beauty, power, and counterintuitive nature of the subject Written with a reader-friendly approach, Complex Analysis: A Modern First Course in Function Theory features a self-contained, concise development of the fundamental principles of complex analysis. After laying groundwork on complex numbers and the calculus and geometric mapping properties of functions of a complex variable, the author uses power series as a unifying theme to define and study the many rich and occasionally surprising properties of analytic fun

  18. Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states.

    Science.gov (United States)

    Schlau-Cohen, Gabriela S; Wang, Quan; Southall, June; Cogdell, Richard J; Moerner, W E

    2013-07-02

    Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.

  19. Intersubject information mapping: revealing canonical representations of complex natural stimuli

    Directory of Open Access Journals (Sweden)

    Nikolaus Kriegeskorte

    2015-03-01

    Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

  20. Complex harmonic modal analysis of rotor systems

    International Nuclear Information System (INIS)

    Han, Dong Ju

    2015-01-01

    Complex harmonic analysis for rotor systems has been proposed from the strict complex modal analysis based upon Floquet theory. In this process the harmonic balance method is adopted, effectively associated with conventional eigenvalue analysis. Also, the harmonic coefficients equivalent to dFRFs in harmonic mode has been derived in practice. The modes are classified from identifying the modal characteristics, and the adaptation of harmonic balance method has been proven by comparing the results of the stability analyses from Floque theory and the eigen analysis. The modal features of each critical speed are depicted in quantitatively and qualitatively by showing that the strengths of each component of the harmonic coefficients are estimated from the order of magnitude analysis according to their harmonic patterns. This effectiveness has been verified by comparing with the numerical solutions

  1. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays

    Directory of Open Access Journals (Sweden)

    Chen David P

    2010-10-01

    Full Text Available Abstract Background Diagnosis and treatment of patients in the clinical setting is often driven by known symptomatic factors that distinguish one particular condition from another. Treatment based on noticeable symptoms, however, is limited to the types of clinical biomarkers collected, and is prone to overlooking dysfunctions in physiological factors not easily evident to medical practitioners. We used a vector-based representation of patient clinical biomarkers, or clinarrays, to search for latent physiological factors that underlie human diseases directly from clinical laboratory data. Knowledge of these factors could be used to improve assessment of disease severity and help to refine strategies for diagnosis and monitoring disease progression. Results Applying Independent Component Analysis on clinarrays built from patient laboratory measurements revealed both known and novel concomitant physiological factors for asthma, types 1 and 2 diabetes, cystic fibrosis, and Duchenne muscular dystrophy. Serum sodium was found to be the most significant factor for both type 1 and type 2 diabetes, and was also significant in asthma. TSH3, a measure of thyroid function, and blood urea nitrogen, indicative of kidney function, were factors unique to type 1 diabetes respective to type 2 diabetes. Platelet count was significant across all the diseases analyzed. Conclusions The results demonstrate that large-scale analyses of clinical biomarkers using unsupervised methods can offer novel insights into the pathophysiological basis of human disease, and suggest novel clinical utility of established laboratory measurements.

  2. Complex surveys analysis of categorical data

    CERN Document Server

    Mukhopadhyay, Parimal

    2016-01-01

    The primary objective of this book is to study some of the research topics in the area of analysis of complex surveys which have not been covered in any book yet. It discusses the analysis of categorical data using three models: a full model, a log-linear model and a logistic regression model. It is a valuable resource for survey statisticians and practitioners in the field of sociology, biology, economics, psychology and other areas who have to use these procedures in their day-to-day work. It is also useful for courses on sampling and complex surveys at the upper-undergraduate and graduate levels. The importance of sample surveys today cannot be overstated. From voters’ behaviour to fields such as industry, agriculture, economics, sociology, psychology, investigators generally resort to survey sampling to obtain an assessment of the behaviour of the population they are interested in. Many large-scale sample surveys collect data using complex survey designs like multistage stratified cluster designs. The o...

  3. Evidence that the respiratory syncytial virus polymerase complex associates with lipid rafts in virus-infected cells: a proteomic analysis

    International Nuclear Information System (INIS)

    McDonald, Terence P.; Pitt, Andrew R.; Brown, Gaie; Rixon, Helen W. McL.; Sugrue, Richard J.

    2004-01-01

    The interaction between the respiratory syncytial virus (RSV) polymerase complex and lipid rafts was examined in HEp2 cells. Lipid-raft membranes were prepared from virus-infected cells and their protein content was analysed by Western blotting and mass spectrometry. This analysis revealed the presence of the N, P, L, M2-1 and M proteins. However, these proteins appeared to differ from one another in their association with these structures, with the M2-1 protein showing a greater partitioning into raft membranes compared to that of the N, P or M proteins. Determination of the polymerase activity profile of the gradient fractions revealed that 95% of the detectable viral enzyme activity was associated with lipid-raft membranes. Furthermore, analysis of virus-infected cells by confocal microscopy suggested an association between these proteins and the raft-lipid, GM1. Together, these results provide evidence that the RSV polymerase complex is able to associate with lipid rafts in virus-infected cells

  4. A Multiple Interaction Analysis Reveals ADRB3 as a Potential Candidate for Gallbladder Cancer Predisposition via a Complex Interaction with Other Candidate Gene Variations

    Directory of Open Access Journals (Sweden)

    Rajani Rai

    2015-11-01

    Full Text Available Gallbladder cancer is the most common and a highly aggressive biliary tract malignancy with a dismal outcome. The pathogenesis of the disease is multifactorial, comprising the combined effect of multiple genetic variations of mild consequence along with numerous dietary and environmental risk factors. Previously, we demonstrated the association of several candidate gene variations with GBC risk. In this study, we aimed to identify the combination of gene variants and their possible interactions contributing towards genetic susceptibility of GBC. Here, we performed Multifactor-Dimensionality Reduction (MDR and Classification and Regression Tree Analysis (CRT to investigate the gene–gene interactions and the combined effect of 14 SNPs in nine genes (DR4 (rs20576, rs6557634; FAS (rs2234767; FASL (rs763110; DCC (rs2229080, rs4078288, rs7504990, rs714; PSCA (rs2294008, rs2978974; ADRA2A (rs1801253; ADRB1 (rs1800544; ADRB3 (rs4994; CYP17 (rs2486758 involved in various signaling pathways. Genotyping was accomplished by PCR-RFLP or Taqman allelic discrimination assays. SPSS software version 16.0 and MDR software version 2.0 were used for all the statistical analysis. Single locus investigation demonstrated significant association of DR4 (rs20576, rs6557634, DCC (rs714, rs2229080, rs4078288 and ADRB3 (rs4994 polymorphisms with GBC risk. MDR analysis revealed ADRB3 (rs4994 to be crucial candidate in GBC susceptibility that may act either alone (p < 0.0001, CVC = 10/10 or in combination with DCC (rs714 and rs2229080, p < 0.0001, CVC = 9/10. Our CRT results are in agreement with the above findings. Further, in-silico results of studied SNPs advocated their role in splicing, transcriptional and/or protein coding regulation. Overall, our result suggested complex interactions amongst the studied SNPs and ADRB3 rs4994 as candidate influencing GBC susceptibility.

  5. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum.

    Science.gov (United States)

    Venkataramanan, Keerthi P; Min, Lie; Hou, Shuyu; Jones, Shawn W; Ralston, Matthew T; Lee, Kelvin H; Papoutsakis, E Terry

    2015-01-01

    Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.

  6. Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids.

    Directory of Open Access Journals (Sweden)

    Pitter F Huesgen

    Full Text Available In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.

  7. Mathematical Analysis of Evolution, Information, and Complexity

    CERN Document Server

    Arendt, Wolfgang

    2009-01-01

    Mathematical Analysis of Evolution, Information, and Complexity deals with the analysis of evolution, information and complexity. The time evolution of systems or processes is a central question in science, this text covers a broad range of problems including diffusion processes, neuronal networks, quantum theory and cosmology. Bringing together a wide collection of research in mathematics, information theory, physics and other scientific and technical areas, this new title offers elementary and thus easily accessible introductions to the various fields of research addressed in the book.

  8. Intraparticulate Metal Speciation Analysis of Soft Complexing Nanoparticles. The Intrinsic Chemical Heterogeneity of Metal-Humic Acid Complexes

    DEFF Research Database (Denmark)

    Town, R. M.; van Leeuwen, Herman P.

    2016-01-01

    ion condensation potential for higher valency counterions within the intraparticulate double layer zone of the soft NP. The approach offers new insights into the intrinsic heterogeneity of the HA. complexes, as revealed by the intraparticulate speciation as a function of the true degree of inner......-sphere complexation, theta(M). The ensuing intrinsic heterogeneity parameters, Gamma, for CdHA and CuHA complexes are in very good agreement with those obtained from dynamic electrochemical stripping chronopotentiometric measurements. The overall intraparticulate metal ion speciation is found to depend on theta...

  9. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

    Directory of Open Access Journals (Sweden)

    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  10. Analysis of complex networks using aggressive abstraction.

    Energy Technology Data Exchange (ETDEWEB)

    Colbaugh, Richard; Glass, Kristin.; Willard, Gerald

    2008-10-01

    This paper presents a new methodology for analyzing complex networks in which the network of interest is first abstracted to a much simpler (but equivalent) representation, the required analysis is performed using the abstraction, and analytic conclusions are then mapped back to the original network and interpreted there. We begin by identifying a broad and important class of complex networks which admit abstractions that are simultaneously dramatically simplifying and property preserving we call these aggressive abstractions -- and which can therefore be analyzed using the proposed approach. We then introduce and develop two forms of aggressive abstraction: 1.) finite state abstraction, in which dynamical networks with uncountable state spaces are modeled using finite state systems, and 2.) onedimensional abstraction, whereby high dimensional network dynamics are captured in a meaningful way using a single scalar variable. In each case, the property preserving nature of the abstraction process is rigorously established and efficient algorithms are presented for computing the abstraction. The considerable potential of the proposed approach to complex networks analysis is illustrated through case studies involving vulnerability analysis of technological networks and predictive analysis for social processes.

  11. Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

    Science.gov (United States)

    Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

    2018-05-19

    Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

    International Nuclear Information System (INIS)

    Elbasyouny, A.

    1983-01-01

    This dissertation reports about studies on the chemical coordination behaviour of uranium of oxidation stages IV and VI with regard to twelve different macrocyclic ligands. For the preparation of the complexes, for every system a different method has been developed. The elementary analysis of the various complexes including the uranium had been done by X-ray fluorescence analysis, and the structural characterization proceeded via vibrational, uv-vis and emission spectroscopy as well as 1 H-NMR and 13 C-spin-lattice relaxation time studies. Conformational analysis of the polyethers used allowed the structural changes in the complexes to be observed. The structural analysis of the hydrous uranium VI crown ether complexes yielded information of characteristic features of these types of complexes. The first coordination sphere of the uranyl ion with covalently bonded anion remains unchanged. As to the water content, there is a certain range. Depending upon the solvent used, the complexes have two or four H 2 O molecules per formula unit. (orig./EF) [de

  13. Multifractal analysis of complex networks

    International Nuclear Information System (INIS)

    Wang Dan-Ling; Yu Zu-Guo; Anh V

    2012-01-01

    Complex networks have recently attracted much attention in diverse areas of science and technology. Many networks such as the WWW and biological networks are known to display spatial heterogeneity which can be characterized by their fractal dimensions. Multifractal analysis is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns. In this paper, we introduce a new box-covering algorithm for multifractal analysis of complex networks. This algorithm is used to calculate the generalized fractal dimensions D q of some theoretical networks, namely scale-free networks, small world networks, and random networks, and one kind of real network, namely protein—protein interaction networks of different species. Our numerical results indicate the existence of multifractality in scale-free networks and protein—protein interaction networks, while the multifractal behavior is not clear-cut for small world networks and random networks. The possible variation of D q due to changes in the parameters of the theoretical network models is also discussed. (general)

  14. Multi-signal sedimentation velocity analysis with mass conservation for determining the stoichiometry of protein complexes.

    Directory of Open Access Journals (Sweden)

    Chad A Brautigam

    Full Text Available Multi-signal sedimentation velocity analytical ultracentrifugation (MSSV is a powerful tool for the determination of the number, stoichiometry, and hydrodynamic shape of reversible protein complexes in two- and three-component systems. In this method, the evolution of sedimentation profiles of macromolecular mixtures is recorded simultaneously using multiple absorbance and refractive index signals and globally transformed into both spectrally and diffusion-deconvoluted component sedimentation coefficient distributions. For reactions with complex lifetimes comparable to the time-scale of sedimentation, MSSV reveals the number and stoichiometry of co-existing complexes. For systems with short complex lifetimes, MSSV reveals the composition of the reaction boundary of the coupled reaction/migration process, which we show here may be used to directly determine an association constant. A prerequisite for MSSV is that the interacting components are spectrally distinguishable, which may be a result, for example, of extrinsic chromophores or of different abundances of aromatic amino acids contributing to the UV absorbance. For interacting components that are spectrally poorly resolved, here we introduce a method for additional regularization of the spectral deconvolution by exploiting approximate knowledge of the total loading concentrations. While this novel mass conservation principle does not discriminate contributions to different species, it can be effectively combined with constraints in the sedimentation coefficient range of uncomplexed species. We show in theory, computer simulations, and experiment, how mass conservation MSSV as implemented in SEDPHAT can enhance or even substitute for the spectral discrimination of components. This should broaden the applicability of MSSV to the analysis of the composition of reversible macromolecular complexes.

  15. Korean Conference on Several Complex Variables

    CERN Document Server

    Byun, Jisoo; Gaussier, Hervé; Hirachi, Kengo; Kim, Kang-Tae; Shcherbina, Nikolay

    2015-01-01

    This volume includes 28 chapters by authors who are leading researchers of the world describing many of the up-to-date aspects in the field of several complex variables (SCV). These contributions are based upon their presentations at the 10th Korean Conference on Several Complex Variables (KSCV10), held as a satellite conference to the International Congress of Mathematicians (ICM) 2014 in Seoul, Korea. SCV has been the term for multidimensional complex analysis, one of the central research areas in mathematics. Studies over time have revealed a variety of rich, intriguing, new knowledge in complex analysis and geometry of analytic spaces and holomorphic functions which were "hidden" in the case of complex dimension one. These new theories have significant intersections with algebraic geometry, differential geometry, partial differential equations, dynamics, functional analysis and operator theory, and sheaves and cohomology, as well as the traditional analysis of holomorphic functions in all dimensions. This...

  16. Evidence for proposed ICD-11 PTSD and complex PTSD: a latent profile analysis

    Directory of Open Access Journals (Sweden)

    Marylène Cloitre

    2013-05-01

    Full Text Available Background: The WHO International Classification of Diseases, 11th version (ICD-11, has proposed two related diagnoses, posttraumatic stress disorder (PTSD and complex PTSD within the spectrum of trauma and stress-related disorders. Objective: To use latent profile analysis (LPA to determine whether there are classes of individuals that are distinguishable according to the PTSD and complex PTSD symptom profiles and to identify potential differences in the type of stressor and severity of impairment associated with each profile. Method: An LPA and related analyses were conducted on 302 individuals who had sought treatment for interpersonal traumas ranging from chronic trauma (e.g., childhood abuse to single-incident events (e.g., exposure to 9/11 attacks. Results: The LPA revealed three classes of individuals: (1 a complex PTSD class defined by elevated PTSD symptoms as well as disturbances in three domains of self-organization: affective dysregulation, negative self-concept, and interpersonal problems; (2 a PTSD class defined by elevated PTSD symptoms but low scores on the three self-organization symptom domains; and (3 a low symptom class defined by low scores on all symptoms and problems. Chronic trauma was more strongly predictive of complex PTSD than PTSD and, conversely, single-event trauma was more strongly predictive of PTSD. In addition, complex PTSD was associated with greater impairment than PTSD. The LPA analysis was completed both with and without individuals with borderline personality disorder (BPD yielding identical results, suggesting the stability of these classes regardless of BPD comorbidity. Conclusion: Preliminary data support the proposed ICD-11 distinction between PTSD and complex PTSD and support the value of testing the clinical utility of this distinction in field trials. Replication of results is necessary.For the abstract or full text in other languages, please see Supplementary files under Article Tools online

  17. [Social-professional status, identity, social participation and media utilization. Analysis of a complex dynamics].

    Science.gov (United States)

    Laflamme, Simon; Roggero, Pascal; Southcott, Chris

    2010-08-01

    This article examines the link between the domain and level of occupation, on the one hand, and use of media, including internet, on the other. It adds to this investigation an analysis of identity in its relation to media use and accessibility. It challenges the hypothesis of a strong correlation between level of occupation and use and accessibility to media. It reveals complex phenomena of social homogenization and differentiation. Data is extracted from a sample of workers who completed a questionnaire which focused on use of media.

  18. Coping with Complexity Model Reduction and Data Analysis

    CERN Document Server

    Gorban, Alexander N

    2011-01-01

    This volume contains the extended version of selected talks given at the international research workshop 'Coping with Complexity: Model Reduction and Data Analysis', Ambleside, UK, August 31 - September 4, 2009. This book is deliberately broad in scope and aims at promoting new ideas and methodological perspectives. The topics of the chapters range from theoretical analysis of complex and multiscale mathematical models to applications in e.g., fluid dynamics and chemical kinetics.

  19. Time series analysis of embodied interaction: Movement variability and complexity matching as dyadic properties

    Directory of Open Access Journals (Sweden)

    Leonardo Zapata-Fonseca

    2016-12-01

    Full Text Available There is a growing consensus that a fuller understanding of social cognition depends on more systematic studies of real-time social interaction. Such studies require methods that can deal with the complex dynamics taking place at multiple interdependent temporal and spatial scales, spanning sub-personal, personal, and dyadic levels of analysis. We demonstrate the value of adopting an extended multi-scale approach by re-analyzing movement time series generated in a study of embodied dyadic interaction in a minimal virtual reality environment (a perceptual crossing experiment. Reduced movement variability revealed an interdependence between social awareness and social coordination that cannot be accounted for by either subjective or objective factors alone: it picks out interactions in which subjective and objective conditions are convergent (i.e. elevated coordination is perceived as clearly social, and impaired coordination is perceived as socially ambiguous. This finding is consistent with the claim that interpersonal interaction can be partially constitutive of direct social perception. Clustering statistics (Allan Factor of salient events revealed fractal scaling. Complexity matching defined as the similarity between these scaling laws was significantly more pronounced in pairs of participants as compared to surrogate dyads. This further highlights the multi-scale and distributed character of social interaction and extends previous complexity matching results from dyadic conversation to nonverbal social interaction dynamics. Trials with successful joint interaction were also associated with an increase in local coordination. Consequently, a local coordination pattern emerges on the background of complex dyadic interactions in the PCE task and makes joint successful performance possible.

  20. Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

    Science.gov (United States)

    Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

    2016-08-12

    The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

  1. Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors.

    Directory of Open Access Journals (Sweden)

    Scott B Vafai

    Full Text Available Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS. Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as "complex I bypass." In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology.

  2. Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

    Directory of Open Access Journals (Sweden)

    Sepil Irem

    2012-05-01

    Full Text Available Abstract Background The critical role of Major Histocompatibility Complex (Mhc genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. Results In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. Conclusions We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help

  3. Complex of the equipment for instrumental element analysis

    International Nuclear Information System (INIS)

    Borisov, G.I.; Komkov, M.M.; Kuz'michev, V.A.

    1986-01-01

    Complex of the equipment for instrumental element analysis at the IR-8 reactor is designed, fabricated and taken into operation. The complex is provided with a multichannel system of vacuum pneumatic transport with radiation positions in the reactor horizontal tangential channel for neutron-activation analysis by short-lived isotopes; specialized dry vertical channels in a beryllium reflector of the reactor and remote system of radioactive sample replacement for neutron-activation analysis by long-lived isotopes; a specialized horizontal tangential channel for neutron beam extraction by means of a beryllium converter and remote device for studied sample replacement under radiation and measurement of prompt γ-radiation for neutron-radiation analysis; a measuring center using minicomputers for experimental data accumulation and processing and analysis control

  4. Hurst Exponent Analysis of Resting-State fMRI Signal Complexity across the Adult Lifespan

    Directory of Open Access Journals (Sweden)

    Jianxin Dong

    2018-02-01

    Full Text Available Exploring functional information among various brain regions across time enables understanding of healthy aging process and holds great promise for age-related brain disease diagnosis. This paper proposed a method to explore fractal complexity of the resting-state functional magnetic resonance imaging (rs-fMRI signal in the human brain across the adult lifespan using Hurst exponent (HE. We took advantage of the examined rs-fMRI data from 116 adults 19 to 85 years of age (44.3 ± 19.4 years, 49 females from NKI/Rockland sample. Region-wise and voxel-wise analyses were performed to investigate the effects of age, gender, and their interaction on complexity. In region-wise analysis, we found that the healthy aging is accompanied by a loss of complexity in frontal and parietal lobe and increased complexity in insula, limbic, and temporal lobe. Meanwhile, differences in HE between genders were found to be significant in parietal lobe (p = 0.04, corrected. However, there was no interaction between gender and age. In voxel-wise analysis, the significant complexity decrease with aging was found in frontal and parietal lobe, and complexity increase was found in insula, limbic lobe, occipital lobe, and temporal lobe with aging. Meanwhile, differences in HE between genders were found to be significant in frontal, parietal, and limbic lobe. Furthermore, we found age and sex interaction in right parahippocampal gyrus (p = 0.04, corrected. Our findings reveal HE variations of the rs-fMRI signal across the human adult lifespan and show that HE may serve as a new parameter to assess healthy aging process.

  5. Critical Fluctuations in Spatial Complex Networks

    Science.gov (United States)

    Bradde, Serena; Caccioli, Fabio; Dall'Asta, Luca; Bianconi, Ginestra

    2010-05-01

    An anomalous mean-field solution is known to capture the nontrivial phase diagram of the Ising model in annealed complex networks. Nevertheless, the critical fluctuations in random complex networks remain mean field. Here we show that a breakdown of this scenario can be obtained when complex networks are embedded in geometrical spaces. Through the analysis of the Ising model on annealed spatial networks, we reveal, in particular, the spectral properties of networks responsible for critical fluctuations and we generalize the Ginsburg criterion to complex topologies.

  6. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits

    DEFF Research Database (Denmark)

    Macé, Aurélien; Tuke, Marcus A; Deelen, Patrick

    2017-01-01

    There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations......-scale genome-wide meta-analysis of structural variation and find rare CNVs associated with height, weight and BMI with large effect sizes.......)). Burden analysis shows a 0.41 cm decrease in height, a 0.003 increase in waist-to-hip ratio and increase in BMI by 0.14 kg/m(2) for each Mb of total deletion burden (P = 2.5 × 10(-10), 6.0 × 10(-5), and 2.9 × 10(-3)). Our study provides evidence that the same genes (e.g., MC4R, FIBIN, and FMO5) harbor...

  7. Integrative Genomic Analysis of Complex traits

    DEFF Research Database (Denmark)

    Ehsani, Ali Reza

    In the last decade rapid development in biotechnologies has made it possible to extract extensive information about practically all levels of biological organization. An ever-increasing number of studies are reporting miltilayered datasets on the entire DNA sequence, transceroption, protein...... expression, and metabolite abundance of more and more populations in a multitude of invironments. However, a solid model for including all of this complex information in one analysis, to disentangle genetic variation and the underlying genetic architecture of complex traits and diseases, has not yet been...

  8. Dynamic Regulation of a Cell Adhesion Protein Complex Including CADM1 by Combinatorial Analysis of FRAP with Exponential Curve-Fitting

    Science.gov (United States)

    Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori

    2015-01-01

    Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation. PMID:25780926

  9. Agent-based financial dynamics model from stochastic interacting epidemic system and complexity analysis

    International Nuclear Information System (INIS)

    Lu, Yunfan; Wang, Jun; Niu, Hongli

    2015-01-01

    An agent-based financial stock price model is developed and investigated by a stochastic interacting epidemic system, which is one of the statistical physics systems and has been used to model the spread of an epidemic or a forest fire. Numerical and statistical analysis are performed on the simulated returns of the proposed financial model. Complexity properties of the financial time series are explored by calculating the correlation dimension and using the modified multiscale entropy method. In order to verify the rationality of the financial model, the real stock market indexes, Shanghai Composite Index and Shenzhen Component Index, are studied in comparison with the simulation data of the proposed model for the different infectiousness parameters. The empirical research reveals that this financial model can reproduce some important features of the real stock markets. - Highlights: • A new agent-based financial price model is developed by stochastic interacting epidemic system. • The structure of the proposed model allows to simulate the financial dynamics. • Correlation dimension and MMSE are applied to complexity analysis of financial time series. • Empirical results show the rationality of the proposed financial model

  10. Agent-based financial dynamics model from stochastic interacting epidemic system and complexity analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Yunfan, E-mail: yunfanlu@yeah.net; Wang, Jun; Niu, Hongli

    2015-06-12

    An agent-based financial stock price model is developed and investigated by a stochastic interacting epidemic system, which is one of the statistical physics systems and has been used to model the spread of an epidemic or a forest fire. Numerical and statistical analysis are performed on the simulated returns of the proposed financial model. Complexity properties of the financial time series are explored by calculating the correlation dimension and using the modified multiscale entropy method. In order to verify the rationality of the financial model, the real stock market indexes, Shanghai Composite Index and Shenzhen Component Index, are studied in comparison with the simulation data of the proposed model for the different infectiousness parameters. The empirical research reveals that this financial model can reproduce some important features of the real stock markets. - Highlights: • A new agent-based financial price model is developed by stochastic interacting epidemic system. • The structure of the proposed model allows to simulate the financial dynamics. • Correlation dimension and MMSE are applied to complexity analysis of financial time series. • Empirical results show the rationality of the proposed financial model.

  11. DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

    Science.gov (United States)

    Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

    2015-10-01

    The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Characteristics of the tomato chromoplast revealed by proteomic analysis

    OpenAIRE

    Barsan, Cristina; Sanchez-Bel, Paloma; Rombaldi, César Valmor; Egea, Isabel; Rossignol, Michel; Kuntz, Marcel; Zouine, Mohamed; Latché, Alain; Bouzayen, Mondher; Pech, Jean-Claude

    2010-01-01

    Chromoplasts are non-photosynthetic specialized plastids that are important in ripening tomato fruit (Solanum lycopersicum) since, among other functions, they are the site of accumulation of coloured compounds. Analysis of the proteome of red fruit chromoplasts revealed the presence of 988 proteins corresponding to 802 Arabidopsis unigenes, among which 209 had not been listed so far in plastidial databanks. These data revealed several features of the chromoplast. Proteins of lipid metabolism ...

  13. Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird, the Manx Shearwater

    Science.gov (United States)

    Freeman, Robin; Dean, Ben; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

    2013-01-01

    Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover. PMID:23635496

  14. Special Year on Complex Analysis held at the University of Maryland

    CERN Document Server

    1987-01-01

    The past several years have witnessed a striking number of important developments in Complex Analysis. One of the characteristics of these developments has been to bridge the gap existing between the theory of functions of one and of several complex variables. The Special Year in Complex Analysis at the University of Maryland, and these proceedings, were conceived as a forum where these new developments could be presented and where specialists in different areas of complex analysis could exchange ideas. These proceedings contain both surveys of different subjects covered during the year as well as many new results and insights. The manuscripts are accessible not only to specialists but to a broader audience. Among the subjects touched upon are Nevanlinna theory in one and several variables, interpolation problems in Cn, estimations and integral representations of the solutions of the Cauchy-Riemann equations, the complex Monge-Ampère equation, geometric problems in complex analysis in Cn, applications of com...

  15. Deep Neural Networks Reveal a Gradient in the Complexity of Neural Representations across the Ventral Stream.

    Science.gov (United States)

    Güçlü, Umut; van Gerven, Marcel A J

    2015-07-08

    Converging evidence suggests that the primate ventral visual pathway encodes increasingly complex stimulus features in downstream areas. We quantitatively show that there indeed exists an explicit gradient for feature complexity in the ventral pathway of the human brain. This was achieved by mapping thousands of stimulus features of increasing complexity across the cortical sheet using a deep neural network. Our approach also revealed a fine-grained functional specialization of downstream areas of the ventral stream. Furthermore, it allowed decoding of representations from human brain activity at an unsurpassed degree of accuracy, confirming the quality of the developed approach. Stimulus features that successfully explained neural responses indicate that population receptive fields were explicitly tuned for object categorization. This provides strong support for the hypothesis that object categorization is a guiding principle in the functional organization of the primate ventral stream. Copyright © 2015 the authors 0270-6474/15/3510005-10$15.00/0.

  16. Meta-analysis of mismatch negativity to simple versus complex deviants in schizophrenia.

    Science.gov (United States)

    Avissar, Michael; Xie, Shanghong; Vail, Blair; Lopez-Calderon, Javier; Wang, Yuanjia; Javitt, Daniel C

    2018-01-01

    Mismatch negativity (MMN) deficits in schizophrenia (SCZ) have been studied extensively since the early 1990s, with the vast majority of studies using simple auditory oddball task deviants that vary in a single acoustic dimension such as pitch or duration. There has been a growing interest in using more complex deviants that violate more abstract rules to probe higher order cognitive deficits. It is still unclear how sensory processing deficits compare to and contribute to higher order cognitive dysfunction, which can be investigated with later attention-dependent auditory event-related potential (ERP) components such as a subcomponent of P300, P3b. In this meta-analysis, we compared MMN deficits in SCZ using simple deviants to more complex deviants. We also pooled studies that measured MMN and P3b in the same study sample and examined the relationship between MMN and P3b deficits within study samples. Our analysis reveals that, to date, studies using simple deviants demonstrate larger deficits than those using complex deviants, with effect sizes in the range of moderate to large. The difference in effect sizes between deviant types was reduced significantly when accounting for magnitude of MMN measured in healthy controls. P3b deficits, while large, were only modestly greater than MMN deficits (d=0.21). Taken together, our findings suggest that MMN to simple deviants may still be optimal as a biomarker for SCZ and that sensory processing dysfunction contributes significantly to MMN deficit and disease pathophysiology. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Complex Wavelet Based Modulation Analysis

    DEFF Research Database (Denmark)

    Luneau, Jean-Marc; Lebrun, Jérôme; Jensen, Søren Holdt

    2008-01-01

    Low-frequency modulation of sound carry important information for speech and music. The modulation spectrum i commonly obtained by spectral analysis of the sole temporal envelopes of the sub-bands out of a time-frequency analysis. Processing in this domain usually creates undesirable distortions...... polynomial trends. Moreover an analytic Hilbert-like transform is possible with complex wavelets implemented as an orthogonal filter bank. By working in an alternative transform domain coined as “Modulation Subbands”, this transform shows very promising denoising capabilities and suggests new approaches for joint...

  18. Complexity Analysis of Industrial Organizations Based on a Perspective of Systems Engineering Analysts

    Directory of Open Access Journals (Sweden)

    I. H. Garbie

    2011-12-01

    Full Text Available Complexity in industrial organizations became more difficult and complex to be solved and it needs more attention from academicians and technicians. For these reasons, complexity in industrial organizations represents a new challenge in the next decades. Until now, analysis of industrial organizations complexity is still remaining a research topic of immense international interest and they require reduction in their complexity. In this paper, analysis of complexity in industrial organizations is shown based on the perspective of systems engineering analyst. In this perspective, analysis of complexity was divided into different levels and these levels were defined as complexity levels. A framework of analyzing these levels was proposed and suggested based on the complexity in industrial organizations. This analysis was divided into four main issues: industrial system vision, industrial system structure, industrial system operating, and industrial system evaluating. This analysis shows that the complexity of industrial organizations is still an ill-structured and a multi-dimensional problem.

  19. An Alternative Front End Analysis Strategy for Complex Systems

    Science.gov (United States)

    2014-12-01

    missile ( ABM ) system . Patriot is employed in the field through a battalion echelon organizational structure. The line battery is the basic building...Research Report 1981 An Alternative Front End Analysis Strategy for Complex Systems M. Glenn Cobb U.S. Army Research Institute...NUMBER W5J9CQ11D0003 An Alternative Front End Analysis Strategy for Complex Systems 5b. PROGRAM ELEMENT NUMBER 633007 6

  20. A finite element framework for multiscale/multiphysics analysis of structures with complex microstructures

    Science.gov (United States)

    Varghese, Julian

    This research work has contributed in various ways to help develop a better understanding of textile composites and materials with complex microstructures in general. An instrumental part of this work was the development of an object-oriented framework that made it convenient to perform multiscale/multiphysics analyses of advanced materials with complex microstructures such as textile composites. In addition to the studies conducted in this work, this framework lays the groundwork for continued research of these materials. This framework enabled a detailed multiscale stress analysis of a woven DCB specimen that revealed the effect of the complex microstructure on the stress and strain energy release rate distribution along the crack front. In addition to implementing an oxidation model, the framework was also used to implement strategies that expedited the simulation of oxidation in textile composites so that it would take only a few hours. The simulation showed that the tow architecture played a significant role in the oxidation behavior in textile composites. Finally, a coupled diffusion/oxidation and damage progression analysis was implemented that was used to study the mechanical behavior of textile composites under mechanical loading as well as oxidation. A parametric study was performed to determine the effect of material properties and the number of plies in the laminate on its mechanical behavior. The analyses indicated a significant effect of the tow architecture and other parameters on the damage progression in the laminates.

  1. Genomic Analysis of Complex Microbial Communities in Wounds

    Science.gov (United States)

    2012-01-01

    Permutation Multivariate Analysis of Variance ( PerMANOVA ). We used PerMANOVA to test the null-hypothesis of no... permutation -based version of the multivariate analysis of variance (MANOVA). PerMANOVA uses the distances between samples to partition variance and...coli. Antibiotics, bacteria, community analysis , diabetes, pyrosequencing, wound, wound therapy, 16S rRNA gene Genomic Analysis of Complex

  2. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

    Directory of Open Access Journals (Sweden)

    Matthias Merker

    Full Text Available Multidrug-resistant (MDR Mycobacterium tuberculosis complex (MTBC strains represent a major threat for tuberculosis (TB control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A and nine (Patient B polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and

  3. Analysis of Metal-Binding Features of the Wild Type and Two Domain-Truncated Mutant Variants of Littorina littorea Metallothionein Reveals Its Cd-Specific Character

    Directory of Open Access Journals (Sweden)

    Òscar Palacios

    2017-07-01

    Full Text Available After the resolution of the 3D structure of the Cd9-aggregate of the Littorina littorea metallothionein (MT, we report here a detailed analysis of the metal binding capabilities of the wild type MT, LlwtMT, and of two truncated mutants lacking either the N-terminal domain, Lltr2MT, or both the N-terminal domain, plus four extra flanking residues (SSVF, Lltr1MT. The recombinant synthesis and in vitro studies of these three proteins revealed that LlwtMT forms unique M9-LlwtMT complexes with Zn(II and Cd(II, while yielding a complex mixture of heteronuclear Zn,Cu-LlwtMT species with Cu(I. As expected, the truncated mutants gave rise to unique M6-LltrMT complexes and Zn,Cu-LltrMT mixtures of lower stoichiometry with respect to LlwtMT, with the SSVF fragment having an influence on their metal binding performance. Our results also revealed a major specificity, and therefore a better metal-coordinating performance of the three proteins for Cd(II than for Zn(II, although the analysis of the Zn(II/Cd(II displacement reaction clearly demonstrates a lack of any type of cooperativity in Cd(II binding. Contrarily, the analysis of their Cu(I binding abilities revealed that every LlMT domain is prone to build Cu4-aggregates, the whole MT working by modules analogously to, as previously described, certain fungal MTs, like those of C. neoformans and T. mesenterica. It is concluded that the Littorina littorea MT is a Cd-specific protein that (beyond its extended binding capacity through an additional Cd-binding domain confers to Littorina littorea a particular adaptive advantage in its changeable marine habitat.

  4. Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

    Science.gov (United States)

    2013-01-01

    Background Analysis of global gene expression by DNA microarrays is widely used in experimental molecular biology. However, the complexity of such high-dimensional data sets makes it difficult to fully understand the underlying biological features present in the data. The aim of this study is to introduce a method for DNA microarray analysis that provides an intuitive interpretation of data through dimension reduction and pattern recognition. We present the first “Archetypal Analysis” of global gene expression. The analysis is based on microarray data from five integrated studies of Pseudomonas aeruginosa isolated from the airways of cystic fibrosis patients. Results Our analysis clustered samples into distinct groups with comprehensible characteristics since the archetypes representing the individual groups are closely related to samples present in the data set. Significant changes in gene expression between different groups identified adaptive changes of the bacteria residing in the cystic fibrosis lung. The analysis suggests a similar gene expression pattern between isolates with a high mutation rate (hypermutators) despite accumulation of different mutations for these isolates. This suggests positive selection in the cystic fibrosis lung environment, and changes in gene expression for these isolates are therefore most likely related to adaptation of the bacteria. Conclusions Archetypal analysis succeeded in identifying adaptive changes of P. aeruginosa. The combination of clustering and matrix factorization made it possible to reveal minor similarities among different groups of data, which other analytical methods failed to identify. We suggest that this analysis could be used to supplement current methods used to analyze DNA microarray data. PMID:24059747

  5. Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

    Energy Technology Data Exchange (ETDEWEB)

    Rockel, Beate [Department of Molecular Structural Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried (Germany); Schmaler, Tilo; Huang, Xiaohua [Division of Molecular Biology, Department of General, Visceral, Vascular and Thoracic Surgery, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin (Germany); Dubiel, Wolfgang, E-mail: Wolfgang.dubiel@charite.de [Division of Molecular Biology, Department of General, Visceral, Vascular and Thoracic Surgery, Charité – Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin (Germany)

    2014-07-25

    Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

  6. Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

    International Nuclear Information System (INIS)

    Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua; Dubiel, Wolfgang

    2014-01-01

    Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

  7. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    Science.gov (United States)

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells

    DEFF Research Database (Denmark)

    Vandamme, Julien; Völkel, Pamela; Rosnoblet, Claire

    2011-01-01

    Polycomb group (PcG) proteins maintain transcriptional repression of hundreds of genes involved in development, signaling or cancer using chromatin-based epigenetic mechanisms. Biochemical studies in Drosophila have revealed that PcG proteins associate in at least two classes of protein complexes...... known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Drosophila core PRC1 is composed of four subunits, Polycomb (Pc), Sex combs extra (Sce), Polyhomeotic (Ph), and Posterior sex combs (Psc). Each of these proteins has multiple orthologs in vertebrates classified respectively as the CBX, RING...... in order to identify interacting partners of CBX family proteins under the same experimental conditions. Our analysis identified with high confidence about 20 proteins co-eluted with CBX2 and CBX7 tagged proteins, about 40 with CBX4, and around 60 with CBX6 and CBX8. We provide evidences that the CBX...

  9. Lipid clustering correlates with membrane curvature as revealed by molecular simulations of complex lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Heidi Koldsø

    2014-10-01

    Full Text Available Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2, in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

  10. Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species

    NARCIS (Netherlands)

    Thompson, S.M.; Tan, Y.P.; Young, A.J.; Neate, S.M.; Aitken, E.A.B.; Shivas, R.G.

    2012-01-01

    The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are

  11. Current topics in pure and computational complex analysis

    CERN Document Server

    Dorff, Michael; Lahiri, Indrajit

    2014-01-01

    The book contains 13 articles, some of which are survey articles and others research papers. Written by eminent mathematicians, these articles were presented at the International Workshop on Complex Analysis and Its Applications held at Walchand College of Engineering, Sangli. All the contributing authors are actively engaged in research fields related to the topic of the book. The workshop offered a comprehensive exposition of the recent developments in geometric functions theory, planar harmonic mappings, entire and meromorphic functions and their applications, both theoretical and computational. The recent developments in complex analysis and its applications play a crucial role in research in many disciplines.

  12. (VI) ML6 Complexes

    African Journals Online (AJOL)

    A geometric analysis revealed that beta-(C-H) and alpha-(C-C) can occupy the seventh and eighth coordination sites in the title Fischer carbene complexes as agostic interactions, which allows classifying the carbene as a η3 ligand in these cases. This theory was supported by the relative energies of the conformers and an ...

  13. Application of «Sensor signal analysis network» complex for distributed, time synchronized analysis of electromagnetic radiation

    Science.gov (United States)

    Mochalov, Vladimir; Mochalova, Anastasia

    2017-10-01

    The paper considers a developing software-hardware complex «Sensor signal analysis network» for distributed and time synchronized analysis of electromagnetic radiations. The areas of application and the main features of the complex are described. An example of application of the complex to monitor natural electromagnetic radiation sources is considered based on the data recorded in VLF range. A generalized functional scheme of stream analysis of signals by a complex functional node is suggested and its application for stream detection of atmospherics, whistlers and tweaks is considered.

  14. Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

    Science.gov (United States)

    Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

    2016-04-26

    The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

  15. Music analysis and Kolmogorov complexity

    DEFF Research Database (Denmark)

    Meredith, David

    The goal of music analysis is to find the most satisfying explanations for musical works. It is proposed that this can best be achieved by attempting to write computer programs that are as short as possible and that generate representations that are as detailed as possible of the music...... that the program represents. If such an effective measure of analysis quality can be found, it could be used in a system that automatically finds the optimal analysis for any passage of music. Measuring program length in terms of number of source-code characters is shown to be problematic and an expression...... is proposed that overcomes some but not all of these problems. It is suggested that the solutions to the remaining problems may lie either in the field of concrete Kolmogorov complexity or in the design of languages specialized for expressing musical structure....

  16. Correlation analysis of the Taurus molecular cloud complex

    International Nuclear Information System (INIS)

    Kleiner, S.C.

    1985-01-01

    Autocorrelation and power spectrum methods were applied to the analysis of the density and velocity structure of the Taurus Complex and Heiles Cloud 2 as traced out by 13 CO J = 1 → 0 molecular line observations obtained with the 14m antenna of the Five College Radio Astronomy Observatory. Statistically significant correlations in the spacing of density fluctuations within the Taurus Complex and Heiles 2 were uncovered. The length scales of the observed correlations correspond in magnitude to the Jeans wavelengths characterizing gravitational instabilities with (i) interstellar atomic hydrogen gas for the case of the Taurus complex, and (ii) molecular hydrogen for Heiles 2. The observed correlations may be the signatures of past and current gravitational instabilities frozen into the structure of the molecular gas. The appendices provide a comprehensive description of the analytical and numerical methods developed for the correlation analysis of molecular clouds

  17. Big and complex data analysis methodologies and applications

    CERN Document Server

    2017-01-01

    This volume conveys some of the surprises, puzzles and success stories in high-dimensional and complex data analysis and related fields. Its peer-reviewed contributions showcase recent advances in variable selection, estimation and prediction strategies for a host of useful models, as well as essential new developments in the field. The continued and rapid advancement of modern technology now allows scientists to collect data of increasingly unprecedented size and complexity. Examples include epigenomic data, genomic data, proteomic data, high-resolution image data, high-frequency financial data, functional and longitudinal data, and network data. Simultaneous variable selection and estimation is one of the key statistical problems involved in analyzing such big and complex data. The purpose of this book is to stimulate research and foster interaction between researchers in the area of high-dimensional data analysis. More concretely, its goals are to: 1) highlight and expand the breadth of existing methods in...

  18. Complex analysis with applications to flows and fields

    CERN Document Server

    Braga da Costa Campos, Luis Manuel

    2012-01-01

    Complex Analysis with Applications to Flows and Fields presents the theory of functions of a complex variable, from the complex plane to the calculus of residues to power series to conformal mapping. The book explores numerous physical and engineering applications concerning potential flows, the gravity field, electro- and magnetostatics, steady heat conduction, and other problems. It provides the mathematical results to sufficiently justify the solution of these problems, eliminating the need to consult external references.The book is conveniently divided into four parts. In each part, the ma

  19. Water Complexes of Cytochrome P450: Insights from Energy Decomposition Analysis

    Directory of Open Access Journals (Sweden)

    Hajime Hirao

    2013-06-01

    Full Text Available Water is a small molecule that nevertheless perturbs, sometimes significantly, the electronic properties of an enzyme’s active site. In this study, interactions of a water molecule with the ferric heme and the compound I (Cpd I intermediate of cytochrome P450 are studied. Energy decomposition analysis (EDA schemes are used to investigate the physical origins of these interactions. Localized molecular orbital EDA (LMOEDA implemented in the quantum chemistry software GAMESS and the EDA method implemented in the ADF quantum chemistry program are used. EDA reveals that the electrostatic and polarization effects act as the major driving force in both of these interactions. The hydrogen bonding in the Cpd I•••H2O complex is similar to that in the water dimer; however, the relative importance of the electrostatic effect is somewhat larger in the water dimer.

  20. Time irreversibility and intrinsics revealing of series with complex network approach

    Science.gov (United States)

    Xiong, Hui; Shang, Pengjian; Xia, Jianan; Wang, Jing

    2018-06-01

    In this work, we analyze time series on the basis of the visibility graph algorithm that maps the original series into a graph. By taking into account the all-round information carried by the signals, the time irreversibility and fractal behavior of series are evaluated from a complex network perspective, and considered signals are further classified from different aspects. The reliability of the proposed analysis is supported by numerical simulations on synthesized uncorrelated random noise, short-term correlated chaotic systems and long-term correlated fractal processes, and by the empirical analysis on daily closing prices of eleven worldwide stock indices. Obtained results suggest that finite size has a significant effect on the evaluation, and that there might be no direct relation between the time irreversibility and long-range correlation of series. Similarity and dissimilarity between stock indices are also indicated from respective regional and global perspectives, showing the existence of multiple features of underlying systems.

  1. β-cyclodextrin inclusion complexes containing Citrus sinensis (L.) Osbeck essential oil: An alternative to control Aedes aegypti larvae

    Energy Technology Data Exchange (ETDEWEB)

    Galvão, J.G., E-mail: julianaggalvao@gmail.com [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Silva, V.F.; Ferreira, S.G. [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); França, F.R.M. [Chemical Engineering Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Santos, D.A.; Freitas, L.S.; Alves, P.B. [Chemistry Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil); Araújo, A.A.S.; Cavalcanti, S.C.H.; Nunes, R.S. [Pharmacy Department, Federal University of Sergipe, 49100-000 São Cristóvão, SE (Brazil)

    2015-05-20

    Highlights: • Thermal analysis was useful to determine the formation of inclusion complexes by paste and co-precipitation methods. • HS/GC-FID quantitative analysis revealed that the best method of obtaining a CSEO/β-CD complex was the PWE, with the largest inclusion content [78.5%]. • The inclusion complex revealed LC{sub 50} of 23.01 ppm, close to CSEO LC{sub 50} 21.5 ppm. - Abstract: The development of β-cyclodextrin (β-CD) complexes is an interesting way for increasing the aqueous solubility of essential oils. The aim of this study was to prepare inclusion complexes of Citrus sinensis essential oil (CSEO) with β-CD using paste complexation (with and without co-solvent) and co-precipitation methods. Additionally, the physicochemical properties of the inclusion complexes using thermal analysis, X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy were evaluated. Furthermore, CSEO content (%) and solubility of complexes were measured. The biological activity against the Aedes aegypti Linn. larvae was further evaluated. For comparison purposes, a physical mixture between β-CD and CSEO was prepared and evaluated. Thermal analysis clearly indicated the formation of complexes by paste and co-precipitation methods. The headspace/gas chromatography quantitative analysis showed inclusions contents higher than 50%. On the other hand, the product revealed LC{sub 50} of 23.01 ppm, close to CSEO LC{sub 50} 21.5 ppm.

  2. β-cyclodextrin inclusion complexes containing Citrus sinensis (L.) Osbeck essential oil: An alternative to control Aedes aegypti larvae

    International Nuclear Information System (INIS)

    Galvão, J.G.; Silva, V.F.; Ferreira, S.G.; França, F.R.M.; Santos, D.A.; Freitas, L.S.; Alves, P.B.; Araújo, A.A.S.; Cavalcanti, S.C.H.; Nunes, R.S.

    2015-01-01

    Highlights: • Thermal analysis was useful to determine the formation of inclusion complexes by paste and co-precipitation methods. • HS/GC-FID quantitative analysis revealed that the best method of obtaining a CSEO/β-CD complex was the PWE, with the largest inclusion content [78.5%]. • The inclusion complex revealed LC 50 of 23.01 ppm, close to CSEO LC 50 21.5 ppm. - Abstract: The development of β-cyclodextrin (β-CD) complexes is an interesting way for increasing the aqueous solubility of essential oils. The aim of this study was to prepare inclusion complexes of Citrus sinensis essential oil (CSEO) with β-CD using paste complexation (with and without co-solvent) and co-precipitation methods. Additionally, the physicochemical properties of the inclusion complexes using thermal analysis, X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy were evaluated. Furthermore, CSEO content (%) and solubility of complexes were measured. The biological activity against the Aedes aegypti Linn. larvae was further evaluated. For comparison purposes, a physical mixture between β-CD and CSEO was prepared and evaluated. Thermal analysis clearly indicated the formation of complexes by paste and co-precipitation methods. The headspace/gas chromatography quantitative analysis showed inclusions contents higher than 50%. On the other hand, the product revealed LC 50 of 23.01 ppm, close to CSEO LC 50 21.5 ppm

  3. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

    Science.gov (United States)

    Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P; Rai, Vandna; Singh, Ashok K; Singh, Nagendra K

    2018-01-01

    Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India's huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon , and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated 'Pro-Indica,' 'Pro-Aus,' and 'Mid-Gangetic,' which showed poor correspondence with the morpho - taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the 'Pro-Indica' and 'Pro-Aus' sub-populations across agro-climatic zones, indicating a more

  4. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

    Science.gov (United States)

    Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

    2018-01-01

    Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

  5. CT-Guided Microwave Ablation of 45 Renal Tumors: Analysis of Procedure Complexity Utilizing a Percutaneous Renal Ablation Complexity Scoring System.

    Science.gov (United States)

    Mansilla, Alberto V; Bivins, Eugene E; Contreras, Francisco; Hernandez, Manuel A; Kohler, Nathan; Pepe, Julie W

    2017-02-01

    To develop a scoring system that stratifies complexity of percutaneous ablation of renal tumors. Analysis was performed of 36 consecutive patients (mean age, 64 y; range, 30-89 y) who underwent CT-guided microwave (MW) ablation of 45 renal tumors (mean tumor diameter, 2.4 cm; range, 1.2-4.0 cm). Technical success and effectiveness were determined based on intraprocedural and follow-up imaging studies. The RENAL score and the proposed percutaneous renal ablation complexity (P-RAC) score were calculated for each tumor. Technical success was 93.3% (n = 42). Biopsy of 38 of 45 renal tumors revealed 23 renal cell carcinomas. Median follow-up period was 9.7 months (range, 2.9-46.8 months). There were no tumor recurrences. One major complication, ureteropelvic junction stricture, occurred (2.6%). The P-RAC score was found to differ statistically from the RENAL score (t = 3.754, df = 44, P = .001). A positive correlation was found between the P-RAC score and number of antenna insertions (r = .378, n = 45, P = .011) and procedure duration (r = .328, n = 45, P = .028). No correlation was found between the RENAL score and number of MW antenna insertions (r = .110, n = 45, P = .472) or procedure duration (r = .263, n = 45, P = .081). Hydrodissection was significantly more common in the P-RAC high-complexity category than in low-complexity category (χ 2 = 12.073, df = 2, P = .002). The P-RAC score may be useful in stratifying percutaneous renal ablation complexity. Further studies with larger sample sizes are necessary to validate the P-RAC score and to determine if it can predict risk of complications. Copyright © 2016 SIR. Published by Elsevier Inc. All rights reserved.

  6. Pan-Cancer Mutational and Transcriptional Analysis of the Integrator Complex

    Directory of Open Access Journals (Sweden)

    Antonio Federico

    2017-04-01

    Full Text Available The integrator complex has been recently identified as a key regulator of RNA Polymerase II-mediated transcription, with many functions including the processing of small nuclear RNAs, the pause-release and elongation of polymerase during the transcription of protein coding genes, and the biogenesis of enhancer derived transcripts. Moreover, some of its components also play a role in genome maintenance. Thus, it is reasonable to hypothesize that their functional impairment or altered expression can contribute to malignancies. Indeed, several studies have described the mutations or transcriptional alteration of some Integrator genes in different cancers. Here, to draw a comprehensive pan-cancer picture of the genomic and transcriptomic alterations for the members of the complex, we reanalyzed public data from The Cancer Genome Atlas. Somatic mutations affecting Integrator subunit genes and their transcriptional profiles have been investigated in about 11,000 patients and 31 tumor types. A general heterogeneity in the mutation frequencies was observed, mostly depending on tumor type. Despite the fact that we could not establish them as cancer drivers, INTS7 and INTS8 genes were highly mutated in specific cancers. A transcriptome analysis of paired (normal and tumor samples revealed that the transcription of INTS7, INTS8, and INTS13 is significantly altered in several cancers. Experimental validation performed on primary tumors confirmed these findings.

  7. Basic complex analysis a comprehensive course in analysis, part 2a

    CERN Document Server

    Simon, Barry

    2015-01-01

    A Comprehensive Course in Analysis by Poincaré Prize winner Barry Simon is a five-volume set that can serve as a graduate-level analysis textbook with a lot of additional bonus information, including hundreds of problems and numerous notes that extend the text and provide important historical background. Depth and breadth of exposition make this set a valuable reference source for almost all areas of classical analysis. Part 2A is devoted to basic complex analysis. It interweaves three analytic threads associated with Cauchy, Riemann, and Weierstrass, respectively. Cauchy's view focuses on th

  8. Metrical and dynamical aspects in complex analysis

    CERN Document Server

    2017-01-01

    The central theme of this reference book is the metric geometry of complex analysis in several variables. Bridging a gap in the current literature, the text focuses on the fine behavior of the Kobayashi metric of complex manifolds and its relationships to dynamical systems, hyperbolicity in the sense of Gromov and operator theory, all very active areas of research. The modern points of view expressed in these notes, collected here for the first time, will be of interest to academics working in the fields of several complex variables and metric geometry. The different topics are treated coherently and include expository presentations of the relevant tools, techniques and objects, which will be particularly useful for graduate and PhD students specializing in the area.

  9. Invitation to complex analysis

    CERN Document Server

    Boas, Ralph P

    2010-01-01

    Ideal for a first course in complex analysis, this book can be used either as a classroom text or for independent study. Written at a level accessible to advanced undergraduates and beginning graduate students, the book is suitable for readers acquainted with advanced calculus or introductory real analysis. The treatment goes beyond the standard material of power series, Cauchy's theorem, residues, conformal mapping, and harmonic functions by including accessible discussions of intriguing topics that are uncommon in a book at this level. The flexibility afforded by the supplementary topics and applications makes the book adaptable either to a short, one-term course or to a comprehensive, full-year course. Detailed solutions of the exercises both serve as models for students and facilitate independent study. Supplementary exercises, not solved in the book, provide an additional teaching tool. This second edition has been painstakingly revised by the author's son, himself an award-winning mathematical expositor...

  10. Scale-free crystallization of two-dimensional complex plasmas: Domain analysis using Minkowski tensors

    Science.gov (United States)

    Böbel, A.; Knapek, C. A.; Räth, C.

    2018-05-01

    Experiments of the recrystallization processes in two-dimensional complex plasmas are analyzed to rigorously test a recently developed scale-free phase transition theory. The "fractal-domain-structure" (FDS) theory is based on the kinetic theory of Frenkel. It assumes the formation of homogeneous domains, separated by defect lines, during crystallization and a fractal relationship between domain area and boundary length. For the defect number fraction and system energy a scale-free power-law relation is predicted. The long-range scaling behavior of the bond-order correlation function shows clearly that the complex plasma phase transitions are not of the Kosterlitz, Thouless, Halperin, Nelson, and Young type. Previous preliminary results obtained by counting the number of dislocations and applying a bond-order metric for structural analysis are reproduced. These findings are supplemented by extending the use of the bond-order metric to measure the defect number fraction and furthermore applying state-of-the-art analysis methods, allowing a systematic testing of the FDS theory with unprecedented scrutiny: A morphological analysis of lattice structure is performed via Minkowski tensor methods. Minkowski tensors form a complete family of additive, motion covariant and continuous morphological measures that are sensitive to nonlinear properties. The FDS theory is rigorously confirmed and predictions of the theory are reproduced extremely well. The predicted scale-free power-law relation between defect fraction number and system energy is verified for one more order of magnitude at high energies compared to the inherently discontinuous bond-order metric. It is found that the fractal relation between crystalline domain area and circumference is independent of the experiment, the particular Minkowski tensor method, and the particular choice of parameters. Thus, the fractal relationship seems to be inherent to two-dimensional phase transitions in complex plasmas. Minkowski

  11. Host-guest complex of N-(2-chloroethyl), N-nitroso, N‧, N‧ -dicyclohexylsulfamid with β-cyclodextrin: Fluorescence, QTAIM analysis and structure-chemical reactivity

    Science.gov (United States)

    Bensouilah, Nadjia; Fisli, Hassina; Bensouilah, Hamza; Zaater, Sihem; Abdaoui, Mohamed; Boutemeur-Kheddis, Baya

    2017-10-01

    In this work, the inclusion complex of DCY/CENS: N-(2-chloroethyl), N-nitroso, N‧, N‧-dicyclohexylsulfamid and β-cyclodextrin (β-CD) is investigated using the fluorescence spectroscopy, PM3, ONIOM2 and DFT methods. The experimental part reveals that DCY/CENS forms a 1:1 stoichiometric ratio inclusion complex with β-CD. The constant of stability is evaluated using the Benesi-Hildebrand equation. The results of the theoretical optimization showed that the lipophilic fraction of molecule (cyclohexyl group) is inside of β-CD. Accordingly, the Nitroso-Chloroethyl moiety is situated outside the cavity of the macromolecule host. The favorable structure of the optimized complex indicates the existence of weak intermolecular hydrogen bonds and the most important van der Waals (vdW) interactions which are studied on the basis of Natural Bonding Orbital (NBO) analysis. The NBO is employed to compute the electronic donor-acceptor exchanges between drug and β-CD. Furthermore, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), has been accomplished on the most favorable complex using B3LYP/6-31G(d) method. The presence of stabilizing intermolecular hydrogen bonds and van der Waals interactions in the most favorable complex is predicted. Also, the energies of these interactions are estimated with Espinosa's formula. The findings of this investigation reveal that the correlation between the structural parameters and the electronic density is good. Finally, and based on DFT calculations, the reactivity of the interesting molecule in free state was studied and compared with that in the complexed state using chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors.

  12. Camelid genomes reveal evolution and adaptation to desert environments.

    Science.gov (United States)

    Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

    2014-10-21

    Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

  13. Analysis and design of complex impedance transforming marchand baluns

    DEFF Research Database (Denmark)

    Michaelsen, Rasmus Schandorph; Johansen, Tom Keinicke; Tamborg, Kjeld M.

    2014-01-01

    A new type of Marchand balun is presented in this paper, which has the property of complex impedance transformation. To allow the Marchand balun to transform between arbitrary complex impedances, three reactances should be added to the circuit. A detailed analysis of the circuit gives the governing...

  14. Multifractal analysis of forest fires in complex regions

    Science.gov (United States)

    Vega Orozco, C. D.; Kanevski, M.; Golay, J.; Tonini, M.; Conedera, M.

    2012-04-01

    Forest fires can be studied as point processes where the ignition points represent the set of locations of the observed events in a defined study region. Their spatial and temporal patterns can be characterized by their fractal properties; which quantify the global aspect of the geometry of the support data. However, a monofractal dimension can not completely describe the pattern structure and related scaling properties. Enhancements in fractal theory had developed the multifractal concept which describes the measures from which interlinked fractal sets can be retrieved and characterized by their fractal dimension and singularity strength [1, 2]. The spatial variability of forest fires is conditioned by an intermixture of human, topographic, meteorological and vegetation factors. This heterogeneity makes fire patterns complex scale-invariant processes difficult to be depicted by a single scale. Therefore, this study proposes an exploratory data analysis through a multifractal formalism to characterize and quantify the multiscaling behaviour of the spatial distribution pattern of this phenomenon in a complex region like the Swiss Alps. The studied dataset is represented by 2,401 georeferenced forest fire ignition points in canton Ticino, Switzerland, in a 40-years period from 1969 to 2008. Three multifractal analyses are performed: one assesses the multiscaling behaviour of fire occurrence probability of the support data (raw data) and four random patterns simulated within three different support domains; second analysis studies the multifractal behavior of patterns from anthropogenic and natural ignited fires (arson-, accident- and lightning-caused fires); and third analysis aims at detecting scale-dependency of the size of burned area. To calculate the generalized dimensions, Dq, a generalization of the box counting methods is carried out based on the generalization of Rényi information of the qth order moment of the probability distribution. For q > 0, Dq

  15. Molecular Epidemiology Reveals Genetic Diversity amongst Isolates of the Cryptococcus neoformans/C. gattii Species Complex in Thailand

    Science.gov (United States)

    Kaocharoen, Sirada; Ngamskulrungroj, Popchai; Firacative, Carolina; Trilles, Luciana; Piyabongkarn, Dumrongdej; Banlunara, Wijit; Poonwan, Natteewan; Chaiprasert, Angkana; Meyer, Wieland; Chindamporn, Ariya

    2013-01-01

    To gain a more detailed picture of cryptococcosis in Thailand, a retrospective study of 498 C. neoformans and C. gattii isolates has been conducted. Among these, 386, 83 and 29 strains were from clinical, environmental and veterinary sources, respectively. A total of 485 C. neoformans and 13 C. gattii strains were studied. The majority of the strains (68.9%) were isolated from males (mean age of 37.97 years), 88.5% of C. neoformans and only 37.5% of C. gattii strains were from HIV patients. URA5-RFLP and/or M13 PCR-fingerprinting analysis revealed that the majority of the isolates were C. neoformans molecular type VNI regardless of their sources (94.8%; 94.6% of the clinical, 98.8% of the environmental and 86.2% of the veterinary isolates). In addition, the molecular types VNII (2.4%; 66.7% of the clinical and 33.3% of the veterinary isolates), VNIV (0.2%; 100% environmental isolate), VGI (0.2%; 100% clinical isolate) and VGII (2.4%; 100% clinical isolates) were found less frequently. Multilocus Sequence Type (MLST) analysis using the ISHAM consensus MLST scheme for the C. neoformans/C. gattii species complex identified a total of 20 sequence types (ST) in Thailand combining current and previous data. The Thai isolates are an integrated part of the global cryptococcal population genetic structure, with ST30 for C. gattii and ST82, ST83, ST137, ST141, ST172 and ST173 for C. neoformans being unique to Thailand. Most of the C. gattii isolates were ST7 = VGIIb, which is identical to the less virulent minor Vancouver island outbreak genotype, indicating Thailand as a stepping stone in the global spread of this outbreak strain. The current study revealed a greater genetic diversity and a wider range of major molecular types being present amongst Thai cryptococcal isolates than previously reported. PMID:23861989

  16. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    The importance of data analysis in quantitative assessment of natural resources remains significant in the sustainable management of complex tropical forest resources. Analyses of data from complex tropical forest stands have not been easy or clear due to improper data management. It is pivotal to practical researches ...

  17. Association genetics and transcriptome analysis reveal a gibberellin-responsive pathway involved in regulating photosynthesis.

    Science.gov (United States)

    Xie, Jianbo; Tian, Jiaxing; Du, Qingzhang; Chen, Jinhui; Li, Ying; Yang, Xiaohui; Li, Bailian; Zhang, Deqiang

    2016-05-01

    Gibberellins (GAs) regulate a wide range of important processes in plant growth and development, including photosynthesis. However, the mechanism by which GAs regulate photosynthesis remains to be understood. Here, we used multi-gene association to investigate the effect of genes in the GA-responsive pathway, as constructed by RNA sequencing, on photosynthesis, growth, and wood property traits, in a population of 435 Populus tomentosa By analyzing changes in the transcriptome following GA treatment, we identified many key photosynthetic genes, in agreement with the observed increase in measurements of photosynthesis. Regulatory motif enrichment analysis revealed that 37 differentially expressed genes related to photosynthesis shared two essential GA-related cis-regulatory elements, the GA response element and the pyrimidine box. Thus, we constructed a GA-responsive pathway consisting of 47 genes involved in regulating photosynthesis, including GID1, RGA, GID2, MYBGa, and 37 photosynthetic differentially expressed genes. Single nucleotide polymorphism (SNP)-based association analysis showed that 142 SNPs, representing 40 candidate genes in this pathway, were significantly associated with photosynthesis, growth, and wood property traits. Epistasis analysis uncovered interactions between 310 SNP-SNP pairs from 37 genes in this pathway, revealing possible genetic interactions. Moreover, a structural gene-gene matrix based on a time-course of transcript abundances provided a better understanding of the multi-gene pathway affecting photosynthesis. The results imply a functional role for these genes in mediating photosynthesis, growth, and wood properties, demonstrating the potential of combining transcriptome-based regulatory pathway construction and genetic association approaches to detect the complex genetic networks underlying quantitative traits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights

  18. Global terrestrial water storage connectivity revealed using complex climate network analyses

    Science.gov (United States)

    Sun, A. Y.; Chen, J.; Donges, J.

    2015-07-01

    Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

  19. Structural Analysis of Complex Networks

    CERN Document Server

    Dehmer, Matthias

    2011-01-01

    Filling a gap in literature, this self-contained book presents theoretical and application-oriented results that allow for a structural exploration of complex networks. The work focuses not only on classical graph-theoretic methods, but also demonstrates the usefulness of structural graph theory as a tool for solving interdisciplinary problems. Applications to biology, chemistry, linguistics, and data analysis are emphasized. The book is suitable for a broad, interdisciplinary readership of researchers, practitioners, and graduate students in discrete mathematics, statistics, computer science,

  20. Outlier-resilient complexity analysis of heartbeat dynamics

    Science.gov (United States)

    Lo, Men-Tzung; Chang, Yi-Chung; Lin, Chen; Young, Hsu-Wen Vincent; Lin, Yen-Hung; Ho, Yi-Lwun; Peng, Chung-Kang; Hu, Kun

    2015-03-01

    Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals with outliers remains a major barrier for translating this novel concept of nonlinear dynamic theory to clinical practice. Here we propose a new approach to estimate the complexity in a signal by analyzing the irregularity of the sign time series of its coarse-grained time series at different time scales. Using surrogate data, we show that the method can reliably assess the complexity in noisy data while being highly resilient to outliers. We further apply this method to the analysis of human heartbeat recordings. Without removing any outliers due to ectopic beats, the method is able to detect a degradation of cardiac control in patients with congestive heart failure and a more degradation in critically ill patients whose life continuation relies on extracorporeal membrane oxygenator (ECMO). Moreover, the derived complexity measures can predict the mortality of ECMO patients. These results indicate that the proposed method may serve as a promising tool for monitoring cardiac function of patients in clinical settings.

  1. Symmetry analysis in parametrisation of complex systems

    International Nuclear Information System (INIS)

    Sikora, W; Malinowski, J

    2010-01-01

    The symmetry analysis method based on the theory of group representations is used for description of complex systems and their behavior in this work. The first trial of using the symmetry analysis in modeling of behavior of complex social system is presented. The evacuation of large building scenarios are discussed as transition from chaotic to ordered states, described as movements of individuals according to fields of displacements, calculated correspondingly to given scenario. The symmetry of the evacuation space is taken into account in calculation of displacements field - the displacements related to every point of this space are presented in the coordinate frame in the best way adapted to given symmetry space group, which is the set of basic vectors of irreducible representation of given symmetry group. The results got with using the symmetry consideration are compared with corresponding results calculated under assumption of shortest way to exits (Voronoi assumption).

  2. Symmetry analysis in parametrisation of complex systems

    Energy Technology Data Exchange (ETDEWEB)

    Sikora, W; Malinowski, J, E-mail: sikora@novell.ftj.agh.edu.p [Faculty of Physics and Applied Computer Science, AGH - University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow (Poland)

    2010-03-01

    The symmetry analysis method based on the theory of group representations is used for description of complex systems and their behavior in this work. The first trial of using the symmetry analysis in modeling of behavior of complex social system is presented. The evacuation of large building scenarios are discussed as transition from chaotic to ordered states, described as movements of individuals according to fields of displacements, calculated correspondingly to given scenario. The symmetry of the evacuation space is taken into account in calculation of displacements field - the displacements related to every point of this space are presented in the coordinate frame in the best way adapted to given symmetry space group, which is the set of basic vectors of irreducible representation of given symmetry group. The results got with using the symmetry consideration are compared with corresponding results calculated under assumption of shortest way to exits (Voronoi assumption).

  3. Advanced complex analysis a comprehensive course in analysis, part 2b

    CERN Document Server

    Simon, Barry

    2015-01-01

    A Comprehensive Course in Analysis by Poincaré Prize winner Barry Simon is a five-volume set that can serve as a graduate-level analysis textbook with a lot of additional bonus information, including hundreds of problems and numerous notes that extend the text and provide important historical background. Depth and breadth of exposition make this set a valuable reference source for almost all areas of classical analysis. Part 2B provides a comprehensive look at a number of subjects of complex analysis not included in Part 2A. Presented in this volume are the theory of conformal metrics (includ

  4. Structural characterization and Hirshfeld surface analysis of a CoII complex with imidazo[1,2-a]pyridine

    Directory of Open Access Journals (Sweden)

    Saikat Kumar Seth

    2018-05-01

    Full Text Available A new mononuclear tetrahedral CoII complex, dichloridobis(imidazo[1,2-a]pyridine-κN1cobalt(II, [CoCl2(C7H6N22], has been synthesized using a bioactive imidazopyridine ligand. X-ray crystallography reveals that the solid-state structure of the title complex exhibits both C—H...Cl and π–π stacking interactions in building supramolecular assemblies. Indeed, the molecules are linked by C—H...Cl interactions into a two-dimensional framework, with finite zero-dimensional dimeric units as building blocks, whereas π–π stacking plays a crucial role in building a supramolecular layered network. An exhaustive investigation of the diverse intermolecular interactions via Hirshfeld surface analysis enables contributions to the crystal packing of the title complex to be quantified. The fingerprint plots associated with the Hirshfeld surface clearly display each significant interaction involved in the structure, by quantifying them in an effective visual manner.

  5. Principles of assembly reveal a periodic table of protein complexes.

    Science.gov (United States)

    Ahnert, Sebastian E; Marsh, Joseph A; Hernández, Helena; Robinson, Carol V; Teichmann, Sarah A

    2015-12-11

    Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering. Copyright © 2015, American Association for the Advancement of Science.

  6. Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation

    Directory of Open Access Journals (Sweden)

    Marangoni Sérgio

    2009-04-01

    Full Text Available Abstract Background Schizophrenia is likely to be a consequence of DNA alterations that, together with environmental factors, will lead to protein expression differences and the ultimate establishment of the illness. The superior temporal gyrus is implicated in schizophrenia and executes functions such as the processing of speech, language skills and sound processing. Methods We performed an individual comparative proteome analysis using two-dimensional gel electrophoresis of 9 schizophrenia and 6 healthy control patients' left posterior superior temporal gyrus (Wernicke's area – BA22p identifying by mass spectrometry several protein expression alterations that could be related to the disease. Results Our analysis revealed 11 downregulated and 14 upregulated proteins, most of them related to energy metabolism. Whereas many of the identified proteins have been previously implicated in schizophrenia, such as fructose-bisphosphate aldolase C, creatine kinase and neuron-specific enolase, new putative disease markers were also identified such as dihydrolipoyl dehydrogenase, tropomyosin 3, breast cancer metastasis-suppressor 1, heterogeneous nuclear ribonucleoproteins C1/C2 and phosphate carrier protein, mitochondrial precursor. Besides, the differential expression of peroxiredoxin 6 (PRDX6 and glial fibrillary acidic protein (GFAP were confirmed by western blot in schizophrenia prefrontal cortex. Conclusion Our data supports a dysregulation of energy metabolism in schizophrenia as well as suggests new markers that may contribute to a better understanding of this complex disease.

  7. Spectral simplicity of apparent complexity. II. Exact complexities and complexity spectra

    Science.gov (United States)

    Riechers, Paul M.; Crutchfield, James P.

    2018-03-01

    The meromorphic functional calculus developed in Part I overcomes the nondiagonalizability of linear operators that arises often in the temporal evolution of complex systems and is generic to the metadynamics of predicting their behavior. Using the resulting spectral decomposition, we derive closed-form expressions for correlation functions, finite-length Shannon entropy-rate approximates, asymptotic entropy rate, excess entropy, transient information, transient and asymptotic state uncertainties, and synchronization information of stochastic processes generated by finite-state hidden Markov models. This introduces analytical tractability to investigating information processing in discrete-event stochastic processes, symbolic dynamics, and chaotic dynamical systems. Comparisons reveal mathematical similarities between complexity measures originally thought to capture distinct informational and computational properties. We also introduce a new kind of spectral analysis via coronal spectrograms and the frequency-dependent spectra of past-future mutual information. We analyze a number of examples to illustrate the methods, emphasizing processes with multivariate dependencies beyond pairwise correlation. This includes spectral decomposition calculations for one representative example in full detail.

  8. International Conference on Finite or Infinite Dimensional Complex Analysis and Applications

    CERN Document Server

    Tutschke, W; Yang, C

    2004-01-01

    There is almost no field in Mathematics which does not use Mathe­ matical Analysis. Computer methods in Applied Mathematics, too, are often based on statements and procedures of Mathematical Analysis. An important part of Mathematical Analysis is Complex Analysis because it has many applications in various branches of Mathematics. Since the field of Complex Analysis and its applications is a focal point in the Vietnamese research programme, the Hanoi University of Technology organized an International Conference on Finite or Infinite Dimensional Complex Analysis and Applications which took place in Hanoi from August 8 - 12, 2001. This conference th was the 9 one in a series of conferences which take place alternately in China, Japan, Korea and Vietnam each year. The first one took place th at Pusan University in Korea in 1993. The preceding 8 conference was th held in Shandong in China in August 2000. The 9 conference of the was the first one which took place above mentioned series of conferences in Vietnam....

  9. Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

    Science.gov (United States)

    Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

    2014-01-01

    The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

  10. Analysis of the High-Frequency Content in Human QRS Complexes by the Continuous Wavelet Transform: An Automatized Analysis for the Prediction of Sudden Cardiac Death.

    Science.gov (United States)

    García Iglesias, Daniel; Roqueñi Gutiérrez, Nieves; De Cos, Francisco Javier; Calvo, David

    2018-02-12

    Fragmentation and delayed potentials in the QRS signal of patients have been postulated as risk markers for Sudden Cardiac Death (SCD). The analysis of the high-frequency spectral content may be useful for quantification. Forty-two consecutive patients with prior history of SCD or malignant arrhythmias (patients) where compared with 120 healthy individuals (controls). The QRS complexes were extracted with a modified Pan-Tompkins algorithm and processed with the Continuous Wavelet Transform to analyze the high-frequency content (85-130 Hz). Overall, the power of the high-frequency content was higher in patients compared with controls (170.9 vs. 47.3 10³nV²Hz -1 ; p = 0.007), with a prolonged time to reach the maximal power (68.9 vs. 64.8 ms; p = 0.002). An analysis of the signal intensity (instantaneous average of cumulative power), revealed a distinct function between patients and controls. The total intensity was higher in patients compared with controls (137.1 vs. 39 10³nV²Hz -1 s -1 ; p = 0.001) and the time to reach the maximal intensity was also prolonged (88.7 vs. 82.1 ms; p content of the QRS complexes was distinct between patients at risk of SCD and healthy controls. The wavelet transform is an efficient tool for spectral analysis of the QRS complexes that may contribute to stratification of risk.

  11. Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; Treur, J.

    2005-01-01

    This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

  12. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification.

    Science.gov (United States)

    Jones, Christopher M; Stres, Blaz; Rosenquist, Magnus; Hallin, Sara

    2008-09-01

    Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene

  13. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

    Science.gov (United States)

    Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J; Abdo, Zaid

    2018-01-01

    The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future

  14. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

    Directory of Open Access Journals (Sweden)

    Noelle Noyes

    Full Text Available The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV. While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae, the Nugent score (a BV diagnostic and vaginal pH (a risk symptom of BV. Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly

  15. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis

    Science.gov (United States)

    Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J.

    2018-01-01

    The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future

  16. Single molecule analysis of c-myb alternative splicing reveals novel classifiers for precursor B-ALL.

    Directory of Open Access Journals (Sweden)

    Ye E Zhou

    Full Text Available The c-Myb transcription factor, a key regulator of proliferation and differentiation in hematopoietic and other cell types, has an N-terminal DNA binding domain and a large C-terminal domain responsible for transcriptional activation, negative regulation and determining target gene specificity. Overexpression and rearrangement of the c-myb gene (MYB has been reported in some patients with leukemias and other types of cancers, implicating activated alleles of c-myb in the development of human tumors. Alternative RNA splicing can produce variants of c-myb with qualitatively distinct transcriptional activities that may be involved in transformation and leukemogenesis. Here, by performing a detailed, single molecule assay we found that c-myb alternative RNA splicing was elevated and much more complex in leukemia samples than in cell lines or CD34+ hematopoietic progenitor cells from normal donors. The results revealed that leukemia samples express more than 60 different c-myb splice variants, most of which have multiple alternative splicing events and were not detectable by conventional microarray or PCR approaches. For example, the single molecule assay detected 21 and 22 splice variants containing the 9B and 9S exons, respectively, most of which encoded unexpected variant forms of c-Myb protein. Furthermore, the detailed analysis identified some splice variants whose expression correlated with poor survival in a small cohort of precursor B-ALL samples. Our findings indicate that single molecule assays can reveal complexities in c-myb alternative splicing that have potential as novel biomarkers and could help explain the role of c-Myb variants in the development of human leukemia.

  17. An equipment complex for instrumental elementary analysis

    International Nuclear Information System (INIS)

    Borisov, G.I.; Komkov, M.M.; Kuz'michev, V.A.; Leonov, V.F.; Tarasov, Y.F.

    1986-01-01

    The competitiveness of elementary analysis on a research reactor depends, in many respects, on the provision of equipment which would permit the realization of the advantages of the analytical method. This paper describes the IR-8 reactor at the I.V. Kurchatov Institute of Atomic energy. In the design of the complex considerable attention was focused on automation and the radiation safety of the operations, which is of particular importance in the light of the large volumes of analysis

  18. Simple, complex and hyper-complex understanding - enhanced sensitivity in observation of information

    DEFF Research Database (Denmark)

    Bering Keiding, Tina

    for construction and analysis of empirical information. A quick overview on empirical research drawing on Luhmann reveals a diverse complex of analytical strategies and empirical methods. Despite differences between strategies and methods they have in common that understanding of uttered information is crucial...... in their production of empirically founded knowledge. However research generally seems to pay more attention to production of uttered information than to selection of understanding. The aim of this contribution is to sketch out a suggestion to how selection of understanding can be systematized in order to produce...... enhanced transparency in selection of understanding as well as enhanced sensitivity and definition in dept. The contribution suggest that we distinguish between three types of understanding; simple, complex and hyper-complex understanding. Simple understanding is the simultaneous selection of understanding...

  19. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  20. Cyclodextrin inclusion complexes with thiocholesterol and their self-assembly on gold: A combined electrochemical and lateral force microscopy analysis

    International Nuclear Information System (INIS)

    Pandey, Rakesh K.; Lakshminarayanan, V.

    2014-01-01

    The present study is an attempt to understand the properties of an interesting self-assembled monolayer system composed of inclusion complexes of thiocholesterol and cyclodextrins. Cyclodextrins were used as host compound while thiocholesterol was used as the entrant molecule into the cavity of cyclodextrins. The improved electron transfer barrier property towards a redox couple indicates a sturdy inclusion complex monolayer. A very large R ct value, 64.6 kΩ·cm 2 for a redox system was obtained in the case of methyl-β-cyclodextrin and thiocholesterol inclusion complex self-assembled monolayer. A rather low value of capacitance 1.2 μF cm −2 measured in supporting electrolyte further signifies the fact that inclusion complex monolayer is quite impermeable for ionic species. In addition lateral force microscopy combined with force–distance analysis revealed the presence of an interesting mixed hydrophilic/hydrophobic surface. - Highlights: • Self-assembled monolayer of inclusion complexes on gold surface • Lateral force microscopy study of the regions of varying hydrophilicities • Could find applications in patterning surfaces to be hydrophilic/hydrophobic • Improved electron transfer barrier properties

  1. Elementary real and complex analysis

    CERN Document Server

    Shilov, Georgi E

    1996-01-01

    In this book the renowned Russian mathematician Georgi E. Shilov brings his unique perspective to real and complex analysis, an area of perennial interest in mathematics. Although there are many books available on the topic, the present work is specially designed for undergraduates in mathematics, science and engineering. A high level of mathematical sophistication is not required.The book begins with a systematic study of real numbers, understood to be a set of objects satisfying certain definite axioms. The concepts of a mathematical structure and an isomorphism are introduced in Chapter 2,

  2. Diethylenetriamine/diamines/copper (II complexes [Cu(dien(NN]Br2: Synthesis, solvatochromism, thermal, electrochemistry, single crystal, Hirshfeld surface analysis and antibacterial activity

    Directory of Open Access Journals (Sweden)

    Fatima Abu Saleemh

    2017-09-01

    Full Text Available Two dicationic water soluble mixed triamine/diamine copper (II complexes, of general formula [Cu(dienNN]Br2 (1–2 [dien = diethelenetriamine and NN is en = ethylenediamine or Me4en = N,N′,N,N′-tetramethylethylenediamine] were prepared under ultrasonic mode with a relatively high yield. These complexes were characterized by elemental microanalysis, UV visible IR spectroscopy, and thermal and electrochemical techniques. In addition, complex 2 structure was solved by X-ray single crystal and Hirshfeld surface analysis. The complex exhibits a distorted square pyramidal coordination environment around Cu(II centre. The solvatochromism of the desired complexes was investigated in water and other suitable organic solvents. The results show that the Guttmann’s DN parameter values of the solvents have mainly contributed to the shift of the d–d absorption band towards the linear increase in the wavelength of the absorption maxima of the complexes. The complex 1 showed higher antibacterial activity against the studied microorganisms compared to complex 2. Both complexes revealed promising antibacterial activities.

  3. Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis

    Science.gov (United States)

    Li, Yuanyuan; Jin, Suoqin; Lei, Lei; Pan, Zishu; Zou, Xiufen

    2015-03-01

    The early diagnosis and investigation of the pathogenic mechanisms of complex diseases are the most challenging problems in the fields of biology and medicine. Network-based systems biology is an important technique for the study of complex diseases. The present study constructed dynamic protein-protein interaction (PPI) networks to identify dynamical network biomarkers (DNBs) and analyze the underlying mechanisms of complex diseases from a systems level. We developed a model-based framework for the construction of a series of time-sequenced networks by integrating high-throughput gene expression data into PPI data. By combining the dynamic networks and molecular modules, we identified significant DNBs for four complex diseases, including influenza caused by either H3N2 or H1N1, acute lung injury and type 2 diabetes mellitus, which can serve as warning signals for disease deterioration. Function and pathway analyses revealed that the identified DNBs were significantly enriched during key events in early disease development. Correlation and information flow analyses revealed that DNBs effectively discriminated between different disease processes and that dysfunctional regulation and disproportional information flow may contribute to the increased disease severity. This study provides a general paradigm for revealing the deterioration mechanisms of complex diseases and offers new insights into their early diagnoses.

  4. Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.

    Science.gov (United States)

    Staats, Charley Christian; Junges, Angela; Guedes, Rafael Lucas Muniz; Thompson, Claudia Elizabeth; de Morais, Guilherme Loss; Boldo, Juliano Tomazzoni; de Almeida, Luiz Gonzaga Paula; Andreis, Fábio Carrer; Gerber, Alexandra Lehmkuhl; Sbaraini, Nicolau; da Paixão, Rana Louise de Andrade; Broetto, Leonardo; Landell, Melissa; Santi, Lucélia; Beys-da-Silva, Walter Orlando; Silveira, Carolina Pereira; Serrano, Thaiane Rispoli; de Oliveira, Eder Silva; Kmetzsch, Lívia; Vainstein, Marilene Henning; de Vasconcelos, Ana Tereza Ribeiro; Schrank, Augusto

    2014-09-29

    Metarhizium anisopliae is an entomopathogenic fungus used in the biological control of some agricultural insect pests, and efforts are underway to use this fungus in the control of insect-borne human diseases. A large repertoire of proteins must be secreted by M. anisopliae to cope with the various available nutrients as this fungus switches through different lifestyles, i.e., from a saprophytic, to an infectious, to a plant endophytic stage. To further evaluate the predicted secretome of M. anisopliae, we employed genomic and transcriptomic analyses, coupled with phylogenomic analysis, focusing on the identification and characterization of secreted proteins. We determined the M. anisopliae E6 genome sequence and compared this sequence to other entomopathogenic fungi genomes. A robust pipeline was generated to evaluate the predicted secretomes of M. anisopliae and 15 other filamentous fungi, leading to the identification of a core of secreted proteins. Transcriptomic analysis using the tick Rhipicephalus microplus cuticle as an infection model during two periods of infection (48 and 144 h) allowed the identification of several differentially expressed genes. This analysis concluded that a large proportion of the predicted secretome coding genes contained altered transcript levels in the conditions analyzed in this study. In addition, some specific secreted proteins from Metarhizium have an evolutionary history similar to orthologs found in Beauveria/Cordyceps. This similarity suggests that a set of secreted proteins has evolved to participate in entomopathogenicity. The data presented represents an important step to the characterization of the role of secreted proteins in the virulence and pathogenicity of M. anisopliae.

  5. Complexity analysis based on generalized deviation for financial markets

    Science.gov (United States)

    Li, Chao; Shang, Pengjian

    2018-03-01

    In this paper, a new modified method is proposed as a measure to investigate the correlation between past price and future volatility for financial time series, known as the complexity analysis based on generalized deviation. In comparison with the former retarded volatility model, the new approach is both simple and computationally efficient. The method based on the generalized deviation function presents us an exhaustive way showing the quantization of the financial market rules. Robustness of this method is verified by numerical experiments with both artificial and financial time series. Results show that the generalized deviation complexity analysis method not only identifies the volatility of financial time series, but provides a comprehensive way distinguishing the different characteristics between stock indices and individual stocks. Exponential functions can be used to successfully fit the volatility curves and quantify the changes of complexity for stock market data. Then we study the influence for negative domain of deviation coefficient and differences during the volatile periods and calm periods. after the data analysis of the experimental model, we found that the generalized deviation model has definite advantages in exploring the relationship between the historical returns and future volatility.

  6. High-resolution crystal structure of Streptococcus pyogenes β-NAD+ glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    International Nuclear Information System (INIS)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin; Kim, Hyoun Sook; Lee, Sang Jae; Im, Ha Na; Jang, Jun Young; Suh, Se Won

    2013-01-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD + glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD + glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN ct –IFS complex, which consists of the SPN C-terminal domain (SPN ct ; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN ct and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope

  7. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  8. Myocardial ischemia analysis based on electrocardiogram QRS complex

    International Nuclear Information System (INIS)

    Song, J.; Yan, H.; Xu, Z.; Yu, X.; Zhu, R.

    2011-01-01

    Full text: Electrocardiogram (ECG) is an economic, convenient, and non-invasive detecting tool in myocardial ischemia (MI), and its clinical appearance is mainly exhibited by the changes in ST-T complex. Recently, QRS complex characters were proposed to analyze MI by more and more researchers. In this paper, various QRS complex characters were extracted in ECG signals, and their relationship was analyzed systematically. As a result, these characters were divided into two groups, and there existed good relationship among them for each group, while the poor relationship between the groups. Then these QRS complex characters were applied for statistical analysis on MI, and five characters had significant differences after ECG recording verification, which were: QRS upward and downward slopes, transient heart rate, angle R and angle Q. On the other hand, these QRS complex characters were analyzed in frequency domain. Experimental results showed that the frequency features of RR interval series (Heart Rate Variability, HRV), and QRS barycenter sequence had signjficant differences between MI states and normal states. Moreover, QRS barycenter sequence performed better. (author)

  9. Exploring the Anti-Burkholderia cepacia Complex Activity of Essential Oils: A Preliminary Analysis

    Directory of Open Access Journals (Sweden)

    Isabel Maida

    2014-01-01

    Full Text Available In this work we have checked the ability of the essential oils extracted from six different medicinal plants (Eugenia caryophyllata, Origanum vulgare, Rosmarinus officinalis, Lavandula officinalis, Melaleuca alternifolia, and Thymus vulgaris to inhibit the growth of 18 bacterial type strains belonging to the 18 known species of the Burkholderia cepacia complex (Bcc. These bacteria are opportunistic human pathogens that can cause severe infection in immunocompromised patients, especially those affected by cystic fibrosis (CF, and are often resistant to multiple antibiotics. The analysis of the aromatograms produced by the six oils revealed that, in spite of their different chemical composition, all of them were able to contrast the growth of Bcc members. However, three of them (i.e., Eugenia caryophyllata, Origanum vulgare, and Thymus vulgaris were particularly active versus the Bcc strains, including those exhibiting a high degree or resistance to ciprofloxacin, one of the most used antibiotics to treat Bcc infections. These three oils are also active toward both environmental and clinical strains (isolated from CF patients, suggesting that they might be used in the future to fight B. cepacia complex infections.

  10. Complex analysis and geometry

    CERN Document Server

    Silva, Alessandro

    1993-01-01

    The papers in this wide-ranging collection report on the results of investigations from a number of linked disciplines, including complex algebraic geometry, complex analytic geometry of manifolds and spaces, and complex differential geometry.

  11. Fire hazard analysis for Plutonium Finishing Plant complex

    International Nuclear Information System (INIS)

    MCKINNIS, D.L.

    1999-01-01

    A fire hazards analysis (FHA) was performed for the Plutonium Finishing Plant (PFP) Complex at the Department of Energy (DOE) Hanford site. The scope of the FHA focuses on the nuclear facilities/structures in the Complex. The analysis was conducted in accordance with RLID 5480.7, [DOE Directive RLID 5480.7, 1/17/94] and DOE Order 5480.7A, ''Fire Protection'' [DOE Order 5480.7A, 2/17/93] and addresses each of the sixteen principle elements outlined in paragraph 9.a(3) of the Order. The elements are addressed in terms of the fire protection objectives stated in paragraph 4 of DOE 5480.7A. In addition, the FHA also complies with WHC-CM-4-41, Fire Protection Program Manual, Section 3.4 [1994] and WHC-SD-GN-FHA-30001, Rev. 0 [WHC, 1994]. Objectives of the FHA are to determine: (1) the fire hazards that expose the PFP facilities, or that are inherent in the building operations, (2) the adequacy of the fire safety features currently located in the PFP Complex, and (3) the degree of compliance of the facility with specific fire safety provisions in DOE orders, related engineering codes, and standards

  12. New heteroleptic Zn(II) complexes of thiosemicarbazone and diimine Co-Ligands: Structural analysis and their biological impacts

    Science.gov (United States)

    Mathan Kumar, Shanmugaiah; Kesavan, Mookkandi Palsamy; Vinoth Kumar, Gujuluva Gangatharan; Sankarganesh, Murugesan; Chakkaravarthi, Ganesan; Rajagopal, Gurusamy; Rajesh, Jegathalaprathaban

    2018-02-01

    A thiosemicarbazone ligand HL appended new Zn(II) complexes [Zn(L)(bpy)] (1) and [Zn(L)(phen)] (2) (where, HL = {2-(3-bromo-5-chloro-2-hydroxybenzylidene)-N-phenylhydrazinecarbothioamide}, bpy = 2, 2‧-bipyridine and phen = 1, 10-phenanthroline) have been synthesized and well characterized using conventional spectroscopic techniques viz.,1H NMR, FTIR and UV-Vis spectra. The crystal structures of complexes 1 and 2 have been determined by single crystal X-ray diffraction studies. Both the complex 1 (τ = 0.5) and 2 (τ = 0.37) possesses square based pyramidally distorted trigonal bipyramidal geometry. The ground state electronic structures of complexes 1 and 2 were investigated by DFT/B3LYP theoretical analysis using 6-311G (d,p) and LANL2DZ basis set level. The superior DNA binding ability of complex 2 has been evaluated using absorption and fluorescence spectral titration studies. Antimicrobial evaluation reveals that complex 2 endowed better screening than HL and complex 1 against both bacterial as well as fungal species. Consequently, complex 2 possesses highest antibacterial screening against Staphylococcus aureus (MIC = 3.0 ± 0.23 mM) and antifungal screening against Candida albicans (MIC = 6.0 ± 0.11 mM). Furthermore, the anticancer activity of the ligand HL, complexes 1 and 2 have been examined against the MCF-7 cell line (Human breast cancer cell line) using MTT assay. It is remarkable that complex 2 (12 ± 0.67 μM) show highest anticancer activity than HL (25.0 ± 0.91 μM) and complex 1 (15 ± 0.88 μM) due to the presence of phen ligand moiety.

  13. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

    Science.gov (United States)

    Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

    2013-01-01

    Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

  14. A theoretical lens for revealing the complexity of chronic care

    NARCIS (Netherlands)

    Borgermans, L.; de Maeseneer, J.; Wollersheim, H.; Vrijhoef, H.J.M.; Devroey, D.

    2013-01-01

    The increasing prevalence of co-occurring multiple chronic conditions in an aging population has influenced the debate on complexity in chronic care and nowadays provides an impetus to the reform of numerous health systems. This article presents a theoretical lens for understanding the complexity of

  15. Intentional risk management through complex networks analysis

    CERN Document Server

    Chapela, Victor; Moral, Santiago; Romance, Miguel

    2015-01-01

    This book combines game theory and complex networks to examine intentional technological risk through modeling. As information security risks are in constant evolution,  the methodologies and tools to manage them must evolve to an ever-changing environment. A formal global methodology is explained  in this book, which is able to analyze risks in cyber security based on complex network models and ideas extracted from the Nash equilibrium. A risk management methodology for IT critical infrastructures is introduced which provides guidance and analysis on decision making models and real situations. This model manages the risk of succumbing to a digital attack and assesses an attack from the following three variables: income obtained, expense needed to carry out an attack, and the potential consequences for an attack. Graduate students and researchers interested in cyber security, complex network applications and intentional risk will find this book useful as it is filled with a number of models, methodologies a...

  16. Complex eigenvalue analysis of railway wheel/rail squeal

    African Journals Online (AJOL)

    DR OKE

    Squeal noise from wheel/rail and brake disc/pad frictional contact is typical in railways. ... squeal noise by multibody simulation of a rail car running on rigid rails. ... system, traditional complex eigenvalue analysis by finite element was used.

  17. In Planta Single-Molecule Pull-Down Reveals Tetrameric Stoichiometry of HD-ZIPIII:LITTLE ZIPPER Complexes.

    Science.gov (United States)

    Husbands, Aman Y; Aggarwal, Vasudha; Ha, Taekjip; Timmermans, Marja C P

    2016-08-01

    Deciphering complex biological processes markedly benefits from approaches that directly assess the underlying biomolecular interactions. Most commonly used approaches to monitor protein-protein interactions typically provide nonquantitative readouts that lack statistical power and do not yield information on the heterogeneity or stoichiometry of protein complexes. Single-molecule pull-down (SiMPull) uses single-molecule fluorescence detection to mitigate these disadvantages and can quantitatively interrogate interactions between proteins and other compounds, such as nucleic acids, small molecule ligands, and lipids. Here, we establish SiMPull in plants using the HOMEODOMAIN LEUCINE ZIPPER III (HD-ZIPIII) and LITTLE ZIPPER (ZPR) interaction as proof-of-principle. Colocalization analysis of fluorophore-tagged HD-ZIPIII and ZPR proteins provides strong statistical evidence of complex formation. In addition, we use SiMPull to directly quantify YFP and mCherry maturation probabilities, showing these differ substantially from values obtained in mammalian systems. Leveraging these probabilities, in conjunction with fluorophore photobleaching assays on over 2000 individual complexes, we determined HD-ZIPIII:ZPR stoichiometry. Intriguingly, these complexes appear as heterotetramers, comprising two HD-ZIPIII and two ZPR molecules, rather than heterodimers as described in the current model. This surprising result raises new questions about the regulation of these key developmental factors and is illustrative of the unique contribution SiMPull is poised to make to in planta protein interaction studies. © 2016 American Society of Plant Biologists. All rights reserved.

  18. Molecular Epidemiology and Phylogeny Reveal Complex Spatial Dynamics in Areas Where Canine Parvovirus Is Endemic ▿†

    Science.gov (United States)

    Clegg, S. R.; Coyne, K. P.; Parker, J.; Dawson, S.; Godsall, S. A.; Pinchbeck, G.; Cripps, P. J.; Gaskell, R. M.; Radford, A. D.

    2011-01-01

    Canine parvovirus type 2 (CPV-2) is a severe enteric pathogen of dogs, causing high mortality in unvaccinated dogs. After emerging, CPV-2 spread rapidly worldwide. However, there is now some evidence to suggest that international transmission appears to be more restricted. In order to investigate the transmission and evolution of CPV-2 both nationally and in relation to the global situation, we have used a long-range PCR to amplify and sequence the full VP2 gene of 150 canine parvoviruses obtained from a large cross-sectional sample of dogs presenting with severe diarrhea to veterinarians in the United Kingdom, over a 2-year period. Among these 150 strains, 50 different DNA sequence types (S) were identified, and apart from one case, all appeared unique to the United Kingdom. Phylogenetic analysis provided clear evidence for spatial clustering at the international level and for the first time also at the national level, with the geographical range of some sequence types appearing to be highly restricted within the United Kingdom. Evolution of the VP2 gene in this data set was associated with a lack of positive selection. In addition, the majority of predicted amino acid sequences were identical to those found elsewhere in the world, suggesting that CPV VP2 has evolved a highly fit conformation. Based on typing systems using key amino acid mutations, 43% of viruses were CPV-2a, and 57% CPV-2b, with no type 2 or 2c found. However, phylogenetic analysis suggested complex antigenic evolution of this virus, with both type 2a and 2b viruses appearing polyphyletic. As such, typing based on specific amino acid mutations may not reflect the true epidemiology of this virus. The geographical restriction that we observed both within the United Kingdom and between the United Kingdom and other countries, together with the lack of CPV-2c in this population, strongly suggests the spread of CPV within its population may be heterogeneously subject to limiting factors. This cross

  19. Multistationary and oscillatory modes of free radicals generation by the mitochondrial respiratory chain revealed by a bifurcation analysis.

    Directory of Open Access Journals (Sweden)

    Vitaly A Selivanov

    Full Text Available The mitochondrial electron transport chain transforms energy satisfying cellular demand and generates reactive oxygen species (ROS that act as metabolic signals or destructive factors. Therefore, knowledge of the possible modes and bifurcations of electron transport that affect ROS signaling provides insight into the interrelationship of mitochondrial respiration with cellular metabolism. Here, a bifurcation analysis of a sequence of the electron transport chain models of increasing complexity was used to analyze the contribution of individual components to the modes of respiratory chain behavior. Our algorithm constructed models as large systems of ordinary differential equations describing the time evolution of the distribution of redox states of the respiratory complexes. The most complete model of the respiratory chain and linked metabolic reactions predicted that condensed mitochondria produce more ROS at low succinate concentration and less ROS at high succinate levels than swelled mitochondria. This prediction was validated by measuring ROS production under various swelling conditions. A numerical bifurcation analysis revealed qualitatively different types of multistationary behavior and sustained oscillations in the parameter space near a region that was previously found to describe the behavior of isolated mitochondria. The oscillations in transmembrane potential and ROS generation, observed in living cells were reproduced in the model that includes interaction of respiratory complexes with the reactions of TCA cycle. Whereas multistationarity is an internal characteristic of the respiratory chain, the functional link of respiration with central metabolism creates oscillations, which can be understood as a means of auto-regulation of cell metabolism.

  20. Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

    Science.gov (United States)

    Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

    2017-11-28

    We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

  1. Complex finite element sensitivity method for creep analysis

    International Nuclear Information System (INIS)

    Gomez-Farias, Armando; Montoya, Arturo; Millwater, Harry

    2015-01-01

    The complex finite element method (ZFEM) has been extended to perform sensitivity analysis for mechanical and structural systems undergoing creep deformation. ZFEM uses a complex finite element formulation to provide shape, material, and loading derivatives of the system response, providing an insight into the essential factors which control the behavior of the system as a function of time. A complex variable-based quadrilateral user element (UEL) subroutine implementing the power law creep constitutive formulation was incorporated within the Abaqus commercial finite element software. The results of the complex finite element computations were verified by comparing them to the reference solution for the steady-state creep problem of a thick-walled cylinder in the power law creep range. A practical application of the ZFEM implementation to creep deformation analysis is the calculation of the skeletal point of a notched bar test from a single ZFEM run. In contrast, the standard finite element procedure requires multiple runs. The value of the skeletal point is that it identifies the location where the stress state is accurate, regardless of the certainty of the creep material properties. - Highlights: • A novel finite element sensitivity method (ZFEM) for creep was introduced. • ZFEM has the capability to calculate accurate partial derivatives. • ZFEM can be used for identification of the skeletal point of creep structures. • ZFEM can be easily implemented in a commercial software, e.g. Abaqus. • ZFEM results were shown to be in excellent agreement with analytical solutions

  2. Chemical Information revealed by Mössbauer spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Nakashima, Satoru, E-mail: snaka@hiroshima-u.ac.jp [Hiroshima University, Natural Science Center for Basic Research and Development (Japan)

    2017-11-15

    Mixed-valence state of binuclear metallocene derivatives and spin-crossover (SCO) phenomena of the assembled Fe(II) complexes have been studied by using Mössbauer spectroscopy. The understanding of the results obtained by Mössbauer spectra is well supported by means of X-ray structural analysis and density functional theory (DFT) calculation. Benchmark study of relativisitic DFT calculation by using Mössbauer isomer shifts of Eu, Np complexes reveals the validity of the calculation. Such study sheds light on the bonding character of 4f and 5f electron. These results are reviewed.

  3. Synthesis and physicochemical analysis of Sm (II, III) acetylacetone chelate complexes

    International Nuclear Information System (INIS)

    Kostyuk, N.N.; Dik, T.A.; Trebnikov, A.G.

    2004-01-01

    Sm (II, III) acetylacetone chelate complexes were synthesized by electrochemical method. It was shown that anode dissolution of the metal samarium over acetylacetone leads to formation of the Sm (II, III) chelate complexes: xSm(acac)2 · ySm(acac)3 · zH(acac). Factors x, y and z depend on quantity of the electricity, which flew through the electrolysis cell. The compositions of the obtained substances were confirmed by the physicochemical analysis (ultimate analysis, IR-, mass spectroscopy and thermal analysis (thermogravimetric, isothermal warming-up and differential scanning colorimetry). (Authors)

  4. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

    Science.gov (United States)

    Toan, Ngo Minh; Thirumalai, D.

    2018-03-01

    Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the

  5. Comparative analysis of carbohydrate active enzymes in Clostridium termitidis CT1112 reveals complex carbohydrate degradation ability.

    Directory of Open Access Journals (Sweden)

    Riffat I Munir

    Full Text Available Clostridium termitidis strain CT1112 is an anaerobic, gram positive, mesophilic, cellulolytic bacillus isolated from the gut of the wood-feeding termite, Nasutitermes lujae. It produces biofuels such as hydrogen and ethanol from cellulose, cellobiose, xylan, xylose, glucose, and other sugars, and therefore could be used for biofuel production from biomass through consolidated bioprocessing. The first step in the production of biofuel from biomass by microorganisms is the hydrolysis of complex carbohydrates present in biomass. This is achieved through the presence of a repertoire of secreted or complexed carbohydrate active enzymes (CAZymes, sometimes organized in an extracellular organelle called cellulosome. To assess the ability and understand the mechanism of polysaccharide hydrolysis in C. termitidis, the recently sequenced strain CT1112 of C. termitidis was analyzed for both CAZymes and cellulosomal components, and compared to other cellulolytic bacteria. A total of 355 CAZyme sequences were identified in C. termitidis, significantly higher than other Clostridial species. Of these, high numbers of glycoside hydrolases (199 and carbohydrate binding modules (95 were identified. The presence of a variety of CAZymes involved with polysaccharide utilization/degradation ability suggests hydrolysis potential for a wide range of polysaccharides. In addition, dockerin-bearing enzymes, cohesion domains and a cellulosomal gene cluster were identified, indicating the presence of potential cellulosome assembly.

  6. Widening the scope of incident analysis in complex work environments

    NARCIS (Netherlands)

    Vuuren, van W.; Kanse, L.; Manser, T.

    2003-01-01

    Incident analysis is commonly used as a tooi to provide information on how to improve health and safety in complex work environments. The effectiveness of this tooi, however, depends on how the analysis is actually carried out. The traditional view on incident analysis highlights the role of human

  7. Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors

    Science.gov (United States)

    Giner, Xavier C; Cotnoir-White, David; Mader, Sylvie; Lévesque, Daniel

    2017-01-01

    Retinoid X receptors (RXR) play a role as master regulators due to their capacity to form heterodimers with other nuclear receptors. Accordingly, retinoid signaling is involved in multiple biological processes, including development, cell differentiation, metabolism and cell death. However, the role and functions of RXR in different heterodimer complexes remain unsolved, mainly because most RXR drugs (called rexinoids) are not selective to specific heterodimer complexes. This also strongly limits the use of rexinoids for specific therapeutic approaches. In order to better characterize rexinoids at specific nuclear receptor complexes, we have developed and optimized luciferase protein complementation-based Bioluminescence Resonance Energy Transfer (BRET) assays, which can directly measure recruitment of a co-activator motif fused to yellow fluorescent protein (YFP) by specific nuclear receptor dimers. To validate the assays, we compared rexinoid modulation of co-activator recruitment by RXR homodimer, and heterodimers Nur77/RXR and Nurr1/RXR. Results reveal that some rexinoids display selective co-activator recruitment activities with homo- or hetero-dimer complexes. In particular, SR11237 (BMS649) has increased potency for recruitment of co-activator motif and transcriptional activity with the Nur77/RXR heterodimer compared to other complexes. This technology should prove useful to identify new compounds with specificity for individual dimeric species formed by nuclear receptors. PMID:26148973

  8. Complex Network Analysis of Guangzhou Metro

    OpenAIRE

    Yasir Tariq Mohmand; Fahad Mehmood; Fahd Amjad; Nedim Makarevic

    2015-01-01

    The structure and properties of public transportation networks can provide suggestions for urban planning and public policies. This study contributes a complex network analysis of the Guangzhou metro. The metro network has 236 kilometers of track and is the 6th busiest metro system of the world. In this paper topological properties of the network are explored. We observed that the network displays small world properties and is assortative in nature. The network possesses a high average degree...

  9. Risk Analysis for Road Tunnels – A Metamodel to Efficiently Integrate Complex Fire Scenarios

    DEFF Research Database (Denmark)

    Berchtold, Florian; Knaust, Christian; Arnold, Lukas

    2018-01-01

    Fires in road tunnels constitute complex scenarios with interactions between the fire, tunnel users and safety measures. More and more methodologies for risk analysis quantify the consequences of these scenarios with complex models. Examples for complex models are the computational fluid dynamics...... complex scenarios in risk analysis. To face this challenge, we improved the metamodel used in the methodology for risk analysis presented on ISTSS 2016. In general, a metamodel quickly interpolates the consequences of few scenarios simulated with the complex models to a large number of arbitrary scenarios...... used in risk analysis. Now, our metamodel consists of the projection array-based design, the moving least squares method, and the prediction interval to quantify the metamodel uncertainty. Additionally, we adapted the projection array-based design in two ways: the focus of the sequential refinement...

  10. Complex history of admixture during citrus domestication revealed by genome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry; Salse, Jerome; Hellsten, Uffe; Murat, Florent; Perrier, Xavier; Ruiz, Manuel; Scalabrin, Simone; Terol, Javier; Takita, Marco Aur& #233; lio,; Labadie, Karine; Poulain, Julie; Couloux, Arnaud; Jabbari, Kamel; Cattonaro, Federica; Fabbro, Cristian Del; Pinosio, Sara; Zuccolo, Andrea; Chapman, Jarrod; Grimwood, Jane; Tadeo, Francisco; Estornell, Leandro H.; Mu?oz-Sanz, Juan V.; Ibanez, Victoria; Herrero-Ortega, Amparo; Aleza, Pablo; P& #233; rez, Juli& #225; n P& #233; rez,; Ramon, Daniel; Brunel, Dominique; Luro, Francois; Chen, Chunxian; Farmerie, William G.; Desany, Brian; Kodira, Chinnappa; Mohiuddin, Mohammed; Harkins, Tim; Fredrikson, Karin; Burns, Paul; Lomsadze, Alexandre; Borodovsky, Mark; Reforgiato, Giuseppe; Freitas-Astua, Juliana; Quetier, Francis; Navarro, Luis; Roose, Mikeal; Wincker, Patrick; Schmutz, Jeremy; Morgante, Michele; Machado, Marcos Antonio; Talon, Manuel; Jaillon, Olivier; Ollitrault, Patrick; Gmitter, Frederick; Rokhsar, Daniel

    2014-06-30

    Although Citrus is the most globally significant tree fruit, its domestication history is poorly understood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm. Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China shows substantial sequence divergence from C. reticulata and appears to represent a distinct taxon. Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement. Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly

  11. Generalised power graph compression reveals dominant relationship patterns in complex networks.

    Science.gov (United States)

    Ahnert, Sebastian E

    2014-03-25

    We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

  12. Complexity, Analysis and Control of Singular Biological Systems

    CERN Document Server

    Zhang, Qingling; Zhang, Xue

    2012-01-01

    Complexity, Analysis and Control of Singular Biological Systems follows the control of real-world biological systems at both ecological and phyisological levels concentrating on the application of now-extensively-investigated singular system theory. Much effort has recently been dedicated to the modelling and analysis of developing bioeconomic systems and the text establishes singular examples of these, showing how proper control can help to maintain sustainable economic development of biological resources. The book begins from the essentials of singular systems theory and bifurcations before tackling  the use of various forms of control in singular biological systems using examples including predator-prey relationships and viral vaccination and quarantine control. Researchers and graduate students studying the control of complex biological systems are shown how a variety of methods can be brought to bear and practitioners working with the economics of biological systems and their control will also find the ...

  13. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2014-01-01

    . Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity. PMID:24422981

  14. Fire hazard analysis for Plutonium Finishing Plant complex

    Energy Technology Data Exchange (ETDEWEB)

    MCKINNIS, D.L.

    1999-02-23

    A fire hazards analysis (FHA) was performed for the Plutonium Finishing Plant (PFP) Complex at the Department of Energy (DOE) Hanford site. The scope of the FHA focuses on the nuclear facilities/structures in the Complex. The analysis was conducted in accordance with RLID 5480.7, [DOE Directive RLID 5480.7, 1/17/94] and DOE Order 5480.7A, ''Fire Protection'' [DOE Order 5480.7A, 2/17/93] and addresses each of the sixteen principle elements outlined in paragraph 9.a(3) of the Order. The elements are addressed in terms of the fire protection objectives stated in paragraph 4 of DOE 5480.7A. In addition, the FHA also complies with WHC-CM-4-41, Fire Protection Program Manual, Section 3.4 [1994] and WHC-SD-GN-FHA-30001, Rev. 0 [WHC, 1994]. Objectives of the FHA are to determine: (1) the fire hazards that expose the PFP facilities, or that are inherent in the building operations, (2) the adequacy of the fire safety features currently located in the PFP Complex, and (3) the degree of compliance of the facility with specific fire safety provisions in DOE orders, related engineering codes, and standards.

  15. Structured analysis and modeling of complex systems

    Science.gov (United States)

    Strome, David R.; Dalrymple, Mathieu A.

    1992-01-01

    The Aircrew Evaluation Sustained Operations Performance (AESOP) facility at Brooks AFB, Texas, combines the realism of an operational environment with the control of a research laboratory. In recent studies we collected extensive data from the Airborne Warning and Control Systems (AWACS) Weapons Directors subjected to high and low workload Defensive Counter Air Scenarios. A critical and complex task in this environment involves committing a friendly fighter against a hostile fighter. Structured Analysis and Design techniques and computer modeling systems were applied to this task as tools for analyzing subject performance and workload. This technology is being transferred to the Man-Systems Division of NASA Johnson Space Center for application to complex mission related tasks, such as manipulating the Shuttle grappler arm.

  16. New levels of language processing complexity and organization revealed by granger causation.

    Science.gov (United States)

    Gow, David W; Caplan, David N

    2012-01-01

    Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all non-redundant potentially interacting signals, and has shown that even "early" processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of "language-specific" localized processes.

  17. Mathematical analysis of complex cellular activity

    CERN Document Server

    Bertram, Richard; Teka, Wondimu; Vo, Theodore; Wechselberger, Martin; Kirk, Vivien; Sneyd, James

    2015-01-01

    This book contains two review articles on mathematical physiology that deal with closely related topics but were written and can be read independently. The first article reviews the basic theory of calcium oscillations (common to almost all cell types), including spatio-temporal behaviors such as waves. The second article uses, and expands on, much of this basic theory to show how the interaction of cytosolic calcium oscillators with membrane ion channels can result in highly complex patterns of electrical spiking. Through these examples one can see clearly how multiple oscillatory processes interact within a cell, and how mathematical methods can be used to understand such interactions better. The two reviews provide excellent examples of how mathematics and physiology can learn from each other, and work jointly towards a better understanding of complex cellular processes. Review 1: Richard Bertram, Joel Tabak, Wondimu Teka, Theodore Vo, Martin Wechselberger: Geometric Singular Perturbation Analysis of Burst...

  18. State analysis requirements database for engineering complex embedded systems

    Science.gov (United States)

    Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.

    2004-01-01

    It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.

  19. Protein complex prediction via dense subgraphs and false positive analysis.

    Directory of Open Access Journals (Sweden)

    Cecilia Hernandez

    Full Text Available Many proteins work together with others in groups called complexes in order to achieve a specific function. Discovering protein complexes is important for understanding biological processes and predict protein functions in living organisms. Large-scale and throughput techniques have made possible to compile protein-protein interaction networks (PPI networks, which have been used in several computational approaches for detecting protein complexes. Those predictions might guide future biologic experimental research. Some approaches are topology-based, where highly connected proteins are predicted to be complexes; some propose different clustering algorithms using partitioning, overlaps among clusters for networks modeled with unweighted or weighted graphs; and others use density of clusters and information based on protein functionality. However, some schemes still require much processing time or the quality of their results can be improved. Furthermore, most of the results obtained with computational tools are not accompanied by an analysis of false positives. We propose an effective and efficient mining algorithm for discovering highly connected subgraphs, which is our base for defining protein complexes. Our representation is based on transforming the PPI network into a directed acyclic graph that reduces the number of represented edges and the search space for discovering subgraphs. Our approach considers weighted and unweighted PPI networks. We compare our best alternative using PPI networks from Saccharomyces cerevisiae (yeast and Homo sapiens (human with state-of-the-art approaches in terms of clustering, biological metrics and execution times, as well as three gold standards for yeast and two for human. Furthermore, we analyze false positive predicted complexes searching the PDBe (Protein Data Bank in Europe database in order to identify matching protein complexes that have been purified and structurally characterized. Our analysis shows

  20. Twenty-one lectures on complex analysis a first course

    CERN Document Server

    Isaev, Alexander

    2017-01-01

    At its core, this concise textbook presents standard material for a first course in complex analysis at the advanced undergraduate level. This distinctive text will prove most rewarding for students who have a genuine passion for mathematics as well as certain mathematical maturity. Primarily aimed at undergraduates with working knowledge of real analysis and metric spaces, this book can also be used to instruct a graduate course. The text uses a conversational style with topics purposefully apportioned into 21 lectures, providing a suitable format for either independent study or lecture-based teaching. Instructors are invited to rearrange the order of topics according to their own vision. A clear and rigorous exposition is supported by engaging examples and exercises unique to each lecture; a large number of exercises contain useful calculation problems. Hints are given for a selection of the more difficult exercises. This text furnishes the reader with a means of learning complex analysis as well as a subtl...

  1. Characterization and biological activity of Solidago canadensis complex.

    Science.gov (United States)

    Šutovská, M; Capek, P; Kocmálová, M; Fraňová, S; Pawlaczyk, I; Gancarz, R

    2013-01-01

    Polyphenolic-polysaccharide-protein complex has been isolated from flowers of Solidago canadensis L. by hot alkaline extraction procedure. Compositional analyses of S canadensis complex revealed the presence of carbohydrates (43 wt%), protein (27 wt%), phenolics (12 wt%), uronic acids (10 wt%) and inorganic material (8 wt%). The carbohydrate part was rich in neutral sugars (81 wt%) while uronids were determined in lower amount (19 wt%). Monosaccharide analysis of carbohydrate part revealed the presence of five main sugar components, i.e. rhamnose (~23 wt%), arabinose (~20 wt%), uronic acids (~19 wt%), galactose (~17 wt%) and glucose (~14 wt%), and indicated thus the presence of rhamnogalacturonan and arabinogalactan in S. canadensis complex. HPLC analysis of complex showed one single peak of molecule mass at 11.2 kDa. Antitussive activity tests, performed in three doses of Solidago complex, showed the reduction of the number of cough efforts in the dose-dependent manner. Higher doses (50 and 75 mg/kg b.w.) were shown to be by 15 and 20% more effective than that of lower one (25mg/kg b.w.). However, the antitussive effect of the highest dose (75 mg/kg b.w.) was by 10% lower in comparison with that of codeine, the strongest antitussive agent. Besides, the highest dose of the complex (75 mg/kg b.w.) significantly decreased values of specific airways resistance and their effect remained longer as that of salbutamol, a representative of classic antiasthmatic drugs. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties

    International Nuclear Information System (INIS)

    Mikeska, Ruth; Wacker, Roland; Arni, Raghuvir; Singh, Tej P.; Mikhailov, Albert; Gabdoulkhakov, Azat; Voelter, Wolfgang; Betzel, Christian

    2004-01-01

    The structures of mistletoe lectin I in complex with lactose and galactose reveal differences in binding by the two known sites in subdomains α1 and γ2 and suggest the presence of a third low-affinity site in subdomain β1. The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (R free = 23.6%) and 20.9 (R free = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML-I B-chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose-binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit β1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound

  3. A systems level approach reveals new gene regulatory modules in the developing ear

    OpenAIRE

    Chen, Jingchen; Tambalo, Monica; Barembaum, Meyer; Ranganathan, Ramya; Simões-Costa, Marcos; Bronner, Marianne E.; Streit, Andrea

    2017-01-01

    The inner ear is a complex vertebrate sense organ, yet it arises from a simple epithelium, the otic placode. Specification towards otic fate requires diverse signals and transcriptional inputs that act sequentially and/or in parallel. Using the chick embryo, we uncover novel genes in the gene regulatory network underlying otic commitment and reveal dynamic changes in gene expression. Functional analysis of selected transcription factors reveals the genetic hierarchy underlying the transition ...

  4. A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto.

    Science.gov (United States)

    Rito, Teresa; Matos, Carlos; Carvalho, Carlos; Machado, Henrique; Rodrigues, Gabriela; Oliveira, Olena; Ferreira, Eduarda; Gonçalves, Jorge; Maio, Lurdes; Morais, Clara; Ramos, Helena; Guimarães, João Tiago; Santos, Catarina L; Duarte, Raquel; Correia-Neves, Margarida

    2018-01-25

    Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.

  5. The application of complex network time series analysis in turbulent heated jets

    International Nuclear Information System (INIS)

    Charakopoulos, A. K.; Karakasidis, T. E.; Liakopoulos, A.; Papanicolaou, P. N.

    2014-01-01

    In the present study, we applied the methodology of the complex network-based time series analysis to experimental temperature time series from a vertical turbulent heated jet. More specifically, we approach the hydrodynamic problem of discriminating time series corresponding to various regions relative to the jet axis, i.e., time series corresponding to regions that are close to the jet axis from time series originating at regions with a different dynamical regime based on the constructed network properties. Applying the transformation phase space method (k nearest neighbors) and also the visibility algorithm, we transformed time series into networks and evaluated the topological properties of the networks such as degree distribution, average path length, diameter, modularity, and clustering coefficient. The results show that the complex network approach allows distinguishing, identifying, and exploring in detail various dynamical regions of the jet flow, and associate it to the corresponding physical behavior. In addition, in order to reject the hypothesis that the studied networks originate from a stochastic process, we generated random network and we compared their statistical properties with that originating from the experimental data. As far as the efficiency of the two methods for network construction is concerned, we conclude that both methodologies lead to network properties that present almost the same qualitative behavior and allow us to reveal the underlying system dynamics

  6. CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

    Directory of Open Access Journals (Sweden)

    Charalambos Chrysostomou

    2015-01-01

    Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

  7. Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

    Science.gov (United States)

    Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

    2017-01-01

    A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

  8. High frequency vibration analysis by the complex envelope vectorization.

    Science.gov (United States)

    Giannini, O; Carcaterra, A; Sestieri, A

    2007-06-01

    The complex envelope displacement analysis (CEDA) is a procedure to solve high frequency vibration and vibro-acoustic problems, providing the envelope of the physical solution. CEDA is based on a variable transformation mapping the high frequency oscillations into signals of low frequency content and has been successfully applied to one-dimensional systems. However, the extension to plates and vibro-acoustic fields met serious difficulties so that a general revision of the theory was carried out, leading finally to a new method, the complex envelope vectorization (CEV). In this paper the CEV method is described, underlying merits and limits of the procedure, and a set of applications to vibration and vibro-acoustic problems of increasing complexity are presented.

  9. CW EPR parameters reveal cytochrome P450 ligand binding modes.

    Science.gov (United States)

    Lockart, Molly M; Rodriguez, Carlo A; Atkins, William M; Bowman, Michael K

    2018-06-01

    Cytochrome P450 (CYP) monoxygenses utilize heme cofactors to catalyze oxidation reactions. They play a critical role in metabolism of many classes of drugs, are an attractive target for drug development, and mediate several prominent drug interactions. Many substrates and inhibitors alter the spin state of the ferric heme by displacing the heme's axial water ligand in the resting enzyme to yield a five-coordinate iron complex, or they replace the axial water to yield a nitrogen-ligated six-coordinate iron complex, which are traditionally assigned by UV-vis spectroscopy. However, crystal structures and recent pulsed electron paramagnetic resonance (EPR) studies find a few cases where molecules hydrogen bond to the axial water. The water-bridged drug-H 2 O-heme has UV-vis spectra similar to nitrogen-ligated, six-coordinate complexes, but are closer to "reverse type I" complexes described in older liteature. Here, pulsed and continuous wave (CW) EPR demonstrate that water-bridged complexes are remarkably common among a range of nitrogenous drugs or drug fragments that bind to CYP3A4 or CYP2C9. Principal component analysis reveals a distinct clustering of CW EPR spectral parameters for water-bridged complexes. CW EPR reveals heterogeneous mixtures of ligated states, including multiple directly-coordinated complexes and water-bridged complexes. These results suggest that water-bridged complexes are under-represented in CYP structural databases and can have energies similar to other ligation modes. The data indicates that water-bridged binding modes can be identified and distinguished from directly-coordinated binding by CW EPR. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    FIRST LADY

    The importance of data analysis in quantitative assessment of natural resources .... Data collection design is an important process in complex forest statistical ... Ideally, the sample size should be equal among groups and sufficiently large.

  11. Complexity and corporate governance: an analysis of companies listed on the BM&FBOVESPA

    Directory of Open Access Journals (Sweden)

    Renata Rouquayrol Assunção

    2017-03-01

    Full Text Available ABSTRACT In light of the need to develop mechanisms of control, protection, and transparency regarding the relationships between principal and agent, and with the aim of eliminating or reducing the agency problem, corporate governance has emerged. Based on Agency Theory, separation of ownership and control of activities derives from the complexity of organizations. In this context, this study aims to analyze the relationship between dimensions of complexity and corporate governance in companies listed on the São Paulo Stock, Commodities, and Futures Exchange (BM&FBOVESPA, in which contingency factors might influence organizational characteristics. The investigation gathers data from a sample of 162 companies listed on the BM&FBOVESPA. The following statistical tests were used in the data analysis: Factor Analysis, Multiple Linear Regression, Correspondence Analysis, and Correlation Analysis. For measuring complexity, contingency variables such as age, size, diversification, and internationalization were adopted; and, to assess corporate governance, a representative index of the adoption of good governance practices was used. The results show that organizational complexity is explained by the size and diversification variables, whereas operational complexity is explained by the size, diversification, and internationalization variables. It was observed that in the two dimensions of complexity - organizational and operational - corporate governance was influenced by the diversification, internationalization, and age variables, with the latter involving an inverse relationship. It is concluded that companies displaying more complexity, in its two dimensions, record a higher level of corporate governance, which confirms the research hypothesis.

  12. High-resolution crystal structure of Streptococcus pyogenes β-NAD{sup +} glycohydrolase in complex with its endogenous inhibitor IFS reveals a highly water-rich interface

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ji Young; An, Doo Ri; Yoon, Hye-Jin [Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyoun Sook [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Sang Jae [Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Ha Na; Jang, Jun Young [Seoul National University, Seoul 151-747 (Korea, Republic of); Suh, Se Won, E-mail: sewonsuh@snu.ac.kr [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of)

    2013-11-01

    The crystal structure of the complex between the C-terminal domain of Streptococcus pyogenes β-NAD{sup +} glycohydrolase and an endogenous inhibitor for SPN was determined at 1.70 Å. It reveals that the interface between the two proteins is highly rich in water molecules. One of the virulence factors produced by Streptococcus pyogenes is β-NAD{sup +} glycohydrolase (SPN). S. pyogenes injects SPN into the cytosol of an infected host cell using the cytolysin-mediated translocation pathway. As SPN is toxic to bacterial cells themselves, S. pyogenes possesses the ifs gene that encodes an endogenous inhibitor for SPN (IFS). IFS is localized intracellularly and forms a complex with SPN. This intracellular complex must be dissociated during export through the cell envelope. To provide a structural basis for understanding the interactions between SPN and IFS, the complex was overexpressed between the mature SPN (residues 38–451) and the full-length IFS (residues 1–161), but it could not be crystallized. Therefore, limited proteolysis was used to isolate a crystallizable SPN{sub ct}–IFS complex, which consists of the SPN C-terminal domain (SPN{sub ct}; residues 193–451) and the full-length IFS. Its crystal structure has been determined by single anomalous diffraction and the model refined at 1.70 Å resolution. Interestingly, our high-resolution structure of the complex reveals that the interface between SPN{sub ct} and IFS is highly rich in water molecules and many of the interactions are water-mediated. The wet interface may facilitate the dissociation of the complex for translocation across the cell envelope.

  13. Survey of large protein complexes D. vulgaris reveals great structural diversity

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  14. Complex analysis and CR geometry

    CERN Document Server

    Zampieri, Giuseppe

    2008-01-01

    Cauchy-Riemann (CR) geometry is the study of manifolds equipped with a system of CR-type equations. Compared to the early days when the purpose of CR geometry was to supply tools for the analysis of the existence and regularity of solutions to the \\bar\\partial-Neumann problem, it has rapidly acquired a life of its own and has became an important topic in differential geometry and the study of non-linear partial differential equations. A full understanding of modern CR geometry requires knowledge of various topics such as real/complex differential and symplectic geometry, foliation theory, the geometric theory of PDE's, and microlocal analysis. Nowadays, the subject of CR geometry is very rich in results, and the amount of material required to reach competence is daunting to graduate students who wish to learn it. However, the present book does not aim at introducing all the topics of current interest in CR geometry. Instead, an attempt is made to be friendly to the novice by moving, in a fairly relaxed way, f...

  15. Stein manifolds and holomorphic mappings the homotopy principle in complex analysis

    CERN Document Server

    Forstnerič, Franc

    2017-01-01

    This book, now in a carefully revised second edition, provides an up-to-date account of Oka theory, including the classical Oka-Grauert theory and the wide array of applications to the geometry of Stein manifolds. Oka theory is the field of complex analysis dealing with global problems on Stein manifolds which admit analytic solutions in the absence of topological obstructions. The exposition in the present volume focuses on the notion of an Oka manifold introduced by the author in 2009. It explores connections with elliptic complex geometry initiated by Gromov in 1989, with the Andersén-Lempert theory of holomorphic automorphisms of complex Euclidean spaces and of Stein manifolds with the density property, and with topological methods such as homotopy theory and the Seiberg-Witten theory. Researchers and graduate students interested in the homotopy principle in complex analysis will find this book particularly useful. It is currently the only work that offers a comprehensive introduction to both the Oka t...

  16. Two conformational states of the membrane-associated Bacillus thuringiensis Cry4Ba δ-endotoxin complex revealed by electron crystallography: Implications for toxin-pore formation

    International Nuclear Information System (INIS)

    Ounjai, Puey; Unger, Vinzenz M.; Sigworth, Fred J.; Angsuthanasombat, Chanan

    2007-01-01

    The insecticidal nature of Cry δ-endotoxins produced by Bacillus thuringiensis is generally believed to be caused by their ability to form lytic pores in the midgut cell membrane of susceptible insect larvae. Here we have analyzed membrane-associated structures of the 65-kDa dipteran-active Cry4Ba toxin by electron crystallography. The membrane-associated toxin complex was crystallized in the presence of DMPC via detergent dialysis. Depending upon the charge of the adsorbed surface, 2D crystals of the oligomeric toxin complex have been captured in two distinct conformations. The projection maps of those crystals have been generated at 17 A resolution. Both complexes appeared to be trimeric; as in one crystal form, its projection structure revealed a symmetrical pinwheel-like shape with virtually no depression in the middle of the complex. The other form revealed a propeller-like conformation displaying an obvious hole in the center region, presumably representing the toxin-induced pore. These crystallographic data thus demonstrate for the first time that the 65-kDa activated Cry4Ba toxin in association with lipid membranes could exist in at least two different trimeric conformations, conceivably implying the closed and open states of the pore

  17. High pH reversed-phase chromatography as a superior fractionation scheme compared to off-gel isoelectric focusing for complex proteome analysis.

    Science.gov (United States)

    Stein, Derek R; Hu, Xiaojie; McCorrister, Stuart J; Westmacott, Garrett R; Plummer, Francis A; Ball, Terry B; Carpenter, Michael S

    2013-10-01

    MS/MS is the technology of choice for analyzing complex protein mixtures. However, due to the intrinsic complexity and dynamic range present in higher eukaryotic proteomes, prefractionation is an important step to maximize the number of proteins identified. Off-gel IEF (OG-IEF) and high pH RP (Hp-RP) column chromatography have both been successfully utilized as a first-dimension peptide separation technique in shotgun proteomic experiments. Here, a direct comparison of the two methodologies was performed on ex vivo peripheral blood mononuclear cell lysate. In 12-fraction replicate analysis, Hp-RP resulted in more peptides and proteins identified than OG-IEF fractionation. Distributions of peptide pIs and hydropathy did not reveal any appreciable bias in either technique. Resolution, defined here as the ability to limit a specific peptide to one particular fraction, was significantly better for Hp-RP. This leads to a more uniform distribution of total and unique peptides for Hp-RP across all fractions collected. These results suggest that fractionation by Hp-RP over OG-IEF is the better choice for typical complex proteome analysis. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. New levels of language processing complexity and organization revealed by Granger causation

    Directory of Open Access Journals (Sweden)

    David W Gow

    2012-11-01

    Full Text Available Granger causation analysis of high spatiotemporal resolution reconstructions of brain activation offers a new window on the dynamic interactions between brain areas that support language processing. Premised on the observation that causes both precede and uniquely predict their effects, this approach provides an intuitive, model-free means of identifying directed causal interactions in the brain. It requires the analysis of all nonredundant potentially interacting signals, and has shown that even early processes such as speech perception involve interactions of many areas in a strikingly large network that extends well beyond traditional left hemisphere perisylvian cortex that play out over hundreds of milliseconds. In this paper we describe this technique and review several general findings that reframe the way we think about language processing and brain function in general. These include the extent and complexity of language processing networks, the central role of interactive processing dynamics, the role of processing hubs where the input from many distinct brain regions are integrated, and the degree to which task requirements and stimulus properties influence processing dynamics and inform our understanding of language-specific localized processes.

  19. The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs.

    Directory of Open Access Journals (Sweden)

    Hongtao Hu

    Full Text Available MicroRNAs (miRNAs and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs are two distinct subfamilies of small RNAs (sRNAs that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs are processed from longer RNA precursors by DICER-LIKE proteins (DCLs. Gossypium arboreum L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid Gossypium hirsutum L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in G. arboreum, a bioinformatics analysis was performed on G. arboreum small RNAs produced from G. arboreum leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs and 108 novel lineage-specific miRNAs (ls-miRNAs. Along with miRNAs, 2,033 miRNA variants (isomiRNAs were identified as well. Those isomiRNAs with variation at the 3'-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called cis- or trans-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers

  20. The Complexity of Posttranscriptional Small RNA Regulatory Networks Revealed by In Silico Analysis of Gossypium arboreum L. Leaf, Flower and Boll Small Regulatory RNAs.

    Science.gov (United States)

    Hu, Hongtao; Rashotte, Aaron M; Singh, Narendra K; Weaver, David B; Goertzen, Leslie R; Singh, Shree R; Locy, Robert D

    2015-01-01

    MicroRNAs (miRNAs) and secondary small interfering RNAs (principally phased siRNAs or trans-acting siRNAs) are two distinct subfamilies of small RNAs (sRNAs) that are emerging as key regulators of posttranscriptional gene expression in plants. Both miRNAs and secondary-siRNAs (sec-siRNAs) are processed from longer RNA precursors by DICER-LIKE proteins (DCLs). Gossypium arboreum L., also known as tree cotton or Asian cotton, is a diploid, possibly ancestral relative of tetraploid Gossypium hirsutum L., the predominant type of commercially grown cotton worldwide known as upland cotton. To understand the biological significance of these gene regulators in G. arboreum, a bioinformatics analysis was performed on G. arboreum small RNAs produced from G. arboreum leaf, flower, and boll tissues. Consequently, 263 miRNAs derived from 353 precursors, including 155 conserved miRNAs (cs-miRNAs) and 108 novel lineage-specific miRNAs (ls-miRNAs). Along with miRNAs, 2,033 miRNA variants (isomiRNAs) were identified as well. Those isomiRNAs with variation at the 3'-miRNA end were expressed at the highest levels, compared to other types of variants. In addition, 755 pha-siRNAs derived 319 pha-siRNA gene transcripts (PGTs) were identified, and the potential pha-siRNA initiators were predicted. Also, 2,251 non-phased siRNAs were found as well, of which 1,088 appeared to be produced by so-called cis- or trans-cleavage of the PGTs observed at positions differing from pha-siRNAs. Of those sRNAs, 148 miRNAs/isomiRNAs and 274 phased/non-phased siRNAs were differentially expressed in one or more pairs of tissues examined. Target analysis revealed that target genes for both miRNAs and pha-siRNAs are involved a broad range of metabolic and enzymatic activities. We demonstrate that secondary siRNA production could result from initial cleavage of precursors by both miRNAs or isomiRNAs, and that subsequently produced phased and unphased siRNAs could result that also serve as triggers of a second

  1. Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae.

    Science.gov (United States)

    Uthe, Henriette; Vanselow, Jens T; Schlosser, Andreas

    2017-02-27

    Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15 N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis.

  2. Analysis of Dynamic Complexity of the Cyber Security Ecosystem of Colombia

    Directory of Open Access Journals (Sweden)

    Angélica Flórez

    2016-07-01

    Full Text Available This paper presents two proposals for the analysis of the complexity of the Cyber security Ecosystem of Colombia (CEC. This analysis shows the available knowledge about entities engaged in cyber security in Colombia and the relationships between them, which allow an understanding of the synergy between the different existing components. The complexity of the CEC is detailed from the view of the Influence Diagram of System Dynamics and the Domain Diagram of Software Engineering. The resulting model makes cyber security evident as a strategic component of national security.

  3. The Complexome of Dehalococcoides mccartyi Reveals Its Organohalide Respiration-Complex Is Modular

    Directory of Open Access Journals (Sweden)

    Katja Seidel

    2018-06-01

    Full Text Available Dehalococcoides mccartyi strain CBDB1 is a slow growing strictly anaerobic microorganism dependent on halogenated compounds as terminal electron acceptor for anaerobic respiration. Indications have been described that the membrane-bound proteinaceous organohalide respiration complex of strain CBDB1 is functional without quinone-mediated electron transfer. We here study this multi-subunit protein complex in depth in regard to participating protein subunits and interactions between the subunits using blue native gel electrophoresis coupled to mass spectrometric label-free protein quantification. Applying three different solubilization modes to detach the respiration complex from the membrane we describe different solubilization snapshots of the organohalide respiration complex. The results demonstrate the existence of a two-subunit hydrogenase module loosely binding to the rest of the complex, tight binding of the subunit HupX to OmeA and OmeB, predicted to be the two subunits of a molybdopterin-binding redox subcomplex, to form a second module, and the presence of two distinct reductive dehalogenase module variants with different sizes. In our data we obtained biochemical evidence for the specificity between a reductive dehalogenase RdhA (CbdbA80 and its membrane anchor protein RdhB (CbdbB3. We also observed weak interactions between the reductive dehalogenase and the hydrogenase module suggesting a not yet recognized contact surface between these two modules. Especially an interaction between the two integral membrane subunits OmeB and RdhB seems to promote the integrity of the complex. With the different solubilization strengths we observe successive disintegration of the complex into its subunits. The observed architecture would allow the association of different reductive dehalogenase modules RdhA/RdhB with the other two protein complex modules when the strain is growing on different electron acceptors. In the search for other respiratory

  4. Economical andgeographical analysis of publishing and printing complex of Ukraine. N. O. Podorozhko

    Directory of Open Access Journals (Sweden)

    Podorozhko N.O.

    2009-08-01

    Full Text Available Actuality and the theoretical foundations of the geographical analysis of publishing and printing complex of Ukraine are substantiated. The analysis of the main indicators of the publishing industry in dynamics for 2000-2007are submitted. In an unfolded state presents complex for 2007 as a whole in Ukraine as in some regions.

  5. Analysis of gene expression profile microarray data in complex regional pain syndrome.

    Science.gov (United States)

    Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

    2017-09-01

    The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

  6. Structure of UreG/UreF/UreH Complex Reveals How Urease Accessory Proteins Facilitate Maturation of Helicobacter pylori Urease

    Science.gov (United States)

    Fong, Yu Hang; Wong, Ho Chun; Yuen, Man Hon; Lau, Pak Ho; Chen, Yu Wai; Wong, Kam-Bo

    2013-01-01

    Urease is a metalloenzyme essential for the survival of Helicobacter pylori in acidic gastric environment. Maturation of urease involves carbamylation of Lys219 and insertion of two nickel ions at its active site. This process requires GTP hydrolysis and the formation of a preactivation complex consisting of apo-urease and urease accessory proteins UreF, UreH, and UreG. UreF and UreH form a complex to recruit UreG, which is a SIMIBI class GTPase, to the preactivation complex. We report here the crystal structure of the UreG/UreF/UreH complex, which illustrates how UreF and UreH facilitate dimerization of UreG, and assembles its metal binding site by juxtaposing two invariant Cys66-Pro67-His68 metal binding motif at the interface to form the (UreG/UreF/UreH)2 complex. Interaction studies revealed that addition of nickel and GTP to the UreG/UreF/UreH complex releases a UreG dimer that binds a nickel ion at the dimeric interface. Substitution of Cys66 and His68 with alanine abolishes the formation of the nickel-charged UreG dimer. This nickel-charged UreG dimer can activate urease in vitro in the presence of the UreF/UreH complex. Static light scattering and atomic absorption spectroscopy measurements demonstrated that the nickel-charged UreG dimer, upon GTP hydrolysis, reverts to its monomeric form and releases nickel to urease. Based on our results, we propose a mechanism on how urease accessory proteins facilitate maturation of urease. PMID:24115911

  7. Communication complexity and information complexity

    Science.gov (United States)

    Pankratov, Denis

    Information complexity enables the use of information-theoretic tools in communication complexity theory. Prior to the results presented in this thesis, information complexity was mainly used for proving lower bounds and direct-sum theorems in the setting of communication complexity. We present three results that demonstrate new connections between information complexity and communication complexity. In the first contribution we thoroughly study the information complexity of the smallest nontrivial two-party function: the AND function. While computing the communication complexity of AND is trivial, computing its exact information complexity presents a major technical challenge. In overcoming this challenge, we reveal that information complexity gives rise to rich geometrical structures. Our analysis of information complexity relies on new analytic techniques and new characterizations of communication protocols. We also uncover a connection of information complexity to the theory of elliptic partial differential equations. Once we compute the exact information complexity of AND, we can compute exact communication complexity of several related functions on n-bit inputs with some additional technical work. Previous combinatorial and algebraic techniques could only prove bounds of the form theta( n). Interestingly, this level of precision is typical in the area of information theory, so our result demonstrates that this meta-property of precise bounds carries over to information complexity and in certain cases even to communication complexity. Our result does not only strengthen the lower bound on communication complexity of disjointness by making it more exact, but it also shows that information complexity provides the exact upper bound on communication complexity. In fact, this result is more general and applies to a whole class of communication problems. In the second contribution, we use self-reduction methods to prove strong lower bounds on the information

  8. Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion.

    Science.gov (United States)

    Rosenthal, Sara Brin; Twomey, Colin R; Hartnett, Andrew T; Wu, Hai Shan; Couzin, Iain D

    2015-04-14

    Coordination among social animals requires rapid and efficient transfer of information among individuals, which may depend crucially on the underlying structure of the communication network. Establishing the decision-making circuits and networks that give rise to individual behavior has been a central goal of neuroscience. However, the analogous problem of determining the structure of the communication network among organisms that gives rise to coordinated collective behavior, such as is exhibited by schooling fish and flocking birds, has remained almost entirely neglected. Here, we study collective evasion maneuvers, manifested through rapid waves, or cascades, of behavioral change (a ubiquitous behavior among taxa) in schooling fish (Notemigonus crysoleucas). We automatically track the positions and body postures, calculate visual fields of all individuals in schools of ∼150 fish, and determine the functional mapping between socially generated sensory input and motor response during collective evasion. We find that individuals use simple, robust measures to assess behavioral changes in neighbors, and that the resulting networks by which behavior propagates throughout groups are complex, being weighted, directed, and heterogeneous. By studying these interaction networks, we reveal the (complex, fractional) nature of social contagion and establish that individuals with relatively few, but strongly connected, neighbors are both most socially influential and most susceptible to social influence. Furthermore, we demonstrate that we can predict complex cascades of behavioral change at their moment of initiation, before they actually occur. Consequently, despite the intrinsic stochasticity of individual behavior, establishing the hidden communication networks in large self-organized groups facilitates a quantitative understanding of behavioral contagion.

  9. Pentacoordinated organoaluminum complexes: A computational insight

    KAUST Repository

    Milione, Stefano

    2012-12-24

    The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

  10. Pentacoordinated organoaluminum complexes: A computational insight

    KAUST Repository

    Milione, Stefano; Milano, Giuseppe; Cavallo, Luigi

    2012-01-01

    The geometry and the electronic structure of a series of organometallic pentacoordinated aluminum complexes bearing tri- or tetradentate N,O-based ligands have been investigated with theoretical methods. The BP86, B3LYP, and M06 functionals reproduce with low accuracy the geometry of the selected complexes. The worst result was obtained for the complex bearing a Schiff base ligand with a pendant donor arm, aeimpAlMe2 (aeimp = N-2-(dimethylamino)ethyl-(3,5-di-tert-butyl)salicylaldimine). In particular, the Al-Namine bond distance was unacceptably overestimated. This failure suggests a reasonably flat potential energy surface with respect to Al-N elongation, indicating a weak interaction with probably a strong component of dispersion forces. MP2 and M06-2X methods led to an acceptable value for the same Al-N distance. Better results were obtained with the addition of the dispersion correction to the hybrid B3LYP functional (B3LYP-D). Natural bond orbital analysis revealed that the contribution of the d orbital to the bonding is very small, in agreement with several previous studies of hypervalent molecules. The donation of electronic charge from the ligand to metal mainly consists in the interactions of the lone pairs on the donor atoms of the ligands with the s and p valence orbitals of the aluminum. The covalent bonding of the Al with the coordinated ligand is weak, and the interactions between Al and the coordinated ligands are largely ionic. To further explore the geometrical and electronic factors affecting the formation of these pentacoordianted aluminum complexes, we considered the tetracoordinated complex impAlMe2 (imp = N-isopropyl-(3,5-di-tert-butyl)salicylaldimine)), analogous to aeimpAlMe 2, and we investigated the potential energy surface around the aluminum atom corresponding to the approach of NMe3 to the metal center. At the MP2/6-31G(d) level of theory, a weak attraction was revealed only when NMe3 heads toward the metal center through the directions

  11. Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

    Science.gov (United States)

    Kachhap, Sangita; Singh, Balvinder

    2015-01-01

    In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

  12. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  13. Factors influencing efficient structure of fuel and energy complex

    Science.gov (United States)

    Sidorova, N. G.; Novikova, S. A.

    2017-10-01

    The development of the Russian fuel-energy complex is a priority for the national economic policy, and the Far East is a link between Russia and the Asia-Pacific region. Large-scale engineering of numerous resources of the Far East will force industrial development, increase living standard and strengthen Russia’s position in the global energy market. So, revealing the factors which influence rational structure of the fuel-energy complex is very urgent nowadays. With the use of depth analysis of development tendencies of the complex and its problems the authors show ways of its efficiency improvement.

  14. Functional dissection of the proton pumping modules of mitochondrial complex I.

    Directory of Open Access Journals (Sweden)

    Stefan Dröse

    2011-08-01

    Full Text Available Mitochondrial complex I, the largest and most complicated proton pump of the respiratory chain, links the electron transfer from NADH to ubiquinone to the pumping of four protons from the matrix into the intermembrane space. In humans, defects in complex I are involved in a wide range of degenerative disorders. Recent progress in the X-ray structural analysis of prokaryotic and eukaryotic complex I confirmed that the redox reactions are confined entirely to the hydrophilic peripheral arm of the L-shaped molecule and take place at a remarkable distance from the membrane domain. While this clearly implies that the proton pumping within the membrane arm of complex I is driven indirectly via long-range conformational coupling, the molecular mechanism and the number, identity, and localization of the pump-sites remains unclear. Here, we report that upon deletion of the gene for a small accessory subunit of the Yarrowia complex I, a stable subcomplex (nb8mΔ is formed that lacks the distal part of the membrane domain as revealed by single particle analysis. The analysis of the subunit composition of holo and subcomplex by three complementary proteomic approaches revealed that two (ND4 and ND5 of the three subunits with homology to bacterial Mrp-type Na(+/H(+ antiporters that have been discussed as prime candidates for harbouring the proton pumps were missing in nb8mΔ. Nevertheless, nb8mΔ still pumps protons at half the stoichiometry of the complete enzyme. Our results provide evidence that the membrane arm of complex I harbours two functionally distinct pump modules that are connected in series by the long helical transmission element recently identified by X-ray structural analysis.

  15. Real and complex analysis

    CERN Document Server

    Apelian, Christopher; Taft, Earl; Nashed, Zuhair

    2009-01-01

    The Spaces R, Rk, and CThe Real Numbers RThe Real Spaces RkThe Complex Numbers CPoint-Set Topology Bounded SetsClassification of Points Open and Closed SetsNested Intervals and the Bolzano-Weierstrass Theorem Compactness and Connectedness Limits and Convergence Definitions and First Properties Convergence Results for SequencesTopological Results for Sequences Properties of Infinite SeriesManipulations of Series in RFunctions: Definitions and Limits DefinitionsFunctions as MappingsSome Elementary Complex FunctionsLimits of FunctionsFunctions: Continuity and Convergence Continuity Uniform Continuity Sequences and Series of FunctionsThe DerivativeThe Derivative for f: D1 → RThe Derivative for f: Dk → RThe Derivative for f: Dk → RpThe Derivative for f: D → CThe Inverse and Implicit Function TheoremsReal IntegrationThe Integral of f: [a, b] → RProperties of the Riemann Integral Further Development of Integration TheoryVector-Valued and Line IntegralsComplex IntegrationIntroduction to Complex Integrals Fu...

  16. Design of glass-ceramic complex microstructure with using onset point of crystallization in differential thermal analysis

    International Nuclear Information System (INIS)

    Hwang, Seongjin; Kim, Jinho; Shin, Hyo-Soon; Kim, Jong-Hee; Kim, Hyungsun

    2008-01-01

    Two types of frits with different compositions were used to develop a high strength substrate in electronic packaging using a low temperature co-fired ceramic process. In order to reveal the crystallization stage during heating to approximately 900 deg. C, a glass-ceramic consisting of the two types of frits, which had been crystallized to diopside and anorthite after firing, was tested at different mixing ratios of the frits. The exothermal peaks deconvoluted by a Gauss function in the differential thermal analysis curves were used to determine the onset point of crystallization of diopside or anorthite. The onset points of crystallization were affected by the mixing ratio of the frits, and the microstructure of the glass-ceramic depended on the onset point of crystallization. It was found that when multicrystalline phases appear in the microstructure, the resulting complex microstructure could be predicted from the onset point of crystallization obtained by differential thermal analysis

  17. Synthesis, Characterization, and Antibacterial Studies of Mixed Ligand Dioxouranium Complexes with 8-Hydroxyquinoline and Some Amino Acids

    Science.gov (United States)

    Patil, Sunil S.; Thakur, Ganesh A.; Shaikh, Manzoor M.

    2011-01-01

    Mixed ligand complexes of dioxouranium (VI) of the type [UO2(Q)(L)·2H2O] have been synthesized using 8-hydroxyquinoline (HQ) as a primary ligand and amino acids (HL) such as L-threonine, L-tryptophan, and L-isoleucine as secondary ligands. The metal complexes have been characterized by elemental analysis, electrical conductance, magnetic susceptibility measurements, and spectral and thermal studies. The electrical conductance studies of the complexes indicate their nonelectrolytic nature. Magnetic susceptibility measurements revealed diamagnetic nature of the complexes. Electronic absorption spectra of the complexes show intraligand and charge transfer transitions, respectively. Bonding of the metal ion through N- and O-donor atoms of the ligands is revealed by IR studies, and the chemical environment of the protons is confirmed by NMR studies. The thermal analysis data of the complexes indicate the presence of coordinated water molecules. The agar cup and tube dilution methods have been used to study the antibacterial activity of the complexes against the pathogenic bacteria S. aureus, C. diphtheriae, S. typhi, and E. coli. PMID:22389843

  18. Synthesis, analysis and radiolysis of the cobalt III 8 hydroxyquinolinate complex

    International Nuclear Information System (INIS)

    Mestnik, S.A.C.; Silva, C.P.G. da.

    1981-11-01

    The cobalt III 8-hidroxyquinolinate complex was syntetized from a solution of cobalt II. The compound was analysed by IR absorption spectroscopy, elemental analysis and by the determination of number of ligands. The radiolytic degradation was verified by spectrophotometry after submitting samples of 10 - 3 M complex in ethanolic solution to different doses of gamma radiation from a 60 Co source. The change of maximum absorbance of the complex with different doses of gamma radiation and its UV-VIS absorption spectra are presented. The complex in the solid state was also irradiated with 6,9 Mrad of gamma radiation but it didn't present degradation. (Author) [pt

  19. Using neutral theory to reveal the contribution of meta-community processes to assembly in complex landscapes

    Directory of Open Access Journals (Sweden)

    Dominique Gravel

    2014-04-01

    Full Text Available The metacommunity perspective appears as an appropriate conceptual framework to make ecology more predictive. It is particularly relevant to limnology, where exchanges of organisms and nutrients affect community and ecosystem properties from the local to the regional scales. The recent development of neutral theory appears as a step back in that direction because of the assumption of ecological equivalence and the absence of any effect of the environment on community organization. A remarkable strength of neutral theory is nonetheless to provide a general theory of diversity that accounts for a wide range of empirical observations. In this paper, we argue that neutral theory can be useful to understand the impact of dispersal on community assembly in landscapes of various complexities. Our analysis focus on spatially explicit landscapes conceptualized as networks of local communities (e.g., lakes connected to each other by dispersal channels (e.g., rivers. The main objective of the paper is to use neutral theory to stress the importance of landscape structure on the distribution of diversity. We refer to the landscape organization as a spatial contingency that could potentially affect the coexistence mechanisms at play. We briefly review the main approaches to describe spatial networks and describe three simple toy models of metacommunity dynamics. We take this opportunity to review their assumptions and main predictions. We then conduct simulations of these models to reveal with simple examples the impact of spatial network structure on diversity distribution. The simulation results show that competitive interactions buffer the potential impact of landscape structure. The strongest relationship between node position in the landscape and species richness was observed for the patch dynamics model without any interactions. On the other hand, strong and unequal competitive interactions minimized the effect of node position. We conclude that the

  20. Terbutaline causes immobilization of single β2-adrenergic receptor-ligand complexes in the plasma membrane of living A549 cells as revealed by single-molecule microscopy

    Science.gov (United States)

    Sieben, Anne; Kaminski, Tim; Kubitscheck, Ulrich; Häberlein, Hanns

    2011-02-01

    G-protein-coupled receptors are important targets for various drugs. After signal transduction, regulatory processes, such as receptor desensitization and internalization, change the lateral receptor mobility. In order to study the lateral diffusion of β2-adrenergic receptors (β2AR) complexed with fluorescently labeled noradrenaline (Alexa-NA) in plasma membranes of A549 cells, trajectories of single receptor-ligand complexes were monitored using single-particle tracking. We found that a fraction of 18% of all β2ARs are constitutively immobile. About 2/3 of the β2ARs moved with a diffusion constant of D2 = 0.03+/-0.001 μm2/s and about 17% were diffusing five-fold faster (D3 = 0.15+/-0.02 μm2/s). The mobile receptors moved within restricted domains and also showed a discontinuous diffusion behavior. Analysis of the trajectory lengths revealed two different binding durations with τ1 = 77+/-1 ms and τ2 = 388+/-11 ms. Agonistic stimulation of the β2AR-Alexa-NA complexes with 1 μM terbutaline caused immobilization of almost 50% of the receptors within 35 min. Simultaneously, the mean area covered by the mobile receptors decreased significantly. Thus, we demonstrated that agonistic stimulation followed by cell regulatory processes results in a change in β2AR mobility suggesting that different receptor dynamics characterize different receptor states.

  1. System for decision analysis support on complex waste management issues

    International Nuclear Information System (INIS)

    Shropshire, D.E.

    1997-01-01

    A software system called the Waste Flow Analysis has been developed and applied to complex environmental management processes for the United States Department of Energy (US DOE). The system can evaluate proposed methods of waste retrieval, treatment, storage, transportation, and disposal. Analysts can evaluate various scenarios to see the impacts to waste slows and schedules, costs, and health and safety risks. Decision analysis capabilities have been integrated into the system to help identify preferred alternatives based on a specific objectives may be to maximize the waste moved to final disposition during a given time period, minimize health risks, minimize costs, or combinations of objectives. The decision analysis capabilities can support evaluation of large and complex problems rapidly, and under conditions of variable uncertainty. The system is being used to evaluate environmental management strategies to safely disposition wastes in the next ten years and reduce the environmental legacy resulting from nuclear material production over the past forty years

  2. A low complexity visualization tool that helps to perform complex systems analysis

    International Nuclear Information System (INIS)

    Beiro, M G; Alvarez-Hamelin, J I; Busch, J R

    2008-01-01

    In this paper, we present an extension of large network visualization (LaNet-vi), a tool to visualize large scale networks using the k-core decomposition. One of the new features is how vertices compute their angular position. While in the later version it is done using shell clusters, in this version we use the angular coordinate of vertices in higher k-shells, and arrange the highest shell according to a cliques decomposition. The time complexity goes from O(n√n) to O(n) upon bounds on a heavy-tailed degree distribution. The tool also performs a k-core-connectivity analysis, highlighting vertices that are not k-connected; e.g. this property is useful to measure robustness or quality of service (QoS) capabilities in communication networks. Finally, the actual version of LaNet-vi can draw labels and all the edges using transparencies, yielding an accurate visualization. Based on the obtained figure, it is possible to distinguish different sources and types of complex networks at a glance, in a sort of 'network iris-print'.

  3. A low complexity visualization tool that helps to perform complex systems analysis

    Science.gov (United States)

    Beiró, M. G.; Alvarez-Hamelin, J. I.; Busch, J. R.

    2008-12-01

    In this paper, we present an extension of large network visualization (LaNet-vi), a tool to visualize large scale networks using the k-core decomposition. One of the new features is how vertices compute their angular position. While in the later version it is done using shell clusters, in this version we use the angular coordinate of vertices in higher k-shells, and arrange the highest shell according to a cliques decomposition. The time complexity goes from O(n\\sqrt n) to O(n) upon bounds on a heavy-tailed degree distribution. The tool also performs a k-core-connectivity analysis, highlighting vertices that are not k-connected; e.g. this property is useful to measure robustness or quality of service (QoS) capabilities in communication networks. Finally, the actual version of LaNet-vi can draw labels and all the edges using transparencies, yielding an accurate visualization. Based on the obtained figure, it is possible to distinguish different sources and types of complex networks at a glance, in a sort of 'network iris-print'.

  4. Histological analysis of thelohaniasis in white-clawed crayfish Austropotamobius pallipes complex

    Directory of Open Access Journals (Sweden)

    Quaglio F.

    2011-09-01

    Full Text Available From 2004 to 2006, a parasitological survey aimed at the detection of the microsporidian parasite Thelohania contejeani Henneguy was carried out on 177 wild white-clawed crayfish (Austropotamobius pallipes complex captured in six streams and rivers of the province of Belluno in north-eastern Italy. Microscopical examination of the skeletal muscles, and histological analysis applying different histochemical stains to full transverse and sagittal sections of the cephalothorax and abdomen were carried out. Transmission electron microscopy (TEM was also conducted on the parasites recovered during the survey. Out of 177 crayfish examined, Thelohania contejeani (Microsporidia, Thelohaniidae was present in only one crayfish from the Vena d’oro creek. The parasite was detected in the skeletal muscles in several developmental stages, including mature spores, which represented the most common stage recovered. Sporophorous vesicles were also present. Histological examination revealed that the fibres of the skeletal, cardiac and intestinal muscles were filled with spores. Melanin infiltrations were focally present in the infected striated muscles. The gill phagocytic nephrocytes were engulfed by small masses of spores. Among the staining techniques applied, Crossman’s trichrome stain represented the most effective method of detecting T. contejeani.

  5. Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress.

    Directory of Open Access Journals (Sweden)

    Henry D Priest

    Full Text Available Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

  6. Structure, magnetic behavior, and anisotropy of homoleptic trinuclear lanthanoid 8-quinolinolate complexes.

    Science.gov (United States)

    Chilton, Nicholas F; Deacon, Glen B; Gazukin, Olga; Junk, Peter C; Kersting, Berthold; Langley, Stuart K; Moubaraki, Boujemaa; Murray, Keith S; Schleife, Frederik; Shome, Mahasish; Turner, David R; Walker, Julia A

    2014-03-03

    Three complexes of the form [Ln(III)3(OQ)9] (Ln = Gd, Tb, Dy; OQ = 8-quinolinolate) have been synthesized and their magnetic properties studied. The trinuclear complexes adopt V-shaped geometries with three bridging 8-quinolinolate oxygen atoms between the central and peripheral eight-coordinate metal atoms. The magnetic properties of these three complexes differ greatly. Variable-temperature direct-current (dc) magnetic susceptibility measurements reveal that the gadolinium and terbium complexes display weak antiferromagnetic nearest-neighbor magnetic exchange interactions. This was quantified in the isotropic gadolinium case with an exchangecoupling parameter of J = -0.068(2) cm(-1). The dysprosium compound displays weak ferromagnetic exchange. Variable-frequency and -temperature alternating-current magnetic susceptibility measurements on the anisotropic cases reveal that the dysprosium complex displays single-molecule-magnet behavior, in zero dc field, with two distinct relaxation modes of differing time scales within the same molecule. Analysis of the data revealed anisotropy barriers of Ueff = 92 and 48 K for the two processes. The terbium complex, on the other hand, displays no such behavior in zero dc field, but upon application of a static dc field, slow magnetic relaxation can be observed. Ab initio and electrostatic calculations were used in an attempt to explain the origin of the experimentally observed slow relaxation of the magnetization for the dysprosium complex.

  7. Chitosan-based Schiff base-metal complexes (Mn, Cu, Co) as ...

    Indian Academy of Sciences (India)

    and A C PISE. Chemistry Research ... Data obtained by thermal analysis revealed that these complexes showed good thermal ... vents along with its inherent chirality makes chitosan .... resulting Schiff base IC was cooled, filtered and washed with ethanol ..... experiments with homogeneous Mn-salen catalyst at different ...

  8. Re-Analysis of Metagenomic Sequences from Acute Flaccidmyelitis Patients Reveals Alternatives to Enterovirus D68 Infection

    Science.gov (United States)

    2015-07-13

    caused in some cases by infection with enterovirus D68. We found that among the patients whose symptoms were previously attributed to enterovirus D68...distribution is unlimited. Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus D68...Street Baltimore, MD 21218 -2685 ABSTRACT Re-analysis of metagenomic sequences from acute flaccidmyelitis patients reveals alternatives to enterovirus

  9. HLA-DR Genotyping and Mitochondrial DNA Analysis Reveal the Presence of Family Burials in a Fourth Century Romano-British Christian Cemetery

    Directory of Open Access Journals (Sweden)

    Canh P. Voong

    2017-12-01

    Full Text Available In Colchester, Britain's oldest recorded town, during the Roman period there were areas which were clearly used solely as cemeteries. One of the most significant is at Butt Road, which includes a late Roman probable Christian cemetery with an associated building, apparently a church, that overlies and developed from a pagan inhumation cemetery. DNA was extracted from the long bones (femurs of 29 individuals, mostly from a large complex of burials centered on two timber vaults. These were thought to comprise a number of family groupings, deduced from osteological analysis, stratigraphical and other considerations. The use of a modified version of the silica-based purification method recovered nanogram quantities of DNA/gram of bone. Two-stage amplification, incorporating primer-extension preamplification-polymerase chain reaction, permitted simultaneous amplification of both mitochondrial and nuclear DNA. Sequence-specific oligonucleotide probes yielded human leukocyte antigen (HLA-DR typing of seven samples, with four revealing the infrequent HLA-DR10 genotype. Examination of the control region of mitochondrial DNA (mtDNA by direct sequencing revealed polymorphisms yet to be reported in the modern population. HLA-DRB typing and mtDNA analysis affirmatively supported kinship among some, if not all, individuals in the “vault complex” and demonstrate a continental European origin of the individuals investigated.

  10. A Comparative Study of the Application of Fluorescence Excitation-Emission Matrices Combined with Parallel Factor Analysis and Nonnegative Matrix Factorization in the Analysis of Zn Complexation by Humic Acids

    Directory of Open Access Journals (Sweden)

    Patrycja Boguta

    2016-10-01

    Full Text Available The main aim of this study was the application of excitation-emission fluorescence matrices (EEMs combined with two decomposition methods: parallel factor analysis (PARAFAC and nonnegative matrix factorization (NMF to study the interaction mechanisms between humic acids (HAs and Zn(II over a wide concentration range (0–50 mg·dm−3. The influence of HA properties on Zn(II complexation was also investigated. Stability constants, quenching degree and complexation capacity were estimated for binding sites found in raw EEM, EEM-PARAFAC and EEM-NMF data using mathematical models. A combination of EEM fluorescence analysis with one of the proposed decomposition methods enabled separation of overlapping binding sites and yielded more accurate calculations of the binding parameters. PARAFAC and NMF processing allowed finding binding sites invisible in a few raw EEM datasets as well as finding totally new maxima attributed to structures of the lowest humification. Decomposed data showed an increase in Zn complexation with an increase in humification, aromaticity and molecular weight of HAs. EEM-PARAFAC analysis also revealed that the most stable compounds were formed by structures containing the highest amounts of nitrogen. The content of oxygen-functional groups did not influence the binding parameters, mainly due to fact of higher competition of metal cation with protons. EEM spectra coupled with NMF and especially PARAFAC processing gave more adequate assessments of interactions as compared to raw EEM data and should be especially recommended for modeling of complexation processes where the fluorescence intensities (FI changes are weak or where the processes are interfered with by the presence of other fluorophores.

  11. A Cost-Effectiveness Analysis of Reverse Total Shoulder Arthroplasty versus Hemiarthroplasty for the Management of Complex Proximal Humeral Fractures in the Elderly.

    Science.gov (United States)

    Osterhoff, Georg; O'Hara, Nathan N; D'Cruz, Jennifer; Sprague, Sheila A; Bansback, Nick; Evaniew, Nathan; Slobogean, Gerard P

    2017-03-01

    There is ongoing debate regarding the optimal surgical treatment of complex proximal humeral fractures in elderly patients. To evaluate the cost-effectiveness of reverse total shoulder arthroplasty (RTSA) compared with hemiarthroplasty (HA) in the management of complex proximal humeral fractures, using a cost-utility analysis. On the basis of data from published literature, a cost-utility analysis was conducted using decision tree and Markov modeling. A single-payer perspective, with a willingness-to-pay (WTP) threshold of Can$50,000 (Canadian dollars), and a lifetime time horizon were used. The incremental cost-effectiveness ratio (ICER) was used as the study's primary outcome measure. In comparison with HA, the incremental cost per quality-adjusted life-year gained for RTSA was Can$13,679. One-way sensitivity analysis revealed the model to be sensitive to the RTSA implant cost and the RTSA procedural cost. The ICER of Can$13,679 is well below the WTP threshold of Can$50,000, and probabilistic sensitivity analysis demonstrated that 92.6% of model simulations favored RTSA. Our economic analysis found that RTSA for the treatment of complex proximal humeral fractures in the elderly is the preferred economic strategy when compared with HA. The ICER of RTSA is well below standard WTP thresholds, and its estimate of cost-effectiveness is similar to other highly successful orthopedic strategies such as total hip arthroplasty for the treatment of hip arthritis. Copyright © 2017 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  12. A Complexity Analysis of Functional Interpretations

    DEFF Research Database (Denmark)

    Hernest, Mircea-Dan; Kohlenbach, Ulrich

    2003-01-01

    We give a quantitative analysis of G ̈odel’s functional interpretation and its monotone variant. The two have been used for the extraction of programs and numerical bounds as well as for conservation results. They apply both to (semi-)intuitionistic as well as (combined with negative translation...... of the verifying proof. In all cases terms of size linear in the size of the proof at input can be extracted and the corresponding extraction algorithms have cubic worst-time complexity. The verifying proofs have depth linear in the depth of the proof at input and the maximal size of a formula of this proof....

  13. Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the human Rod–Zwilch–ZW10 (RZZ) complex

    Energy Technology Data Exchange (ETDEWEB)

    Altenfeld, Anika; Wohlgemuth, Sabine [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Wehenkel, Annemarie [Institut Curie, CNRS UMR 3348/INSERM U1005, Bâtiment 110, Centre Universitaire, 91405 Orsay CEDEX (France); Vetter, Ingrid R. [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); Musacchio, Andrea, E-mail: andrea.musacchio@mpi-dortmund.mpg.de [Max Planck Institute of Molecular Physiology, Otto Hahn Strasse 11, 44227 Dortmund (Germany); University of Duisburg-Essen, Universitätstrasse 1, 45141 Essen (Germany)

    2015-03-20

    The 800 kDa complex of the human Rod, Zwilch and ZW10 proteins (the RZZ complex) was reconstituted in insect cells, purified, crystallized and subjected to preliminary X-ray diffraction analysis. The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted by co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3{sub 1} (No. 144) or P3{sub 2} (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.

  14. Analysis of complex systems using neural networks

    International Nuclear Information System (INIS)

    Uhrig, R.E.

    1992-01-01

    The application of neural networks, alone or in conjunction with other advanced technologies (expert systems, fuzzy logic, and/or genetic algorithms), to some of the problems of complex engineering systems has the potential to enhance the safety, reliability, and operability of these systems. Typically, the measured variables from the systems are analog variables that must be sampled and normalized to expected peak values before they are introduced into neural networks. Often data must be processed to put it into a form more acceptable to the neural network (e.g., a fast Fourier transformation of the time-series data to produce a spectral plot of the data). Specific applications described include: (1) Diagnostics: State of the Plant (2) Hybrid System for Transient Identification, (3) Sensor Validation, (4) Plant-Wide Monitoring, (5) Monitoring of Performance and Efficiency, and (6) Analysis of Vibrations. Although specific examples described deal with nuclear power plants or their subsystems, the techniques described can be applied to a wide variety of complex engineering systems

  15. Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B.

    Science.gov (United States)

    Krause-Kyora, Ben; Susat, Julian; Key, Felix M; Kühnert, Denise; Bosse, Esther; Immel, Alexander; Rinne, Christoph; Kornell, Sabin-Christin; Yepes, Diego; Franzenburg, Sören; Heyne, Henrike O; Meier, Thomas; Lösch, Sandra; Meller, Harald; Friederich, Susanne; Nicklisch, Nicole; Alt, Kurt W; Schreiber, Stefan; Tholey, Andreas; Herbig, Alexander; Nebel, Almut; Krause, Johannes

    2018-05-10

    The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses. © 2018, Krause-Kyora et al.

  16. Structural analysis of the Rubjerg Knude Glaciotectonic Complex, Vendsyssel, Northern Denmark

    Directory of Open Access Journals (Sweden)

    Pedersen, Stig A. Schack

    2005-12-01

    Full Text Available The Rubjerg Knude Glaciotectonic Complex is a thin-skinned thrust-fault complex that was formed during the advance of the Scandinavian Ice Sheet (30 000 – 26 000 B.P.; it is well exposed in a 6 km long coastal profile bordering the North Sea in northern Denmark. Theglaciotectonic thrust-fault deformation revealed by this cliff section has been subjected to detailed structural analysis based on photogrammetric measurement and construction of a balanced cross-section. Thirteen sections are differentiated, characterising the distal to proximal structural development of the complex. The deformation affected three stratigraphic units: the Middle Weichselian arctic marine Stortorn Formation, the mainly glaciolacustrine Lønstrup Klint Formation and the dominantly fluvial Rubjerg Knude Formation; these three formations are formally defined herein, together with the Skærumhede Group which includes the Stortorn and Lønstrup Klint Formations. The Rubjerg Knude Formation was deposited on a regional unconformity that caps the Lønstrup Klint Formation and separates pre-tectonic deposits below from syntectonic deposits above.In the distal part of the complex, the thrust-fault architecture is characterised by thin flatlying thrust sheets displaced over the footwall flat of the foreland for a distance of more than 500 m. Towards the proximal part of the complex, the dip of the thrust faults increases, and over long stretches they are over-steepened to an upright position. The lowest décollement zone is about 40 m below sea level in the proximal part of the system, and shows a systematicstep-wise change to higher levels in a distal (southwards direction. The structural elements are ramps and flats related to hanging-wall and footwall positions. Above upper ramp-hinges,hanging-wall anticlines developed; footwall synclines are typically related to growth-fault sedimentation in syntectonic piggyback basins, represented by the Rubjerg Knude Formation. Blocks

  17. Phylogenetic analysis of glycerol 3-phosphate acyltransferases in opisthokonts reveals unexpected ancestral complexity and novel modern biosynthetic components.

    Directory of Open Access Journals (Sweden)

    Heather C Smart

    Full Text Available Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT, have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of 'fungal' orthologs in the basal taxa of the holozoa and 'animal' orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.

  18. Training Revising Based Traversability Analysis of Complex Terrains for Mobile Robot

    Directory of Open Access Journals (Sweden)

    Rui Song

    2014-05-01

    Full Text Available Traversability analysis is one of the core issues in the autonomous navigation for mobile robots to identify the accessible area by the information of sensors on mobile robots. This paper proposed a model to analyze the traversability of complex terrains based on rough sets and training revising. The model described the traversability for mobile robots by traversability cost. Through the experiment, the paper gets the conclusion that traversability analysis model based on rough sets and training revising can be used where terrain features are rich and complex, can effectively handle the unstructured environment, and can provide reliable and effective decision rules in the autonomous navigation for mobile robots.

  19. Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

    Science.gov (United States)

    Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

    2013-12-06

    Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

  20. Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina

    DEFF Research Database (Denmark)

    Gallo, G.; Renzone, G.; Alduina, R.

    2010-01-01

    A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially...... available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-proteome-maps). Functional clustering analysis revealed that differentially expressed proteins belong to functional groups involved in central carbon metabolism, amino acid metabolism and protein biosynthesis...... intermediates, were upregulated during antibiotic production. qRT-PCR analysis revealed that 8 out of 14 upregulated genes showed a positive correlation between changes at translational and transcriptional expression level. Furthermore, proteomic analysis of two nonproducing mutants, restricted to a sub...

  1. Binding affinities of Schiff base Fe(II) complex with BSA and calf-thymus DNA: Spectroscopic investigations and molecular docking analysis

    Science.gov (United States)

    Rudra, Suparna; Dasmandal, Somnath; Patra, Chiranjit; Kundu, Arjama; Mahapatra, Ambikesh

    2016-09-01

    The binding interaction of a synthesized Schiff base Fe(II) complex with biological macromolecules viz., bovine serum albumin (BSA) and calf thymus(ct)-DNA have been investigated using different spectroscopic techniques coupled with viscosity measurements at physiological pH and 298 K. Regular amendments in emission intensities of BSA upon the action of the complex indicate significant interaction between them, and the binding interaction have been characterized by Stern Volmer plots and thermodynamic binding parameters. On the basis of this quenching technique one binding site with binding constant (Kb = (7.6 ± 0.21) × 105) between complex and protein have been obtained at 298 K. Time-resolved fluorescence studies have also been encountered to understand the mechanism of quenching induced by the complex. Binding affinities of the complex to the fluorophores of BSA namely tryptophan (Trp) and tyrosine (Tyr) have been judged by synchronous fluorescence studies. Secondary structural changes of BSA rooted by the complex has been revealed by CD spectra. On the other hand, hypochromicity of absorption spectra of the complex with the addition of ct-DNA and the gradual reduction in emission intensities of ethidium bromide bound ct-DNA in presence of the complex indicate noticeable interaction between ct-DNA and the complex with the binding constant (4.2 ± 0.11) × 106 M- 1. Life-time measurements have been studied to determine the relative amplitude of binding of the complex to ct-DNA base pairs. Mode of binding interaction of the complex with ct-DNA has been deciphered by viscosity measurements. CD spectra have also been used to understand the changes in ct-DNA structure upon binding with the metal complex. Density functional theory (DFT) and molecular docking analysis have been employed in highlighting the interactive phenomenon and binding location of the complex with the macromolecules.

  2. Progress of studies on traditional chinese medicine based on complex network analysis

    Directory of Open Access Journals (Sweden)

    Qian-Ru Zhang

    2017-01-01

    Full Text Available Traditional Chinese medicine (TCM is a distinct medical system that deals with the life–health–disease–environment relationship using holistic, dynamic, and dialectical thinking. However, reductionism has often restricted the conventional studies on TCM, and these studies did not investigate the central concepts of TCM theory about the multiple relationships among life, health, disease, and environment. Complex network analysis describes a wide variety of complex systems in the real world, and it has the potential to bridge the gap between TCM and modern science owing to the holism of TCM theory. This article summarizes the current research involving TCM network analysis and highlights the computational tools and analysis methods involved in this research. Finally, to inspire a new approach, the article discussed the potential problems underlying the application of TCM network analysis.

  3. Central Waste Complex (CWC) Waste Analysis Plan

    International Nuclear Information System (INIS)

    ELLEFSON, M.D.

    2000-01-01

    The purpose of this waste analysis plan (WAP) is to document the waste acceptance process, sampling methodologies, analytical techniques, and overall processes that are undertaken for waste accepted for storage at the Central Waste Complex (CWC), which is located in the 200 West Area of the Hanford Facility, Richland, Washington. Because dangerous waste does not include the source special nuclear and by-product material components of mixed waste, radionuclides are not within the scope of this document. The information on radionuclides is provided only for general knowledge. This document has been revised to meet the interim status waste analysis plan requirements of Washington Administrative Code (WAC) 173 303-300(5). When the final status permit is issued, permit conditions will be incorporated and this document will be revised accordingly

  4. MANAGEMENT OF SPORT COMPLEXES

    Directory of Open Access Journals (Sweden)

    Marian STAN

    2015-07-01

    Full Text Available The actuality of the investigated theme. Nowadays, human evolution, including his intellectual development, proves the fact that especially the creation manpower and the employment was the solution of all life’s ambitions in society. So, the fact is that in reality, man is the most important capital of the society. Also, in an individual’s life, the practice of sport plays a significant role and that’s why the initiation, the launch and the management of sports complexes activity reveal the existence of specific management features that we will identify and explain in the current study. The aim of the research refers to the elaboration of a theoretical base of the management of the sport complexes, to the pointing of the factors that influence the efficient existence and function of a sport complex in our country and to the determination of the responsibilities that have a manager who directs successfully the activity of the sport complexes. The investigation is based on theoretical methods, such as: scientific documentation, analysis, synthesis, comparison and on empirical research methods, like: study of researched literature and observation. The results of the research indicate the fact that the profitability of a sport complex must assure a particular structure to avoid the bankruptcy risk and also, that the administration of the sport complexes activity must keep in view the reliable functions of the contemporaneous management.

  5. Chemical genetics analysis of an aniline mustard anticancer agent reveals complex I of the electron transport chain as a target.

    Science.gov (United States)

    Fedeles, Bogdan I; Zhu, Angela Y; Young, Kellie S; Hillier, Shawn M; Proffitt, Kyle D; Essigmann, John M; Croy, Robert G

    2011-09-30

    The antitumor agent 11β (CAS 865070-37-7), consisting of a DNA-damaging aniline mustard linked to an androgen receptor (AR) ligand, is known to form covalent DNA adducts and to induce apoptosis potently in AR-positive prostate cancer cells in vitro; it also strongly prevents growth of LNCaP xenografts in mice. The present study describes the unexpectedly strong activity of 11β against the AR-negative HeLa cells, both in cell culture and tumor xenografts, and uncovers a new mechanism of action that likely explains this activity. Cellular fractionation experiments indicated that mitochondria are the major intracellular sink for 11β; flow cytometry studies showed that 11β exposure rapidly induced oxidative stress, mitochondria being an important source of reactive oxygen species (ROS). Additionally, 11β inhibited oxygen consumption both in intact HeLa cells and in isolated mitochondria. Specifically, 11β blocked uncoupled oxygen consumption when mitochondria were incubated with complex I substrates, but it had no effect on oxygen consumption driven by substrates acting downstream of complex I in the mitochondrial electron transport chain. Moreover, 11β enhanced ROS generation in isolated mitochondria, suggesting that complex I inhibition is responsible for ROS production. At the cellular level, the presence of antioxidants (N-acetylcysteine or vitamin E) significantly reduced the toxicity of 11β, implicating ROS production as an important contributor to cytotoxicity. Collectively, our findings establish complex I inhibition and ROS generation as a new mechanism of action for 11β, which supplements conventional DNA adduct formation to promote cancer cell death.

  6. Strategic directions of personnel potential forming of a building complex

    Directory of Open Access Journals (Sweden)

    Simonova Marina

    2016-01-01

    Full Text Available The analysis of directions of strategic approach forming of labor potential management of a building complex is carried out in this paper. On the basis of this analysis the system of actions for strategy forming divided into consecutive stages is offered. The development of the personnel forecast is a strategic planning basis. One of personnel forecast variants is the correlation of needs estimates in personnel of a building complex with available allowances. On the basis of the personnel forecast strategic analysis it is possible to compose working programs for the stated goals of implementation. Operational assessment of personnel requirements of a building complex is proved to be combined with strategic objectives. Some assessment approaches to qualitative and quantitative need for specialists of a building complex are offered. The fact that high-quality labor power supply system of a building complex with should be based on industry development forecast and increase in construction products competitiveness is revealed in the article. Strategic management priority will allow to react immediately to the current situation changes, to introduce amendments both into tactical, and operational management.

  7. Complex cytogeographical patterns reveal a dynamic tetraploid–octoploid contact zone

    Science.gov (United States)

    Castro, Mariana; Castro, Sílvia; Figueiredo, Albano; Husband, Brian; Loureiro, João

    2018-01-01

    Abstract The distribution of cytotypes in mixed-ploidy species is crucial for evaluating ecological processes involved in the establishment and evolution of polyploid taxa. Here, we use flow cytometry and chromosome counts to explore cytotype diversity and distributions within a tetraploid–octoploid contact zone. We then use niche modelling and ploidy seed screening to assess the roles of niche differentiation among cytotypes and reproductive interactions, respectively, in promoting cytotype coexistence. Two cytotypes, tetraploids and octoploids, were dominant within the contact zone. They were most often distributed parapatrically or allopatrically, resulting in high geographic isolation. Still, 16.7 % of localities comprised two or more cytotypes, including the intermediate hexaploid cytotype. Tetraploids and octoploids had high environmental niche overlap and associated with similar climatic environments, suggesting they have similar ecological requirements. Given the geographical separation and habitat similarity among cytotypes, mixed-ploidy populations may be transitional and subject to the forces of minority cytotype exclusion which lead to pure-ploidy populations. However, seed ploidy analysis suggests that strong reproductive barriers may enforce assortative mating which favours stable cytotype coexistence. High cytogenetic diversity detected in the field suggests that unreduced gamete formation and hybridization events seem frequent in the studied polyploid complex and might be involved with the recurrent polyploid formation, governing, as well, the gene flow between cytogenetic entities. PMID:29593853

  8. Tandem mass spectrometry: analysis of complex mixtures

    International Nuclear Information System (INIS)

    Singleton, K.E.

    1985-01-01

    Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction products of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated

  9. Analysis of costs-benefits tradeoffs of complex security systems

    International Nuclear Information System (INIS)

    Hicks, M.J.

    1996-01-01

    Essential to a systems approach to design of security systems is an analysis of the cost effectiveness of alternative designs. While the concept of analysis of costs and benefits is straightforward, implementation can be at the least tedious and, for complex designs and alternatives, can become nearly intractable without the help of structured analysis tools. PACAIT--Performance and Cost Analysis Integrated Tools--is a prototype tool. The performance side of the analysis collates and reduces data from ASSESS, and existing DOE PC-based security systems performance analysis tool. The costs side of the analysis uses ACE, an existing DOD PC-based costs analysis tool. Costs are reported over the full life-cycle of the system, that is, the costs to procure, operate, maintain and retire the system and all of its components. Results are collected in Microsoft reg-sign Excel workbooks and are readily available to analysts and decision makers in both tabular and graphical formats and at both the system and path-element levels

  10. Molecular fingerprinting of complex grass allergoids: size assessments reveal new insights in epitope repertoires and functional capacities.

    Science.gov (United States)

    Starchenka, S; Bell, A J; Mwange, J; Skinner, M A; Heath, M D

    2017-01-01

    Subcutaneous allergen immunotherapy (SCIT) is a well-documented treatment for allergic disease which involves injections of native allergen or modified (allergoid) extracts. The use of allergoid vaccines is a growing sector of the allergy immunotherapy market, associated with shorter-course therapy. The aim of this study was the structural and immunological characterisation of group 1 (Lol p 1) IgG-binding epitopes within a complex mix grass allergoid formulation containing rye grass. HP-SEC was used to resolve a mix grass allergoid preparation of high molecular weight into several distinct fractions with defined molecular weight and elution profiles. Allergen verification of the HP-SEC allergoid fractions was confirmed by mass spectrometry analysis. IgE and IgG immunoreactivity of the allergoid preparations was explored and Lol p 1 specific IgG-binding epitopes mapped by SPOT synthesis technology (PepSpot™) with structural analysis based on a Lol p 1 homology model. Grass specific IgE reactivity of the mix grass modified extract (allergoid) was diminished in comparison with the mix grass native extract. A difference in IgG profiles was observed between an intact mix grass allergoid preparation and HP-SEC allergoid fractions, which indicated enhancement of accessible reactive IgG epitopes across size distribution profiles of the mix grass allergoid formulation. Detailed analysis of the epitope specificity showed retention of six Lol p 1 IgG-binding epitopes in the mix grass modified extract. The structural and immunological changes which take place following the grass allergen modification process was further unravelled revealing distinct IgG immunological profiles. All epitopes were mapped on the solvent exposed area of Lol p 1 homology model accessible for IgG binding. One of the epitopes was identified as an 'immunodominant' Lol p 1 IgG-binding epitope (62-IFKDGRGCGSCFEIK-76) and classified as a novel epitope. The results from this study support the concept

  11. Automated analysis and design of complex structures

    International Nuclear Information System (INIS)

    Wilson, E.L.

    1977-01-01

    The present application of optimum design appears to be restricted to components of the structure rather than to the total structural system. Since design normally involved many analysis of the system any improvement in the efficiency of the basic methods of analysis will allow more complicated systems to be designed by optimum methods. The evaluation of the risk and reliability of a structural system can be extremely important. Reliability studies have been made of many non-structural systems for which the individual components have been extensively tested and the service environment is known. For such systems the reliability studies are valid. For most structural systems, however, the properties of the components can only be estimated and statistical data associated with the potential loads is often minimum. Also, a potentially critical loading condition may be completely neglected in the study. For these reasons and the previous problems associated with the reliability of both linear and nonlinear analysis computer programs it appears to be premature to place a significant value on such studies for complex structures. With these comments as background the purpose of this paper is to discuss the following: the relationship of analysis to design; new methods of analysis; new of improved finite elements; effect of minicomputer on structural analysis methods; the use of system of microprocessors for nonlinear structural analysis; the role of interacting graphics systems in future analysis and design. This discussion will focus on the impact of new, inexpensive computer hardware on design and analysis methods

  12. GlcNAc-1-P-transferase–tunicamycin complex structure reveals basis for inhibition of N-glycosylation

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Jiho; Mashalidis, Ellene H.; Kuk, Alvin C. Y.; Yamamoto, Kazuki; Kaeser, Benjamin; Ichikawa, Satoshi; Lee, Seok-Yong

    2018-02-19

    N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. In conclusion, structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. We demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.

  13. Comparative analysis reveals that polyploidy does not decelerate diversification in fish.

    Science.gov (United States)

    Zhan, S H; Glick, L; Tsigenopoulos, C S; Otto, S P; Mayrose, I

    2014-02-01

    While the proliferation of the species-rich teleost fish has been ascribed to an ancient genome duplication event at the base of this group, the broader impact of polyploidy on fish evolution and diversification remains poorly understood. Here, we investigate the association between polyploidy and diversification in several fish lineages: the sturgeons (Acipenseridae: Acipenseriformes), the botiid loaches (Botiidae: Cypriniformes), Cyprininae fishes (Cyprinidae: Cypriniformes) and the salmonids (Salmonidae: Salmoniformes). Using likelihood-based evolutionary methodologies, we co-estimate speciation and extinction rates associated with polyploid vs. diploid fish lineages. Family-level analysis of Acipenseridae and Botiidae revealed no significant difference in diversification rates between polyploid and diploid relatives, while analysis of the subfamily Cyprininae revealed higher polyploid diversification. Additionally, order-level analysis of the polyploid Salmoniformes and its diploid sister clade, the Esociformes, did not support a significantly different net diversification rate between the two groups. Taken together, our results suggest that polyploidy is generally not associated with decreased diversification in fish - a pattern that stands in contrast to that previously observed in plants. While there are notable differences in the time frame examined in the two studies, our results suggest that polyploidy is associated with different diversification patterns in these two major branches of the eukaryote tree of life. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  14. Synthesis, structural characterization, Hirshfeld surface analysis and spectroscopic studies of cadmium (II) chloride complex with 4-hydroxy-1-methylpiperidine

    Energy Technology Data Exchange (ETDEWEB)

    Soudani, S. [Université de Carthage, Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna (Tunisia); Ferretti, V. [Department of Chemical and Pharmaceutical Sciences and Center for Structural Diffractometry, via Fossato di Mortara 17, I-44121 Ferrara (Italy); Jelsch, C. [CRM2, CNRS, Institut Jean Barriol, Université de Lorraine, Vandoeuvre les Nancy CEDEX (France); Lefebvre, F. [Laboratoire de Chimie Organométallique de Surface (LCOMS), Ecole Supérieure de Chimie Physique Electronique, 69626 Villeurbanne Cedex (France); Nasr, C. Ben, E-mail: cherif_bennasr@yahoo.fr [Université de Carthage, Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, 7021 Zarzouna (Tunisia)

    2016-05-15

    The chemical preparation, crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the novel cadmium (II) 4-hydroxy-1-methylpiperidine complex, Cd{sub 4}Cl{sub 10}(C{sub 6}H{sub 14}NO){sub 2}·2H{sub 2}O, have been reported. The atomic arrangement can be described as built up by an anionic framework, formed by edge sharing CdCl{sub 6} and CdCl{sub 5}O octahedral linear chains spreading along the a-axis. These chains are interconnected by water molecules via O–H⋯Cl and O–H⋯O hydrogen bonds to form layers parallel to (011) plane. The organic cations are inserted between layers through C–H⋯Cl hydrogen bonds. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that the H{sub C}⋯Cl and H{sub C}⋯H{sub C} intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The statistical analysis of crystal contacts reveals the driving forces in the packing formation. The {sup 13}C and {sup 15}N CP-MAS NMR spectra are in agreement with the X-ray structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.

  15. Analysis of a hysteresis motor on asynchronous speed using complex permeability

    International Nuclear Information System (INIS)

    Horii, T.; Yuge, N.; Wakui, G.

    1994-01-01

    Although hysteresis motors have a comparatively small output for their mechanical dimensions compared with other types of motor, they offer the advantages of extremely low vibration and noise levels, and so are widely used as driving motors in acoustic equipment and uranium gas centrifuges. This paper deals with a method for determining the complex permeability in analysis of hysteresis motors. The method assumes that the magnetic intensity distribution is sinusoidal in the direction of rotation. Analysis of the asynchronous speed of a hysteresis motor is then performed for cylindrical coordinates, using modified Bessel functions. The results of calculations are in good agreement with experimental results, confirming the effectiveness of the proposed model and method for determining the complex permeability

  16. Complex experimental analysis of rifle-shooter interaction

    Directory of Open Access Journals (Sweden)

    Michał Taraszewski, M.ScEng, PhD. candidate

    2017-10-01

    Full Text Available In this study, a complex analysis of a man-weapon interaction based on experimental effort is presented. The attention is focused on how a shooter can influence on a rifle, opposite to generally considered in literature rifle's impact on a shooter. It is shown, based on the kbk AKM weapon, that each support point of the rifle has an substantial impact on the system. It is said that identifying human reactions on weapon may let to describe gun movement and thus may be applied to weapon accuracy determination.

  17. Isolation and characterization of PSI-LHCI super-complex and their sub-complexes from a red alga Cyanidioschyzon merolae.

    Science.gov (United States)

    Tian, Lirong; Liu, Zheyi; Wang, Fangjun; Shen, Liangliang; Chen, Jinghua; Chang, Lijing; Zhao, Songhao; Han, Guangye; Wang, Wenda; Kuang, Tingyun; Qin, Xiaochun; Shen, Jian-Ren

    2017-09-01

    Photosystem I (PSI)-light-harvesting complex I (LHCI) super-complex and its sub-complexes PSI core and LHCI, were purified from a unicellular red alga Cyanidioschyzon merolae and characterized. PSI-LHCI of C. merolae existed as a monomer with a molecular mass of 580 kDa. Mass spectrometry analysis identified 11 subunits (PsaA, B, C, D, E, F, I, J, K, L, O) in the core complex and three LHCI subunits, CMQ142C, CMN234C, and CMN235C in LHCI, indicating that at least three Lhcr subunits associate with the red algal PSI core. PsaG was not found in the red algae PSI-LHCI, and we suggest that the position corresponding to Lhca1 in higher plant PSI-LHCI is empty in the red algal PSI-LHCI. The PSI-LHCI complex was separated into two bands on native PAGE, suggesting that two different complexes may be present with slightly different protein compositions probably with respective to the numbers of Lhcr subunits. Based on the results obtained, a structural model was proposed for the red algal PSI-LHCI. Furthermore, pigment analysis revealed that the C. merolae PSI-LHCI contained a large amount of zeaxanthin, which is mainly associated with the LHCI complex whereas little zeaxanthin was found in the PSI core. This indicates a unique feature of the carotenoid composition of the Lhcr proteins and may suggest an important role of Zea in the light-harvesting and photoprotection of the red algal PSI-LHCI complex.

  18. Synthesis, structural characterization and cytotoxic activity of two new organoruthenium(II complexes

    Directory of Open Access Journals (Sweden)

    SANJA GRGURIC-SIPKA

    2008-06-01

    Full Text Available Two new p-cymene ruthenium(II complexes containing as additional ligands N-methylpiperazine ([(η6-p-cymeneRuCl2(CH3NH(CH24NH]PF6, complex 1 or vitamin K3-thiosemicarbazone ([(η6-p-cymeneRuCl2(K3tsc], complex 2 were synthesized starting from [(η6-p-cymene2RuCl2]2 and the corresponding ligand. The complexes were characterized by elemental analysis, IR, electronic absorption and NMR spectroscopy. The X-ray crystal structure determination of complex 1 revealed “piano-stool” geometry. The differences in the cytotoxic activity of the two complexes are discussed in terms of the ligand present.

  19. Proteomic analysis of the dysferlin protein complex unveils its importance for sarcolemmal maintenance and integrity.

    Directory of Open Access Journals (Sweden)

    Antoine de Morrée

    Full Text Available Dysferlin is critical for repair of muscle membranes after damage. Mutations in dysferlin lead to a progressive muscular dystrophy. Recent studies suggest additional roles for dysferlin. We set out to study dysferlin's protein-protein interactions to obtain comprehensive knowledge of dysferlin functionalities in a myogenic context. We developed a robust and reproducible method to isolate dysferlin protein complexes from cells and tissue. We analyzed the composition of these complexes in cultured myoblasts, myotubes and skeletal muscle tissue by mass spectrometry and subsequently inferred potential protein functions through bioinformatics analyses. Our data confirm previously reported interactions and support a function for dysferlin as a vesicle trafficking protein. In addition novel potential functionalities were uncovered, including phagocytosis and focal adhesion. Our data reveal that the dysferlin protein complex has a dynamic composition as a function of myogenic differentiation. We provide additional experimental evidence and show dysferlin localization to, and interaction with the focal adhesion protein vinculin at the sarcolemma. Finally, our studies reveal evidence for cross-talk between dysferlin and its protein family member myoferlin. Together our analyses show that dysferlin is not only a membrane repair protein but also important for muscle membrane maintenance and integrity.

  20. Conformational Complexity in the LH2 Antenna of the Purple Sulfur Bacterium Allochromatium vinosum Revealed by Hole-Burning Spectroscopy.

    Science.gov (United States)

    Kell, Adam; Jassas, Mahboobe; Acharya, Khem; Hacking, Kirsty; Cogdell, Richard J; Jankowiak, Ryszard

    2017-06-15

    This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800 R and B800 B . The energy differences between average site energies of conformations 1 and 2, and B800 R and B800 B are similar (∼200 cm -1 ), suggesting weak and strong hydrogen bonds linking two major subpopulations of BChls and the protein scaffolding. Although conformations 1 and 2 of the B850 chromophores, and B800 R and B800 B , exist in the ground state, selective excitation leads to 1 → 2 and B800 R → B800 B phototransformations. Different static inhomogeneous broadening is revealed for the lowest energy exciton states of B850 (fwhm ∼195 cm -1 ) and B800 R (fwhm ∼140 cm -1 ). To describe the 5 K absorption spectrum and the above-mentioned conformations, we employ an exciton model with dichotomous protein conformation disorder. We show that both experimental data and the modeling study support a two-site model with strongly and weakly hydrogen-bonded B850 and B800 BChls, which under illumination undergo conformational changes, most likely caused by proton dynamics.

  1. Optimal fatigue analysis of structures during complex loadings

    Directory of Open Access Journals (Sweden)

    Karaouni Habib

    2016-01-01

    Full Text Available A new framework for high cycle fatigue analysis of metallic structures under complex multi-parameter loadings was here developed. This allows to reduce the analysis on a 2-D window with a characterized one-parameter cyclic loading thanks to an equivalence rule relative to damage between any two loadings. The simplified inelastic analysis introduced by J. Zarka [J. Zarka et al. 1990. A new approach in inelastic analysis of structures. CADLM] was used to find the limit state of the structure. A new design rules for fatigue analysis by utilizing automatic learning systems was successfully performed. A database was built by coupling numerical simulations and experimental results on several welded specimens which are considered as a general structure in the proposed approach. This could be possible by the introduction of an intelligent description of a general fatigue case based on the actual theories and models. A software, FATPRO [M.I. Systems, FatPro, available at http://www.mzintsys.com/our_products_fatpro.html], based on this work has been developed at MZ Intelligent Systems.

  2. Nostradamus 2014 prediction, modeling and analysis of complex systems

    CERN Document Server

    Suganthan, Ponnuthurai; Chen, Guanrong; Snasel, Vaclav; Abraham, Ajith; Rössler, Otto

    2014-01-01

    The prediction of behavior of complex systems, analysis and modeling of its structure is a vitally important problem in engineering, economy and generally in science today. Examples of such systems can be seen in the world around us (including our bodies) and of course in almost every scientific discipline including such “exotic” domains as the earth’s atmosphere, turbulent fluids, economics (exchange rate and stock markets), population growth, physics (control of plasma), information flow in social networks and its dynamics, chemistry and complex networks. To understand such complex dynamics, which often exhibit strange behavior, and to use it in research or industrial applications, it is paramount to create its models. For this purpose there exists a rich spectrum of methods, from classical such as ARMA models or Box Jenkins method to modern ones like evolutionary computation, neural networks, fuzzy logic, geometry, deterministic chaos amongst others. This proceedings book is a collection of accepted ...

  3. Global transit: from critical technologies to complex practice

    Directory of Open Access Journals (Sweden)

    Aleksandr Ivanovich Neklessa

    2015-03-01

    Full Text Available Objective to study the dynamics of global economic socialcultural and militarypolitical transformations of the humanity in the end of 20th ndash beginning of the 21st c. Methods systemicprognostic approach to analysis of social reality determined the ldquoregisterrdquo of specific research methods phenomenological reduction hermeneutic comparative method systemic analysis. Results general trends of social transformations in the global community are revealed strategic risks of the global society development are defined. Scientific novelty the article presents a complex analysis of the modern world structure and reveals the probable scenarios of the scientific community responses to the challenges of modern times. Practical value the main provisions and conclusions of the article are topical for the scientificresearch and educational activity when viewing the global issues of modern times in economic socialcultural and militarypolitical perspective as well as for development of scientific methodology in socialhumanitarian studies. nbsp

  4. A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape.

    Science.gov (United States)

    Castellanos, Elisabeth; Gel, Bernat; Rosas, Inma; Tornero, Eva; Santín, Sheila; Pluvinet, Raquel; Velasco, Juan; Sumoy, Lauro; Del Valle, Jesús; Perucho, Manuel; Blanco, Ignacio; Navarro, Matilde; Brunet, Joan; Pineda, Marta; Feliubadaló, Lidia; Capellá, Gabi; Lázaro, Conxi; Serra, Eduard

    2017-01-04

    We wanted to implement an NGS strategy to globally analyze hereditary cancer with diagnostic quality while retaining the same degree of understanding and control we had in pre-NGS strategies. To do this, we developed the I2HCP panel, a custom bait library covering 122 hereditary cancer genes. We improved bait design, tested different NGS platforms and created a clinically driven custom data analysis pipeline. The I2HCP panel was developed using a training set of hereditary colorectal cancer, hereditary breast and ovarian cancer and neurofibromatosis patients and reached an accuracy, analytical sensitivity and specificity greater than 99%, which was maintained in a validation set. I2HCP changed our diagnostic approach, involving clinicians and a genetic diagnostics team from panel design to reporting. The new strategy improved diagnostic sensitivity, solved uncertain clinical diagnoses and identified mutations in new genes. We assessed the genetic variation in the complete set of hereditary cancer genes, revealing a complex variation landscape that coexists with the disease-causing mutation. We developed, validated and implemented a custom NGS-based strategy for hereditary cancer diagnostics that improved our previous workflows. Additionally, the existence of a rich genetic variation in hereditary cancer genes favors the use of this panel to investigate their role in cancer risk.

  5. Complexity in White Noise Analysis

    Science.gov (United States)

    Hida, Takeyuki

    We restrict our attention to random complex systems and discuss degree their degree of complexity based on a white noise. The white noise is realized as the time derivative of a Brownian motion B(t), and denoted by Ḃ(t). The collection {Ḃ(t)}, is a system of idealized elementary variables and at the same time the system is a stochastic representation of the time t, in other words it is time-oriented. Having expressed the given evolutional random phenomena in question in terms of the Ḃ(t), we introduce the notion of spectral multiplicity, which describes how much the phenomena are complex. The multiplicity is the number of cyclic subspaces that are spanned by the given random phenomena. Each cyclic subspace has further structure. Typical property is multiple Markov property, although this property appears only particular cases. As a related property, in fact as a characteristic of a complex system, one can speak of the time reversibility and irreversibility of certain random phenomena in terms of the white noise. We expect an irreversible random complex system may be decomposed into reversible systems.

  6. Analysis of nanoparticle biomolecule complexes.

    Science.gov (United States)

    Gunnarsson, Stefán B; Bernfur, Katja; Mikkelsen, Anders; Cedervall, Tommy

    2018-03-01

    Nanoparticles exposed to biological fluids adsorb biomolecules on their surface forming a biomolecular corona. This corona determines, on a molecular level, the interactions and impact the newly formed complex has on cells and organisms. The corona formation as well as the physiological and toxicological relevance are commonly investigated. However, an acknowledged but rarely addressed problem in many fields of nanobiotechnology is aggregation and broadened size distribution of nanoparticles following their interactions with the molecules of biological fluids. In blood serum, TiO 2 nanoparticles form complexes with a size distribution from 30 nm to more than 500 nm. In this study we have separated these complexes, with good resolution, using preparative centrifugation in a sucrose gradient. Two main apparent size populations were obtained, a fast sedimenting population of complexes that formed a pellet in the preparative centrifugation tube, and a slow sedimenting complex population still suspended in the gradient after centrifugation. Concentration and surface area dependent differences are found in the biomolecular corona between the slow and fast sedimenting fractions. There are more immunoglobulins, lipid binding proteins, and lipid-rich complexes at higher serum concentrations. Sedimentation rate and the biomolecular corona are important factors for evaluating any experiment including nanoparticle exposure. Our results show that traditional description of nanoparticles in biological fluids is an oversimplification and that more thorough characterisations are needed.

  7. Tracking Glideosome-associated protein 50 reveals the development and organization of the inner membrane complex of Plasmodium falciparum.

    Science.gov (United States)

    Yeoman, Jeffrey A; Hanssen, Eric; Maier, Alexander G; Klonis, Nectarios; Maco, Bohumil; Baum, Jake; Turnbull, Lynne; Whitchurch, Cynthia B; Dixon, Matthew W A; Tilley, Leann

    2011-04-01

    The most deadly of the human malaria parasites, Plasmodium falciparum, has different stages specialized for invasion of hepatocytes, erythrocytes, and the mosquito gut wall. In each case, host cell invasion is powered by an actin-myosin motor complex that is linked to an inner membrane complex (IMC) via a membrane anchor called the glideosome-associated protein 50 (PfGAP50). We generated P. falciparum transfectants expressing green fluorescent protein (GFP) chimeras of PfGAP50 (PfGAP50-GFP). Using immunoprecipitation and fluorescence photobleaching, we show that C-terminally tagged PfGAP50-GFP can form a complex with endogenous copies of the linker protein PfGAP45 and the myosin A tail domain-interacting protein (MTIP). Full-length PfGAP50-GFP is located in the endoplasmic reticulum in early-stage parasites and then redistributes to apical caps during the formation of daughter merozoites. In the final stage of schizogony, the PfGAP50-GFP profile extends further around the merozoite surface. Three-dimensional (3D) structured illumination microscopy reveals the early-stage IMC as a doubly punctured flat ellipsoid that separates to form claw-shaped apposed structures. A GFP fusion of PfGAP50 lacking the C-terminal membrane anchor is misdirected to the parasitophorous vacuole. Replacement of the acid phosphatase homology domain of PfGAP50 with GFP appears to allow correct trafficking of the chimera but confers a growth disadvantage.

  8. Modeling data irregularities and structural complexities in data envelopment analysis

    CERN Document Server

    Zhu, Joe

    2007-01-01

    In a relatively short period of time, Data Envelopment Analysis (DEA) has grown into a powerful quantitative, analytical tool for measuring and evaluating performance. It has been successfully applied to a whole variety of problems in many different contexts worldwide. This book deals with the micro aspects of handling and modeling data issues in modeling DEA problems. DEA's use has grown with its capability of dealing with complex "service industry" and the "public service domain" types of problems that require modeling of both qualitative and quantitative data. This handbook treatment deals with specific data problems including: imprecise or inaccurate data; missing data; qualitative data; outliers; undesirable outputs; quality data; statistical analysis; software and other data aspects of modeling complex DEA problems. In addition, the book will demonstrate how to visualize DEA results when the data is more than 3-dimensional, and how to identify efficiency units quickly and accurately.

  9. Time Series Analysis OF SAR Image Fractal Maps: The Somma-Vesuvio Volcanic Complex Case Study

    Science.gov (United States)

    Pepe, Antonio; De Luca, Claudio; Di Martino, Gerardo; Iodice, Antonio; Manzo, Mariarosaria; Pepe, Susi; Riccio, Daniele; Ruello, Giuseppe; Sansosti, Eugenio; Zinno, Ivana

    2016-04-01

    The fractal dimension is a significant geophysical parameter describing natural surfaces representing the distribution of the roughness over different spatial scale; in case of volcanic structures, it has been related to the specific nature of materials and to the effects of active geodynamic processes. In this work, we present the analysis of the temporal behavior of the fractal dimension estimates generated from multi-pass SAR images relevant to the Somma-Vesuvio volcanic complex (South Italy). To this aim, we consider a Cosmo-SkyMed data-set of 42 stripmap images acquired from ascending orbits between October 2009 and December 2012. Starting from these images, we generate a three-dimensional stack composed by the corresponding fractal maps (ordered according to the acquisition dates), after a proper co-registration. The time-series of the pixel-by-pixel estimated fractal dimension values show that, over invariant natural areas, the fractal dimension values do not reveal significant changes; on the contrary, over urban areas, it correctly assumes values outside the natural surfaces fractality range and show strong fluctuations. As a final result of our analysis, we generate a fractal map that includes only the areas where the fractal dimension is considered reliable and stable (i.e., whose standard deviation computed over the time series is reasonably small). The so-obtained fractal dimension map is then used to identify areas that are homogeneous from a fractal viewpoint. Indeed, the analysis of this map reveals the presence of two distinctive landscape units corresponding to the Mt. Vesuvio and Gran Cono. The comparison with the (simplified) geological map clearly shows the presence in these two areas of volcanic products of different age. The presented fractal dimension map analysis demonstrates the ability to get a figure about the evolution degree of the monitored volcanic edifice and can be profitably extended in the future to other volcanic systems with

  10. Gene Coexpression Analysis Reveals Complex Metabolism of the Monoterpene Alcohol Linalool in Arabidopsis FlowersW

    NARCIS (Netherlands)

    Ginglinger, J.F.; Boachon, B.; Hofer, R.; Paetz, C.; Kollner, T.G.; Miesch, L.; Lugan, R.; Baltenweck, R.; Mutterer, J.; Ullman, P.; Verstappen, F.W.A.; Bouwmeester, H.J.

    2013-01-01

    The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus

  11. Complexity Analysis of Reed-Solomon Decoding over GF without Using Syndromes

    Directory of Open Access Journals (Sweden)

    Chen Ning

    2008-01-01

    Full Text Available Abstract There has been renewed interest in decoding Reed-Solomon (RS codes without using syndromes recently. In this paper, we investigate the complexity of syndromeless decoding, and compare it to that of syndrome-based decoding. Aiming to provide guidelines to practical applications, our complexity analysis focuses on RS codes over characteristic-2 fields, for which some multiplicative FFT techniques are not applicable. Due to moderate block lengths of RS codes in practice, our analysis is complete, without big notation. In addition to fast implementation using additive FFT techniques, we also consider direct implementation, which is still relevant for RS codes with moderate lengths. For high-rate RS codes, when compared to syndrome-based decoding algorithms, not only syndromeless decoding algorithms require more field operations regardless of implementation, but also decoder architectures based on their direct implementations have higher hardware costs and lower throughput. We also derive tighter bounds on the complexities of fast polynomial multiplications based on Cantor's approach and the fast extended Euclidean algorithm.

  12. Quantitative analysis of ribosome–mRNA complexes at different translation stages

    Science.gov (United States)

    Shirokikh, Nikolay E.; Alkalaeva, Elena Z.; Vassilenko, Konstantin S.; Afonina, Zhanna A.; Alekhina, Olga M.; Kisselev, Lev L.; Spirin, Alexander S.

    2010-01-01

    Inhibition of primer extension by ribosome–mRNA complexes (toeprinting) is a proven and powerful technique for studying mechanisms of mRNA translation. Here we have assayed an advanced toeprinting approach that employs fluorescently labeled DNA primers, followed by capillary electrophoresis utilizing standard instruments for sequencing and fragment analysis. We demonstrate that this improved technique is not merely fast and cost-effective, but also brings the primer extension inhibition method up to the next level. The electrophoretic pattern of the primer extension reaction can be characterized with a precision unattainable by the common toeprint analysis utilizing radioactive isotopes. This method allows us to detect and quantify stable ribosomal complexes at all stages of translation, including initiation, elongation and termination, generated during the complete translation process in both the in vitro reconstituted translation system and the cell lysate. We also point out the unique advantages of this new methodology, including the ability to assay sites of the ribosomal complex assembly on several mRNA species in the same reaction mixture. PMID:19910372

  13. Using qualitative comparative analysis in a systematic review of a complex intervention.

    Science.gov (United States)

    Kahwati, Leila; Jacobs, Sara; Kane, Heather; Lewis, Megan; Viswanathan, Meera; Golin, Carol E

    2016-05-04

    Systematic reviews evaluating complex interventions often encounter substantial clinical heterogeneity in intervention components and implementation features making synthesis challenging. Qualitative comparative analysis (QCA) is a non-probabilistic method that uses mathematical set theory to study complex phenomena; it has been proposed as a potential method to complement traditional evidence synthesis in reviews of complex interventions to identify key intervention components or implementation features that might explain effectiveness or ineffectiveness. The objective of this study was to describe our approach in detail and examine the suitability of using QCA within the context of a systematic review. We used data from a completed systematic review of behavioral interventions to improve medication adherence to conduct two substantive analyses using QCA. The first analysis sought to identify combinations of nine behavior change techniques/components (BCTs) found among effective interventions, and the second analysis sought to identify combinations of five implementation features (e.g., agent, target, mode, time span, exposure) found among effective interventions. For each substantive analysis, we reframed the review's research questions to be designed for use with QCA, calibrated sets (i.e., transformed raw data into data used in analysis), and identified the necessary and/or sufficient combinations of BCTs and implementation features found in effective interventions. Our application of QCA for each substantive analysis is described in detail. We extended the original review findings by identifying seven combinations of BCTs and four combinations of implementation features that were sufficient for improving adherence. We found reasonable alignment between several systematic review steps and processes used in QCA except that typical approaches to study abstraction for some intervention components and features did not support a robust calibration for QCA. QCA was

  14. [Tissue-specific nucleoprotein complexes].

    Science.gov (United States)

    Riadnova, I Iu; Shataeva, L K; Khavinson, V Kh

    2000-01-01

    A method of isolation of native nucleorprotein complexes from cattle cerebral cortex, thymus, and liver was developed. Compositions of these complexes were studied by means of gel-chromatography and ion-exchange chromatography. These preparations were shown to consist of several fractions of proteins and their complexes differ by molecular mass and electro-chemical properties. Native nucleoprotein complexes revealed high tissue specific activity, which was not species-specific.

  15. Exergy Analysis of Complex Ship Energy Systems

    Directory of Open Access Journals (Sweden)

    Pierre Marty

    2016-04-01

    Full Text Available With multiple primary and secondary energy converters (diesel engines, steam turbines, waste heat recovery (WHR and oil-fired boilers, etc. and extensive energy networks (steam, cooling water, exhaust gases, etc., ships may be considered as complex energy systems. Understanding and optimizing such systems requires advanced holistic energy modeling. This modeling can be done in two ways: The simpler approach focuses on energy flows, and has already been tested, approved and presented; a new, more complicated approach, focusing on energy quality, i.e., exergy, is presented in this paper. Exergy analysis has rarely been applied to ships, and, as a general rule, the shipping industry is not familiar with this tool. This paper tries to fill this gap. We start by giving a short reminder of what exergy is and describe the principles of exergy modeling to explain what kind of results should be expected from such an analysis. We then apply these principles to the analysis of a large two-stroke diesel engine with its cooling and exhaust systems. Simulation results are then presented along with the exergy analysis. Finally, we propose solutions for energy and exergy saving which could be applied to marine engines and ships in general.

  16. Pan-Cancer Analysis of the Mediator Complex Transcriptome Identifies CDK19 and CDK8 as Therapeutic Targets in Advanced Prostate Cancer.

    Science.gov (United States)

    Brägelmann, Johannes; Klümper, Niklas; Offermann, Anne; von Mässenhausen, Anne; Böhm, Diana; Deng, Mario; Queisser, Angela; Sanders, Christine; Syring, Isabella; Merseburger, Axel S; Vogel, Wenzel; Sievers, Elisabeth; Vlasic, Ignacija; Carlsson, Jessica; Andrén, Ove; Brossart, Peter; Duensing, Stefan; Svensson, Maria A; Shaikhibrahim, Zaki; Kirfel, Jutta; Perner, Sven

    2017-04-01

    Purpose: The Mediator complex is a multiprotein assembly, which serves as a hub for diverse signaling pathways to regulate gene expression. Because gene expression is frequently altered in cancer, a systematic understanding of the Mediator complex in malignancies could foster the development of novel targeted therapeutic approaches. Experimental Design: We performed a systematic deconvolution of the Mediator subunit expression profiles across 23 cancer entities ( n = 8,568) using data from The Cancer Genome Atlas (TCGA). Prostate cancer-specific findings were validated in two publicly available gene expression cohorts and a large cohort of primary and advanced prostate cancer ( n = 622) stained by immunohistochemistry. The role of CDK19 and CDK8 was evaluated by siRNA-mediated gene knockdown and inhibitor treatment in prostate cancer cell lines with functional assays and gene expression analysis by RNAseq. Results: Cluster analysis of TCGA expression data segregated tumor entities, indicating tumor-type-specific Mediator complex compositions. Only prostate cancer was marked by high expression of CDK19 In primary prostate cancer, CDK19 was associated with increased aggressiveness and shorter disease-free survival. During cancer progression, highest levels of CDK19 and of its paralog CDK8 were present in metastases. In vitro , inhibition of CDK19 and CDK8 by knockdown or treatment with a selective CDK8/CDK19 inhibitor significantly decreased migration and invasion. Conclusions: Our analysis revealed distinct transcriptional expression profiles of the Mediator complex across cancer entities indicating differential modes of transcriptional regulation. Moreover, it identified CDK19 and CDK8 to be specifically overexpressed during prostate cancer progression, highlighting their potential as novel therapeutic targets in advanced prostate cancer. Clin Cancer Res; 23(7); 1829-40. ©2016 AACR . ©2016 American Association for Cancer Research.

  17. PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

    Science.gov (United States)

    Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

    2016-03-10

    Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and

  18. Structural analysis of d(GCAATTGC)2 and its complex with berenil by nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Yoshida, Mitsuru; Banville, D.L.; Shafer, R.H.

    1990-01-01

    The structures of d(GCAATTGC) 2 and its complex with berenil in solution were analyzed by two-dimensional 1 H NMR spectroscopy. Intra- and internucleotide nuclear Overhauser effect (NOE) connectivities demonstrate that the octanucleotide duplex is primarily in the B conformation. Binding with berenil stabilizes the duplex with respect to thermal denaturation by about 10 degree C, based on the appearance of the imino proton signals. The berenil-d(GCAATTGC) 2 system is in fast exchange on the NMR time scale. The two-dimensional NMR data reveal that berenil binds in the minor groove of d(GCAATTGC) 2 . The aromatic drug protons are placed within 5 angstrom of the H2 proton of both adenines, the H1', H5', and H5 double-prime of both thymidines, and the H4', H5', and H5 double-prime of the internal guanosine. The amidine protons on berenil are also close to the H2 proton of both adenines. The duplex retains an overall B conformation in the complex with berenil. At 18 degree C, NOE contacts at longer mixing times indicate the presence of end-to-end association both in the duplex alone and also in its complex with berenil. These intermolecular contacts either vanished or diminished substantially at 45 degree C. Two molecular models are proposed for the berenil-(GCAATTGC) 2 complex; one has hydrogen bonds between the berenil amidine protons and the carbonyl oxygen, O2, of the external thymines, and the other has hydrogen bonds between the drug amidine protons and the purine nitrogen, N3, of the internal adenines. Quantitative analysis of the NOE data favors the second model

  19. Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation

    Directory of Open Access Journals (Sweden)

    Rismani-Yazdi Hamid

    2012-09-01

    Full Text Available Abstract Background The lack of sequenced genomes for oleaginous microalgae limits our understanding of the mechanisms these organisms utilize to become enriched in triglycerides. Here we report the de novo transcriptome assembly and quantitative gene expression analysis of the oleaginous microalga Neochloris oleoabundans, with a focus on the complex interaction of pathways associated with the production of the triacylglycerol (TAG biofuel precursor. Results After growth under nitrogen replete and nitrogen limiting conditions, we quantified the cellular content of major biomolecules including total lipids, triacylglycerides, starch, protein, and chlorophyll. Transcribed genes were sequenced, the transcriptome was assembled de novo, and the expression of major functional categories, relevant pathways, and important genes was quantified through the mapping of reads to the transcriptome. Over 87 million, 77 base pair high quality reads were produced on the Illumina HiSeq sequencing platform. Metabolite measurements supported by genes and pathway expression results indicated that under the nitrogen-limiting condition, carbon is partitioned toward triglyceride production, which increased fivefold over the nitrogen-replete control. In addition to the observed overexpression of the fatty acid synthesis pathway, TAG production during nitrogen limitation was bolstered by repression of the β-oxidation pathway, up-regulation of genes encoding for the pyruvate dehydrogenase complex which funnels acetyl-CoA to lipid biosynthesis, activation of the pentose phosphate pathway to supply reducing equivalents to inorganic nitrogen assimilation and fatty acid biosynthesis, and the up-regulation of lipases—presumably to reconstruct cell membranes in order to supply additional fatty acids for TAG biosynthesis. Conclusions Our quantitative transcriptome study reveals a broad overview of how nitrogen stress results in excess TAG production in N. oleoabundans, and

  20. Simultaneous measurement of amyloid fibril formation by dynamic light scattering and fluorescence reveals complex aggregation kinetics.

    Directory of Open Access Journals (Sweden)

    Aaron M Streets

    Full Text Available An apparatus that combines dynamic light scattering and Thioflavin T fluorescence detection is used to simultaneously probe fibril formation in polyglutamine peptides, the aggregating subunit associated with Huntington's disease, in vitro. Huntington's disease is a neurodegenerative disorder in a class of human pathologies that includes Alzheimer's and Parkinson's disease. These pathologies are all related by the propensity of their associated protein or polypeptide to form insoluble, β-sheet rich, amyloid fibrils. Despite the wide range of amino acid sequence in the aggregation prone polypeptides associated with these diseases, the resulting amyloids display strikingly similar physical structure, an observation which suggests a physical basis for amyloid fibril formation. Thioflavin T fluorescence reports β-sheet fibril content while dynamic light scattering measures particle size distributions. The combined techniques allow elucidation of complex aggregation kinetics and are used to reveal multiple stages of amyloid fibril formation.

  1. Fault Correspondence Analysis in Complex Electric Power Systems

    Directory of Open Access Journals (Sweden)

    WANG, C.

    2015-02-01

    Full Text Available Wide area measurement system (WAMS mainly serves for the requirement of time synchronization in complex electric power systems. The analysis and control of power system mostly depends on the measurement of state variables, and WAMS provides the basis for dynamic monitoring of power system by these measurements, which can also satisfy the demands of observable, controllable, real-time analysis and decision, self-adaptive etc. requested by smart grid. In this paper, based on the principles of fault correspondence analysis, by calculating row characteristic which represents nodal electrical information and column characteristic which represents acquisition time information, we will conduct intensive research on fault detection. The research results indicate that the fault location is determined by the first dimensional variable, and the occurrence time of fault is determined by the second dimensional variable. The research in this paper will contribute to the development of future smart grid.

  2. Sleep spindle and K-complex detection using tunable Q-factor wavelet transform and morphological component analysis

    Directory of Open Access Journals (Sweden)

    Tarek eLajnef

    2015-07-01

    Full Text Available A novel framework for joint detection of sleep spindles and K-complex events, two hallmarks of sleep stage S2, is proposed. Sleep electroencephalography (EEG signals are split into oscillatory (spindles and transient (K-complex components. This decomposition is conveniently achieved by applying morphological component analysis (MCA to a sparse representation of EEG segments obtained by the recently introduced discrete tunable Q-factor wavelet transform (TQWT. Tuning the Q-factor provides a convenient and elegant tool to naturally decompose the signal into an oscillatory and a transient component. The actual detection step relies on thresholding (i the transient component to reveal K-complexes and (ii the time-frequency representation of the oscillatory component to identify sleep spindles. Optimal thresholds are derived from ROC-like curves (sensitivity versus FDR on training sets and the performance of the method is assessed on test data sets. We assessed the performance of our method using full-night sleep EEG data we collected from 14 participants. In comparison to visual scoring (Expert 1, the proposed method detected spindles with a sensitivity of 83.18% and false discovery rate (FDR of 39%, while K-complexes were detected with a sensitivity of 81.57% and an FDR of 29.54%. Similar performances were obtained when using a second expert as benchmark. In addition, when the TQWT and MCA steps were excluded from the pipeline the detection sensitivities dropped down to 70% for spindles and to 76.97% for K-complexes, while the FDR rose up to 43.62% and 49.09% respectively. Finally, we also evaluated the performance of the proposed method on a set of publicly available sleep EEG recordings. Overall, the results we obtained suggest that the TQWT-MCA method may be a valuable alternative to existing spindle and K-complex detection methods. Paths for improvements and further validations with large-scale standard open-access benchmarking data sets are

  3. Economic development and wage inequality: A complex system analysis.

    Directory of Open Access Journals (Sweden)

    Angelica Sbardella

    Full Text Available Adapting methods from complex system analysis, this paper analyzes the features of the complex relationship between wage inequality and the development and industrialization of a country. Development is understood as a combination of a monetary index, GDP per capita, and a recently introduced measure of a country's economic complexity: Fitness. Initially the paper looks at wage inequality on a global scale, over the time period 1990-2008. Our empirical results show that globally the movement of wage inequality along with the ongoing industrialization of countries has followed a longitudinally persistent pattern comparable to the one theorized by Kuznets in the fifties: countries with an average level of development suffer the highest levels of wage inequality. Next, the study narrows its focus on wage inequality within the United States. By using data on wages and employment in the approximately 3100 US counties over the time interval 1990-2014, it generalizes the Fitness-Complexity metric for geographic units and industrial sectors, and then investigates wage inequality between NAICS industries. The empirical time and scale dependencies are consistent with a relation between wage inequality and development driven by institutional factors comparing countries, and by change in the structural compositions of sectors in a homogeneous institutional environment, such as the counties of the United States.

  4. Economic development and wage inequality: A complex system analysis.

    Science.gov (United States)

    Sbardella, Angelica; Pugliese, Emanuele; Pietronero, Luciano

    2017-01-01

    Adapting methods from complex system analysis, this paper analyzes the features of the complex relationship between wage inequality and the development and industrialization of a country. Development is understood as a combination of a monetary index, GDP per capita, and a recently introduced measure of a country's economic complexity: Fitness. Initially the paper looks at wage inequality on a global scale, over the time period 1990-2008. Our empirical results show that globally the movement of wage inequality along with the ongoing industrialization of countries has followed a longitudinally persistent pattern comparable to the one theorized by Kuznets in the fifties: countries with an average level of development suffer the highest levels of wage inequality. Next, the study narrows its focus on wage inequality within the United States. By using data on wages and employment in the approximately 3100 US counties over the time interval 1990-2014, it generalizes the Fitness-Complexity metric for geographic units and industrial sectors, and then investigates wage inequality between NAICS industries. The empirical time and scale dependencies are consistent with a relation between wage inequality and development driven by institutional factors comparing countries, and by change in the structural compositions of sectors in a homogeneous institutional environment, such as the counties of the United States.

  5. Objective high Resolution Analysis over Complex Terrain with VERA

    Science.gov (United States)

    Mayer, D.; Steinacker, R.; Steiner, A.

    2012-04-01

    VERA (Vienna Enhanced Resolution Analysis) is a model independent, high resolution objective analysis of meteorological fields over complex terrain. This system consists of a special developed quality control procedure and a combination of an interpolation and a downscaling technique. Whereas the so called VERA-QC is presented at this conference in the contribution titled "VERA-QC, an approved Data Quality Control based on Self-Consistency" by Andrea Steiner, this presentation will focus on the method and the characteristics of the VERA interpolation scheme which enables one to compute grid point values of a meteorological field based on irregularly distributed observations and topography related aprior knowledge. Over a complex topography meteorological fields are not smooth in general. The roughness which is induced by the topography can be explained physically. The knowledge about this behavior is used to define the so called Fingerprints (e.g. a thermal Fingerprint reproducing heating or cooling over mountainous terrain or a dynamical Fingerprint reproducing positive pressure perturbation on the windward side of a ridge) under idealized conditions. If the VERA algorithm recognizes patterns of one or more Fingerprints at a few observation points, the corresponding patterns are used to downscale the meteorological information in a greater surrounding. This technique allows to achieve an analysis with a resolution much higher than the one of the observational network. The interpolation of irregularly distributed stations to a regular grid (in space and time) is based on a variational principle applied to first and second order spatial and temporal derivatives. Mathematically, this can be formulated as a cost function that is equivalent to the penalty function of a thin plate smoothing spline. After the analysis field has been divided into the Fingerprint components and the unexplained part respectively, the requirement of a smooth distribution is applied to the

  6. Correlation between detrended fluctuation analysis and the Lempel-Ziv complexity in nonlinear time series analysis

    International Nuclear Information System (INIS)

    Tang You-Fu; Liu Shu-Lin; Jiang Rui-Hong; Liu Ying-Hui

    2013-01-01

    We study the correlation between detrended fluctuation analysis (DFA) and the Lempel-Ziv complexity (LZC) in nonlinear time series analysis in this paper. Typical dynamic systems including a logistic map and a Duffing model are investigated. Moreover, the influence of Gaussian random noise on both the DFA and LZC are analyzed. The results show a high correlation between the DFA and LZC, which can quantify the non-stationarity and the nonlinearity of the time series, respectively. With the enhancement of the random component, the exponent a and the normalized complexity index C show increasing trends. In addition, C is found to be more sensitive to the fluctuation in the nonlinear time series than α. Finally, the correlation between the DFA and LZC is applied to the extraction of vibration signals for a reciprocating compressor gas valve, and an effective fault diagnosis result is obtained

  7. Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting α-glycosidase.

    Science.gov (United States)

    Miyazaki, Takatsugu; Nishikawa, Atsushi; Tonozuka, Takashi

    2016-12-01

    Glycoside hydrolases are divided into two groups, known as inverting and retaining enzymes, based on their hydrolytic mechanisms. Glycoside hydrolase family 63 (GH63) is composed of inverting α-glycosidases, which act mainly on α-glucosides. We previously found that Escherichia coli GH63 enzyme, YgjK, can hydrolyze 2-O-α-d-glucosyl-d-galactose. Two constructed glycosynthase mutants, D324N and E727A, which catalyze the transfer of a β-glucosyl fluoride donor to galactose, lactose, and melibiose. Here, we determined the crystal structures of D324N and E727A soaked with a mixture of glucose and lactose at 1.8- and 2.1-Å resolutions, respectively. Because glucose and lactose molecules are found at the active sites in both structures, it is possible that these structures mimic the enzyme-product complex of YgjK. A glucose molecule found at subsite -1 in both structures adopts an unusual 1 S 3 skew-boat conformation. Comparison between these structures and the previously determined enzyme-substrate complex structure reveals that the glucose pyranose ring might be distorted immediately after nucleophilic attack by a water molecule. These structures represent the first enzyme-product complex for the GH63 family, as well as the structurally-related glycosidases, and it may provide insight into the catalytic mechanism of these enzymes. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Connectivity-enhanced diffusion analysis reveals white matter density disruptions in first episode and chronic schizophrenia

    Directory of Open Access Journals (Sweden)

    Rachael G. Grazioplene

    Full Text Available Reduced fractional anisotropy (FA is a well-established correlate of schizophrenia, but it remains unclear whether these tensor-based differences are the result of axon damage and/or organizational changes and whether the changes are progressive in the adult course of illness. Diffusion MRI data were collected in 81 schizophrenia patients (54 first episode and 27 chronic and 64 controls. Analysis of FA was combined with “fixel-based” analysis, the latter of which leverages connectivity and crossing-fiber information to assess both fiber bundle density and organizational complexity (i.e., presence and magnitude of off-axis diffusion signal. Compared with controls, patients with schizophrenia displayed clusters of significantly lower FA in the bilateral frontal lobes, right dorsal centrum semiovale, and the left anterior limb of the internal capsule. All FA-based group differences overlapped substantially with regions containing complex fiber architecture. FA within these clusters was positively correlated with principal axis fiber density, but inversely correlated with both secondary/tertiary axis fiber density and voxel-wise fiber complexity. Crossing fiber complexity had the strongest (inverse association with FA (r = −0.82. When crossing fiber structure was modeled in the MRtrix fixel-based analysis pipeline, patients exhibited significantly lower fiber density compared to controls in the dorsal and posterior corpus callosum (central, postcentral, and forceps major. Findings of lower FA in patients with schizophrenia likely reflect two inversely related signals: reduced density of principal axis fiber tracts and increased off-axis diffusion sources. Whereas the former confirms at least some regions where myelin and or/axon count are lower in schizophrenia, the latter indicates that the FA signal from principal axis fiber coherence is broadly contaminated by macrostructural complexity, and therefore does not necessarily reflect

  9. CFD three dimensional wake analysis in complex terrain

    Science.gov (United States)

    Castellani, F.; Astolfi, D.; Terzi, L.

    2017-11-01

    Even if wind energy technology is nowadays fully developed, the use of wind energy in very complex terrain is still challenging. In particular, it is challenging to characterize the combination effects of wind ow over complex terrain and wake interactions between nearby turbines and this has a practical relevance too, for the perspective of mitigating anomalous vibrations and loads as well improving the farm efficiency. In this work, a very complex terrain site has been analyzed through a Reynolds-averaged CFD (Computational Fluid Dynamics) numerical wind field model; in the simulation the inuence of wakes has been included through the Actuator Disk (AD) approach. In particular, the upstream turbine of a cluster of 4 wind turbines having 2.3 MW of rated power is studied. The objective of this study is investigating the full three-dimensional wind field and the impact of three-dimensionality on the evolution of the waked area between nearby turbines. A post-processing method of the output of the CFD simulation is developed and this allows to estimate the wake lateral deviation and the wake width. The reliability of the numerical approach is inspired by and crosschecked through the analysis of the operational SCADA (Supervisory Control and Data Acquisition) data of the cluster of interest.

  10. A Mathematical Approach to Supply Complexity Management Efficiency Evaluation for Supply Chain

    Directory of Open Access Journals (Sweden)

    Changhee Kim

    2015-01-01

    Full Text Available This study aims to identify the factors of complexity due to the globalization of supply chain and to measure the management efficiency of the factors which cause the supply complexity within supply chain. This study conducts an analysis to utilize linear programming and bootstrapping, targeting 12 Korean companies among the selected companies in Fortune Global 500. According to the results from the analysis, 4 companies with relatively high management efficiency of the factors which cause the supply complexity and 8 companies with relatively low management efficiency are found. The research findings reveal that public companies with the small number of products, factories, and providers relatively manage the supply complexity compared to private companies. Moreover, this study suggests projection point as a direction for relatively less efficient companies and excess quantity of input which should reduce for its achievement. This study also has an implication to establish a further standard of efficiency to manage the supply complexity for companies.

  11. GEOMETRIC COMPLEXITY ANALYSIS IN AN INTEGRATIVE TECHNOLOGY EVALUATION MODEL (ITEM FOR SELECTIVE LASER MELTING (SLM#

    Directory of Open Access Journals (Sweden)

    S. Merkt

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT: Selective laser melting (SLM is becoming an economically viable choice for manufacturing complex serial parts. This paper focuses on a geometric complexity analysis as part of the integrative technology evaluation model (ITEM presented here. In contrast to conventional evaluation methodologies, the ITEM considers interactions between product and process innovations generated by SLM. The evaluation of manufacturing processes that compete with SLM is the main goal of ITEM. The paper includes a complexity analysis of a test part from Festo AG. The paper closes with a discussion of how the expanded design freedom of SLM can be used to improve company operations, and how the complexity analysis presented here can be seen as a starting point for feature-based complexity analysis..

    AFRIKAANSE OPSOMMING: Selektiewe lasersmelting word geleidelik ’n gangbare ekonomiese keuse vir die vervaar-diging van opeenvolgende komplekse onderdele. Die navorsing is toegespits op die ontleding van meetkundige kompleksiteit as ’n gedeelte van ’n integrerende tegnologiese evalueringsmodel. Gemeet teen konvensionele evalueringsmodelle behandel die genoemde metode interaksies tussen produkte- en prosesinnovasies wat gegenereer word. Die navorsing behandel ’n kompleksiteitsontleding van ’n toetsonderdeel van die firma FESTO AG. Die resultaat toon hoe kompleksiteits-analise gebruik kan word as die vertrekpunt vir eienskapsgebaseerde analise.

  12. Informational analysis involving application of complex information system

    Science.gov (United States)

    Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael

    The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.

  13. The geosystems of complex geographical atlases

    Directory of Open Access Journals (Sweden)

    Jovanović Jasmina

    2012-01-01

    Full Text Available Complex geographical atlases represent geosystems of different hierarchical rank, complexity and diversity, scale and connection. They represent a set of large number of different pieces of information about geospace. Also, they contain systematized, correlative and in the apparent form represented pieces of information about space. The degree of information revealed in the atlas is precisely explained by its content structure and the form of presentation. The quality of atlas depends on the method of visualization of data and the quality of geodata. Cartographic visualization represents cognitive process. The analysis converts geospatial data into knowledge. A complex geographical atlas represents information complex of spatial - temporal coordinated database on geosystems of different complexity and territorial scope. Each geographical atlas defines a concrete geosystem. Systemic organization (structural and contextual determines its complexity and concreteness. In complex atlases, the attributes of geosystems are modeled and pieces of information are given in systematized, graphically unique form. The atlas can be considered as a database. In composing a database, semantic analysis of data is important. The result of semantic modeling is expressed in structuring of data information, in emphasizing logic connections between phenomena and processes and in defining their classes according to the degree of similarity. Accordingly, the efficiency of research of needed pieces of information in the process of the database use is enabled. An atlas map has a special power to integrate sets of geodata and present information contents in user - friendly and understandable visual and tactile way using its visual ability. Composing an atlas by systemic cartography requires the pieces of information on concrete - defined geosystems of different hierarchical level, the application of scientific methods and making of adequate number of analytical, synthetic

  14. Automatic Complexity Analysis

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    1989-01-01

    One way to analyse programs is to to derive expressions for their computational behaviour. A time bound function (or worst-case complexity) gives an upper bound for the computation time as a function of the size of input. We describe a system to derive such time bounds automatically using abstract...

  15. Synthesis and X-ray diffraction study of some nickel(II) complexes of urea and thiourea

    International Nuclear Information System (INIS)

    Sharma, Pradeep; Bhale, Jaishree; Mishra, Ashutosh; Malviya, Pramod

    2014-01-01

    XRD of four biologically important nickel(II) complexes having urea and thiourea as primary ligands and sulphate and nitrate as secondary ligands have been studied using Bruker D8 Advance diffractometer at IUC, Indore. The synthesized metal complexes were characterized by XRD measurements in order to elucidate their geometry. The data obtained has been preceded using XRD data analysis program Origin 6.0 Professional. From the experimental measurements, various parameters, e.g., particle size, lattice parameter have been estimated.Particle size for Ni-urea complexes is found in the range of 4.23-9.01 nm while for Ni-thiourea complexes its range is 0.26-9.76 nm.Lattice parameter for all these complexes is found in the range of 7.47-8.06 Å. The XRD analysis revealed the crystalline nature of all the complexes.

  16. Species of the Colletotrichum gloeosporioides complex associated with anthracnose diseases of Proteaceae

    NARCIS (Netherlands)

    Liu, F.; Damm, U.; Cai, L.; Crous, P.W.

    2013-01-01

    Anthracnose disease of Proteaceae has in the past chiefly been attributed to infections by C. acutatum, C. boninense and C. gloeosporioides. In the present study, a multi-locus phylogenetic analysis (ACT, CAL, CHS-1, GAPDH, GS, ITS, TUB2) revealed that strains of the C. gloeosporioides complex

  17. Simultaneous analysis of qualitative parameters of solid fuel using complex neutron gamma method

    International Nuclear Information System (INIS)

    Dombrovskij, V.P.; Ajtsev, N.I.; Ryashchikov, V.I.; Frolov, V.K.

    1983-01-01

    A study was made on complex neutron gamma method for simultaneous analysis of carbon content, ash content and humidity of solid fuel according to gamma radiation of inelastic fast neutron scattering and radiation capture of thermal neutrons. Metrological characteristics of pulse and stationary neutron gamma methods for determination of qualitative solid fuel parameters were analyzed, taking coke breeze as an example. Optimal energy ranges of gamma radiation detection (2-8 MeV) were determined. The advantages of using pulse neutron generator for complex analysis of qualitative parameters of solid fuel in large masses were shown

  18. Transition metal complexes with oxygen donor ligands: a synthesis, spectral, thermal and antimicrobial study

    Directory of Open Access Journals (Sweden)

    VAIBHAV N. PATANGE

    2008-10-01

    Full Text Available Transition metal complexes of chalcones derived from the conden¬sation of 3-acetyl-6-methyl-2H-pyran-2,4(3H-dione (dehydroacetic acid and p-methoxybenzaldehyde (HL1 or p-nitrobenzaldehyde (HL2 were synthesized and characterized by elemental analysis, conductometry, thermal analysis, magnetic measurements, IR, 1H-NMR, UV–Vis spectroscopy and a microbial study. From the analytical and thermal data, the stoichiometry of the complexes was found to be 1:2 (metal:ligand. The molar conductance data revealed that all the metal chelates were non-electrolytes. The thermal stability of the complexes was studied by thermogravimetry and the decomposition schemes of the complexes are given. The ligands and their metal complexes were screened for antibacterial activity against Staphylococcus aureus and Escherichia coli, and fungicidal activity against Aspergillus flavus, Curvularia lunata and Penicillium notatum.

  19. Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

    Science.gov (United States)

    Hertach, Thomas; Puissant, Stéphane; Gogala, Matija; Trilar, Tomi; Hagmann, Reto; Baur, Hannes; Kunz, Gernot; Wade, Elizabeth J.; Loader, Simon P.; Simon, Chris; Nagel, Peter

    2016-01-01

    Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species. Indeed, two taxa turned out to be especially diverse in that they form a “complex within the complex”: the Cicadetta cerdaniensis song group (four species studied previously) and Cicadetta brevipennis (examined in details here). Based on acoustic, morphological, molecular, ecological and spatial data sampled throughout their broad European distribution, we find that Cicadetta brevipennis s. l. comprises five lineages. The most distinct lineage is identified as Cicadetta petryi Schumacher, 1924, which we re-assign to the species level. Cicadetta brevipennis litoralis Puissant & Hertach ssp. n. and Cicadetta brevipennis hippolaidica Hertach ssp. n. are new to science. The latter hybridizes with Cicadetta brevipennis brevipennis Fieber, 1876 at a zone inferred from intermediate song patterns. The fifth lineage requires additional investigation. The C. cerdaniensis and the C. brevipennis song groups exhibit characteristic, clearly distinct basic song patterns that act as reproductive barriers. However, they remain completely intermixed in the Bayesian and maximum likelihood COI and COII mitochondrial DNA phylogenies. The closest relative of each of the four cerdaniensis group species is a brevipennis group taxon. In our favoured scenario the phylogenetic pairs originated in common Pleistocene glacial refuges where the taxa speciated and experienced sporadic inter-group hybridization leading to extensive

  20. Analysis on complex structure stability under different bar angle with BIM technology

    Directory of Open Access Journals (Sweden)

    Wang Xiongjue

    2016-03-01

    Full Text Available Sun Valley, the landmark building of World Expo in Shanghai, which has free surface with single-layer reticulated shell structure, is a typical complex structure. CAD/CAM integrated information system to design is used for the complex structure; however, it is a very rigorous process to be used widely. The relevant technology of the Sun Valley is not open to the public at present, so we try to use BIM technology to model the Sun Valley, including architecture modelling and structure analysis. By analysis of the Sun Valley structure using this method, it is proved that the problems in modelling may be solved by writing some script codes in Rhino software and the stability of the model can also be analyzed. The new approach is viable and effective in combination with different softwares such as Rhino, Revit, and Midas in solution of the complex shaped surfaces’ structure for modelling and calculation.

  1. [Ultraviolet-visible spectrometry analysis of insoluble xanthate heavy metal complexes].

    Science.gov (United States)

    Qiu, Bo; Liu, Jin-Feng; Liu, Yao-Chi; Yang, Zhao-Guang; Li, Hai-Pu

    2014-11-01

    A ultraviolet-visible spectrometry method of determining insoluble xanthate heavy metal complexes in flotation wastewater was the first time to be put forward. In this work, the changes of ultraviolet-visible spectra of xanthate solution after the addition of various heavy metal ions were investigated firstly. It was found that Pb2+ and Cu2+ can form insoluble complexes with xanthate, while Fe2+, Zn2+ and Mn2+ have little effect on the ultraviolet absorption of xanthate solution. Then the removal efficiencies of filter membrane with different pore sizes were compared, and the 0.22 μm membrane was found to be effective to separate copper xanthate or lead xanthate from the filtrate. Furthermore, the results of the study on the reaction of sodium sulfide and insoluble xanthate heavy metal complexes showed that S(2-) can release the xanthate ion quantitatively from insoluble complexes to solution. Based on the above research, it was concluded that the amount of insoluble xanthate heavy metal complexes in water samples can be obtained through the increase of free xanthate in the filtrate after the addition of sodium sulfide. Finally, the feasibility of this method was verified by the application to the analysis of flotation wastewater from three ore-dressing plants in the Thirty-six Coves in Chenzhou.

  2. 'Fractional recovery' analysis of a presynaptic synaptotagmin 1-anchored endocytic protein complex.

    Directory of Open Access Journals (Sweden)

    Rajesh Khanna

    Full Text Available BACKGROUND: The integral synaptic vesicle protein and putative calcium sensor, synaptotagmin 1 (STG, has also been implicated in synaptic vesicle (SV recovery. However, proteins with which STG interacts during SV endocytosis remain poorly understood. We have isolated an STG-associated endocytic complex (SAE from presynaptic nerve terminals and have used a novel fractional recovery (FR assay based on electrostatic dissociation to identify SAE components and map the complex structure. The location of SAE in the presynaptic terminal was determined by high-resolution quantitative immunocytochemistry at the chick ciliary ganglion giant calyx-type synapse. METHODOLOGY/PRINCIPLE FINDINGS: The first step in FR analysis was to immunoprecipitate (IP the complex with an antibody against one protein component (the IP-protein. The immobilized complex was then exposed to a high salt (1150 mM stress-test that caused shedding of co-immunoprecipitated proteins (co-IP-proteins. A Fractional Recovery ratio (FR: recovery after high salt/recovery with control salt as assayed by Western blot was calculated for each co-IP-protein. These FR values reflect complex structure since an easily dissociated protein, with a low FR value, cannot be intermediary between the IP-protein and a salt-resistant protein. The structure of the complex was mapped and a blueprint generated with a pair of FR analyses generated using two different IP-proteins. The blueprint of SAE contains an AP180/X/STG/stonin 2/intersectin/epsin core (X is unknown and epsin is hypothesized, and an AP2 adaptor, H-/L-clathrin coat and dynamin scission protein perimeter. Quantitative immunocytochemistry (ICA/ICQ method at an isolated calyx-type presynaptic terminal indicates that this complex is associated with STG at the presynaptic transmitter release face but not with STG on intracellular synaptic vesicles. CONCLUSIONS/SIGNIFICANCE: We hypothesize that the SAE serves as a recognition site and also as a

  3. Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

    Science.gov (United States)

    Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

    2016-04-01

    We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

  4. Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

    Energy Technology Data Exchange (ETDEWEB)

    Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

    2014-10-02

    Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

  5. Complex Network Analysis of Guangzhou Metro

    Directory of Open Access Journals (Sweden)

    Yasir Tariq Mohmand

    2015-11-01

    Full Text Available The structure and properties of public transportation networks can provide suggestions for urban planning and public policies. This study contributes a complex network analysis of the Guangzhou metro. The metro network has 236 kilometers of track and is the 6th busiest metro system of the world. In this paper topological properties of the network are explored. We observed that the network displays small world properties and is assortative in nature. The network possesses a high average degree of 17.5 with a small diameter of 5. Furthermore, we also identified the most important metro stations based on betweenness and closeness centralities. These could help in identifying the probable congestion points in the metro system and provide policy makers with an opportunity to improve the performance of the metro system.

  6. A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility

    NARCIS (Netherlands)

    Bush, W.S.; McCauley, J.L.; DeJager, P.L.; Dudek, S.M.; Hafler, D.A.; Gibson, R.A.; Matthews, P.M.; Kappos, L.; Naegelin, Y.; Polman, C.H.; Hauser, S.L.; Oksenberg, J.; Haines, J.L.; Ritchie, M.D.

    2011-01-01

    Gene-gene interactions are proposed as an important component of the genetic architecture of complex diseases, and are just beginning to be evaluated in the context of genome-wide association studies (GWAS). In addition to detecting epistasis, a benefit to interaction analysis is that it also

  7. Revealing the equivalence of two clonal survival models by principal component analysis

    International Nuclear Information System (INIS)

    Lachet, Bernard; Dufour, Jacques

    1976-01-01

    The principal component analysis of 21 chlorella cell survival curves, adjusted by one-hit and two-hit target models, lead to quite similar projections on the principal plan: the homologous parameters of these models are linearly correlated; the reason for the statistical equivalence of these two models, in the present state of experimental inaccuracy, is revealed [fr

  8. Changes in cod muscle proteins during frozen storage revealed by proteome analysis and multivariate data analysis

    DEFF Research Database (Denmark)

    Kjærsgård, Inger Vibeke Holst; Nørrelykke, M.R.; Jessen, Flemming

    2006-01-01

    Multivariate data analysis has been combined with proteomics to enhance the recovery of information from 2-DE of cod muscle proteins during different storage conditions. Proteins were extracted according to 11 different storage conditions and samples were resolved by 2-DE. Data generated by 2-DE...... was subjected to principal component analysis (PCA) and discriminant partial least squares regression (DPLSR). Applying PCA to 2-DE data revealed the samples to form groups according to frozen storage time, whereas differences due to different storage temperatures or chilled storage in modified atmosphere...... light chain 1, 2 and 3, triose-phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, aldolase A and two ?-actin fragments, and a nuclease diphosphate kinase B fragment to change in concentration, during frozen storage. Application of proteomics, multivariate data analysis and MS/MS to analyse...

  9. Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

    Science.gov (United States)

    Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

  10. Phosphoproteome analysis of streptomyces development reveals extensive protein phosphorylation accompanying bacterial differentiation

    DEFF Research Database (Denmark)

    Manteca, Angel; Ye, Juanying; Sánchez, Jesús

    2011-01-01

    Streptomycetes are bacterial species that undergo a complex developmental cycle that includes programmed cell death (PCD) events and sporulation. They are widely used in biotechnology because they produce most clinically relevant secondary metabolites. Although Streptomyces coelicolor is one...... events were detected during the presporulation and sporulation stages (80%). Most of these phosphorylations were not reported before in Streptomyces, and included sporulation factors, transcriptional regulators, protein kinases and other regulatory proteins. Several of the identified phosphorylated...... proteins, FtsZ, DivIVA, and FtsH2, were previously demonstrated to be involved in the sporulation process. We thus established for the first time the widespread occurrence and dynamic features of Ser/Thr/Tyr protein phosphorylation in a bacteria species and also revealed a previously unrecognized...

  11. Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.

    Science.gov (United States)

    Lee, Kenneth K; Sardiu, Mihaela E; Swanson, Selene K; Gilmore, Joshua M; Torok, Michael; Grant, Patrick A; Florens, Laurence; Workman, Jerry L; Washburn, Michael P

    2011-07-05

    Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.

  12. Investigation of the complex structure, comparative DNA-binding and DNA cleavage of two water-soluble mono-nuclear lanthanum(III) complexes and cytotoxic activity of chitosan-coated magnetic nanoparticles as drug delivery for the complexes

    Science.gov (United States)

    Asadi, Zahra; Nasrollahi, Neda; Karbalaei-Heidari, Hamidreza; Eigner, Vaclav; Dusek, Michal; Mobaraki, Nabiallah; Pournejati, Roya

    2017-05-01

    Two water-soluble mono-nuclear macrocyclic lanthanum(III) complexes of 2,6-diformyl-4-methylphenol with 1,3-diamino-2-propanol (C1) or 1,3-propylenediamine (C2) were synthesized and characterized by UV-Vis, FT-IR, 13C and 1H NMR spectroscopy and elemental analysis. C1 complex was structurally characterized by single-crystal X-ray diffraction, which revealed that the complex was mononuclear and ten-coordinated. The coordination sites around lanthanum(III) were occupied with a five-dentate ligand, two bidentate nitrates, and one water molecule. The interaction of complexes with DNA was studied in buffered aqueous solution at pH 7.4. UV-Vis absorption spectroscopy, emission spectroscopy, circular dichroism (CD) and viscometric measurements provided clear evidence of the intercalation mechanism of binding. The obtained intrinsic binding constants (Kb) 9.3 × 103 and 1.2 × 103 M- 1 for C1 and C2, respectively confirmed that C1 is better intercalator than C2. The DNA docking studies suggested that the complexes bind with DNA in a groove binding mode with the binding affinity of C1 > C2. Moreover, agarose gel electrophoresis study of the DNA-complex for both compounds revealed that the C1 intercalation cause ethidium bromide replacement in a competitive manner which confirms the suggested mechanism of binding. Finally, the anticancer experiments for the treated cancerous cell lines with both synthesized compounds show that these hydrophilic molecules need a suitable carrier to pass through the hydrophobic nature of cell membrane efficiently.

  13. Complexity Plots

    KAUST Repository

    Thiyagalingam, Jeyarajan

    2013-06-01

    In this paper, we present a novel visualization technique for assisting the observation and analysis of algorithmic complexity. In comparison with conventional line graphs, this new technique is not sensitive to the units of measurement, allowing multivariate data series of different physical qualities (e.g., time, space and energy) to be juxtaposed together conveniently and consistently. It supports multivariate visualization as well as uncertainty visualization. It enables users to focus on algorithm categorization by complexity classes, while reducing visual impact caused by constants and algorithmic components that are insignificant to complexity analysis. It provides an effective means for observing the algorithmic complexity of programs with a mixture of algorithms and black-box software through visualization. Through two case studies, we demonstrate the effectiveness of complexity plots in complexity analysis in research, education and application. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and Blackwell Publishing Ltd.

  14. Complexity of EEG-signal in Time Domain - Possible Biomedical Application

    Science.gov (United States)

    Klonowski, Wlodzimierz; Olejarczyk, Elzbieta; Stepien, Robert

    2002-07-01

    Human brain is a highly complex nonlinear system. So it is not surprising that in analysis of EEG-signal, which represents overall activity of the brain, the methods of Nonlinear Dynamics (or Chaos Theory as it is commonly called) can be used. Even if the signal is not chaotic these methods are a motivating tool to explore changes in brain activity due to different functional activation states, e.g. different sleep stages, or to applied therapy, e.g. exposure to chemical agents (drugs) and physical factors (light, magnetic field). The methods supplied by Nonlinear Dynamics reveal signal characteristics that are not revealed by linear methods like FFT. Better understanding of principles that govern dynamics and complexity of EEG-signal can help to find `the signatures' of different physiological and pathological states of human brain, quantitative characteristics that may find applications in medical diagnostics.

  15. X-ray structure of a transition state analog complex reveals the molecular origins of the catalytic power and substrate specificity of acetylcholinesterase

    Energy Technology Data Exchange (ETDEWEB)

    Harel, M.; Silman, I. [Weizmann Inst. of Science, Rehovot (Israel); Quinn, D.M.; Nair, H.K. [Univ. of Iowa, Iowa City, IA (United States); Sussman, J.L. [Weizmann Inst. of Science, Rehovot (Israel)]|[Brookhaven National Lab., Upton, NY (United States)

    1996-03-13

    The structure of a complex of Torpedo californica acetylcholinesterase with the transition state analog inhibitor m-(N, N,N-trimethylammonio)-2,2,2-trifluoroacetophenone has been solved by X-ray crystallographic methods to 2.8 A resolution. Since the inhibitor binds to the enzyme about 10{sup 10}-fold more tightly than the substrate acetylcholine, this complex provides a visual accounting of the enzyme-ligand interactions that provide the molecular basis for the catalytic power of acetylcholinesterase. The acetyl ester hydrolytic specificity of the enzyme is revealed by the interaction of the CF{sub 3} function of the transition state analog with a concave binding site comprised of the residues G119, W233, F288, F290, and F331. The highly geometrically convergent array of enzyme-ligand interactions visualized in the complex described herein envelopes the acylation transition state and sequesters it from solvent, this being consistent with the location of the active site at the bottom of a deep and narrow gorge. 82 refs., 5 figs.

  16. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression

    Directory of Open Access Journals (Sweden)

    Yeates Todd O

    2009-12-01

    Full Text Available Abstract Background Many of the functional units in cells are multi-protein complexes such as RNA polymerase, the ribosome, and the proteasome. For such units to work together, one might expect a high level of regulation to enable co-appearance or repression of sets of complexes at the required time. However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships. Results We detect coordinated regulation of multiple protein complexes using logic analysis of gene expression data. Specifically, we identify gene triplets composed of genes whose expression profiles are found to be related by various types of logic functions. In order to focus on complexes, we associate the members of a gene triplet with the distinct protein complexes to which they belong. In this way, we identify complexes related by specific kinds of regulatory relationships. For example, we may find that the transcription of complex C is increased only if the transcription of both complex A AND complex B is repressed. We identify hundreds of examples of coordinated regulation among complexes under various stress conditions. Many of these examples involve the ribosome. Some of our examples have been previously identified in the literature, while others are novel. One notable example is the relationship between the transcription of the ribosome, RNA polymerase and mannosyltransferase II, which is involved in N-linked glycan processing in the Golgi. Conclusions The analysis proposed here focuses on relationships among triplets of genes that are not evident when genes are examined in a pairwise fashion as in typical clustering methods. By grouping gene triplets, we are able to decipher coordinated regulation among sets of three complexes. Moreover, using all triplets that involve coordinated regulation with the ribosome

  17. System Testability Analysis for Complex Electronic Devices Based on Multisignal Model

    International Nuclear Information System (INIS)

    Long, B; Tian, S L; Huang, J G

    2006-01-01

    It is necessary to consider the system testability problems for electronic devices during their early design phase because modern electronic devices become smaller and more compositive while their function and structure are more complex. Multisignal model, combining advantage of structure model and dependency model, is used to describe the fault dependency relationship for the complex electronic devices, and the main testability indexes (including optimal test program, fault detection rate, fault isolation rate, etc.) to evaluate testability and corresponding algorithms are given. The system testability analysis process is illustrated for USB-GPIB interface circuit with TEAMS toolbox. The experiment results show that the modelling method is simple, the computation speed is rapid and this method has important significance to improve diagnostic capability for complex electronic devices

  18. Economic development and wage inequality: A complex system analysis

    Science.gov (United States)

    Pugliese, Emanuele; Pietronero, Luciano

    2017-01-01

    Adapting methods from complex system analysis, this paper analyzes the features of the complex relationship between wage inequality and the development and industrialization of a country. Development is understood as a combination of a monetary index, GDP per capita, and a recently introduced measure of a country’s economic complexity: Fitness. Initially the paper looks at wage inequality on a global scale, over the time period 1990–2008. Our empirical results show that globally the movement of wage inequality along with the ongoing industrialization of countries has followed a longitudinally persistent pattern comparable to the one theorized by Kuznets in the fifties: countries with an average level of development suffer the highest levels of wage inequality. Next, the study narrows its focus on wage inequality within the United States. By using data on wages and employment in the approximately 3100 US counties over the time interval 1990–2014, it generalizes the Fitness-Complexity metric for geographic units and industrial sectors, and then investigates wage inequality between NAICS industries. The empirical time and scale dependencies are consistent with a relation between wage inequality and development driven by institutional factors comparing countries, and by change in the structural compositions of sectors in a homogeneous institutional environment, such as the counties of the United States. PMID:28926577

  19. Synthesis, Crystal Structure, Gas Absorption, and Separation Properties of a Novel Complex Based on Pr and a Three-Connected Ligand

    Directory of Open Access Journals (Sweden)

    Jie Sun

    2017-12-01

    Full Text Available A novel Pr complex, constructed from a rigid three-connected H3TMTA and praseodymium(III ion, has been synthesized in a mixed solvent system and characterized by X-ray single crystal diffraction, infrared spectroscopy, a thermogravimetric analysis, an element analysis, and powder X-ray diffraction, which reveals that complex 1 crystallizes in a three-dimensional porous framework. Moreover, the thermal stabilities and the fluorescent and gas adsorption and separation properties of complex 1 were investigated systematically.

  20. freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

    Science.gov (United States)

    Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

    2015-01-01

    Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

  1. Extrinsic and intrinsic complexities of the Los Alamos plutonium processing facility

    International Nuclear Information System (INIS)

    Bearse, R.C.; Roberts, N.J.; Longmire, V.L.

    1985-01-01

    Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. The authors have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. The authors have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities

  2. Computer aided approach to qualitative and quantitative common cause failure analysis for complex systems

    International Nuclear Information System (INIS)

    Cate, C.L.; Wagner, D.P.; Fussell, J.B.

    1977-01-01

    Common cause failure analysis, also called common mode failure analysis, is an integral part of a complete system reliability analysis. Existing methods of computer aided common cause failure analysis are extended by allowing analysis of the complex systems often encountered in practice. The methods aid in identifying potential common cause failures and also address quantitative common cause failure analysis

  3. Co-occurrence correlations of heavy metals in sediments revealed using network analysis.

    Science.gov (United States)

    Liu, Lili; Wang, Zhiping; Ju, Feng; Zhang, Tong

    2015-01-01

    In this study, the correlation-based study was used to identify the co-occurrence correlations among metals in marine sediment of Hong Kong, based on the long-term (from 1991 to 2011) temporal and spatial monitoring data. 14 stations out of the total 45 marine sediment monitoring stations were selected from three representative areas, including Deep Bay, Victoria Harbour and Mirs Bay. Firstly, Spearman's rank correlation-based network analysis was conducted as the first step to identify the co-occurrence correlations of metals from raw metadata, and then for further analysis using the normalized metadata. The correlations patterns obtained by network were consistent with those obtained by the other statistic normalization methods, including annual ratios, R-squared coefficient and Pearson correlation coefficient. Both Deep Bay and Victoria Harbour have been polluted by heavy metals, especially for Pb and Cu, which showed strong co-occurrence with other heavy metals (e.g. Cr, Ni, Zn and etc.) and little correlations with the reference parameters (Fe or Al). For Mirs Bay, which has better marine sediment quality compared with Deep Bay and Victoria Harbour, the co-occurrence patterns revealed by network analysis indicated that the metals in sediment dominantly followed the natural geography process. Besides the wide applications in biology, sociology and informatics, it is the first time to apply network analysis in the researches of environment pollutions. This study demonstrated its powerful application for revealing the co-occurrence correlations among heavy metals in marine sediments, which could be further applied for other pollutants in various environment systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. 6th international symposium on finite volumes for complex applications

    CERN Document Server

    Halama, Jan; Herbin, Raphaèle; Hubert, Florence; Fort, Jaroslav; FVCA 6; Finite Volumes for Complex Applications VI : Problems and perspectives

    2011-01-01

    Finite volume methods are used for various applications in fluid dynamics, magnetohydrodynamics, structural analysis or nuclear physics. A closer look reveals many interesting phenomena and mathematical or numerical difficulties, such as true error analysis and adaptivity, modelling of multi-phase phenomena or fitting problems, stiff terms in convection/diffusion equations and sources. To overcome existing problems and to find solution methods for future applications requires many efforts and always new developments. The goal of The International Symposium on Finite Volumes for Complex Applica

  5. Complexes of uranyl nitrate with 2,6-pyridinedicarboxamides: synthesis, crystal structure, and DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Alyapyshev, Mikhail; Babain, Vasiliy [ITMO University, 49, Kronverksky pr., 197101, St. Petersburg (Russian Federation); ThreeArc Mining Ltd., 5, Stary Tolmachevskiy per., 115184, Moscow (Russian Federation); Tkachenko, Lyudmila; Lumpov, Alexander [Khlopin Radium Institute, 28, 2nd Murinskiy pr., 194021, St. Petersburg (Russian Federation); Gurzhiy, Vladislav; Zolotarev, Andrey; Dar' in, Dmitriy [St. Petersburg State University, 7-9, Universitetskaya nab., 199034, St. Petersburg (Russian Federation); Ustynyuk, Yuriy; Gloriozov, Igor [M.V. Lomonosov Moscow State University, 119991, Moscow (Russian Federation); Paulenova, Alena [Department of Nuclear Engineering, Oregon State University, Corvallis, OR (United States)

    2017-05-04

    Two complexes of uranyl nitrate with N,N,N',N'-tetrabutyl-2,6-pyridinedicarboxamide (TBuDPA) and N,N'-diethyl-N,N'-diphenyl-2,6-pyridinedicarboxamide (EtPhDPA) were synthesized and studied. The complex of tetraalkyl-2,6-pyridinedicarboxamide with metal nitrate was synthesized for the first time. XRD analysis revealed the different type of complexation: a 1:1 metal:ligand complex for EtPhDPA and complex with polymeric structure for TBuDPA. The quantum chemical calculations (DFT) confirm that both ligands form the most stable complexes that match the minimal values pre-organization energy of the ligands. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Data-Independent Acquisition-Based Quantitative Proteomic Analysis Reveals Potential Biomarkers of Kidney Cancer.

    Science.gov (United States)

    Song, Yimeng; Zhong, Lijun; Zhou, Juntuo; Lu, Min; Xing, Tianying; Ma, Lulin; Shen, Jing

    2017-12-01

    Renal cell carcinoma (RCC) is a malignant and metastatic cancer with 95% mortality, and clear cell RCC (ccRCC) is the most observed among the five major subtypes of RCC. Specific biomarkers that can distinguish cancer tissues from adjacent normal tissues should be developed to diagnose this disease in early stages and conduct a reliable prognostic evaluation. Data-independent acquisition (DIA) strategy has been widely employed in proteomic analysis because of various advantages, including enhanced protein coverage and reliable data acquisition. In this study, a DIA workflow is constructed on a quadrupole-Orbitrap LC-MS platform to reveal dysregulated proteins between ccRCC and adjacent normal tissues. More than 4000 proteins are identified, 436 of these proteins are dysregulated in ccRCC tissues. Bioinformatic analysis reveals that multiple pathways and Gene Ontology items are strongly associated with ccRCC. The expression levels of L-lactate dehydrogenase A chain, annexin A4, nicotinamide N-methyltransferase, and perilipin-2 examined through RT-qPCR, Western blot, and immunohistochemistry confirm the validity of the proteomic analysis results. The proposed DIA workflow yields optimum time efficiency and data reliability and provides a good choice for proteomic analysis in biological and clinical studies, and these dysregulated proteins might be potential biomarkers for ccRCC diagnosis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. A Stylistic Analysis of Complexity in William Faulkner's "A Rose for Emily"

    Science.gov (United States)

    Abdurrahman, Israa' Burhanuddin

    2016-01-01

    Applying a stylistic analysis on certain texts refers to the identification of patterns of usage in writing. However, such an analysis is not restricted just to the description of the formal characteristics of texts, but it also tries to elucidate their functional importance for the interpretation of the text. This paper highlights complexity as a…

  8. Oxovanadium (iv) complexes with n/o- and o-donor ligands: their synthesis, characterization, semiempirical study and alkaline phosphatase activity (abstract)

    International Nuclear Information System (INIS)

    Munawar, K.S.; Ali, S.; Khan, A.N.

    2011-01-01

    Various N/O- and O-donor ligands and their oxovanadium complexes have been synthesized and characterized by different techniques such as FTIR, elemental analysis, thermogravimetery and conductometry. The IR data show the bidentate nature of the ligands and reveals hexa-coordinated geometry in the solid state which is also confirmed by semi-empirical study. Conductance measurements reveal the non-electrolytic nature of the complexes. These complexes have been checked for their alkaline phosphatase activity in the presence and absence of inhibitor which shows that by the addition of inhibitor the activity of enzyme decreases and at higher concentration it is completely inhibited. (author)

  9. Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts

    Science.gov (United States)

    Eldarov, Mikhail A.; Beletsky, Alexey V.; Tanashchuk, Tatiana N.; Kishkovskaya, Svetlana A.; Ravin, Nikolai V.; Mardanov, Andrey V.

    2018-01-01

    Flor yeast strains represent a specialized group of Saccharomyces cerevisiae yeasts used for biological wine aging. We have sequenced the genomes of three flor strains originated from different geographic regions and used for production of sherry-like wines in Russia. According to the obtained phylogeny of 118 yeast strains, flor strains form very tight cluster adjacent to the main wine clade. SNP analysis versus available genomes of wine and flor strains revealed 2,270 genetic variants in 1,337 loci specific to flor strains. Gene ontology analysis in combination with gene content evaluation revealed a complex landscape of possibly adaptive genetic changes in flor yeast, related to genes associated with cell morphology, mitotic cell cycle, ion homeostasis, DNA repair, carbohydrate metabolism, lipid metabolism, and cell wall biogenesis. Pangenomic analysis discovered the presence of several well-known “non-reference” loci of potential industrial importance. Events of gene loss included deletions of asparaginase genes, maltose utilization locus, and FRE-FIT locus involved in iron transport. The latter in combination with a flor-yeast-specific mutation in the Aft1 transcription factor gene is likely to be responsible for the discovered phenotype of increased iron sensitivity and improved iron uptake of analyzed strains. Expansion of the coding region of the FLO11 flocullin gene and alteration of the balance between members of the FLO gene family are likely to positively affect the well-known propensity of flor strains for velum formation. Our study provides new insights in the nature of genetic variation in flor yeast strains and demonstrates that different adaptive properties of flor yeast strains could have evolved through different mechanisms of genetic variation. PMID:29867869

  10. SPICE: exploration and analysis of post-cytometric complex multivariate datasets.

    Science.gov (United States)

    Roederer, Mario; Nozzi, Joshua L; Nason, Martha C

    2011-02-01

    Polychromatic flow cytometry results in complex, multivariate datasets. To date, tools for the aggregate analysis of these datasets across multiple specimens grouped by different categorical variables, such as demographic information, have not been optimized. Often, the exploration of such datasets is accomplished by visualization of patterns with pie charts or bar charts, without easy access to statistical comparisons of measurements that comprise multiple components. Here we report on algorithms and a graphical interface we developed for these purposes. In particular, we discuss thresholding necessary for accurate representation of data in pie charts, the implications for display and comparison of normalized versus unnormalized data, and the effects of averaging when samples with significant background noise are present. Finally, we define a statistic for the nonparametric comparison of complex distributions to test for difference between groups of samples based on multi-component measurements. While originally developed to support the analysis of T cell functional profiles, these techniques are amenable to a broad range of datatypes. Published 2011 Wiley-Liss, Inc.

  11. Structural Analysis of the Tobramycin and Gentamicin Clinical Resistome Reveals Limitations for Next-generation Aminoglycoside Design.

    Science.gov (United States)

    Bassenden, Angelia V; Rodionov, Dmitry; Shi, Kun; Berghuis, Albert M

    2016-05-20

    Widespread use and misuse of antibiotics has allowed for the selection of resistant bacteria capable of avoiding the effects of antibiotics. The primary mechanism for resistance to aminoglycosides, a broad-spectrum class of antibiotics, is through covalent enzymatic modification of the drug, waning their bactericidal effect. Tobramycin and gentamicin are two medically important aminoglycosides targeted by several different resistance factors, including aminoglycoside 2″-nucleotidyltransferase [ANT(2″)], the primary cause of aminoglycoside resistance in North America. We describe here two crystal structures of ANT(2″), each in complex with AMPCPP, Mn(2+), and either tobramycin or gentamicin. Together these structures outline ANT(2″)'s specificity for clinically used substrates. Importantly, these structures complete our structural knowledge for the set of enzymes that most frequently confer clinically observed resistance to tobramycin and gentamicin. Comparison of tobramycin and gentamicin binding to enzymes in this resistome, as well as to the intended target, the bacterial ribosome, reveals surprising diversity in observed drug-target interactions. Analysis of the diverse binding modes informs that there are limited opportunities for developing aminoglycoside analogs capable of evading resistance.

  12. Readability, complexity, and suitability analysis of online lymphedema resources.

    Science.gov (United States)

    Tran, Bao Ngoc N; Singh, Mansher; Lee, Bernard T; Rudd, Rima; Singhal, Dhruv

    2017-06-01

    Over 72% of Americans use online health information to assist in health care decision-making. Previous studies of lymphedema literature have focused only on reading level of patient-oriented materials online. Findings indicate they are too advanced for most patients to comprehend. This, more comprehensive study, expands the previous analysis to include critical elements of health materials beyond readability using assessment tools to report on the complexity and density of data as well as text design, vocabulary, and organization. The top 10 highest ranked websites on lymphedema were identified using the most popular search engine (Google). Website content was analyzed for readability, complexity, and suitability using Simple Measure of Gobbledygook, PMOSE/iKIRSCH, and Suitability Assessment of Materials (SAM), respectively. PMOSE/iKIRSCH and SAM were performed by two independent raters. Fleiss' kappa score was calculated to ensure inter-rater reliability. Online lymphedema literature had a reading grade level of 14.0 (SMOG). Overall complexity score was 6.7 (PMOSE/iKIRSCH) corresponding to "low" complexity and requiring a 8th-12th grade education. Fleiss' kappa score was 80% (P = 0.04, "substantial" agreement). Overall suitability score was 45% (SAM) correlating to the lowest level of "adequate" suitability. Fleiss' kappa score was 76% (P = 0.06, "substantial" agreement). Online resources for lymphedema are above the recommended levels for readability and complexity. The suitability level is barely adequate for the intended audience. Overall, these materials are too sophisticated for the average American adult, whose literacy skills are well documented. Further efforts to revise these materials are needed to improve patient comprehension and understanding. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Complexity and Intensionality in a Type-1 Framework for Computable Analysis

    DEFF Research Database (Denmark)

    Lambov, Branimir Zdravkov

    2005-01-01

    This paper describes a type-1 framework for computable analysis designed to facilitate efficient implementations and discusses properties that have not been well studied before for type-1 approaches: the introduction of complexity measures for type-1 representations of real functions, and ways...

  14. Analysis of the landscape complexity and heterogeneity of the Pantanal wetland.

    Science.gov (United States)

    Miranda, C S; Gamarra, R M; Mioto, C L; Silva, N M; Conceição Filho, A P; Pott, A

    2018-05-01

    This is the first report on analysis of habitat complexity and heterogeneity of the Pantanal wetland. The Pantanal encompasses a peculiar mosaic of environments, being important to evaluate and monitor this area concerning conservation of biodiversity. Our objective was to indirectly measure the habitat complexity and heterogeneity of the mosaic forming the sub-regions of the Pantanal, by means of remote sensing. We obtained free images of Normalized Difference Vegetation Index (NDVI) from the sensor MODIS and calculated the mean value (complexity) and standard deviation (heterogeneity) for each sub-region in the years 2000, 2008 and 2015. The sub-regions of Poconé, Canoeira, Paraguai and Aquidauana presented the highest values of complexity (mean NDVI), between 0.69 and 0.64 in the evaluated years. The highest horizontal heterogeneity (NDVI standard deviation) was observed in the sub-region of Tuiuiú, with values of 0.19 in the years 2000 and 2015, and 0.21 in the year 2008. We concluded that the use of NDVI to estimate landscape parameters is an efficient tool for assessment and monitoring of the complexity and heterogeneity of the Pantanal habitats, applicable in other regions.

  15. The complexity of nurses' attitudes toward euthanasia: a review of the literature.

    Science.gov (United States)

    Berghs, M; Dierckx de Casterlé, B; Gastmans, C

    2005-08-01

    In this literature review, a picture is given of the complexity of nursing attitudes toward euthanasia. The myriad of data found in empirical literature is mostly framed within a polarised debate and inconclusive about the complex reality behind attitudes toward euthanasia. Yet, a further examination of the content as well as the context of attitudes is more revealing. The arguments for euthanasia have to do with quality of life and respect for autonomy. Arguments against euthanasia have to do with non-maleficence, sanctity of life, and the notion of the slippery slope. When the context of attitudes is examined a number of positive correlates for euthanasia such as age, nursing specialty, and religion appear. In a further analysis of nurses' comments on euthanasia, it is revealed that part of the complexity of nursing attitudes toward euthanasia arises because of the needs of nurses at the levels of clinical practice, communication, emotions, decision making, and ethics.

  16. Complexity and competition in appetitive and aversive neural circuits

    Directory of Open Access Journals (Sweden)

    Crista L. Barberini

    2012-11-01

    Full Text Available Decision-making often involves using sensory cues to predict possible rewarding or punishing reinforcement outcomes before selecting a course of action. Recent work has revealed complexity in how the brain learns to predict rewards and punishments. Analysis of neural signaling during and after learning in the amygdala and orbitofrontal cortex, two brain areas that process appetitive and aversive stimuli, reveals a dynamic relationship between appetitive and aversive circuits. Specifically, the relationship between signaling in appetitive and aversive circuits in these areas shifts as a function of learning. Furthermore, although appetitive and aversive circuits may often drive opposite behaviors – approaching or avoiding reinforcement depending upon its valence – these circuits can also drive similar behaviors, such as enhanced arousal or attention; these processes also may influence choice behavior. These data highlight the formidable challenges ahead in dissecting how appetitive and aversive neural circuits interact to produce a complex and nuanced range of behaviors.

  17. Procedure for the analysis of americium in complex matrices

    International Nuclear Information System (INIS)

    Knab, D.

    1978-02-01

    A radioanalytical procedure for the analysis of americium in complex matrices has been developed. Clean separations of americium can be obtained from up to 100 g of sample ash, regardless of the starting material. The ability to analyze large masses of material provides the increased sensitivity necessary to detect americium in many environmental samples. The procedure adequately decontaminates from rare earth elements and natural radioactive nuclides that interfere with the alpha spectrometric measurements

  18. Analysis of a complex shape chain plate using Transmission Photoelasticity

    Directory of Open Access Journals (Sweden)

    Dasari N.

    2010-06-01

    -3]. A loading fixture was used to load the model during stress freezing in the furnace. The integrated fringe pattern of the offset chain plate is shown in Figure 2. Slices are cut in the offset zone to understand the nature of the stress distribution. A Simple photoelastic analysis of this has revealed a wealth of information to take suitable decision on the design of such plates taking into account the constraints in manufacturing.

  19. Managing Complexity in Evidence Analysis: A Worked Example in Pediatric Weight Management.

    Science.gov (United States)

    Parrott, James Scott; Henry, Beverly; Thompson, Kyle L; Ziegler, Jane; Handu, Deepa

    2018-05-02

    Nutrition interventions are often complex and multicomponent. Typical approaches to meta-analyses that focus on individual causal relationships to provide guideline recommendations are not sufficient to capture this complexity. The objective of this study is to describe the method of meta-analysis used for the Pediatric Weight Management (PWM) Guidelines update and provide a worked example that can be applied in other areas of dietetics practice. The effects of PWM interventions were examined for body mass index (BMI), body mass index z-score (BMIZ), and waist circumference at four different time periods. For intervention-level effects, intervention types were identified empirically using multiple correspondence analysis paired with cluster analysis. Pooled effects of identified types were examined using random effects meta-analysis models. Differences in effects among types were examined using meta-regression. Context-level effects are examined using qualitative comparative analysis. Three distinct types (or families) of PWM interventions were identified: medical nutrition, behavioral, and missing components. Medical nutrition and behavioral types showed statistically significant improvements in BMIZ across all time points. Results were less consistent for BMI and waist circumference, although four distinct patterns of weight status change were identified. These varied by intervention type as well as outcome measure. Meta-regression indicated statistically significant differences between the medical nutrition and behavioral types vs the missing component type for both BMIZ and BMI, although the pattern varied by time period and intervention type. Qualitative comparative analysis identified distinct configurations of context characteristics at each time point that were consistent with positive outcomes among the intervention types. Although analysis of individual causal relationships is invaluable, this approach is inadequate to capture the complexity of dietetics

  20. How a submarine returns to periscope depth: analysing complex socio-technical systems using Cognitive Work Analysis.

    Science.gov (United States)

    Stanton, Neville A; Bessell, Kevin

    2014-01-01

    This paper presents the application of Cognitive Work Analysis to the description of the functions, situations, activities, decisions, strategies, and competencies of a Trafalgar class submarine when performing the function of returning to periscope depth. All five phases of Cognitive Work Analysis are presented, namely: Work Domain Analysis, Control Task Analysis, Strategies Analysis, Social Organisation and Cooperation Analysis, and Worker Competencies Analysis. Complex socio-technical systems are difficult to analyse but Cognitive Work Analysis offers an integrated way of analysing complex systems with the core of functional means-ends analysis underlying all of the other representations. The joined-up analysis offers a coherent framework for understanding how socio-technical systems work. Data were collected through observation and interviews at different sites across the UK. The resultant representations present a statement of how the work domain and current activities are configured in this complex socio-technical system. This is intended to provide a baseline, from which all future conceptions of the domain may be compared. The strength of the analysis is in the multiple representations from which the constraints acting on the work may be analysed. Future research needs to challenge the assumptions behind these constraints in order to develop new ways of working. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  1. Recent Developments in Complex Analysis and Computer Algebra

    CERN Document Server

    Kajiwara, Joji; Xu, Yongzhi

    1999-01-01

    This volume consists of papers presented in the special sessions on "Complex and Numerical Analysis", "Value Distribution Theory and Complex Domains", and "Use of Symbolic Computation in Mathematics Education" of the ISAAC'97 Congress held at the University of Delaware, during June 2-7, 1997. The ISAAC Congress coincided with a U.S.-Japan Seminar also held at the University of Delaware. The latter was supported by the National Science Foundation through Grant INT-9603029 and the Japan Society for the Promotion of Science through Grant MTCS-134. It was natural that the participants of both meetings should interact and consequently several persons attending the Congress also presented papers in the Seminar. The success of the ISAAC Congress and the U.S.-Japan Seminar has led to the ISAAC'99 Congress being held in Fukuoka, Japan during August 1999. Many of the same participants will return to this Seminar. Indeed, it appears that the spirit of the U.S.-Japan Seminar will be continued every second year as part of...

  2. Extrinsic and intrinsic complexities of the Los Alamos Plutonium Processing Facility

    International Nuclear Information System (INIS)

    Bearse, R.C.; Longmire, V.L.; Roberts, N.J.

    1985-01-01

    Analysis of the data obtained in one year of plutonium accounting at Los Alamos reveals significant complexity. Much of this complexity arises from the complexity of the processes themselves. Additional complexity is induced by errors in the data entry process. It is important to note that there is no evidence that this complexity is adversely affecting the accounting in the plant. We have been analyzing transaction data from fiscal year 1983 processing. This study involved 62,595 transactions. The data have been analyzed using the relational database program INGRES on a VAX 11/780 computer. This software allows easy manipulation of the original data and subsets drawn from it. We have been attempting for several years to understand the global features of the TA-55 accounting data. This project has underscored several of the system's complexities. Examples that will be reported here include audit trails, lot-name multiplicity, etc

  3. Physiological and comparative proteomic analysis reveals different drought responses in roots and leaves of drought-tolerant wild wheat (Triticum boeoticum.

    Directory of Open Access Journals (Sweden)

    Hui Liu

    Full Text Available To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum, physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control, 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs (corresponding to 87 and 80 unique proteins, respectively in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism

  4. An approach to measuring adolescents' perception of complexity for pictures of fruit and vegetable mixes

    DEFF Research Database (Denmark)

    Mielby, Line Holler; Bennedbæk-Jensen, Sidsel; Edelenbos, Merete

    2013-01-01

    . An adolescent consumer group (n = 242) and an adult consumer group (n = 86) subsequently rated the pictures on simplicity and attractiveness. Pearson's correlation coefficients revealed strong correlations between the sensory panel and both consumer groups' usage of simplicity. This suggests that simplicity can...... adolescents' perception of complexity of pictures of fruit and vegetable mixes. A sensory panel evaluated 10 descriptive attributes, including simplicity and complexity, for 24 pictures of fruit and vegetable mixes. The descriptive analysis found strong inverse correlation between complexity and simplicity...

  5. Characterization of La2MoO6 prepared by the cation complexation technique

    International Nuclear Information System (INIS)

    Rocha, R.A.; Muccillo, E.N.S.

    2005-01-01

    The La 2 MoO 6 mixed oxide was prepared by the cation complexation technique using citric acid as complexant agent. The main purpose of this work was to obtain a mesoporous powder with relatively high specific surface area. The thermal decomposition behavior of the metal complex was studied by thermal analysis and Fourier transform infrared spectroscopy. A specific surface area value of ∼15 m 2 g -1 was obtained by nitrogen adsorption/desorption measurements. X-ray diffraction patterns of calcined mesoporous materials reveal that even though a low degree of crystallinity is attained, this phase may be obtained at low temperatures

  6. Analysis and Perspective from the Complex Aerospace Systems Exchange (CASE) 2013

    Science.gov (United States)

    Jones, Kennie H.; Parker, Peter A.; Detweiler, Kurt N.; McGowan, Anna-Maria R.; Dress, David A.; Kimmel, William M.

    2014-01-01

    NASA Langley Research Center embedded four rapporteurs at the Complex Aerospace Systems Exchange (CASE) held in August 2013 with the objective to capture the essence of the conference presentations and discussions. CASE was established to provide a discussion forum among chief engineers, program managers, and systems engineers on challenges in the engineering of complex aerospace systems. The meeting consists of invited presentations and panels from industry, academia, and government followed by discussions among attendees. This report presents the major and reoccurring themes captured throughout the meeting and provides analysis and insights to further the CASE mission.

  7. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    DEFF Research Database (Denmark)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

    2016-01-01

    to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

  8. On the complexity of numerical analysis

    DEFF Research Database (Denmark)

    Miltersen, Peter Bro; Allender, Eric; Burgisser, Peter

    2009-01-01

    an integer N, decide whether N>0. • In the Blum-Shub-Smale model, polynomial time computation over the reals (on discrete inputs) is polynomial-time equivalent to PosSLP, when there are only algebraic constants. We conjecture that using transcendental constants provides no additional power, beyond nonuniform...... reductions to PosSLP, and we present some preliminary results supporting this conjecture. • The Generic Task of Numerical Computation is also polynomial-time equivalent to PosSLP. We prove that PosSLP lies in the counting hierarchy. Combining this with work of Tiwari, we obtain that the Euclidean Traveling......We study two quite different approaches to understanding the complexity of fundamental problems in numerical analysis: • The Blum-Shub-Smale model of computation over the reals. • A problem we call the “Generic Task of Numerical Computation,” which captures an aspect of doing numerical computation...

  9. Spontaneous brain network activity: Analysis of its temporal complexity

    Directory of Open Access Journals (Sweden)

    Mangor Pedersen

    2017-06-01

    Full Text Available The brain operates in a complex way. The temporal complexity underlying macroscopic and spontaneous brain network activity is still to be understood. In this study, we explored the brain’s complexity by combining functional connectivity, graph theory, and entropy analyses in 25 healthy people using task-free functional magnetic resonance imaging. We calculated the pairwise instantaneous phase synchrony between 8,192 brain nodes for a total of 200 time points. This resulted in graphs for which time series of clustering coefficients (the “cliquiness” of a node and participation coefficients (the between-module connectivity of a node were estimated. For these two network metrics, sample entropy was calculated. The procedure produced a number of results: (1 Entropy is higher for the participation coefficient than for the clustering coefficient. (2 The average clustering coefficient is negatively related to its associated entropy, whereas the average participation coefficient is positively related to its associated entropy. (3 The level of entropy is network-specific to the participation coefficient, but not to the clustering coefficient. High entropy for the participation coefficient was observed in the default-mode, visual, and motor networks. These results were further validated using an independent replication dataset. Our work confirms that brain networks are temporally complex. Entropy is a good candidate metric to explore temporal network alterations in diseases with paroxysmal brain disruptions, including schizophrenia and epilepsy. In recent years, connectomics has provided significant insights into the topological complexity of brain networks. However, the temporal complexity of brain networks still remains somewhat poorly understood. In this study we used entropy analysis to demonstrate that the properties of network segregation (the clustering coefficient and integration (the participation coefficient are temporally complex

  10. The effect of spatial micro-CT image resolution and surface complexity on the morphological 3D analysis of open porous structures

    Energy Technology Data Exchange (ETDEWEB)

    Pyka, Grzegorz, E-mail: gregory.pyka@mtm.kuleuven.be [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium); Kerckhofs, Greet [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium); Biomechanics Research Unit, Université de Liege, Chemin des Chevreuils 1 - BAT 52/3, B-4000 Liège (Belgium); Schrooten, Jan; Wevers, Martine [Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44 – PB2450, B-3001 Leuven (Belgium)

    2014-01-15

    In material science microfocus X-ray computed tomography (micro-CT) is one of the most popular non-destructive techniques to visualise and quantify the internal structure of materials in 3D. Despite constant system improvements, state-of-the-art micro-CT images can still hold several artefacts typical for X-ray CT imaging that hinder further image-based processing, structural and quantitative analysis. For example spatial resolution is crucial for an appropriate characterisation as the voxel size essentially influences the partial volume effect. However, defining the adequate image resolution is not a trivial aspect and understanding the correlation between scan parameters like voxel size and the structural properties is crucial for comprehensive material characterisation using micro-CT. Therefore, the objective of this study was to evaluate the influence of the spatial image resolution on the micro-CT based morphological analysis of three-dimensional (3D) open porous structures with a high surface complexity. In particular the correlation between the local surface properties and the accuracy of the micro-CT-based macro-morphology of 3D open porous Ti6Al4V structures produced by selective laser melting (SLM) was targeted and revealed for rough surfaces a strong dependence of the resulting structure characteristics on the scan resolution. Reducing the surface complexity by chemical etching decreased the sensitivity of the overall morphological analysis to the spatial image resolution and increased the detection limit. This study showed that scan settings and image processing parameters need to be customized to the material properties, morphological parameters under investigation and the desired final characteristics (in relation to the intended functional use). Customization of the scan resolution can increase the reliability of the micro-CT based analysis and at the same time reduce its operating costs. - Highlights: • We examine influence of the image resolution

  11. Recent adaptive events in human brain revealed by meta-analysis of positively selected genes.

    Directory of Open Access Journals (Sweden)

    Yue Huang

    Full Text Available BACKGROUND AND OBJECTIVES: Analysis of positively-selected genes can help us understand how human evolved, especially the evolution of highly developed cognitive functions. However, previous works have reached conflicting conclusions regarding whether human neuronal genes are over-represented among genes under positive selection. METHODS AND RESULTS: We divided positively-selected genes into four groups according to the identification approaches, compiling a comprehensive list from 27 previous studies. We showed that genes that are highly expressed in the central nervous system are enriched in recent positive selection events in human history identified by intra-species genomic scan, especially in brain regions related to cognitive functions. This pattern holds when different datasets, parameters and analysis pipelines were used. Functional category enrichment analysis supported these findings, showing that synapse-related functions are enriched in genes under recent positive selection. In contrast, immune-related functions, for instance, are enriched in genes under ancient positive selection revealed by inter-species coding region comparison. We further demonstrated that most of these patterns still hold even after controlling for genomic characteristics that might bias genome-wide identification of positively-selected genes including gene length, gene density, GC composition, and intensity of negative selection. CONCLUSION: Our rigorous analysis resolved previous conflicting conclusions and revealed recent adaptation of human brain functions.

  12. Analysis reveals potential rangeland impacts if Williamson Act eliminated

    Directory of Open Access Journals (Sweden)

    William C. Wetzel

    2012-10-01

    Full Text Available California budget cuts have resulted in dramatic reductions in state funding for the Williamson Act, a land protection program that reduces property taxes for the owners of 15 million acres of California farms and rangeland. With state reimbursements to counties eliminated, the decision to continue Williamson Act contracts lies with individual counties. We investigated the consequences of eliminating the Williamson Act, using a geospatial analysis and a mail questionnaire asking ranchers for plans under a hypothetical elimination scenario. The geospatial analysis revealed that 72% of rangeland parcels enrolled in Williamson Act contracts contained habitat important for statewide conservation goals. Presented with the elimination scenario, survey respondents reported an intention to sell 20% of their total 496,889 acres. The tendency of survey participants to respond that they would sell land was highest among full-time ranchers with low household incomes and without off-ranch employment. A majority (76% of the ranchers who reported that they would sell land predicted that the buyers would develop it for nonagricultural uses, suggesting substantial changes to California's landscape in a future without the Williamson Act.

  13. Analysis and modeling of complex data in behavioral and social sciences

    CERN Document Server

    Okada, Akinori; Ragozini, Giancarlo; Weihs, Claus

    2014-01-01

    This volume presents theoretical developments, applications and computational methods for the analysis and modeling in behavioral and social sciences where data are usually complex to explore and investigate. The challenging proposals provide a connection between statistical methodology and the social domain with particular attention to computational issues in order to effectively address complicated data analysis problems. The papers in this volume stem from contributions initially presented at the joint international meeting JCS-CLADAG held in Anacapri (Italy) where the Japanese Classification Society and the Classification and Data Analysis Group of the Italian Statistical Society had a stimulating scientific discussion and exchange.

  14. Reactions and mass spectra of complex particles using Aerosol CIMS

    Science.gov (United States)

    Hearn, John D.; Smith, Geoffrey D.

    2006-12-01

    Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

  15. Complex ray analysis for plasmas

    International Nuclear Information System (INIS)

    Connor, K.A.

    1980-01-01

    An extension of ray tracing techniques is considered for a variety of cases in which the dispersion relation of the plasma medium is complex. The ray trajectories are permitted to begin and/or at least travel through complex space-time; the wave propagation process so characterized becomes significant only where the rays intersect real space-time. It is found that rules and guidelines can be established for limited application of this idea

  16. Crystallization and preliminary X-ray diffraction analysis of the peripheral light-harvesting complex LH2 from Marichromatium purpuratum.

    Science.gov (United States)

    Cranston, Laura J; Roszak, Aleksander W; Cogdell, Richard J

    2014-06-01

    LH2 from the purple photosynthetic bacterium Marichromatium (formerly known as Chromatium) purpuratum is an integral membrane pigment-protein complex that is involved in harvesting light energy and transferring it to the LH1-RC `core' complex. The purified LH2 complex was crystallized using the sitting-drop vapour-diffusion method at 294 K. The crystals diffracted to a resolution of 6 Å using synchrotron radiation and belonged to the tetragonal space group I4, with unit-cell parameters a=b=109.36, c=80.45 Å. The data appeared to be twinned, producing apparent diffraction symmetry I422. The tetragonal symmetry of the unit cell and diffraction for the crystals of the LH2 complex from this species reveal that this complex is an octamer.

  17. Flavonoids as matrices for MALDI-TOF mass spectrometric analysis of transition metal complexes

    Science.gov (United States)

    Petkovic, Marijana; Petrovic, Biljana; Savic, Jasmina; Bugarcic, Zivadin D.; Dimitric-Markovic, Jasmina; Momic, Tatjana; Vasic, Vesna

    2010-02-01

    Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a suitable method for the analysis of inorganic and organic compounds and biomolecules. This makes MALDI-TOF MS convenient for monitoring the interaction of metallo-drugs with biomolecules. Results presented in this manuscript demonstrate that flavonoids such as apigenin, kaempferol and luteolin are suitable for MALDI-TOF MS analysis of Pt(II), Pd(II), Pt(IV) and Ru(III) complexes, giving different signal-to-noise ratios of the analyte peak. The MALDI-TOF mass spectra of inorganic complexes acquired with these flavonoid matrices are easy to interpret and have some advantages over the application of other commonly used matrices: a low number of matrix peaks are detectable and the coordinative metal-ligand bond is, in most cases, preserved. On the other hand, flavonoids do not act as typical matrices, as their excess is not required for the acquisition of MALDI-TOF mass spectra of inorganic complexes.

  18. Fracture mechanics and residual fatigue life analysis for complex stress fields. Technical report

    International Nuclear Information System (INIS)

    Besuner, P.M.

    1975-07-01

    This report reviews the development and application of an influence function method for calculating stress intensity factors and residual fatigue life for two- and three-dimensional structures with complex stress fields and geometries. Through elastic superposition, the method properly accounts for redistribution of stress as the crack grows through the structure. The analytical methods used and the computer programs necessary for computation and application of load independent influence functions are presented. A new exact solution is obtained for the buried elliptical crack, under an arbitrary Mode I stress field, for stress intensity factors at four positions around the crack front. The IF method is then applied to two fracture mechanics problems with complex stress fields and geometries. These problems are of current interest to the electric power generating industry and include (1) the fatigue analysis of a crack in a pipe weld under nominal and residual stresses and (2) fatigue analysis of a reactor pressure vessel nozzle corner crack under a complex bivariate stress field

  19. Complex network analysis of resting-state fMRI of the brain.

    Science.gov (United States)

    Anwar, Abdul Rauf; Hashmy, Muhammad Yousaf; Imran, Bilal; Riaz, Muhammad Hussnain; Mehdi, Sabtain Muhammad Muntazir; Muthalib, Makii; Perrey, Stephane; Deuschl, Gunther; Groppa, Sergiu; Muthuraman, Muthuraman

    2016-08-01

    Due to the fact that the brain activity hardly ever diminishes in healthy individuals, analysis of resting state functionality of the brain seems pertinent. Various resting state networks are active inside the idle brain at any time. Based on various neuro-imaging studies, it is understood that various structurally distant regions of the brain could be functionally connected. Regions of the brain, that are functionally connected, during rest constitutes to the resting state network. In the present study, we employed the complex network measures to estimate the presence of community structures within a network. Such estimate is named as modularity. Instead of using a traditional correlation matrix, we used a coherence matrix taken from the causality measure between different nodes. Our results show that in prolonged resting state the modularity starts to decrease. This decrease was observed in all the resting state networks and on both sides of the brain. Our study highlights the usage of coherence matrix instead of correlation matrix for complex network analysis.

  20. Waste Sampling and Characterization Facility (WSCF) Complex Safety Analysis

    International Nuclear Information System (INIS)

    MELOY, R.T.

    2003-01-01

    The Waste Sampling and Characterization Facility (WSCF) is an analytical laboratory complex on the Hanford Site that was constructed to perform chemical and low-level radiological analyses on a variety of sample media in support of Hanford Site customer needs. The complex is located in the 600 area of the Hanford Site, east of the 200 West Area. Customers include effluent treatment facilities, waste disposal and storage facilities, and remediation projects. Customers primarily need analysis results for process control and to comply with federal, Washington State, and US. Department of Energy (DOE) environmental or industrial hygiene requirements. This document was prepared to analyze the facility for safety consequences and includes the following steps: Determine radionuclide and highly hazardous chemical inventories; Compare these inventories to the appropriate regulatory limits; Document the compliance status with respect to these limits; and Identify the administrative controls necessary to maintain this status

  1. Solution XAS Analysis for Exploring the Active Species in Homogeneous Vanadium Complex Catalysis

    Science.gov (United States)

    Nomura, Kotohiro; Mitsudome, Takato; Tsutsumi, Ken; Yamazoe, Seiji

    2018-06-01

    Selected examples in V K-edge X-ray Absorption Near Edge Structure (XANES) analysis of a series of vanadium complexes containing imido ligands (possessing metal-nitrogen double bond) in toluene solution have been introduced, and their pre-edge and the edge were affected by their structures and nature of ligands. Selected results in exploring the oxidation states of the active species in ethylene dimerization/polymerization using homogeneous vanadium catalysts [consisting of (imido)vanadium(V) complexes and Al cocatalysts] by X-ray absorption spectroscopy (XAS) analyses have been introduced. It has been demonstrated that the method should provide more clear information concerning the active species in situ, especially by combination with the other methods (NMR and ESR spectra, X-ray crystallographic analysis, and reaction chemistry), and should be powerful tool for study of catalysis mechanism as well as for the structural analysis in solution.

  2. Recurrence Density Enhanced Complex Networks for Nonlinear Time Series Analysis

    Science.gov (United States)

    Costa, Diego G. De B.; Reis, Barbara M. Da F.; Zou, Yong; Quiles, Marcos G.; Macau, Elbert E. N.

    We introduce a new method, which is entitled Recurrence Density Enhanced Complex Network (RDE-CN), to properly analyze nonlinear time series. Our method first transforms a recurrence plot into a figure of a reduced number of points yet preserving the main and fundamental recurrence properties of the original plot. This resulting figure is then reinterpreted as a complex network, which is further characterized by network statistical measures. We illustrate the computational power of RDE-CN approach by time series by both the logistic map and experimental fluid flows, which show that our method distinguishes different dynamics sufficiently well as the traditional recurrence analysis. Therefore, the proposed methodology characterizes the recurrence matrix adequately, while using a reduced set of points from the original recurrence plots.

  3. Complexity science and leadership in healthcare.

    Science.gov (United States)

    Burns, J P

    2001-10-01

    The emerging field of complexity science offers an alternative leadership strategy for the chaotic, complex healthcare environment. A survey revealed that healthcare leaders intuitively support principles of complexity science. Leadership that uses complexity principles offers opportunities in the chaotic healthcare environment to focus less on prediction and control and more on fostering relationships and creating conditions in which complex adaptive systems can evolve to produce creative outcomes.

  4. Ecomorph or endangered coral? DNA and microstructure reveal hawaiian species complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli.

    Directory of Open Access Journals (Sweden)

    Zac H Forsman

    2010-12-01

    Full Text Available M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA, which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I M. patula/M. verrilli, II M. cf. incrassata, III M. capitata, IV M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA, two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity.

  5. Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories.

    Directory of Open Access Journals (Sweden)

    S Elfekih

    Full Text Available Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1 have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO. Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.

  6. Thin-plate spline analysis of allometry and sexual dimorphism in the human craniofacial complex.

    Science.gov (United States)

    Rosas, Antonio; Bastir, Markus

    2002-03-01

    The relationship between allometry and sexual dimorphism in the human craniofacial complex was analyzed using geometric morphometric methods. Thin-plate splines (TPS) analysis has been applied to investigate the lateral profile of complete adult skulls of known sex. Twenty-nine three-dimensional (3D) craniofacial and mandibular landmark coordinates were recorded from a sample of 52 adult females and 52 adult males of known age and sex. No difference in the influence of size on shape was detected between sexes. Both size and sex had significant influences on shape. As expected, the influence of centroid size on shape (allometry) revealed a shift in the proportions of the neurocranium and the viscerocranium, with a marked allometric variation of the lower face. Adjusted for centroid size, males presented a relatively larger size of the nasopharyngeal space than females. A mean-male TPS transformation revealed a larger piriform aperture, achieved by an increase of the angulation of the nasal bones and a downward rotation of the anterior nasal floor. Male pharynx expansion was also reflected by larger choanae and a more posteriorly inclined basilar part of the occipital clivus. Male muscle attachment sites appeared more pronounced. In contrast, the mean-female TPS transformation was characterized by a relatively small nasal aperture. The occipital clivus inclined anteriorly, and muscle insertion areas became smoothed. Besides these variations, both maxillary and mandibular alveolar regions became prognathic. The sex-specific TPS deformation patterns are hypothesized to be associated with sexual differences in body composition and energetic requirements. Copyright 2002 Wiley-Liss, Inc.

  7. A Single-Cell Biochemistry Approach Reveals PAR Complex Dynamics during Cell Polarization.

    Science.gov (United States)

    Dickinson, Daniel J; Schwager, Francoise; Pintard, Lionel; Gotta, Monica; Goldstein, Bob

    2017-08-21

    Regulated protein-protein interactions are critical for cell signaling, differentiation, and development. For the study of dynamic regulation of protein interactions in vivo, there is a need for techniques that can yield time-resolved information and probe multiple protein binding partners simultaneously, using small amounts of starting material. Here we describe a single-cell protein interaction assay. Single-cell lysates are generated at defined time points and analyzed using single-molecule pull-down, yielding information about dynamic protein complex regulation in vivo. We established the utility of this approach by studying PAR polarity proteins, which mediate polarization of many animal cell types. We uncovered striking regulation of PAR complex composition and stoichiometry during Caenorhabditis elegans zygote polarization, which takes place in less than 20 min. PAR complex dynamics are linked to the cell cycle by Polo-like kinase 1 and govern the movement of PAR proteins to establish polarity. Our results demonstrate an approach to study dynamic biochemical events in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. A framework for the analysis of cognitive reliability in complex systems: a recovery centred approach

    International Nuclear Information System (INIS)

    Kontogiannis, Tom

    1997-01-01

    Managing complex industrial systems requires reliable performance of cognitive tasks undertaken by operating crews. The infrequent practice of cognitive skills and the reliance on operator performance for novel situations raised cognitive reliability into an urgent and essential aspect in system design and risk analysis. The aim of this article is to contribute to the development of methods for the analysis of cognitive tasks in complex man-machine interactions. A practical framework is proposed for analysing cognitive errors and enhancing error recovery through interface design. Cognitive errors are viewed as failures in problem solving which are difficult to recover under the task constrains imposed by complex systems. In this sense, the interaction between context and cognition, on the one hand, and the process of error recovery, on the other hand, become the focal points of the proposed framework which is illustrated in an analysis of a simulated emergency

  9. Genomic analysis of primordial dwarfism reveals novel disease genes.

    Science.gov (United States)

    Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

    2014-02-01

    Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

  10. Growth and characterization of barium complex of 1,3,5-triazinane-2,4,6-trione in gel: a corrosion inhibiting material

    Science.gov (United States)

    Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Babu, K. Rajendra

    2018-05-01

    Good quality prismatic crystals of industrially applicable corrosion inhibiting barium complex of 1,3,5-triazinane-2,4,6-trione have been grown by conventional gel method. The crystal structure, packing, and nature of bonds are revealed in the single crystal X-ray diffraction analysis. The crystal has a three-dimensional polymeric structure having a triclinic crystal system with the space group P-1. The powder X-ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal are identified by Fourier transform infrared spectroscopy. Elemental analysis confirms the stoichiometry of the elements present in the complex. Thermogravimetric analysis and differential thermal analysis reveal its good thermal stability. The optical properties like band gap, refractive index and extinction coefficient are evaluated from the UV-visible spectral analysis. The singular property of the material, corrosion inhibition efficiency achieved by the adsorption of the sample molecules is determined by the weight loss method.

  11. Design Analysis Method for Multidisciplinary Complex Product using SysML

    Directory of Open Access Journals (Sweden)

    Liu Jihong

    2017-01-01

    Full Text Available In the design of multidisciplinary complex products, model-based systems engineering methods are widely used. However, the methodologies only contain only modeling order and simple analysis steps, and lack integrated design analysis methods supporting the whole process. In order to solve the problem, a conceptual design analysis method with integrating modern design methods has been proposed. First, based on the requirement analysis of the quantization matrix, the user’s needs are quantitatively evaluated and translated to system requirements. Then, by the function decomposition of the function knowledge base, the total function is semi-automatically decomposed into the predefined atomic function. The function is matched into predefined structure through the behaviour layer using function-structure mapping based on the interface matching. Finally based on design structure matrix (DSM, the structure reorganization is completed. The process of analysis is implemented with SysML, and illustrated through an aircraft air conditioning system for the system validation.

  12. Structural flexibility of the G alpha s alpha-helical domain in the beta2-adrenoceptor Gs complex

    DEFF Research Database (Denmark)

    Westfield, Gerwin H; Rasmussen, Søren Gøgsig Faarup; Su, Min

    2011-01-01

    The active-state complex between an agonist-bound receptor and a guanine nucleotide-free G protein represents the fundamental signaling assembly for the majority of hormone and neurotransmitter signaling. We applied single-particle electron microscopy (EM) analysis to examine the architecture...... of agonist-occupied β(2)-adrenoceptor (β(2)AR) in complex with the heterotrimeric G protein Gs (Gαsβγ). EM 2D averages and 3D reconstructions of the detergent-solubilized complex reveal an overall architecture that is in very good agreement with the crystal structure of the active-state ternary complex...

  13. Network reliability analysis of complex systems using a non-simulation-based method

    International Nuclear Information System (INIS)

    Kim, Youngsuk; Kang, Won-Hee

    2013-01-01

    Civil infrastructures such as transportation, water supply, sewers, telecommunications, and electrical and gas networks often establish highly complex networks, due to their multiple source and distribution nodes, complex topology, and functional interdependence between network components. To understand the reliability of such complex network system under catastrophic events such as earthquakes and to provide proper emergency management actions under such situation, efficient and accurate reliability analysis methods are necessary. In this paper, a non-simulation-based network reliability analysis method is developed based on the Recursive Decomposition Algorithm (RDA) for risk assessment of generic networks whose operation is defined by the connections of multiple initial and terminal node pairs. The proposed method has two separate decomposition processes for two logical functions, intersection and union, and combinations of these processes are used for the decomposition of any general system event with multiple node pairs. The proposed method is illustrated through numerical network examples with a variety of system definitions, and is applied to a benchmark gas transmission pipe network in Memphis TN to estimate the seismic performance and functional degradation of the network under a set of earthquake scenarios.

  14. Engineering Complex Embedded Systems with State Analysis and the Mission Data System

    Science.gov (United States)

    Ingham, Michel D.; Rasmussen, Robert D.; Bennett, Matthew B.; Moncada, Alex C.

    2004-01-01

    It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer s intent, potentially leading to software errors. This problem is addressed by a systems engineering methodology called State Analysis, which provides a process for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using State Analysis and how these requirements inform the design of the system software, using representative spacecraft examples.

  15. Homology modeling and docking of AahII-Nanobody complexes reveal the epitope binding site on AahII scorpion toxin.

    Science.gov (United States)

    Ksouri, Ayoub; Ghedira, Kais; Ben Abderrazek, Rahma; Shankar, B A Gowri; Benkahla, Alia; Bishop, Ozlem Tastan; Bouhaouala-Zahar, Balkiss

    2018-02-19

    Scorpion envenoming and its treatment is a public health problem in many parts of the world due to highly toxic venom polypeptides diffusing rapidly within the body of severely envenomed victims. Recently, 38 AahII-specific Nanobody sequences (Nbs) were retrieved from which the performance of NbAahII10 nanobody candidate, to neutralize the most poisonous venom compound namely AahII acting on sodium channels, was established. Herein, structural computational approach is conducted to elucidate the Nb-AahII interactions that support the biological characteristics, using Nb multiple sequence alignment (MSA) followed by modeling and molecular docking investigations (RosettaAntibody, ZDOCK software tools). Sequence and structural analysis showed two dissimilar residues of NbAahII10 CDR1 (Tyr27 and Tyr29) and an inserted polar residue Ser30 that appear to play an important role. Indeed, CDR3 region of NbAahII10 is characterized by a specific Met104 and two negatively charged residues Asp115 and Asp117. Complex dockings reveal that NbAahII17 and NbAahII38 share one common binding site on the surface of the AahII toxin divergent from the NbAahII10 one's. At least, a couple of NbAahII10 - AahII residue interactions (Gln38 - Asn44 and Arg62, His64, respectively) are mainly involved in the toxic AahII binding site. Altogether, this study gives valuable insights in the design and development of next generation of antivenom. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse.

    Science.gov (United States)

    Dai, Jiajuan; Wang, Xusheng; Chen, Ying; Wang, Xiaodong; Zhu, Jun; Lu, Lu

    2009-11-01

    Previous studies have revealed that the subunit alpha 2 (Gabra2) of the gamma-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.

  17. Revealing effective classifiers through network comparison

    Science.gov (United States)

    Gallos, Lazaros K.; Fefferman, Nina H.

    2014-11-01

    The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured, in ways that are otherwise inaccessible to observation. Here, we introduce the n-tangle method to directly compare two networks for structural similarity, based on the distribution of edge density in network subgraphs. We demonstrate that this method can efficiently introduce comparative analysis into network science and opens the road for many new applications. For example, we show how the construction of a “phylogenetic tree” across animal taxa according to their social structure can reveal commonalities in the behavioral ecology of the populations, or how students create similar networks according to the University size. Our method can be expanded to study many additional properties, such as network classification, changes during time evolution, convergence of growth models, and detection of structural changes during damage.

  18. Meta-analysis, complexity, and heterogeneity: a qualitative interview study of researchers’ methodological values and practices

    Directory of Open Access Journals (Sweden)

    Theo Lorenc

    2016-11-01

    Full Text Available Abstract Background Complex or heterogeneous data pose challenges for systematic review and meta-analysis. In recent years, a number of new methods have been developed to meet these challenges. This qualitative interview study aimed to understand researchers’ understanding of complexity and heterogeneity and the factors which may influence the choices researchers make in synthesising complex data. Methods We conducted interviews with a purposive sample of researchers (N = 19 working in systematic review or meta-analysis across a range of disciplines. We analysed data thematically using a framework approach. Results Participants reported using a broader range of methods and data types in complex reviews than in traditional reviews. A range of techniques are used to explore heterogeneity, but there is some debate about their validity, particularly when applied post hoc. Conclusions Technical considerations of how to synthesise complex evidence cannot be isolated from questions of the goals and contexts of research. However, decisions about how to analyse data appear to be made in a largely informal way, drawing on tacit expertise, and their relation to these broader questions remains unclear.

  19. Meta-analysis, complexity, and heterogeneity: a qualitative interview study of researchers' methodological values and practices.

    Science.gov (United States)

    Lorenc, Theo; Felix, Lambert; Petticrew, Mark; Melendez-Torres, G J; Thomas, James; Thomas, Sian; O'Mara-Eves, Alison; Richardson, Michelle

    2016-11-16

    Complex or heterogeneous data pose challenges for systematic review and meta-analysis. In recent years, a number of new methods have been developed to meet these challenges. This qualitative interview study aimed to understand researchers' understanding of complexity and heterogeneity and the factors which may influence the choices researchers make in synthesising complex data. We conducted interviews with a purposive sample of researchers (N = 19) working in systematic review or meta-analysis across a range of disciplines. We analysed data thematically using a framework approach. Participants reported using a broader range of methods and data types in complex reviews than in traditional reviews. A range of techniques are used to explore heterogeneity, but there is some debate about their validity, particularly when applied post hoc. Technical considerations of how to synthesise complex evidence cannot be isolated from questions of the goals and contexts of research. However, decisions about how to analyse data appear to be made in a largely informal way, drawing on tacit expertise, and their relation to these broader questions remains unclear.

  20. Performance Analysis with Network-Enhanced Complexities: On Fading Measurements, Event-Triggered Mechanisms, and Cyber Attacks

    Directory of Open Access Journals (Sweden)

    Derui Ding

    2014-01-01

    Full Text Available Nowadays, the real-world systems are usually subject to various complexities such as parameter uncertainties, time-delays, and nonlinear disturbances. For networked systems, especially large-scale systems such as multiagent systems and systems over sensor networks, the complexities are inevitably enhanced in terms of their degrees or intensities because of the usage of the communication networks. Therefore, it would be interesting to (1 examine how this kind of network-enhanced complexities affects the control or filtering performance; and (2 develop some suitable approaches for controller/filter design problems. In this paper, we aim to survey some recent advances on the performance analysis and synthesis with three sorts of fashionable network-enhanced complexities, namely, fading measurements, event-triggered mechanisms, and attack behaviors of adversaries. First, these three kinds of complexities are introduced in detail according to their engineering backgrounds, dynamical characteristic, and modelling techniques. Then, the developments of the performance analysis and synthesis issues for various networked systems are systematically reviewed. Furthermore, some challenges are illustrated by using a thorough literature review and some possible future research directions are highlighted.

  1. Computational model of dose response for low-LET-induced complex chromosomal aberrations

    International Nuclear Information System (INIS)

    Eidelman, Y.A.; Andreev, S.G.

    2015-01-01

    Experiments with full-colour mFISH chromosome painting have revealed high yield of radiation-induced complex chromosomal aberrations (CAs). The ratio of complex to simple aberrations is dependent on cell type and linear energy transfer. Theoretical analysis has demonstrated that the mechanism of CA formation as a result of interaction between lesions at a surface of chromosome territories does not explain high complexes-to-simples ratio in human lymphocytes. The possible origin of high yields of γ-induced complex CAs was investigated in the present work by computer simulation. CAs were studied on the basis of chromosome structure and dynamics modelling and the hypothesis of CA formation on nuclear centres. The spatial organisation of all chromosomes in a human interphase nucleus was predicted by simulation of mitosis-to-interphase chromosome structure transition. Two scenarios of CA formation were analysed, 'static' (existing in a nucleus prior to irradiation) centres and 'dynamic' (formed in response to irradiation) centres. The modelling results reveal that under certain conditions, both scenarios explain quantitatively the dose-response relationships for both simple and complex γ-induced inter-chromosomal exchanges observed by mFISH chromosome painting in the first post-irradiation mitosis in human lymphocytes. (authors)

  2. Complex Retrieval of Embedded IVC Filters: Alternative Techniques and Histologic Tissue Analysis

    International Nuclear Information System (INIS)

    Kuo, William T.; Cupp, John S.; Louie, John D.; Kothary, Nishita; Hofmann, Lawrence V.; Sze, Daniel Y.; Hovsepian, David M.

    2012-01-01

    Purpose: We evaluated the safety and effectiveness of alternative endovascular methods to retrieve embedded optional and permanent filters in order to manage or reduce risk of long-term complications from implantation. Histologic tissue analysis was performed to elucidate the pathologic effects of chronic filter implantation. Methods: We studied the safety and effectiveness of alternative endovascular methods for removing embedded inferior vena cava (IVC) filters in 10 consecutive patients over 12 months. Indications for retrieval were symptomatic chronic IVC occlusion, caval and aortic perforation, and/or acute PE (pulmonary embolism) from filter-related thrombus. Retrieval was also performed to reduce risk of complications from long-term filter implantation and to eliminate the need for lifelong anticoagulation. All retrieved specimens were sent for histologic analysis. Results: Retrieval was successful in all 10 patients. Filter types and implantation times were as follows: one Venatech (1,495 days), one Simon-Nitinol (1,485 days), one Optease (300 days), one G2 (416 days), five Günther-Tulip (GTF; mean 606 days, range 154–1,010 days), and one Celect (124 days). There were no procedural complications or adverse events at a mean follow-up of 304 days after removal (range 196–529 days). Histology revealed scant native intima surrounded by a predominance of neointimal hyperplasia and dense fibrosis in all specimens. Histologic evidence of photothermal tissue ablation was confirmed in three laser-treated specimens. Conclusion: Complex retrieval methods can now be used in select patients to safely remove embedded optional and permanent IVC filters previously considered irretrievable. Neointimal hyperplasia and dense fibrosis are the major components that must be separated to achieve successful retrieval of chronic filter implants.

  3. Techniques for Fault Detection and Visualization of Telemetry Dependence Relationships for Root Cause Fault Analysis in Complex Systems

    Science.gov (United States)

    Guy, Nathaniel

    This thesis explores new ways of looking at telemetry data, from a time-correlative perspective, in order to see patterns within the data that may suggest root causes of system faults. It was thought initially that visualizing an animated Pearson Correlation Coefficient (PCC) matrix for telemetry channels would be sufficient to give new understanding; however, testing showed that the high dimensionality and inability to easily look at change over time in this approach impeded understanding. Different correlative techniques, combined with the time curve visualization proposed by Bach et al (2015), were adapted to visualize both raw telemetry and telemetry data correlations. Review revealed that these new techniques give insights into the data, and an intuitive grasp of data families, which show the effectiveness of this approach for enhancing system understanding and assisting with root cause analysis for complex aerospace systems.

  4. SACS2: Dynamic and Formal Safety Analysis Method for Complex Safety Critical System

    International Nuclear Information System (INIS)

    Koh, Kwang Yong; Seong, Poong Hyun

    2009-01-01

    Fault tree analysis (FTA) is one of the most widely used safety analysis technique in the development of safety critical systems. However, over the years, several drawbacks of the conventional FTA have become apparent. One major drawback is that conventional FTA uses only static gates and hence can not capture dynamic behaviors of the complex system precisely. Although several attempts such as dynamic fault tree (DFT), PANDORA, formal fault tree (FFT) and so on, have been made to overcome this problem, they can not still do absolute or actual time modeling because they adapt relative time concept and can capture only sequential behaviors of the system. Second drawback of conventional FTA is its lack of rigorous semantics. Because it is informal in nature, safety analysis results heavily depend on an analyst's ability and are error-prone. Finally reasoning process which is to check whether basic events really cause top events is done manually and hence very labor-intensive and timeconsuming for the complex systems. In this paper, we propose a new safety analysis method for complex safety critical system in qualitative manner. We introduce several temporal gates based on timed computational tree logic (TCTL) which can represent quantitative notion of time. Then, we translate the information of the fault trees into UPPAAL query language and the reasoning process is automatically done by UPPAAL which is the model checker for time critical system

  5. Synthesis and Spectral Evaluation of Some Unsymmetrical Mesoporphyrinic Complexes

    Directory of Open Access Journals (Sweden)

    Rica Boscencu

    2012-06-01

    Full Text Available Synthesis and spectral evaluation of new zinc and copper unsymmetrical mesoporphyrinic complexes are reported. Zn(II-5-(4-acetoxy-3-methoxyphenyl-10,15,20-tris-(4-carboxymethylphenylporphyrin, Zn(II-5-[(3,4-methylenedioxyphenyl]-10,15,20-tris-(4-carboxymethylphenylporphyrin, Cu(II-5-(4-acetoxy-3-methoxyphenyl-10,15,20-tris-(4-carboxymethylphenylporphyrin and Cu(II-5-[(3,4-methylenedioxyphenyl]-10,15,20-tris-(4-carboxymethylphenylporphyrin were synthesized using microwave-assisted synthesis. The complexes were characterized by elemental analysis, FT-IR, UV-Vis, EPR and NMR spectroscopy, which fully confirmed their structure. The spectral absorption properties of the porphyrinic complexes were studied in solvents with different polarities. Fluorescence emission and singlet oxygen formation quantum yields were evaluated for the compounds under study, revealing high yields for the zinc derivatives. The copper complexes are not emissive and only display residual capacity for singlet oxygen formation.

  6. Multivariate Multi-Scale Permutation Entropy for Complexity Analysis of Alzheimer’s Disease EEG

    Directory of Open Access Journals (Sweden)

    Isabella Palamara

    2012-07-01

    Full Text Available An original multivariate multi-scale methodology for assessing the complexity of physiological signals is proposed. The technique is able to incorporate the simultaneous analysis of multi-channel data as a unique block within a multi-scale framework. The basic complexity measure is done by using Permutation Entropy, a methodology for time series processing based on ordinal analysis. Permutation Entropy is conceptually simple, structurally robust to noise and artifacts, computationally very fast, which is relevant for designing portable diagnostics. Since time series derived from biological systems show structures on multiple spatial-temporal scales, the proposed technique can be useful for other types of biomedical signal analysis. In this work, the possibility of distinguish among the brain states related to Alzheimer’s disease patients and Mild Cognitive Impaired subjects from normal healthy elderly is checked on a real, although quite limited, experimental database.

  7. Removal combined with reduction of hexavalent chromium from aqueous solution by Fe-ethylene glycol complex microspheres

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yong-Xing [School of Physics and Electronic Information, Huaibei Normal University, Huaibei 235000 (China); Jia, Yong, E-mail: yjiaahedu@163.com [School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012 (China)

    2016-12-15

    Highlights: • Fe-EG complex microspheres were synthesized by a hydrothermal method. • The removal properties towards Cr(VI) ions were investigated. • The adsorption and reduction mechanism was revealed by FTIR and XPS. - Abstract: Three-dimensional Fe-ethylene glycol (Fe-EG) complex microspheres were synthesized by a facile hydrothermal method, and were characterized by field emission scanning electron microscopy and transmission electron microscopy. The adsorption as well as reduction properties of the obtained Fe-EG complex microspheres towards Cr(VI) ions were studied. The experiment data of adsorption kinetic and isotherm were fitted by nonlinear regression approach. In neutral condition, the maximum adsorption capacity was 49.78 mg g{sup −1} at room temperature, and was increased with the increasing of temperature. Thermodynamic parameters including the Gibbs free energy, standard enthalpy and standard entropy revealed that adsorption of Cr(VI) was a feasible, spontaneous and endothermic process. Spectroscopic analysis revealed the adsorption of Cr(VI) was a physical adsorption process. The adsorbed CrO{sub 4}{sup 2−} ions were partly reduced to Cr(OH){sub 3} by Fe(II) ions and the organic groups in the Fe-EG complex.

  8. Complexity and time asymmetry of heart rate variability are altered in acute mental stress.

    Science.gov (United States)

    Visnovcova, Z; Mestanik, M; Javorka, M; Mokra, D; Gala, M; Jurko, A; Calkovska, A; Tonhajzerova, I

    2014-07-01

    We aimed to study the complexity and time asymmetry of short-term heart rate variability (HRV) as an index of complex neurocardiac control in response to stress using symbolic dynamics and time irreversibility methods. ECG was recorded at rest and during and after two stressors (Stroop, arithmetic test) in 70 healthy students. Symbolic dynamics parameters (NUPI, NCI, 0V%, 1V%, 2LV%, 2UV%), and time irreversibility indices (P%, G%, E) were evaluated. Additionally, HRV magnitude was quantified by linear parameters: spectral powers in low (LF) and high frequency (HF) bands. Our results showed a reduction of HRV complexity in stress (lower NUPI with both stressors, lower NCI with Stroop). Pattern classification analysis revealed significantly higher 0V% and lower 2LV% with both stressors, indicating a shift in sympathovagal balance, and significantly higher 1V% and lower 2UV% with Stroop. An unexpected result was found in time irreversibility: significantly lower G% and E with both stressors, P% index significantly declined only with arithmetic test. Linear HRV analysis confirmed vagal withdrawal (lower HF) with both stressors; LF significantly increased with Stroop and decreased with arithmetic test. Correlation analysis revealed no significant associations between symbolic dynamics and time irreversibility. Concluding, symbolic dynamics and time irreversibility could provide independent information related to alterations of neurocardiac control integrity in stress-related disease.

  9. Complexity and time asymmetry of heart rate variability are altered in acute mental stress

    International Nuclear Information System (INIS)

    Visnovcova, Z; Mestanik, M; Javorka, M; Mokra, D; Calkovska, A; Tonhajzerova, I; Gala, M; Jurko, A

    2014-01-01

    We aimed to study the complexity and time asymmetry of short-term heart rate variability (HRV) as an index of complex neurocardiac control in response to stress using symbolic dynamics and time irreversibility methods. ECG was recorded at rest and during and after two stressors (Stroop, arithmetic test) in 70 healthy students. Symbolic dynamics parameters (NUPI, NCI, 0V%, 1V%, 2LV%, 2UV%), and time irreversibility indices (P%, G%, E) were evaluated. Additionally, HRV magnitude was quantified by linear parameters: spectral powers in low (LF) and high frequency (HF) bands. Our results showed a reduction of HRV complexity in stress (lower NUPI with both stressors, lower NCI with Stroop). Pattern classification analysis revealed significantly higher 0V% and lower 2LV% with both stressors, indicating a shift in sympathovagal balance, and significantly higher 1V% and lower 2UV% with Stroop. An unexpected result was found in time irreversibility: significantly lower G% and E with both stressors, P% index significantly declined only with arithmetic test. Linear HRV analysis confirmed vagal withdrawal (lower HF) with both stressors; LF significantly increased with Stroop and decreased with arithmetic test. Correlation analysis revealed no significant associations between symbolic dynamics and time irreversibility. Concluding, symbolic dynamics and time irreversibility could provide independent information related to alterations of neurocardiac control integrity in stress-related disease. (paper)

  10. Exploring the potential relevance of human-specific genes to complex disease

    Directory of Open Access Journals (Sweden)

    Cooper David N

    2011-01-01

    Full Text Available Abstract Although human disease genes generally tend to be evolutionarily more ancient than non-disease genes, complex disease genes appear to be represented more frequently than Mendelian disease genes among genes of more recent evolutionary origin. It is therefore proposed that the analysis of human-specific genes might provide new insights into the genetics of complex disease. Cross-comparison with the Human Gene Mutation Database (http://www.hgmd.org revealed a number of examples of disease-causing and disease-associated mutations in putatively human-specific genes. A sizeable proportion of these were missense polymorphisms associated with complex disease. Since both human-specific genes and genes associated with complex disease have often experienced particularly rapid rates of evolutionary change, either due to weaker purifying selection or positive selection, it is proposed that a significant number of human-specific genes may play a role in complex disease.

  11. An analysis methodology for impact of new technology in complex sociotechnical systems

    CSIR Research Space (South Africa)

    Oosthuizen, R

    2013-11-01

    Full Text Available in support of Systems Engineering efforts, which is difficult with complex Sociotechnical Systems. Cognitive Work Analysis and System Dynamics are two complementary approaches that can be applied within this context. The products of these methods assist...

  12. REVEAL - A tool for rule driven analysis of safety critical software

    International Nuclear Information System (INIS)

    Miedl, H.; Kersken, M.

    1998-01-01

    As the determination of ultrahigh reliability figures for safety critical software is hardly possible, national and international guidelines and standards give mainly requirements for the qualitative evaluation of software. An analysis whether all these requirements are fulfilled is time and effort consuming and prone to errors, if performed manually by analysts, and should instead be dedicated to tools as far as possible. There are many ''general-purpose'' software analysis tools, both static and dynamic, which help analyzing the source code. However, they are not designed to assess the adherence to specific requirements of guidelines and standards in the nuclear field. Against the background of the development of I and C systems in the nuclear field which are based on digital techniques and implemented in high level language, it is essential that the assessor or licenser has a tool with which he can automatically and uniformly qualify as many aspects as possible of the high level language software. For this purpose the software analysis tool REVEAL has been developed at ISTec and the Halden Reactor Project. (author)

  13. Microwave synthesis, spectral, thermal, and antimicrobial activities of some transition metal complexes involving 5-bromosalicylaldehyde moiety

    Directory of Open Access Journals (Sweden)

    Rajendra K. Jain

    2012-07-01

    Full Text Available The coordination complexes of Co(II, Ni(II and Cu(II derived from 5-bromosalicylidene-3,4-dimethylaniline (BSMA and 5-bromosalicylidene-3,4-dichloroaniline (BSCA have been synthesized by conventional as well as microwave methods. These compounds have been characterized by elemental analysis, FT-IR, molar conductance, electronic spectra, 1H-NMR, FAB-mass, ESR, magnetic susceptibility, electrical conductivity and thermal analysis. The complexes are coloured and stable in air. Analytical data revealed that all the complexes exhibited 1:2 (metal: ligand ratio with coordination number 4 or 6. IR data shows that the ligand coordinates with the metal ions in a bidentate manner through the phenolic oxygen and azomethine nitrogen. FAB-mass and thermal data show degradation pattern of the complexes. Solid state electrical conductivity studies reflect semiconducting nature of the complexes. The Schiff base and metal complexes show a good activity against the Gram-positive bacteria; Staphylococcus aureus and Gram-negative bacteria; Escherichia coli and fungi Aspergillus niger and Candida albicans.

  14. Bilingualism at the core of the brain. Structural differences between bilinguals and monolinguals revealed by subcortical shape analysis.

    Science.gov (United States)

    Burgaleta, Miguel; Sanjuán, Ana; Ventura-Campos, Noelia; Sebastian-Galles, Núria; Ávila, César

    2016-01-15

    Naturally acquiring a language shapes the human brain through a long-lasting learning and practice process. This is supported by previous studies showing that managing more than one language from early childhood has an impact on brain structure and function. However, to what extent bilingual individuals present neuroanatomical peculiarities at the subcortical level with respect to monolinguals is yet not well understood, despite the key role of subcortical gray matter for a number of language functions, including monitoring of speech production and language control - two processes especially solicited by bilinguals. Here we addressed this issue by performing a subcortical surface-based analysis in a sample of monolinguals and simultaneous bilinguals (N=88) that only differed in their language experience from birth. This analysis allowed us to study with great anatomical precision the potential differences in morphology of key subcortical structures, namely, the caudate, accumbens, putamen, globus pallidus and thalamus. Vertexwise analyses revealed significantly expanded subcortical structures for bilinguals compared to monolinguals, localized in bilateral putamen and thalamus, as well as in the left globus pallidus and right caudate nucleus. A topographical interpretation of our results suggests that a more complex phonological system in bilinguals may lead to a greater development of a subcortical brain network involved in monitoring articulatory processes. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

    Science.gov (United States)

    Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

    2017-07-01

    Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

  16. Managing complex research datasets using electronic tools: A meta-analysis exemplar

    Science.gov (United States)

    Brown, Sharon A.; Martin, Ellen E.; Garcia, Theresa J.; Winter, Mary A.; García, Alexandra A.; Brown, Adama; Cuevas, Heather E.; Sumlin, Lisa L.

    2013-01-01

    Meta-analyses of broad scope and complexity require investigators to organize many study documents and manage communication among several research staff. Commercially available electronic tools, e.g., EndNote, Adobe Acrobat Pro, Blackboard, Excel, and IBM SPSS Statistics (SPSS), are useful for organizing and tracking the meta-analytic process, as well as enhancing communication among research team members. The purpose of this paper is to describe the electronic processes we designed, using commercially available software, for an extensive quantitative model-testing meta-analysis we are conducting. Specific electronic tools improved the efficiency of (a) locating and screening studies, (b) screening and organizing studies and other project documents, (c) extracting data from primary studies, (d) checking data accuracy and analyses, and (e) communication among team members. The major limitation in designing and implementing a fully electronic system for meta-analysis was the requisite upfront time to: decide on which electronic tools to use, determine how these tools would be employed, develop clear guidelines for their use, and train members of the research team. The electronic process described here has been useful in streamlining the process of conducting this complex meta-analysis and enhancing communication and sharing documents among research team members. PMID:23681256

  17. Use of neural networks in the analysis of complex systems

    International Nuclear Information System (INIS)

    Uhrig, R.E.

    1992-01-01

    The application of neural networks, alone or in conjunction with other advanced technologies (expert systems, fuzzy logic, and/or genetic algorithms) to some of the problems of complex engineering systems has the potential to enhance the safety reliability and operability of these systems. The work described here deals with complex systems or parts of such systems that can be isolated from the total system. Typically, the measured variables from the systems are analog variables that must be sampled and normalized to expected peak values before they are introduced into neural networks. Often data must be processed to put it into a form more acceptable to the neural network. The neural networks are usually simulated on modern high-speed computers that carry out the calculations serially. However, it is possible to implement neural networks using specially designed microchips where the network calculations are truly carried out in parallel, thereby providing virtually instantaneous outputs for each set of inputs. Specific applications described include: Diagnostics: State of the Plant; Hybrid System for Transient Identification; Detection of Change of Mode in Complex Systems; Sensor Validation; Plant-Wide Monitoring; Monitoring of Performance and Efficiency; and Analysis of Vibrations. Although the specific examples described deal with nuclear power plants or their subsystems, the techniques described can be applied to a wide variety of complex engineering systems

  18. Biogenesis of the yeast cytochrome bc1 complex.

    Science.gov (United States)

    Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

    2009-01-01

    The mitochondrial respiratory chain is composed of four different protein complexes that cooperate in electron transfer and proton pumping across the inner mitochondrial membrane. The cytochrome bc1 complex, or complex III, is a component of the mitochondrial respiratory chain. This review will focus on the biogenesis of the bc1 complex in the mitochondria of the yeast Saccharomyces cerevisiae. In wild type yeast mitochondrial membranes the major part of the cytochrome bc1 complex was found in association with one or two copies of the cytochrome c oxidase complex. The analysis of several yeast mutant strains in which single genes or pairs of genes encoding bc1 subunits had been deleted revealed the presence of a common set of bc1 sub-complexes. These sub-complexes are represented by the central core of the bc1 complex, consisting of cytochrome b bound to subunit 7 and subunit 8, by the two core proteins associated with each other, by the Rieske protein associated with subunit 9, and by those deriving from the unexpected interaction of each of the two core proteins with cytochrome c1. Furthermore, a higher molecular mass sub-complex is that composed of cytochrome b, cytochrome c1, core protein 1 and 2, subunit 6, subunit 7 and subunit 8. The identification and characterization of all these sub-complexes may help in defining the steps and the molecular events leading to bc1 assembly in yeast mitochondria.

  19. Analysis of Proteins, Protein Complexes, and Organellar Proteomes Using Sheathless Capillary Zone Electrophoresis - Native Mass Spectrometry

    Science.gov (United States)

    Belov, Arseniy M.; Viner, Rosa; Santos, Marcia R.; Horn, David M.; Bern, Marshall; Karger, Barry L.; Ivanov, Alexander R.

    2017-12-01

    Native mass spectrometry (MS) is a rapidly advancing field in the analysis of proteins, protein complexes, and macromolecular species of various types. The majority of native MS experiments reported to-date has been conducted using direct infusion of purified analytes into a mass spectrometer. In this study, capillary zone electrophoresis (CZE) was coupled online to Orbitrap mass spectrometers using a commercial sheathless interface to enable high-performance separation, identification, and structural characterization of limited amounts of purified proteins and protein complexes, the latter with preserved non-covalent associations under native conditions. The performance of both bare-fused silica and polyacrylamide-coated capillaries was assessed using mixtures of protein standards known to form non-covalent protein-protein and protein-ligand complexes. High-efficiency separation of native complexes is demonstrated using both capillary types, while the polyacrylamide neutral-coated capillary showed better reproducibility and higher efficiency for more complex samples. The platform was then evaluated for the determination of monoclonal antibody aggregation and for analysis of proteomes of limited complexity using a ribosomal isolate from E. coli. Native CZE-MS, using accurate single stage and tandem-MS measurements, enabled identification of proteoforms and non-covalent complexes at femtomole levels. This study demonstrates that native CZE-MS can serve as an orthogonal and complementary technique to conventional native MS methodologies with the advantages of low sample consumption, minimal sample processing and losses, and high throughput and sensitivity. This study presents a novel platform for analysis of ribosomes and other macromolecular complexes and organelles, with the potential for discovery of novel structural features defining cellular phenotypes (e.g., specialized ribosomes). [Figure not available: see fulltext.

  20. The altered complexity of cardiovascular regulation in depressed patients

    International Nuclear Information System (INIS)

    Schulz, Steffen; Voss, Andreas; Koschke, Mandy; Bär, Karl-Jürgen

    2010-01-01

    Major depressive disorders (MDD) are associated with an increased risk for cardiovascular morbidity and mortality. Even if it is known that MDD are accompanied by an autonomic dysbalance with increased sympathetic and/or reduced parasympathetic activity, to date only limited information is available about the degree and complexity of cardiovascular regulation. The aim of this study was to investigate the influence of MDD on the autonomous nervous system and cardiovascular complexity by means of linear and nonlinear indices from heart rate and blood pressure variability (HRV, BPV). From 57 non-medicated patients and 57 matched healthy controls with respect to age and gender HRV and BPV in time and frequency domain, symbolic dynamics, compression entropy, multiscale entropy, detrended fluctuation analysis, Poincaré plot analysis and baroreflex sensitivity were analysed from 30 min short-term recordings. Complexity indices from nonlinear dynamics demonstrated considerable changes in autonomous regulation due to MDD. For the first time we could show that non-medicated depressed patients who were matched with respect to age and gender reveal a significantly changed short-term as well as long-term complexity of cardiovascular regulation. These results suggest substantial changes in autonomic control probably due to a change of interactions between different physiological control loops in MDD

  1. Superposed ruptile deformational events revealed by field and VOM structural analysis

    Science.gov (United States)

    Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

    2017-04-01

    Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and

  2. The composition-explicit distillation curve technique: Relating chemical analysis and physical properties of complex fluids.

    Science.gov (United States)

    Bruno, Thomas J; Ott, Lisa S; Lovestead, Tara M; Huber, Marcia L

    2010-04-16

    The analysis of complex fluids such as crude oils, fuels, vegetable oils and mixed waste streams poses significant challenges arising primarily from the multiplicity of components, the different properties of the components (polarity, polarizability, etc.) and matrix properties. We have recently introduced an analytical strategy that simplifies many of these analyses, and provides the added potential of linking compositional information with physical property information. This aspect can be used to facilitate equation of state development for the complex fluids. In addition to chemical characterization, the approach provides the ability to calculate thermodynamic properties for such complex heterogeneous streams. The technique is based on the advanced distillation curve (ADC) metrology, which separates a complex fluid by distillation into fractions that are sampled, and for which thermodynamically consistent temperatures are measured at atmospheric pressure. The collected sample fractions can be analyzed by any method that is appropriate. The analytical methods we have applied include gas chromatography (with flame ionization, mass spectrometric and sulfur chemiluminescence detection), thin layer chromatography, FTIR, corrosivity analysis, neutron activation analysis and cold neutron prompt gamma activation analysis. By far, the most widely used analytical technique we have used with the ADC is gas chromatography. This has enabled us to study finished fuels (gasoline, diesel fuels, aviation fuels, rocket propellants), crude oils (including a crude oil made from swine manure) and waste oils streams (used automotive and transformer oils). In this special issue of the Journal of Chromatography, specifically dedicated to extraction technologies, we describe the essential features of the advanced distillation curve metrology as an analytical strategy for complex fluids. Published by Elsevier B.V.

  3. Multi-complexity ensemble measures for gait time series analysis: application to diagnostics, monitoring and biometrics.

    Science.gov (United States)

    Gavrishchaka, Valeriy; Senyukova, Olga; Davis, Kristina

    2015-01-01

    Previously, we have proposed to use complementary complexity measures discovered by boosting-like ensemble learning for the enhancement of quantitative indicators dealing with necessarily short physiological time series. We have confirmed robustness of such multi-complexity measures for heart rate variability analysis with the emphasis on detection of emerging and intermittent cardiac abnormalities. Recently, we presented preliminary results suggesting that such ensemble-based approach could be also effective in discovering universal meta-indicators for early detection and convenient monitoring of neurological abnormalities using gait time series. Here, we argue and demonstrate that these multi-complexity ensemble measures for gait time series analysis could have significantly wider application scope ranging from diagnostics and early detection of physiological regime change to gait-based biometrics applications.

  4. Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy.

    Science.gov (United States)

    Hayes, Dugan; Kohler, Lars; Hadt, Ryan G; Zhang, Xiaoyi; Liu, Cunming; Mulfort, Karen L; Chen, Lin X

    2018-01-28

    The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)-Ru(ii) analogs of the homodinuclear Cu(i)-Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.

  5. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

    Directory of Open Access Journals (Sweden)

    Eileen eLuders

    2013-07-01

    Full Text Available Scientific studies addressing anatomical variations in meditators’ brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM. To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls, where meditators have been practicing close to twenty years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentate, entorhinal cortex, subiculum as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri- hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators – perhaps due to an attenuated release of stress hormones and decreased neurotoxicity.

  6. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

    Science.gov (United States)

    Luders, Eileen; Kurth, Florian; Toga, Arthur W.; Narr, Katherine L.; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators—perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  7. Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed.

    Science.gov (United States)

    Boykin, Laura M; Bell, Charles D; Evans, Gregory; Small, Ian; De Barro, Paul J

    2013-10-18

    Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes. The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification. Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period

  8. Experimental and theoretical investigations on Pd(II) host-guest compound: Deciphering the structural and electronic features of a potential bioactive complex

    Science.gov (United States)

    Sreejith, S. S.; Mohan, Nithya; Prathapachandra Kurup, M. R.

    2017-10-01

    A Pd(II) complex from N,N‧-bis(2-hydroxy-3-ethoxybenzylidene)butane-1,4-diamine salen-type ligand has been synthesized and characterised using single crystal XRD analysis, elemental analysis, IR and UV-Vis spectroscopic methods. Thermal profile of the compound is investigated using TG-DTG-DSC method. The quantification of intermolecular interactions and surface morphology has been done using Hirshfeld surface study mapped using various functions like dnorm, shape index and curvedness. ESP analysis is done to visualize the electrophilic and nucleophilic regions in the complex. Geometry optimization of the structure is done using DFT at B3LYP/def2-TZVP level of theory. Frontier orbital analysis reveals the kinetical stability and chemical inertness of the complex. A detailed charge distribution analysis is done using different analytical methods like Mulliken, Löwdin, NPA and AIM methods. Further bond order analysis and topological analysis are also done. Finally the bioactivity of the titled complex is checked using molecular docking method on both DNA and protein.

  9. Weighted Complex Network Analysis of Pakistan Highways

    Directory of Open Access Journals (Sweden)

    Yasir Tariq Mohmand

    2013-01-01

    Full Text Available The structure and properties of public transportation networks have great implications in urban planning, public policies, and infectious disease control. This study contributes a weighted complex network analysis of travel routes on the national highway network of Pakistan. The network is responsible for handling 75 percent of the road traffic yet is largely inadequate, poor, and unreliable. The highway network displays small world properties and is assortative in nature. Based on the betweenness centrality of the nodes, the most important cities are identified as this could help in identifying the potential congestion points in the network. Keeping in view the strategic location of Pakistan, such a study is of practical importance and could provide opportunities for policy makers to improve the performance of the highway network.

  10. On the complex analysis of the reliability, safety, and economic efficiency of atomic electric power stations

    International Nuclear Information System (INIS)

    Emel'yanov, I.Ya.; Klemin, A.I.; Polyakov, E.F.

    1977-01-01

    The problem is posed of effectively increasing the engineering performance of nuclear electric power stations (APS). The principal components of the engineering performance of modern large APS are considered: economic efficiency, radiation safety, reliability, and their interrelationship. A nomenclature is proposed for the quantitative indices which most completely characterize the enumerated properties and are convenient for the analysis of the engineering performance. The urgent problem of developing a methodology for the complex analysis and optimization of the principal performance components is considered; this methodology is designed to increase the efficiency of the work on high-performance competitive APS. The principle of complex optimization of the reliability, safety, and economic-efficiency indices is formulated; specific recommendations are made for the practical realization of this principle. The structure of the complex quantiative analysis of the enumerated performance components is given. The urgency and promise of the complex approach to solving the problem of APS optimization is demonstrated, i.e., the solution of the problem of creating optimally reliable, fairly safe, and maximally economically efficient stations

  11. Discrete Fourier Transform Analysis in a Complex Vector Space

    Science.gov (United States)

    Dean, Bruce H.

    2009-01-01

    Alternative computational strategies for the Discrete Fourier Transform (DFT) have been developed using analysis of geometric manifolds. This approach provides a general framework for performing DFT calculations, and suggests a more efficient implementation of the DFT for applications using iterative transform methods, particularly phase retrieval. The DFT can thus be implemented using fewer operations when compared to the usual DFT counterpart. The software decreases the run time of the DFT in certain applications such as phase retrieval that iteratively call the DFT function. The algorithm exploits a special computational approach based on analysis of the DFT as a transformation in a complex vector space. As such, this approach has the potential to realize a DFT computation that approaches N operations versus Nlog(N) operations for the equivalent Fast Fourier Transform (FFT) calculation.

  12. Advances in complex analysis and operator theory festschrift in honor of Daniel Alpay’s 60th birthday

    CERN Document Server

    Sabadini, Irene; Struppa, Daniele; Vajiac, Mihaela

    2017-01-01

    This book gathers contributions written by Daniel Alpay’s friends and collaborators. Several of the papers were presented at the International Conference on Complex Analysis and Operator Theory held in honor of Professor Alpay’s 60th birthday at Chapman University in November 2016. The main topics covered are complex analysis, operator theory and other areas of mathematics close to Alpay’s primary research interests. The book is recommended for mathematicians from the graduate level on, working in various areas of mathematical analysis, operator theory, infinite dimensional analysis, linear systems, and stochastic processes.

  13. Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation.

    Directory of Open Access Journals (Sweden)

    Peter Rellos

    2010-07-01

    Full Text Available Long-term potentiation (LTP, a long-lasting enhancement in communication between neurons, is considered to be the major cellular mechanism underlying learning and memory. LTP triggers high-frequency calcium pulses that result in the activation of Calcium/Calmodulin (CaM-dependent kinase II (CaMKII. CaMKII acts as a molecular switch because it remains active for a long time after the return to basal calcium levels, which is a unique property required for CaMKII function. Here we describe the crystal structure of the human CaMKIIdelta/Ca2+/CaM complex, structures of all four human CaMKII catalytic domains in their autoinhibited states, as well as structures of human CaMKII oligomerization domains in their tetradecameric and physiological dodecameric states. All four autoinhibited human CaMKIIs were monomeric in the determined crystal structures but associated weakly in solution. In the CaMKIIdelta/Ca2+/CaM complex, the inhibitory region adopted an extended conformation and interacted with an adjacent catalytic domain positioning T287 into the active site of the interacting protomer. Comparisons with autoinhibited CaMKII structures showed that binding of calmodulin leads to the rearrangement of residues in the active site to a conformation suitable for ATP binding and to the closure of the binding groove for the autoinhibitory helix by helix alphaD. The structural data, together with biophysical interaction studies, reveals the mechanism of CaMKII activation by calmodulin and explains many of the unique regulatory properties of these two essential signaling molecules.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3-D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the Web plugin are available in Text S1.

  14. Complexity Analysis of Reed-Solomon Decoding over GF(2m without Using Syndromes

    Directory of Open Access Journals (Sweden)

    Zhiyuan Yan

    2008-06-01

    Full Text Available There has been renewed interest in decoding Reed-Solomon (RS codes without using syndromes recently. In this paper, we investigate the complexity of syndromeless decoding, and compare it to that of syndrome-based decoding. Aiming to provide guidelines to practical applications, our complexity analysis focuses on RS codes over characteristic-2 fields, for which some multiplicative FFT techniques are not applicable. Due to moderate block lengths of RS codes in practice, our analysis is complete, without big O notation. In addition to fast implementation using additive FFT techniques, we also consider direct implementation, which is still relevant for RS codes with moderate lengths. For high-rate RS codes, when compared to syndrome-based decoding algorithms, not only syndromeless decoding algorithms require more field operations regardless of implementation, but also decoder architectures based on their direct implementations have higher hardware costs and lower throughput. We also derive tighter bounds on the complexities of fast polynomial multiplications based on Cantor's approach and the fast extended Euclidean algorithm.

  15. Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

    Directory of Open Access Journals (Sweden)

    E. Damaraju

    2014-01-01

    Full Text Available Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length, and a dynamic sense, computed using sliding windows (44 s in length and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual, as well as reduced connectivity (hypoconnectivity between sensory networks from all modalities. Dynamic analysis suggests that (1, on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2, that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity

  16. Dissection of the complex phenotype in cuticular mutants of Arabidopsis reveals a role of SERRATE as a mediator.

    Directory of Open Access Journals (Sweden)

    Derry Voisin

    2009-10-01

    Full Text Available Mutations in LACERATA (LCR, FIDDLEHEAD (FDH, and BODYGUARD (BDG cause a complex developmental syndrome that is consistent with an important role for these Arabidopsis genes in cuticle biogenesis. The genesis of their pleiotropic phenotypes is, however, poorly understood. We provide evidence that neither distorted depositions of cutin, nor deficiencies in the chemical composition of cuticular lipids, account for these features, instead suggesting that the mutants alleviate the functional disorder of the cuticle by reinforcing their defenses. To better understand how plants adapt to these mutations, we performed a genome-wide gene expression analysis. We found that apparent compensatory transcriptional responses in these mutants involve the induction of wax, cutin, cell wall, and defense genes. To gain greater insight into the mechanism by which cuticular mutations trigger this response in the plants, we performed an overlap meta-analysis, which is termed MASTA (MicroArray overlap Search Tool and Analysis, of differentially expressed genes. This suggested that different cell integrity pathways are recruited in cesA cellulose synthase and cuticular mutants. Using MASTA for an in silico suppressor/enhancer screen, we identified SERRATE (SE, which encodes a protein of RNA-processing multi-protein complexes, as a likely enhancer. In confirmation of this notion, the se lcr and se bdg double mutants eradicate severe leaf deformations as well as the organ fusions that are typical of lcr and bdg and other cuticular mutants. Also, lcr does not confer resistance to Botrytis cinerea in a se mutant background. We propose that there is a role for SERRATE-mediated RNA signaling in the cuticle integrity pathway.

  17. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    Science.gov (United States)

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Experimental design for optimizing MALDI-TOF-MS analysis of palladium complexes

    Directory of Open Access Journals (Sweden)

    Rakić-Kostić Tijana M.

    2017-01-01

    Full Text Available This paper presents optimization of matrix-assisted laser desorption/ionization (MALDI time-of-flight (TOF mass spectrometer (MS instrumental parameters for the analysis of chloro(2,2'',2"-terpyridinepalladium(II chloride dihydrate complex applying design of experiments methodology (DoE. This complex is of interest for potential use in the cancer therapy. DoE methodology was proved to succeed in optimization of many complex analytical problems. However, it has been poorly used for MALDI-TOF-MS optimization up to now. The theoretical mathematical relationships which explain the influence of important experimental factors (laser energy, grid voltage and number of laser shots on the selected responses (signal to noise – S/N ratio and the resolution – R of the leading peak is established. The optimal instrumental settings providing maximal S/N and R are identified and experimentally verified. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 172052 and Grant no. 172011

  19. Does complexity matter? Meta-analysis of learner performance in artificial grammar tasks.

    Science.gov (United States)

    Schiff, Rachel; Katan, Pesia

    2014-01-01

    Complexity has been shown to affect performance on artificial grammar learning (AGL) tasks (categorization of test items as grammatical/ungrammatical according to the implicitly trained grammar rules). However, previously published AGL experiments did not utilize consistent measures to investigate the comprehensive effect of grammar complexity on task performance. The present study focused on computerizing Bollt and Jones's (2000) technique of calculating topological entropy (TE), a quantitative measure of AGL charts' complexity, with the aim of examining associations between grammar systems' TE and learners' AGL task performance. We surveyed the literature and identified 56 previous AGL experiments based on 10 different grammars that met the sampling criteria. Using the automated matrix-lift-action method, we assigned a TE value for each of these 10 previously used AGL systems and examined its correlation with learners' task performance. The meta-regression analysis showed a significant correlation, demonstrating that the complexity effect transcended the different settings and conditions in which the categorization task was performed. The results reinforced the importance of using this new automated tool to uniformly measure grammar systems' complexity when experimenting with and evaluating the findings of AGL studies.

  20. The use of network analysis to study complex animal communication systems: a study on nightingale song

    OpenAIRE

    Weiss, Michael; Hultsch, Henrike; Adam, Iris; Scharff, Constance; Kipper, Silke

    2014-01-01

    The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (Luscinia megarhynchos) by means of a network analysis. We translated long nocturn...

  1. Multivariate multiscale complex network analysis of vertical upward oil-water two-phase flow in a small diameter pipe.

    Science.gov (United States)

    Gao, Zhong-Ke; Yang, Yu-Xuan; Zhai, Lu-Sheng; Dang, Wei-Dong; Yu, Jia-Liang; Jin, Ning-De

    2016-02-02

    High water cut and low velocity vertical upward oil-water two-phase flow is a typical complex system with the features of multiscale, unstable and non-homogenous. We first measure local flow information by using distributed conductance sensor and then develop a multivariate multiscale complex network (MMCN) to reveal the dispersed oil-in-water local flow behavior. Specifically, we infer complex networks at different scales from multi-channel measurements for three typical vertical oil-in-water flow patterns. Then we characterize the generated multiscale complex networks in terms of network clustering measure. The results suggest that the clustering coefficient entropy from the MMCN not only allows indicating the oil-in-water flow pattern transition but also enables to probe the dynamical flow behavior governing the transitions of vertical oil-water two-phase flow.

  2. The resilience analysis grid taming complexity?

    NARCIS (Netherlands)

    Gallis, R.

    2012-01-01

    In this workshop we will look at the next step in safety: using resilience engineering as a tool for dealing with complexity. Present concepts such as Bow-ties use linear cause & effect relationships. More and more we see that companies are faced with a complex world with non linear systems. This

  3. SMART: A Propositional Logic-Based Trade Analysis and Risk Assessment Tool for a Complex Mission

    Science.gov (United States)

    Ono, Masahiro; Nicholas, Austin; Alibay, Farah; Parrish, Joseph

    2015-01-01

    This paper introduces a new trade analysis software called the Space Mission Architecture and Risk Analysis Tool (SMART). This tool supports a high-level system trade study on a complex mission, such as a potential Mars Sample Return (MSR) mission, in an intuitive and quantitative manner. In a complex mission, a common approach to increase the probability of success is to have redundancy and prepare backups. Quantitatively evaluating the utility of adding redundancy to a system is important but not straightforward, particularly when the failure of parallel subsystems are correlated.

  4. Complexity and Vulnerability Analysis of Critical Infrastructures: A Methodological Approach

    Directory of Open Access Journals (Sweden)

    Yongliang Deng

    2017-01-01

    Full Text Available Vulnerability analysis of network models has been widely adopted to explore the potential impacts of random disturbances, deliberate attacks, and natural disasters. However, almost all these models are based on a fixed topological structure, in which the physical properties of infrastructure components and their interrelationships are not well captured. In this paper, a new research framework is put forward to quantitatively explore and assess the complexity and vulnerability of critical infrastructure systems. Then, a case study is presented to prove the feasibility and validity of the proposed framework. After constructing metro physical network (MPN, Pajek is employed to analyze its corresponding topological properties, including degree, betweenness, average path length, network diameter, and clustering coefficient. With a comprehensive understanding of the complexity of MPN, it would be beneficial for metro system to restrain original near-miss or accidents and support decision-making in emergency situations. Moreover, through the analysis of two simulation protocols for system component failure, it is found that the MPN turned to be vulnerable under the condition that the high-degree nodes or high-betweenness edges are attacked. These findings will be conductive to offer recommendations and proposals for robust design, risk-based decision-making, and prioritization of risk reduction investment.

  5. The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components.

    Directory of Open Access Journals (Sweden)

    Lukas Aeberhard

    2015-06-01

    Full Text Available Chlamydia trachomatis is an important human pathogen that replicates inside the infected host cell in a unique vacuole, the inclusion. The formation of this intracellular bacterial niche is essential for productive Chlamydia infections. Despite its importance for Chlamydia biology, a holistic view on the protein composition of the inclusion, including its membrane, is currently missing. Here we describe the host cell-derived proteome of isolated C. trachomatis inclusions by quantitative proteomics. Computational analysis indicated that the inclusion is a complex intracellular trafficking platform that interacts with host cells' antero- and retrograde trafficking pathways. Furthermore, the inclusion is highly enriched for sorting nexins of the SNX-BAR retromer, a complex essential for retrograde trafficking. Functional studies showed that in particular, SNX5 controls the C. trachomatis infection and that retrograde trafficking is essential for infectious progeny formation. In summary, these findings suggest that C. trachomatis hijacks retrograde pathways for effective infection.

  6. Quantitative Analysis of MicroRNAs in Vaccinia virus Infection Reveals Diversity in Their Susceptibility to Modification and Suppression.

    Directory of Open Access Journals (Sweden)

    Amy H Buck

    Full Text Available Vaccinia virus (VACV is a large cytoplasmic DNA virus that causes dramatic alterations to many cellular pathways including microRNA biogenesis. The virus encodes a poly(A polymerase which was previously shown to add poly(A tails to the 3' end of cellular miRNAs, resulting in their degradation by 24 hours post infection (hpi. Here we used small RNA sequencing to quantify the impact of VACV infection on cellular miRNAs in human cells at both early (6 h and late (24 h times post infection. A detailed quantitative analysis of individual miRNAs revealed marked diversity in the extent of their modification and relative change in abundance during infection. Some miRNAs became highly modified (e.g. miR-29a-3p, miR-27b-3p whereas others appeared resistant (e.g. miR-16-5p. Furthermore, miRNAs that were highly tailed at 6 hpi were not necessarily among the most reduced at 24 hpi. These results suggest that intrinsic features of human cellular miRNAs cause them to be differentially polyadenylated and altered in abundance during VACV infection. We also demonstrate that intermediate and late VACV gene expression are required for optimal repression of some miRNAs including miR-27-3p. Overall this work reveals complex and varied consequences of VACV infection on host miRNAs and identifies miRNAs which are largely resistant to VACV-induced polyadenylation and are therefore present at functional levels during the initial stages of infection and replication.

  7. Governing Influence of Thermodynamic and Chemical Equilibria on the Interfacial Properties in Complex Fluids.

    Science.gov (United States)

    Harikrishnan, A R; Dhar, Purbarun; Gedupudi, Sateesh; Das, Sarit K

    2018-04-12

    We propose a comprehensive analysis and a quasi-analytical mathematical formalism to predict the surface tension and contact angles of complex surfactant-infused nanocolloids. The model rests on the foundations of the interaction potentials for the interfacial adsorption-desorption dynamics in complex multicomponent colloids. Surfactant-infused nanoparticle-laden interface problems are difficult to deal with because of the many-body interactions and interfaces involved at the meso-nanoscales. The model is based on the governing role of thermodynamic and chemical equilibrium parameters in modulating the interfacial energies. The influence of parameters such as the presence of surfactants, nanoparticles, and surfactant-capped nanoparticles on interfacial dynamics is revealed by the analysis. Solely based on the knowledge of interfacial properties of independent surfactant solutions and nanocolloids, the same can be deduced for complex surfactant-based nanocolloids through the proposed approach. The model accurately predicts the equilibrium surface tension and contact angle of complex nanocolloids available in the existing literature and present experimental findings.

  8. Fe(II) and Co (II) complexes of (4-(4-bromophenyl)-[2,2'-bipyridine]-6-carboxylic acid) synthesis, characterization and electrochromic studies

    International Nuclear Information System (INIS)

    Saba, A.; Maqsood, Z.T.; Wasim, A.A.; Basha, F.Z.

    2017-01-01

    In this study novel complexes of substituted bipyridine (4-(4-bromophenyl)-[2,2'-bipyridine]-6-carboxylic acid) with Fe/sup +2/ and Co/sup +2/ were synthesized and characterized by different physical, analytical and spectral techniques which includes /sup 1/ H-NMR, MALDI-MS, FTIR, UV-VIS Spectrophotometry, CHN analysis and conductometry. Mole ratio method revealed that both complexes satisfied ML2 stoichiometry. Other characterization studies showed that substituted bipyridine acted as a tridentate ligand, with two pyridine N and one carboxylic O atom as binding sites per ligand molecule. The complexes were found octahedral, neutral and possessed fairly high molar absorptivities in visible region. Electrochromic studies revealed that Fe (II) complex had relatively good electrochromic properties with a reversible color change from blue to pale yellow. Co (II) complex, however, did not show significant electrochromic properties in the visible region. (author)

  9. Microarray analysis on human neuroblastoma cells exposed to aluminum, β(1-42-amyloid or the β(1-42-amyloid aluminum complex.

    Directory of Open Access Journals (Sweden)

    Valentina Gatta

    Full Text Available BACKGROUND: A typical pathological feature of Alzheimer's disease (AD is the appearance in the brain of senile plaques made up of β-amyloid (Aβ and neurofibrillary tangles. AD is also associated with an abnormal accumulation of some metal ions, and we have recently shown that one of these, aluminum (Al, plays a relevant role in affecting Aβ aggregation and neurotoxicity. METHODOLOGY: In this study, employing a microarray analysis of 35,129 genes, we investigated the effects induced by the exposure to the Aβ(1-42-Al (Aβ-Al complex on the gene expression profile of the neuronal-like cell line, SH-SY5Y. PRINCIPAL FINDINGS: The microarray assay indicated that, compared to Aβ or Al alone, exposure to Aβ-Al complex produced selective changes in gene expression. Some of the genes selectively over or underexpressed are directly related to AD. A further evaluation performed with Ingenuity Pathway analysis revealed that these genes are nodes of networks and pathways that are involved in the modulation of Ca(2+ homeostasis as well as in the regulation of glutamatergic transmission and synaptic plasticity. CONCLUSIONS AND SIGNIFICANCE: Aβ-Al appears to be largely involved in the molecular machinery that regulates neuronal as well as synaptic dysfunction and loss. Aβ-Al seems critical in modulating key AD-related pathways such as glutamatergic transmission, Ca(2+ homeostasis, oxidative stress, inflammation, and neuronal apoptosis.

  10. Competitive binding affinity of two lanthanum(III) macrocycle complexes toward DNA and bovine serum albumin in water

    Energy Technology Data Exchange (ETDEWEB)

    Asadi, Zahra; Mosallaei, Hamta; Sedaghat, Moslem [Shiraz Univ. (Iran, Islamic Republic of). Dept. of Chemistry; Yousefi, Reza [Shiraz Univ. (Iran, Islamic Republic of). Protein Chemistry Lab. (PCL)

    2017-11-15

    In the present study, two water-soluble lanthanum(III) hexaaza Schiff base complexes were synthesized and characterized and also theoretically investigated. The interactions of these complexes with DNA and bovine serum albumin (BSA) were studied using different spectroscopic assessments and docking simulation analysis. The DNA docking studies suggested that these two complexes are able to interact with DNA through the minor groove, and also the binding affinity is in the order of La(L{sup 1}) > La(L{sup 2}). Furthermore, the spectral titration was carried out and viscosity measurements were taken. In this regard, protein-binding studies revealed that these complexes quench the intrinsic fluorescence of BSA, and indicated that the possible binding site is located on the vicinity of Trp 213, which is further validated by docking simulation analysis. The in vitro anticancer activities of these complexes indicated that the La(L{sup 1}) complex is more effective than the other one and also exhibits a better interaction with DNA.

  11. The application of HP-GFC chromatographic method for the analysis of oligosaccharides in bioactive complexes

    Directory of Open Access Journals (Sweden)

    Savić Ivan

    2009-01-01

    Full Text Available The aim of this work was to optimize a GFC method for the analysis of bioactive metal (Cu, Co and Fe complexes with olygosaccharides (dextran and pullulan. Bioactive metal complexes with olygosaccharides were synthesized by original procedure. GFC was used to study the molecular weight distribution, polymerization degree of oligosaccharides and bioactive metal complexes. The metal bounding in complexes depends on the ligand polymerization degree and the presence of OH groups in coordinative sphere of the central metal ion. The interaction between oligosaccharide and metal ions are very important in veterinary medicine, agriculture, pharmacy and medicine.

  12. Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding.

    Science.gov (United States)

    Huang, Kai-Fa; Liaw, Su-Sen; Huang, Wei-Lin; Chia, Cho-Yun; Lo, Yan-Chung; Chen, Yi-Ling; Wang, Andrew H-J

    2011-04-08

    Aberrant pyroglutamate formation at the N terminus of certain peptides and proteins, catalyzed by glutaminyl cyclases (QCs), is linked to some pathological conditions, such as Alzheimer disease. Recently, a glutaminyl cyclase (QC) inhibitor, PBD150, was shown to be able to reduce the deposition of pyroglutamate-modified amyloid-β peptides in brain of transgenic mouse models of Alzheimer disease, leading to a significant improvement of learning and memory in those transgenic animals. Here, we report the 1.05-1.40 Å resolution structures, solved by the sulfur single-wavelength anomalous dispersion phasing method, of the Golgi-luminal catalytic domain of the recently identified Golgi-resident QC (gQC) and its complex with PBD150. We also describe the high-resolution structures of secretory QC (sQC)-PBD150 complex and two other gQC-inhibitor complexes. gQC structure has a scaffold similar to that of sQC but with a relatively wider and negatively charged active site, suggesting a distinct substrate specificity from sQC. Upon binding to PBD150, a large loop movement in gQC allows the inhibitor to be tightly held in its active site primarily by hydrophobic interactions. Further comparisons of the inhibitor-bound structures revealed distinct interactions of the inhibitors with gQC and sQC, which are consistent with the results from our inhibitor assays reported here. Because gQC and sQC may play different biological roles in vivo, the different inhibitor binding modes allow the design of specific inhibitors toward gQC and sQC.

  13. Beam model for seismic analysis of complex shear wall structure based on the strain energy equivalence

    International Nuclear Information System (INIS)

    Reddy, G.R.; Mahajan, S.C.; Suzuki, Kohei

    1997-01-01

    A nuclear reactor building structure consists of shear walls with complex geometry, beams and columns. The complexity of the structure is explained in the section Introduction. Seismic analysis of the complex reactor building structure using the continuum mechanics approach may produce good results but this method is very difficult to apply. Hence, the finite element approach is found to be an useful technique for solving the dynamic equations of the reactor building structure. In this approach, the model which uses finite elements such as brick, plate and shell elements may produce accurate results. However, this model also poses some difficulties which are explained in the section Modeling Techniques. Therefore, seismic analysis of complex structures is generally carried out using a lumped mass beam model. This model is preferred because of its simplicity and economy. Nevertheless, mathematical modeling of a shear wall structure as a beam requires specialized skill and a thorough understanding of the structure. For accurate seismic analysis, it is necessary to model more realistically the stiffness, mass and damping. In linear seismic analysis, modeling of the mass and damping may pose few problems compared to modeling the stiffness. When used to represent a complex structure, the stiffness of the beam is directly related to the shear wall section properties such as area, shear area and moment of inertia. Various beam models which are classified based on the method of stiffness evaluation are also explained under the section Modeling Techniques. In the section Case Studies the accuracy and simplicity of the beam models are explained. Among various beam models, the one which evaluates the stiffness using strain energy equivalence proves to be the simplest and most accurate method for modeling the complex shear wall structure. (author)

  14. LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes.

    Science.gov (United States)

    Carlson, Hanqian L; Quinn, Jeffrey J; Yang, Yul W; Thornburg, Chelsea K; Chang, Howard Y; Stadler, H Scott

    2015-12-01

    Gene expression profiling in E 11 mouse embryos identified high expression of the long noncoding RNA (lncRNA), LNCRNA-HIT in the undifferentiated limb mesenchyme, gut, and developing genital tubercle. In the limb mesenchyme, LncRNA-HIT was found to be retained in the nucleus, forming a complex with p100 and CBP. Analysis of the genome-wide distribution of LncRNA-HIT-p100/CBP complexes by ChIRP-seq revealed LncRNA-HIT associated peaks at multiple loci in the murine genome. Ontological analysis of the genes contacted by LncRNA-HIT-p100/CBP complexes indicate a primary role for these loci in chondrogenic differentiation. Functional analysis using siRNA-mediated reductions in LncRNA-HIT or p100 transcripts revealed a significant decrease in expression of many of the LncRNA-HIT-associated loci. LncRNA-HIT siRNA treatments also impacted the ability of the limb mesenchyme to form cartilage, reducing mesenchymal cell condensation and the formation of cartilage nodules. Mechanistically the LncRNA-HIT siRNA treatments impacted pro-chondrogenic gene expression by reducing H3K27ac or p100 activity, confirming that LncRNA-HIT is essential for chondrogenic differentiation in the limb mesenchyme. Taken together, these findings reveal a fundamental epigenetic mechanism functioning during early limb development, using LncRNA-HIT and its associated proteins to promote the expression of multiple genes whose products are necessary for the formation of cartilage.

  15. Two-center three-electron bonding in ClNH{sub 3} revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH{sub 3} → ClNH{sub 2} + H reaction

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Christopher P.; Douberly, Gary E., E-mail: douberly@uga.edu [Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556 (United States); Xie, Changjian; Guo, Hua [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Kaufmann, Matin [Department of Physical Chemistry II, Ruhr-University Bochum, D-44801 Bochum (Germany)

    2016-04-28

    Pyrolytic dissociation of Cl{sub 2} is employed to dope helium droplets with single Cl atoms. Sequential addition of NH{sub 3} to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH{sub 3} → ClNH{sub 2} + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C{sub 3v} symmetric top. Frequency shifts from NH{sub 3} and dipole moment measurements are consistent with a ClNH{sub 3} complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH{sub 3} is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. Computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH{sub 3}Cl and Cl–HNH{sub 2}, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH{sub 3} → HCl + NH{sub 2}.

  16. Anionic solid lipid nanoparticles supported on protamine/DNA complexes

    International Nuclear Information System (INIS)

    Ye Jiesheng; Liu Chunxi; Chen Zhijin; Zhang Na; Wang Aihua

    2008-01-01

    The objective of this study was to design novel anionic ternary nanoparticles for gene delivery. These ternary nanoparticles were equipped with protamine/DNA binary complexes (150-200 nm) as the support, and the anionic formation was achieved by absorption of anionic solid lipid nanoparticles (≤20 nm) onto the surface of the binary complexes. The small solid lipid nanoparticles (SLNs) were prepared by a modified film dispersion-ultrasonication method, and adsorption of the anionic SLNs onto the binary complexes was typically carried out in water via electrostatic interaction. The formulated ternary nanoparticles were found to be relatively uniform in size (257.7 ± 10.6 nm) with a 'bumpy' surface, and the surface charge inversion from 19.28 ± 1.14 mV to -17.16 ± 1.92 mV could be considered as evidence of the formation of the ternary nanoparticles. The fluorescence intensity measurements from three batches of the ternary nanoparticles gave a mean adsorption efficiency of 96.75 ± 1.13%. Circular dichroism spectra analysis showed that the protamine/DNA complexes had been coated by small SLNs, and that the anionic ternary nanoparticles formed did not disturb the construction of the binary complexes. SYBR Green I analysis suggested that the ternary nanoparticles could protect the DNA from nuclease degradation, and cell viability assay results showed that they exhibit lower cytotoxicity to A549 cells compared with the binary complexes and lipofectamine. The transfection efficiency of the ternary nanoparticles was better than that of naked DNA and the binary complexes, and almost equal to that of lipofectamine/DNA complexes, as revealed by inversion fluorescence microscope observation. These results indicated that the anionic ternary nanoparticles could facilitate gene transfer in cultured cells, and might alleviate the drawbacks of the conventional cationic vector/DNA complexes for gene delivery in vivo

  17. Effect of the substitutional groups on the electrochemistry, kinetic of thermal decomposition and kinetic of substitution of some uranyl Schiff base complexes

    Energy Technology Data Exchange (ETDEWEB)

    Asadi, Zahra; Nasrollahi, Rahele; Ranjkeshshorkaei, Mohammad; Firuzabadi, Fahimeh Dehghani [Shiraz Univ. (Iran, Islamic Republic of). Chemistry Dept.; Dusek, Michal; Fejfarova, Karla [ASCR, Prague (Czech Republic). Inst. of Physics

    2016-05-15

    Uranyl(VI) complexes, [UO{sub 2}(X-saloph)(solvent)], where saloph denotes N,N{sup '}-bis(salicylidene)-1,2-phenylenediamine and X = NO{sub 2}, Cl, Me, H; were synthesized and characterized by 61H NMR, IR, UV-Vis spectroscopy, thermal gravimetry (TG), cyclic voltammetry, elemental analysis (C.H.N) and X-ray crystallography. X-ray crystallography of [UO{sub 2}(4-nitro-saloph)(DMF)] revealed coordination of the uranyl by the tetradentate Schiff base ligand and one solvent molecule, resulting in seven-coordinated uranium. The complex of [UO{sub 2}(4-nitro-saloph)(DMF)] was also synthesized in nano form. Transmission electron microscopy image showed nano-particles with sizes between 30 and 35 nm. The TG method and analysis of Coats-Redfern plots revealed that the kinetics of thermal decomposition of the complexes is of the first-order in all stages. The kinetics and mechanism of the exchange reaction of the coordinated solvent with tributylphosphine was investigated by spectrophotometric method. The second-order rate constants at four temperatures and the activation parameters showed an associative mechanism for all corresponding complexes with the following trend: 4-Nitro > 4-Cl > H > 4-Me. It was concluded that the steric and electronic properties of the complexes were important for the reaction rate. For analysis of anticancer properties of uranyl Schiff base complexes, cell culture and MTT assay was carried out. These results showed a reduction of jurkat cell line concentration across the complexes.

  18. Calibration of a complex activated sludge model for the full-scale wastewater treatment plant

    OpenAIRE

    Liwarska-Bizukojc, Ewa; Olejnik, Dorota; Biernacki, Rafal; Ledakowicz, Stanislaw

    2011-01-01

    In this study, the results of the calibration of the complex activated sludge model implemented in BioWin software for the full-scale wastewater treatment plant are presented. Within the calibration of the model, sensitivity analysis of its parameters and the fractions of carbonaceous substrate were performed. In the steady-state and dynamic calibrations, a successful agreement between the measured and simulated values of the output variables was achieved. Sensitivity analysis revealed that u...

  19. CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenous Drosophila kni-L2 CRM reveals unexpected complexity.

    Science.gov (United States)

    Xu, Xiang-Ru Shannon; Gantz, Valentino Matteo; Siomava, Natalia; Bier, Ethan

    2017-12-23

    The knirps ( kni ) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila . Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. We also demonstrate that self-propagating active genetic elements (CopyCat elements) can efficiently delete and replace the L2-CRM with orthologous sequences from other divergent fly species. Wing vein phenotypes resulting from these trans-species enhancer replacements parallel features of the respective donor fly species. This highly sensitive phenotypic readout of enhancer function in a native genomic context reveals novel features of CRM function undetected by traditional reporter gene analysis. © 2017, Xu et al.

  20. Multi-scale complexity analysis of muscle coactivation during gait in children with cerebral palsy

    Directory of Open Access Journals (Sweden)

    Wen eTao

    2015-07-01

    Full Text Available The objective of this study is to characterize complexity of lower-extremity muscle coactivation and coordination during gait in children with cerebral palsy (CP, children with typical development (TD and healthy adults, by applying recently developed multivariate multi-scale entropy (MMSE analysis to surface EMG signals. Eleven CP children (CP group, eight TD children and seven healthy adults (consider as an entire control group were asked to walk while surface EMG signals were collected from 5 thigh muscles and 3 lower leg muscles on each leg (16 EMG channels in total. The 16-channel surface EMG data, recorded during a series of consecutive gait cycles, were simultaneously processed by multivariate empirical mode decomposition (MEMD, to generate fully aligned data scales for subsequent MMSE analysis. In order to conduct extensive examination of muscle coactivation complexity using the MEMD-enhanced MMSE, 14 data analysis schemes were designed by varying partial muscle combinations and time durations of data segments. Both TD children and healthy adults showed almost consistent MMSE curves over multiple scales for all the 14 schemes, without any significant difference (p > 0.09. However, quite diversity in MMSE curve was observed in the CP group when compared with those in the control group. There appears to be diverse neuropathological processes in CP that may affect dynamical complexity of muscle coactivation and coordination during gait. The abnormal complexity patterns emerging in CP group can be attributed to different factors such as motor control impairments, loss of muscle couplings, and spasticity or paralysis in individual muscles. All these findings expand our knowledge of neuropathology of CP from a novel point of view of muscle co-activation complexity, also indicating the potential to derive a quantitative index for assessing muscle activation characteristics as well as motor function in CP.

  1. Functional analytic methods in complex analysis and applications to partial differential equations

    International Nuclear Information System (INIS)

    Mshimba, A.S.A.; Tutschke, W.

    1990-01-01

    The volume contains 24 lectures given at the Workshop on Functional Analytic Methods in Complex Analysis and Applications to Partial Differential Equations held in Trieste, Italy, between 8-19 February 1988, at the ICTP. A separate abstract was prepared for each of these lectures. Refs and figs

  2. Rac1 regulates neuronal polarization through the WAVE complex

    DEFF Research Database (Denmark)

    Tahirovic, Sabina; Hellal, Farida; Neukirchen, Dorothee

    2010-01-01

    the physiological function of Rac1 in neuronal development, we have generated a conditional knock-out mouse, in which Rac1 is ablated in the whole brain. Rac1-deficient cerebellar granule neurons, which do not express other Rac isoforms, showed impaired neuronal migration and axon formation both in vivo...... and in vitro. In addition, Rac1 ablation disrupts lamellipodia formation in growth cones. The analysis of Rac1 effectors revealed the absence of the Wiskott-Aldrich syndrome protein (WASP) family verprolin-homologous protein (WAVE) complex from the plasma membrane of knock-out growth cones. Loss of WAVE...... function inhibited axon growth, whereas overexpression of a membrane-tethered WAVE mutant partially rescued axon growth in Rac1-knock-out neurons. In addition, pharmacological inhibition of the WAVE complex effector Arp2/3 also reduced axon growth. We propose that Rac1 recruits the WAVE complex...

  3. Multichannel detrended fluctuation analysis reveals synchronized patterns of spontaneous spinal activity in anesthetized cats.

    Directory of Open Access Journals (Sweden)

    Erika E Rodríguez

    Full Text Available The analysis of the interaction and synchronization of relatively large ensembles of neurons is fundamental for the understanding of complex functions of the nervous system. It is known that the temporal synchronization of neural ensembles is involved in the generation of specific motor, sensory or cognitive processes. Also, the intersegmental coherence of spinal spontaneous activity may indicate the existence of synaptic neural pathways between different pairs of lumbar segments. In this study we present a multichannel version of the detrended fluctuation analysis method (mDFA to analyze the correlation dynamics of spontaneous spinal activity (SSA from time series analysis. This method together with the classical detrended fluctuation analysis (DFA were used to find out whether the SSA recorded in one or several segments in the spinal cord of the anesthetized cat occurs either in a random or in an organized manner. Our results are consistent with a non-random organization of the sets of neurons involved in the generation of spontaneous cord dorsum potentials (CDPs recorded either from one lumbar segment (DFA-α mean = 1.04[Formula: see text]0.09 or simultaneously from several lumbar segments (mDFA-α mean = 1.01[Formula: see text]0.06, where α = 0.5 indicates randomness while α = 0.5 indicates long-term correlations. To test the sensitivity of the mDFA method we also examined the effects of small spinal lesions aimed to partially interrupt connectivity between neighboring lumbosacral segments. We found that the synchronization and correlation between the CDPs recorded from the L5 and L6 segments in both sides of the spinal cord were reduced when a lesion comprising the left dorsal quadrant was performed between the segments L5 and L6 (mDFA-[Formula: see text] = 0.992 as compared to initial conditions mDFA-α = 1.186. The synchronization and correlation were reduced even further after a similar additional right spinal lesion (mDFA-α = 0

  4. Surface Structures Formed by a Copper(II Complex of Alkyl-Derivatized Indigo

    Directory of Open Access Journals (Sweden)

    Akinori Honda

    2016-10-01

    Full Text Available Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM analysis revealed that the copper(II complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed.

  5. Spectroscopic analysis of the powdery complex chitosan-iodine

    Science.gov (United States)

    Gegel, Natalia O.; Babicheva, Tatyana S.; Belyakova, Olga A.; Lugovitskaya, Tatyana N.; Shipovskaya, Anna B.

    2018-04-01

    A chitosan-iodine complex was obtained by modification of polymer powder in the vapor of an iodine-containing sorbate and studied by electron and IR spectroscopy, optical rotation dispersion. It was found that the electronic spectra of an aqueous solution of the modified chitosan (the source one and that stored for a year) showed intense absorption bands of triiodide and iodate ions, and also polyiodide ions, bound to the macromolecule by exciton bonding with charge transfer. Analysis of the IR spectra shows destruction of the network of intramolecular and intermolecular hydrogen bonds in the iodinated chitosan powder in comparison with the source polymer and the formation of a new chemical substance. E.g., the absorption band of deformation vibrations of the hydroxyl group disappears in the modified sample, and that of the protonated amino group shifts toward shorter wavelengths. The intensity of the stretching vibration band of the glucopyranose ring atoms significantly reduces. Heating of the modified sample at a temperature below the thermal degradation point of the polymer leads to stabilization of the chitosan-iodine complex. Based on our studies, the hydroxyl and amino groups of the aminopolysaccharide have been recognized as the centers of retention of polyiodide chains in the chitosan matrix.

  6. Method for analysis the complex grounding cables system

    International Nuclear Information System (INIS)

    Ackovski, R.; Acevski, N.

    2002-01-01

    A new iterative method for the analysis of the performances of the complex grounding systems (GS) in underground cable power networks with coated and/or uncoated metal sheathed cables is proposed in this paper. The analyzed grounding system consists of the grounding grid of a high voltage (HV) supplying transformer station (TS), middle voltage/low voltage (MV/LV) consumer TSs and arbitrary number of power cables, connecting them. The derived method takes into consideration the drops of voltage in the cable sheets and the mutual influence among all earthing electrodes, due to the resistive coupling through the soil. By means of the presented method it is possible to calculate the main grounding system performances, such as earth electrode potentials under short circuit fault to ground conditions, earth fault current distribution in the whole complex grounding system, step and touch voltages in the nearness of the earthing electrodes dissipating the fault current in the earth, impedances (resistances) to ground of all possible fault locations, apparent shield impedances to ground of all power cables, e.t.c. The proposed method is based on the admittance summation method [1] and is appropriately extended, so that it takes into account resistive coupling between the elements that the GS. (Author)

  7. Three-Dimensional Numerical Analysis of Compound Lining in Complex Underground Surge-Shaft Structure

    Directory of Open Access Journals (Sweden)

    Juntao Chen

    2015-01-01

    Full Text Available The mechanical behavior of lining structure of deep-embedded cylinder surge shaft with multifork tunnel is analyzed using three-dimensional nonlinear FEM. With the elastic-plastic constitutive relations of rock mass imported and the implicit bolt element and distributed concrete cracking model adopted, a computing method of complex surge shaft is presented for the simulation of underground excavations and concrete lining cracks. In order to reflect the interaction and initial gap between rock mass and concrete lining, a three-dimensional nonlinear interface element is adopted, which can take into account both the normal and tangential characteristics. By an actual engineering computation, the distortion characteristics and stress distribution rules of the dimensional multifork surge-shaft lining structure under different behavior are revealed. The results verify the rationality and feasibility of this computation model and method and provide a new idea and reference for the complex surge-shaft design and construction.

  8. High throughput analysis reveals dissociable gene expression profiles in two independent neural systems involved in the regulation of social behavior

    Directory of Open Access Journals (Sweden)

    Stevenson Tyler J

    2012-10-01

    Full Text Available Abstract Background Production of contextually appropriate social behaviors involves integrated activity across many brain regions. Many songbird species produce complex vocalizations called ‘songs’ that serve to attract potential mates, defend territories, and/or maintain flock cohesion. There are a series of discrete interconnect brain regions that are essential for the successful production of song. The probability and intensity of singing behavior is influenced by the reproductive state. The objectives of this study were to examine the broad changes in gene expression in brain regions that control song production with a brain region that governs the reproductive state. Results We show using microarray cDNA analysis that two discrete brain systems that are both involved in governing singing behavior show markedly different gene expression profiles. We found that cortical and basal ganglia-like brain regions that control the socio-motor production of song in birds exhibit a categorical switch in gene expression that was dependent on their reproductive state. This pattern is in stark contrast to the pattern of expression observed in a hypothalamic brain region that governs the neuroendocrine control of reproduction. Subsequent gene ontology analysis revealed marked variation in the functional categories of active genes dependent on reproductive state and anatomical localization. HVC, one cortical-like structure, displayed significant gene expression changes associated with microtubule and neurofilament cytoskeleton organization, MAP kinase activity, and steroid hormone receptor complex activity. The transitions observed in the preoptic area, a nucleus that governs the motivation to engage in singing, exhibited variation in functional categories that included thyroid hormone receptor activity, epigenetic and angiogenetic processes. Conclusions These findings highlight the importance of considering the temporal patterns of gene expression

  9. Proliferative, necrotizing and crescentic immune complex-mediated glomerulonephritis in a cat

    Directory of Open Access Journals (Sweden)

    Carolyn Gross

    2015-09-01

    Full Text Available Case Summary A 5-year-old cat was examined for vomiting and anorexia of 2 days’ duration. Azotemia, hyperphosphatemia and hypoalbuminemia were the main biochemical findings. Serial analyses of the urine revealed isosthenuria, proteinuria and eventual glucosuria. Hyperechoic perirenal fat was detected surrounding the right kidney by ultrasonography. Histopathologic evaluation of ante-mortem ultrasound-guided needle biopsies of the right kidney was consistent with proliferative, necrotizing and crescentic glomerulonephritis with fibrin thrombi, proteinaceous and red blood cell casts, and moderate multifocal chronic-active interstitial nephritis. Owing to a lack of clinical improvement, the cat was eventually euthanized. Post-mortem renal biopsies were processed for light microscopy, transmission electron microscopy and immunofluorescence. This revealed severe focal proliferative and necrotizing glomerulonephritis with cellular crescent formation, podocyte injury and secondary segmental sclerosis. Ultrastructural analysis revealed scattered electron-dense deposits in the mesangium, and immunofluorescence demonstrated positive granular staining for λ light chains, consistent with immune complex-mediated glomerulonephritis. Severe diffuse acute tubular epithelial injury and numerous red blood cell casts were also seen. Relevance and novel information To our knowledge, this is the first report of naturally occurring proliferative, necrotizing and crescentic immune complex glomerulonephritis in a cat.

  10. Identification of hybrid node and link communities in complex networks.

    Science.gov (United States)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-02

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  11. Identification of hybrid node and link communities in complex networks

    Science.gov (United States)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  12. Predictability, Force and (Anti-)Resonance in Complex Object Control.

    Science.gov (United States)

    Maurice, Pauline; Hogan, Neville; Sternad, Dagmar

    2018-04-18

    Manipulation of complex objects as in tool use is ubiquitous and has given humans an evolutionary advantage. This study examined the strategies humans choose when manipulating an object with underactuated internal dynamics, such as a cup of coffee. The object's dynamics renders the temporal evolution complex, possibly even chaotic, and difficult to predict. A cart-and-pendulum model, loosely mimicking coffee sloshing in a cup, was implemented in a virtual environment with a haptic interface. Participants rhythmically manipulated the virtual cup containing a rolling ball; they could choose the oscillation frequency, while the amplitude was prescribed. Three hypotheses were tested: 1) humans decrease interaction forces between hand and object; 2) humans increase the predictability of the object dynamics; 3) humans exploit the resonances of the coupled object-hand system. Analysis revealed that humans chose either a high-frequency strategy with anti-phase cup-and-ball movements or a low-frequency strategy with in-phase cup-and-ball movements. Counter Hypothesis 1, they did not decrease interaction force; instead, they increased the predictability of the interaction dynamics, quantified by mutual information, supporting Hypothesis 2. To address Hypothesis 3, frequency analysis of the coupled hand-object system revealed two resonance frequencies separated by an anti-resonance frequency. The low-frequency strategy exploited one resonance, while the high-frequency strategy afforded more choice, consistent with the frequency response of the coupled system; both strategies avoided the anti-resonance. Hence, humans did not prioritize interaction force, but rather strategies that rendered interactions predictable. These findings highlight that physical interactions with complex objects pose control challenges not present in unconstrained movements.

  13. Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites

    Directory of Open Access Journals (Sweden)

    Sibley L David

    2005-12-01

    Full Text Available Abstract Background The phylum Apicomplexa is an early-branching eukaryotic lineage that contains a number of important human and animal pathogens. Their complex life cycles and unique cytoskeletal features distinguish them from other model eukaryotes. Apicomplexans rely on actin-based motility for cell invasion, yet the regulation of this system remains largely unknown. Consequently, we focused our efforts on identifying actin-related proteins in the recently completed genomes of Toxoplasma gondii, Plasmodium spp., Cryptosporidium spp., and Theileria spp. Results Comparative genomic and phylogenetic studies of apicomplexan genomes reveals that most contain only a single conventional actin and yet they each have 8–10 additional actin-related proteins. Among these are a highly conserved Arp1 protein (likely part of a conserved dynactin complex, and Arp4 and Arp6 homologues (subunits of the chromatin-remodeling machinery. In contrast, apicomplexans lack canonical Arp2 or Arp3 proteins, suggesting they lost the Arp2/3 actin polymerization complex on their evolutionary path towards intracellular parasitism. Seven of these actin-like proteins (ALPs are novel to apicomplexans. They show no phylogenetic associations to the known Arp groups and likely serve functions specific to this important group of intracellular parasites. Conclusion The large diversity of actin-like proteins in apicomplexans suggests that the actin protein family has diverged to fulfill various roles in the unique biology of intracellular parasites. Conserved Arps likely participate in vesicular transport and gene expression, while apicomplexan-specific ALPs may control unique biological traits such as actin-based gliding motility.

  14. Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

    Science.gov (United States)

    Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

    2016-01-01

    Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

  15. Data Analysis with the Morse-Smale Complex: The msr Package for R

    KAUST Repository

    Gerber, Samuel

    2012-01-01

    In many areas, scientists deal with increasingly high-dimensional data sets. An important aspect for these scientists is to gain a qualitative understanding of the process or system from which the data is gathered. Often, both input variables and an outcome are observed and the data can be characterized as a sample from a high-dimensional scalar function. This work presents the R package msr for exploratory data analysis of multivariate scalar functions based on the Morse-Smale complex. The Morse-Smale complex provides a topologically meaningful decomposition of the domain. The msr package implements a discrete approximation of the Morse-Smale complex for data sets. In previous work this approximation has been exploited for visualization and partition-based regression, which are both supported in the msr package. The visualization combines the Morse-Smale complex with dimension-reduction techniques for a visual summary representation that serves as a guide for interactive exploration of the high-dimensional function. In a similar fashion, the regression employs a combination of linear models based on the Morse-Smale decomposition of the domain. This regression approach yields topologically accurate estimates and facilitates interpretation of general trends and statistical comparisons between partitions. In this manner, the msr package supports high-dimensional data understanding and exploration through the Morse-Smale complex.

  16. Native Liquid Extraction Surface Analysis Mass Spectrometry: Analysis of Noncovalent Protein Complexes Directly from Dried Substrates

    Science.gov (United States)

    Martin, Nicholas J.; Griffiths, Rian L.; Edwards, Rebecca L.; Cooper, Helen J.

    2015-08-01

    Liquid extraction surface analysis (LESA) mass spectrometry is a promising tool for the analysis of intact proteins from biological substrates. Here, we demonstrate native LESA mass spectrometry of noncovalent protein complexes of myoglobin and hemoglobin from a range of surfaces. Holomyoglobin, in which apomyoglobin is noncovalently bound to the prosthetic heme group, was observed following LESA mass spectrometry of myoglobin dried onto glass and polyvinylidene fluoride surfaces. Tetrameric hemoglobin [(αβ)2 4H] was observed following LESA mass spectrometry of hemoglobin dried onto glass and polyvinylidene fluoride (PVDF) surfaces, and from dried blood spots (DBS) on filter paper. Heme-bound dimers and monomers were also observed. The `contact' LESA approach was particularly suitable for the analysis of hemoglobin tetramers from DBS.

  17. Formation of competitive potential of the machine-building complex of the region

    Directory of Open Access Journals (Sweden)

    Oleg Ivanovich Botkin

    2014-03-01

    Full Text Available The article describes the features of competitive potential of regional machine-building complex in a globalized world economy. The purpose of the research is the development of theoretically reasonable economic basis of the machine-building complex considering  the  features of business in the conditions of the WTO. In the work, the hypothesis of a special role of the external economic factors locates in development of the enterprises of regional industrial complexes. The study of the theoretical provisions defining the development of the region revealed the factors determining influence of the international trade agreements on spatial localization of the industry. The main attention is paid to an analytical assessment of the current state and the trends, which have developed in the period of post-crisis economic recovery. Analysis of the main indicators of attractiveness has revealed the weak position of local industrial enterprises in the WTO. The directions of strengthening of the competitive capacity of the local industrial enterprises are defined. The obtained results allow us to increase the sustainability of the industry by means of effective management mechanism improvements and to create favorable operating conditions of a machine-building complex of the region

  18. Complex segregation analysis of craniomandibular osteopathy in Deutsch Drahthaar dogs.

    Science.gov (United States)

    Vagt, J; Distl, O

    2018-01-01

    This study investigated familial relationships among Deutsch Drahthaar dogs with craniomandibular osteopathy and examined the most likely mode of inheritance. Sixteen Deutsch Drahthaar dogs with craniomandibular osteopathy were diagnosed using clinical findings, radiography or computed tomography. All 16 dogs with craniomandibular osteopathy had one common ancestor. Complex segregation analyses rejected models explaining the segregation of craniomandibular osteopathy through random environmental variation, monogenic inheritance or an additive sex effect. Polygenic and mixed major gene models sufficiently explained the segregation of craniomandibular osteopathy in the pedigree analysis and offered the most likely hypotheses. The SLC37A2:c.1332C>T variant was not found in a sample of Deutsch Drahthaar dogs with craniomandibular osteopathy, nor in healthy controls. Craniomandibular osteopathy is an inherited condition in Deutsch Drahthaar dogs and the inheritance seems to be more complex than a simple Mendelian model. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. A symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences

    International Nuclear Information System (INIS)

    Xiao Fanghong

    2004-01-01

    By considering a chaotic pseudo-random sequence as a symbolic sequence, authors present a symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences. The method is applied to the cases of Logistic map and one-way coupled map lattice to demonstrate how it works, and a comparison is made between it and the approximate entropy method. The results show that this method is applicable to distinguish the complexities of different chaotic pseudo-random sequences, and it is superior to the approximate entropy method

  20. Amputation effects on the underlying complexity within transtibial amputee ankle motion

    Energy Technology Data Exchange (ETDEWEB)

    Wurdeman, Shane R., E-mail: shanewurdeman@gmail.com [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); Advanced Prosthetics Center, Omaha, Nebraska 68134 (United States); Myers, Sara A. [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); Stergiou, Nicholas [Nebraska Biomechanics Core Facility, University of Nebraska at Omaha, Omaha, Nebraska 68182 (United States); College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198 (United States)

    2014-03-15

    The presence of chaos in walking is considered to provide a stable, yet adaptable means for locomotion. This study examined whether lower limb amputation and subsequent prosthetic rehabilitation resulted in a loss of complexity in amputee gait. Twenty-eight individuals with transtibial amputation participated in a 6 week, randomized cross-over design study in which they underwent a 3 week adaptation period to two separate prostheses. One prosthesis was deemed “more appropriate” and the other “less appropriate” based on matching/mismatching activity levels of the person and the prosthesis. Subjects performed a treadmill walking trial at self-selected walking speed at multiple points of the adaptation period, while kinematics of the ankle were recorded. Bilateral sagittal plane ankle motion was analyzed for underlying complexity through the pseudoperiodic surrogation analysis technique. Results revealed the presence of underlying deterministic structure in both prostheses and both the prosthetic and sound leg ankle (discriminant measure largest Lyapunov exponent). Results also revealed that the prosthetic ankle may be more likely to suffer loss of complexity than the sound ankle, and a “more appropriate” prosthesis may be better suited to help restore a healthy complexity of movement within the prosthetic ankle motion compared to a “less appropriate” prosthesis (discriminant measure sample entropy). Results from sample entropy results are less likely to be affected by the intracycle periodic dynamics as compared to the largest Lyapunov exponent. Adaptation does not seem to influence complexity in the system for experienced prosthesis users.