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Sample records for burkholderia species causal

  1. Bioactive and Structural Metabolites of Pseudomonas and Burkholderia Species Causal Agents of Cultivated Mushrooms Diseases1

    Science.gov (United States)

    Andolfi, Anna; Cimmino, Alessio; Cantore, Pietro Lo; Iacobellis, Nicola Sante; Evidente, Antonio

    2008-01-01

    Pseudomonas tolaasii, P. reactans and Burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. The main bioactive metabolites produced by both Pseudomonas strains are the lipodepsipeptides (LDPs) tolaasin I and II and the so called White Line Inducing Principle (WLIP), respectively, LDPs which have been extensively studied for their role in the disease process and for their biological properties. In particular, their antimicrobial activity and the alteration of biological and model membranes (red blood cell and liposomes) was established. In the case of tolaasin I interaction with membranes was also related to the tridimensional structure in solution as determined by NMR combined with molecular dynamic calculation techniques. Recently, five news minor tolaasins, tolaasins A–E, were isolated from the culture filtrates of P. tolaasii and their chemical structure was determined by extensive use of NMR and MS spectroscopy. Furthermore, their antimicrobial activity was evaluated on target micro-organisms (fungi—including the cultivated mushrooms Agaricus bisporus, Lentinus edodes, and Pleurotus spp.—chromista, yeast and bacteria). The Gram positive bacteria resulted the most sensible and a significant structure-activity relationships was apparent. The isolation and structure determination of bioactive metabolites produced by B. gladioli pv. agaricicola are still in progress but preliminary results indicate their peptide nature. Furthermore, the exopolysaccharide (EPS) from the culture filtrates of B. gladioli pv. agaricicola, as well as the O-chain and lipid A, from the lipopolysaccharide (LPS) of the three bacteria, were isolated and the structures determined. PMID:19787100

  2. Bioactive and structural metabolites of pseudomonas and burkholderia species causal agents of cultivated mushrooms diseases.

    Science.gov (United States)

    Andolfi, Anna; Cimmino, Alessio; Cantore, Pietro Lo; Iacobellis, Nicola Sante; Evidente, Antonio

    2008-05-09

    Pseudomonas tolaasii, P. reactans and Burkholderia gladioli pv. agaricicola, are responsible of diseases on some species of cultivated mushrooms. The main bioactive metabolites produced by both Pseudomonas strains are the lipodepsipeptides (LDPs) tolaasin I and II and the so called White Line Inducing Principle (WLIP), respectively, LDPs which have been extensively studied for their role in the disease process and for their biological properties. In particular, their antimicrobial activity and the alteration of biological and model membranes (red blood cell and liposomes) was established. In the case of tolaasin I interaction with membranes was also related to the tridimensional structure in solution as determined by NMR combined with molecular dynamic calculation techniques. Recently, five news minor tolaasins, tolaasins A-E, were isolated from the culture filtrates of P. tolaasii and their chemical structure was determined by extensive use of NMR and MS spectroscopy. Furthermore, their antimicrobial activity was evaluated on target micro-organisms (fungi-including the cultivated mushrooms Agaricus bisporus, Lentinus edodes, and Pleurotus spp.-chromista, yeast and bacteria). The Gram positive bacteria resulted the most sensible and a significant structure-activity relationships was apparent. The isolation and structure determination of bioactive metabolites produced by B. gladioli pv. agaricicola are still in progress but preliminary results indicate their peptide nature. Furthermore, the exopolysaccharide (EPS) from the culture filtrates of B. gladioli pv. agaricicola, as well as the O-chain and lipid A, from the lipopolysaccharide (LPS) of the three bacteria, were isolated and the structures determined.

  3. Solution conformation and dynamics of exopolysaccharides from Burkholderia species.

    Science.gov (United States)

    Pol-Fachin, Laercio; Serrato, Rodrigo V; Verli, Hugo

    2010-09-03

    Exopolysaccharides (EPSs) from the Burkholderia genus are proposed to be involved in pathological conditions in humans, such as cystic fibrosis and septicemia, as well as in the stability of soil aggregates. Hence, considering that the conformational and dynamic aspects of such EPSs may influence their biological activity, the current work employs a series of molecular dynamics simulations on di-, oligo-, and polysaccharide fragments of three EPSs, from Burkholderia caribensis, Burkholderia cepacia, and Burkholderia pseudomallei, with previously determined NOE data, to obtain a conformational description of such EPSs at the atomic level. As the obtained results show good agreement with the experimental data, pointing to the adequacy of the employed methodology to accurately describe the dynamics of polysaccharides, the strategy was also employed to predict the conformational behavior of an additional compound, from Burkholderia tropica, for which NOE signals are not available. Taking into account the potential importance of EPSs on the interaction of Burkholderia bacteria with distinct environments, it may be expected that a greater understanding of their structural aspects may contribute to controlling their pathological roles and potential agricultural applications.

  4. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.

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    Jennifer L Ginther

    Full Text Available Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.

  5. Unusual distribution of Burkholderia cepacia complex species in Danish cystic fibrosis clinics may stem from restricted transmission between patients

    DEFF Research Database (Denmark)

    Nørskov-Lauritsen, Niels; Johansen, Helle Krogh; Fenger, Mette G;

    2010-01-01

    Forty-four of 48 Burkholderia cepacia complex strains cultured from Danish cystic fibrosis patients were Burkholderia multivorans, a distribution of species that has not been reported before. Although cases of cross infections were demonstrated, no major epidemic clone was found. The species...... distribution may represent the sporadic acquisition of bacteria from the environment....

  6. Prevalence and Identification of Burkholderia pseudomallei and Near-Neighbor Species in the Malabar Coastal Region of India.

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    Peddayelachagiri, Bhavani V; Paul, Soumya; Nagaraj, Sowmya; Gogoi, Madhurjya; Sripathy, Murali H; Batra, Harsh V

    2016-09-01

    Accurate identification of pathogens with biowarfare importance requires detection tools that specifically differentiate them from near-neighbor species. Burkholderia pseudomallei, the causative agent of a fatal disease melioidosis, is one such biothreat agent whose differentiation from its near-neighbor species is always a challenge. This is because of its phenotypic similarity with other Burkholderia species which have a wide spread geographical distribution with shared environmental niches. Melioidosis is a major public health concern in endemic regions including Southeast Asia and northern Australia. In India, the disease is still considered to be emerging. Prevalence surveys of this saprophytic bacterium in environment are under-reported in the country. A major challenge in this case is the specific identification and differentiation of B. pseudomallei from the growing list of species of Burkholderia genus. The objectives of this study included examining the prevalence of B. pseudomallei and near-neighbor species in coastal region of South India and development of a novel detection tool for specific identification and differentiation of Burkholderia species. Briefly, we analyzed soil and water samples collected from Malabar coastal region of Kerala, South India for prevalence of B. pseudomallei. The presumptive Burkholderia isolates were identified using recA PCR assay. The recA PCR assay identified 22 of the total 40 presumptive isolates as Burkholderia strains (22.72% and 77.27% B. pseudomallei and non-pseudomallei Burkholderia respectively). In order to identify each isolate screened, we performed recA and 16S rDNA sequencing. This two genes sequencing revealed that the presumptive isolates included B. pseudomallei, non-pseudomallei Burkholderia as well as non-Burkholderia strains. Furthermore, a gene termed D-beta hydroxybutyrate dehydrogenase (bdha) was studied both in silico and in vitro for accurate detection of Burkholderia genus. The optimized bdha

  7. Polyphasic characterisation of Burkholderia cepacia complex species isolated from children with cystic fibrosis

    Science.gov (United States)

    Vicenzi, Fernando José; Pillonetto, Marcelo; de Souza, Helena Aguilar Peres Homem de Mello; Palmeiro, Jussara Kasuko; Riedi, Carlos Antônio; Rosario-Filho, Nelson Augusto; Dalla-Costa, Libera Maria

    2016-01-01

    Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recAsequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recAsequencing to identify Bcc species. The recAsequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%),Burkholderia vietnamiensis (30.6%), B. cenocepaciaIIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes. PMID:26814642

  8. Genetic diversity of Burkholderia (Proteobacteria) species from the Caatinga and Atlantic rainforest biomes in Bahia, Brazil.

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    Santini, A C; Santos, H R M; Gross, E; Corrêa, R X

    2013-03-11

    The genus Burkholderia (β-Proteobacteria) currently comprises more than 60 species, including parasites, symbionts and free-living organisms. Several new species of Burkholderia have recently been described showing a great diversity of phenotypes. We examined the diversity of Burkholderia spp in environmental samples collected from Caatinga and Atlantic rainforest biomes of Bahia, Brazil. Legume nodules were collected from five locations, and 16S rDNA and recA genes of the isolated microorganisms were analyzed. Thirty-three contigs of 16S rRNA genes and four contigs of the recA gene related to the genus Burkholderia were obtained. The genetic dissimilarity of the strains ranged from 0 to 2.5% based on 16S rDNA analysis, indicating two main branches: one distinct branch of the dendrogram for the B. cepacia complex and another branch that rendered three major groups, partially reflecting host plants and locations. A dendrogram designed with sequences of this research and those designed with sequences of Burkholderia-type strains and the first hit BLAST had similar topologies. A dendrogram similar to that constructed by analysis of 16S rDNA was obtained using sequences of the fragment of the recA gene. The 16S rDNA sequences enabled sufficient identification of relevant similarities and groupings amongst isolates and the sequences that we obtained. Only 6 of the 33 isolates analyzed via 16S rDNA sequencing showed high similarity with the B. cepacia complex. Thus, over 3/4 of the isolates have potential for biotechnological applications.

  9. Total protein extraction and 2-D gel electrophoresis methods for Burkholderia species.

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    Velapatiño, Billie; Zlosnik, James E A; Hird, Trevor J; Speert, David P

    2013-10-15

    The investigation of the intracellular protein levels of bacterial species is of importance to understanding the pathogenic mechanisms of diseases caused by these organisms. Here we describe a procedure for protein extraction from Burkholderia species based on mechanical lysis using glass beads in the presence of ethylenediamine tetraacetic acid and phenylmethylsulfonyl fluoride in phosphate buffered saline. This method can be used for different Burkholderia species, for different growth conditions, and it is likely suitable for the use in proteomic studies of other bacteria. Following protein extraction, a two-dimensional (2-D) gel electrophoresis proteomic technique is described to study global changes in the proteomes of these organisms. This method consists of the separation of proteins according to their isoelectric point by isoelectric focusing in the first dimension, followed by separation on the basis of molecular weight by acrylamide gel electrophoresis in the second dimension. Visualization of separated proteins is carried out by silver staining.

  10. Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans.

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    Thomas eKost

    2014-01-01

    Full Text Available Plant roots and shoots harbour complex bacterial communities. Early seed and plantlet colonization plays a key role in determining which bacterial populations will successfully invade plant tissues, yet the mechanisms enabling plants to select for beneficial rather than harmful populations are largely unknown. In this study, we demonstrate a role of oxalate as a determinant in this selection process, using members of the genus Burkholderia as model organisms. Oxalotrophy, i.e. the ability to use oxalate as a carbon source, was found to be a property strictly associated with plant-beneficial species of the Burkholderia genus, while plant pathogenic (B. glumae, B. plantarii or human opportunistic pathogens (Burkholderia cepacia complex strains were unable to degrade oxalate. We further show that oxalotrophy is required for successful plant colonization by the broad host endophyte Burkholderia phytofirmans PsJN: an engineered Δoxc mutant, which lost the ability to grow on oxalate, was significantly impaired in early colonization of both lupin and maize compared with the wild-type. This work suggests that in addition to the role of oxalate in heavy metal tolerance of plants and in virulence of phytopathogenic fungi, it is also involved in specifically recruiting plant-beneficial members from complex bacterial communities.

  11. Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

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    Martínez-Aguilar, Lourdes; Salazar-Salazar, Corelly; Méndez, Rafael Díaz; Caballero-Mellado, Jesús; Hirsch, Ann M; Vásquez-Murrieta, María Soledad; Estrada-de los Santos, Paulina

    2013-12-01

    During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

  12. Detection of Burkholderia pseudomallei O-antigen serotypes in near-neighbor species

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    Stone Joshua K

    2012-11-01

    Full Text Available Abstract Background Burkholderia pseudomallei is the etiological agent of melioidosis and a CDC category B select agent with no available effective vaccine. Previous immunizations in mice have utilized the lipopolysaccharide (LPS as a potential vaccine target because it is known as one of the most important antigenic epitopes in B. pseudomallei. Complicating this strategy are the four different B. pseudomallei LPS O-antigen types: A, B, B2, and rough. Sero-crossreactivity is common among O-antigens of Burkholderia species. Here, we identified the presence of multiple B. pseudomallei O-antigen types and sero-crossreactivity in its near-neighbor species. Results PCR screening of O-antigen biosynthesis genes, phenotypic characterization using SDS-PAGE, and immunoblot analysis showed that majority of B. mallei and B. thailandensis strains contained the typical O-antigen type A. In contrast, most of B. ubonensis and B. thailandensis-like strains expressed the atypical O-antigen types B and B2, respectively. Most B. oklahomensis strains expressed a distinct and non-seroreactive O-antigen type, except strain E0147 which expressed O-antigen type A. O-antigen type B2 was also detected in B. thailandensis 82172, B. ubonensis MSMB108, and Burkholderia sp. MSMB175. Interestingly, B. thailandensis-like MSMB43 contained a novel serotype B positive O-antigen. Conclusions This study expands the number of species which express B. pseudomallei O-antigen types. Further work is required to elucidate the full structures and how closely these are to the B. pseudomallei O-antigens, which will ultimately determine the efficacy of the near-neighbor B serotypes for vaccine development.

  13. Transports of acetate and haloacetate in Burkholderia species MBA4 are operated by distinct systems

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    Su Xianbin

    2012-11-01

    Full Text Available Abstract Background Acetate is a commonly used substrate for biosynthesis while monochloroacetate is a structurally similar compound but toxic and inhibits cell metabolism by blocking the citric acid cycle. In Burkholderia species MBA4 haloacetate was utilized as a carbon and energy source for growth. The degradation of haloacid was mediated by the production of an inducible dehalogenase. Recent studies have identified the presence of a concomitantly induced haloacetate-uptake activity in MBA4. This uptake activity has also been found to transport acetate. Since acetate transporters are commonly found in bacteria it is likely that haloacetate was transported by such a system in MBA4. Results The haloacetate-uptake activity of MBA4 was found to be induced by monochloroacetate (MCA and monobromoacetate (MBA. While the acetate-uptake activity was also induced by MCA and MBA, other alkanoates: acetate, propionate and 2-monochloropropionate (2MCPA were also inducers. Competing solute analysis showed that acetate and propionate interrupted the acetate- and MCA- induced acetate-uptake activities. While MCA, MBA, 2MCPA, and butyrate have no effect on acetate uptake they could significantly quenched the MCA-induced MCA-uptake activity. Transmembrane electrochemical potential was shown to be a driving force for both acetate- and MCA- transport systems. Conclusions Here we showed that acetate- and MCA- uptake in Burkholderia species MBA4 are two transport systems that have different induction patterns and substrate specificities. It is envisaged that the shapes and the three dimensional structures of the solutes determine their recognition or exclusion by the two transport systems.

  14. Causality

    OpenAIRE

    Antonakis, J.

    2015-01-01

    Making correct causal claims is important for research and practice. This article explains what causality is, and how it can be established via experimental design. Because experiments are infeasible in many applied settings, researchers often use "observational" methods to estimate causal models. In these situations, it is likely that model estimates are compromised by endogeneity. The article discusses the conditions that engender endogeneity and methods that can eliminate it.

  15. Causality

    Science.gov (United States)

    Pearl, Judea

    2000-03-01

    Written by one of the pre-eminent researchers in the field, this book provides a comprehensive exposition of modern analysis of causation. It shows how causality has grown from a nebulous concept into a mathematical theory with significant applications in the fields of statistics, artificial intelligence, philosophy, cognitive science, and the health and social sciences. Pearl presents a unified account of the probabilistic, manipulative, counterfactual and structural approaches to causation, and devises simple mathematical tools for analyzing the relationships between causal connections, statistical associations, actions and observations. The book will open the way for including causal analysis in the standard curriculum of statistics, artifical intelligence, business, epidemiology, social science and economics. Students in these areas will find natural models, simple identification procedures, and precise mathematical definitions of causal concepts that traditional texts have tended to evade or make unduly complicated. This book will be of interest to professionals and students in a wide variety of fields. Anyone who wishes to elucidate meaningful relationships from data, predict effects of actions and policies, assess explanations of reported events, or form theories of causal understanding and causal speech will find this book stimulating and invaluable.

  16. Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PLAT medium

    NARCIS (Netherlands)

    Salles, JF; Samyn, E; Vandamme, P; van Veen, JA; van Elsas, JD

    2006-01-01

    In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize monocultu

  17. Changes in agricultural management drive the diversity of Burkholderia species isolated from soil on PCAT medium

    NARCIS (Netherlands)

    Salles, J.F.; Samyn, E.; Vandamme, P.; Van Veen, J.A.; van Elsas, J.D.

    2006-01-01

    Abstract In order to assess the diversity of culturable Burkholderia populations in rhizosphere and bulk soil and to evaluate how different agricultural management regimes and land use history affect this diversity, four treatments were evaluated: permanent grassland; grassland converted into maize

  18. Investigating early stages of biocorrosion with XPS: AISI 304 stainless steel exposed to Burkholderia species

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    Johansson, Leena-Sisko; Saastamoinen, Tuomas

    1999-04-01

    We have investigated the interactions of an exopolymer-producing bacteria, Burkholderia sp. with polished AISI 304 stainless steel substrates using X-ray photoelectron spectroscopy (XPS). Steel coupons were exposed to the pure bacteria culture in a specially designed flowcell for 6 h during which the experiment was monitored in situ with an optical microscope. XPS results verified the formation of biofilm containing extracellular polymer on all the samples exposed to bacteria. Sputter results indicated that some ions needed for metabolic processes were trapped within the biofilm. Changes in the relative Fe concentration and Fe 2p peak shape indicated that also iron had accumulated into the biofilm.

  19. The Role of Reactive Oxygen Species in Antibiotic-Induced Cell Death in Burkholderia cepacia Complex Bacteria.

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    Heleen Van Acker

    Full Text Available It was recently proposed that bactericidal antibiotics, besides through specific drug-target interactions, kill bacteria by a common mechanism involving the production of reactive oxygen species (ROS. However, this mechanism involving the production of hydroxyl radicals has become the subject of a lot of debate. Since the contribution of ROS to antibiotic mediated killing most likely depends on the conditions, differences in experimental procedures are expected to be at the basis of the conflicting results. In the present study different methods (ROS specific stainings, gene-expression analyses, electron paramagnetic resonance, genetic and phenotypic experiments, detection of protein carbonylation and DNA oxidation to measure the production of ROS upon antibiotic treatment in Burkholderia cepacia complex (Bcc bacteria were compared. Different classes of antibiotics (tobramycin, ciprofloxacin, meropenem were included, and both planktonic and biofilm cultures were studied. Our results indicate that some of the methods investigated were not sensitive enough to measure antibiotic induced production of ROS, including the spectrophotometric detection of protein carbonylation. Secondly, other methods were found to be useful only in specific conditions. For example, an increase in the expression of OxyR was measured in Burkholderia cenocepacia K56-2 after treatment with ciprofloxacin or meropenem (both in biofilms and planktonic cultures but not after treatment with tobramycin. In addition results vary with the experimental conditions and the species tested. Nevertheless our data strongly suggest that ROS contribute to antibiotic mediated killing in Bcc species and that enhancing ROS production or interfering with the protection against ROS may form a novel strategy to improve antibiotic treatment.

  20. Virulent Burkholderia species mimic host actin polymerases to drive actin-based motility

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    Benanti, Erin L.; Nguyen, Catherine M.; Welch, Matthew D.

    2015-01-01

    Summary Burkholderia pseudomallei and B. mallei are bacterial pathogens that cause melioidosis and glanders, while their close relative B. thailandensis is nonpathogenic. All use the trimeric autotransporter BimA to facilitate actin-based motility, host cell fusion and dissemination. Here, we show that BimA orthologs mimic different host actin-polymerizing proteins. B. thailandensis BimA activates the host Arp2/3 complex. In contrast, B. pseudomallei and B. mallei BimA mimic host Ena/VASP actin polymerases in their ability to nucleate, elongate and bundle filaments by associating with barbed ends, as well as in their use of WH2 motifs and oligomerization for activity. Mechanistic differences among BimA orthologs resulted in distinct actin filament organization and motility parameters, which affected the efficiency of cell fusion during infection. Our results identify bacterial Ena/VASP mimics and reveal that pathogens imitate the full spectrum of host actin-polymerizing pathways, suggesting that mimicry of different polymerization mechanisms influences key parameters of infection. PMID:25860613

  1. Neutrophil elastase causes tissue damage that decreases host tolerance to lung infection with burkholderia species.

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    Manoranjan Sahoo

    2014-08-01

    Full Text Available Two distinct defense strategies can protect the host from infection: resistance is the ability to destroy the infectious agent, and tolerance is the ability to withstand infection by minimizing the negative impact it has on the host's health without directly affecting pathogen burden. Burkholderia pseudomallei is a Gram-negative bacterium that infects macrophages and causes melioidosis. We have recently shown that inflammasome-triggered pyroptosis and IL-18 are equally important for resistance to B. pseudomallei, whereas IL-1β is deleterious. Here we show that the detrimental role of IL-1β during infection with B. pseudomallei (and closely related B. thailandensis is due to excessive recruitment of neutrophils to the lung and consequent tissue damage. Mice deficient in the potentially damaging enzyme neutrophil elastase were less susceptible than the wild type C57BL/6J mice to infection, although the bacterial burdens in organs and the extent of inflammation were comparable between C57BL/6J and elastase-deficient mice. In contrast, lung tissue damage and vascular leakage were drastically reduced in elastase-deficient mice compared to controls. Bradykinin levels were higher in C57BL/6 than in elastase-deficient mice; administration of a bradykinin antagonist protected mice from infection, suggesting that increased vascular permeability mediated by bradykinin is one of the mechanisms through which elastase decreases host tolerance to melioidosis. Collectively, these results demonstrate that absence of neutrophil elastase increases host tolerance, rather than resistance, to infection by minimizing host tissue damage.

  2. Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23

    OpenAIRE

    Lim, Jong Sung; Choi, Beom Soon; Choi, Ah Young; Kim, Kyung Duk; Kim, Dong In; Choi, Ik Young; Ka, Jong-Ok

    2012-01-01

    Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23.

  3. Causality of the relationship between geographic distribution and species abundance

    DEFF Research Database (Denmark)

    Borregaard, Michael Krabbe; Rahbek, Carsten

    2010-01-01

    The positive relationship between a species' geographic distribution and its abundance is one of ecology's most well-documented patterns, yet the causes behind this relationship remain unclear. Although many hypotheses have been proposed to account for distribution-abundance relationships none ha......, in a framework that facilitates a comparison between them. We identify and discuss the central factors governing the individual mechanisms, and elucidate their effect on empirical patterns....

  4. Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes.

    Science.gov (United States)

    De Meyer, Sofie E; Briscoe, Leah; Martínez-Hidalgo, Pilar; Agapakis, Christina M; de-Los Santos, Paulina Estrada; Seshadri, Rekha; Reeve, Wayne; Weinstock, George; O'Hara, Graham; Howieson, John G; Hirsch, Ann M

    2016-08-01

    Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.

  5. Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

    Energy Technology Data Exchange (ETDEWEB)

    Moulin, Lionel [UMR, France; Klonowska, Agnieszka [UMR, France; Caroline, Bournaud [UMR, France; Booth, Kristina [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts; Melkonian, Remy [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom; Bena, Gilles [UMR, France; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lizotte-Waniewski, Michelle [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole

    2014-01-01

    Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

  6. Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.

    Directory of Open Access Journals (Sweden)

    Zhenyue Lin

    Full Text Available BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. RESULT: Two Fusarium species (F. verticillioides and F. proliferatum that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. CONCLUSIONS/SIGNIFICANCE: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng.

  7. CHROMOSOMAL MULTIPLICITY IN BURKHOLDERIA CEPACIA

    Science.gov (United States)

    We have used CHEF gel electrophoresis to screen preparations of large DNA from different Burkholderia cepacia isolates for the presence of DNA species corresponding to the linearized forms of the three chromosomes of 3.4,2.5, and 0.9 Mb identified in B. cepacia strain 17616. DNA ...

  8. Darwin's diagram of divergence of taxa as a causal model for the origin of species.

    Science.gov (United States)

    Bouzat, Juan L

    2014-03-01

    On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, thus representing a comprehensive model of Darwin's theory on the origin of species. I describe Darwin's Tree Diagram in relation to his argumentative strategy under the vera causa principle, and suggest that the testing of his theory based on the evidence from the geological record, the geographical distribution of organisms, and the mutual affinities of organic beings can be framed under the hypothetico-deductive method. Darwin's Diagram of Divergence of Taxa therefore represents a broad conceptual model that helps understanding the causal construction of Darwin's theory of evolution, the structure of his argumentative strategy, and the nature of his scientific methodology.

  9. Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species.

    Directory of Open Access Journals (Sweden)

    Heleen Van Acker

    Full Text Available The presence of persister cells has been proposed as a factor in biofilm resilience. In the present study we investigated whether persister cells are present in Burkholderia cepacia complex (Bcc biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. After treatment of Bcc biofilms with high concentrations of various antibiotics often a small subpopulation survived. To investigate the molecular mechanism of tolerance in this subpopulation, Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin. Using ROS-specific staining and flow cytometry, we showed that tobramycin increased ROS production in treated sessile cells. However, approximately 0.1% of all sessile cells survived the treatment. A transcriptome analysis showed that several genes from the tricarboxylic acid cycle and genes involved in the electron transport chain were downregulated. In contrast, genes from the glyoxylate shunt were upregulated. These data indicate that protection against ROS is important for the survival of persisters. To confirm this, we determined the number of persisters in biofilms formed by catalase mutants. The persister fraction in ΔkatA and ΔkatB biofilms was significantly reduced, confirming the role of ROS detoxification in persister survival. Pretreatment of B. cenocepacia biofilms with itaconate, an inhibitor of isocitrate lyase (ICL, the first enzyme in the glyoxylate shunt, reduced the persister fraction approx. 10-fold when the biofilms were subsequently treated with tobramycin. In conclusion, most Bcc biofilms contain a significant fraction of persisters that survive treatment with high doses of tobramycin. The surviving persister cells downregulate the TCA cycle to avoid production of ROS and at the same time activate an alternative pathway, the glyoxylate shunt. This pathway may present a novel target for combination therapy.

  10. Evaluation of a latex agglutination assay for the identification of Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Duval, Brea D; Elrod, Mindy G; Gee, Jay E; Chantratita, Narisara; Tandhavanant, Sarunporn; Limmathurotsakul, Direk; Hoffmaster, Alex R

    2014-06-01

    Cases of melioidosis and glanders are rare in the United States, but the etiologic agents of each disease (Burkholderia pseudomallei and Burkholderia mallei, respectively) are classified as Tier 1 select agents because of concerns about their potential use as bioterrorism agents. A rapid, highly sensitive, and portable assay for clinical laboratories and field use is required. Our laboratory has further evaluated a latex agglutination assay for its ability to identify B. pseudomallei and B. mallei isolates. This assay uses a monoclonal antibody that specifically recognizes the capsular polysaccharide produced by B. pseudomallei and B. mallei, but is absent in closely related Burkholderia species. A total of 110 B. pseudomallei and B. mallei were tested, and 36 closely related Burkholderia species. The latex agglutination assay was positive for 109 of 110 (99.1% sensitivity) B. pseudomallei and B. mallei isolates tested.

  11. Reactive Oxygen Species and Aging in Caenorhabditis elegans: Causal or Casual Relationship?

    Science.gov (United States)

    Van Raamsdonk, Jeremy Michael; Hekimi, Siegfried

    2010-12-15

    The free radical theory of aging proposes a causal relationship between reactive oxygen species (ROS) and aging. While it is clear that oxidative damage increases with age, its role in the aging process is uncertain. Testing the free radical theory of aging requires experimentally manipulating ROS production or detoxification and examining the resulting effects on lifespan. In this review, we examine the relationship between ROS and aging in the genetic model organism Caenorhabditis elegans, summarizing experiments using long-lived mutants, mutants with altered mitochondrial function, mutants with decreased antioxidant defenses, worms treated with antioxidant compounds, and worms exposed to different environmental conditions. While there is frequently a negative correlation between oxidative damage and lifespan, there are many examples in which they are uncoupled. Neither is resistance to oxidative stress sufficient for a long life nor are all long-lived mutants more resistant to oxidative stress. Similarly, sensitivity to oxidative stress does not necessarily shorten lifespan and is in fact compatible with long life. Overall, the data in C. elegans indicate that oxidative damage can be dissociated from aging in experimental situations.

  12. Genetic Diversity of Burkholderia contaminans Isolates from Cystic Fibrosis Patients in Argentina

    OpenAIRE

    Martina, Pablo F.; Bettiol, Marisa; Vescina, Cecilia; Montanaro, Patricia; Mannino, Maria Constanza; Prieto, Claudia Inés; Vay, Carlos Alberto; Naumann, Dieter; Schmitt, Juergen; Yantorno, Osvaldo Miguel; Lagares, Antonio; Bosch, María Alejandra

    2013-01-01

    A total of 120 Burkholderia cepacia complex isolates collected during 2004?2010 from 66 patients in two cystic fibrosis reference centers in Argentina were analyzed. Burkholderia contaminans was the species most frequently recovered (57.6%), followed by Burkholderia cenocepacia (15%), a species distribution not reported so far. The recA-PCR-based techniques applied to the B. contaminans isolates revealed that 85% of the population carried the recA-ST-71 allele. Our results showed the utili...

  13. Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei

    Directory of Open Access Journals (Sweden)

    Janse Ingmar

    2013-02-01

    Full Text Available Abstract Background Burkholderia mallei and B. pseudomallei are two closely related species of highly virulent bacteria that can be difficult to detect. Pathogenic Burkholderia are endemic in many regions worldwide and cases of infection, sometimes brought by travelers from unsuspected regions, also occur elsewhere. Rapid, sensitive methods for identification of B. mallei and B. pseudomallei are urgently needed in the interests of patient treatment and epidemiological surveillance. Methods Signature sequences for sensitive, specific detection of pathogenic Burkholderia based on published genomes were identified and a qPCR assay was designed and validated. Results A single-reaction quadruplex qPCR assay for the detection of pathogenic Burkholderia, which includes a marker for internal control of DNA extraction and amplification, was developed. The assay permits differentiation of B. mallei and B. pseudomallei strains, and probit analysis showed a very low detection limit. Use of a multicopy signature sequence permits detection of less than 1 genome equivalent per reaction. Conclusions The new assay permits rapid detection of pathogenic Burkholderia and combines enhanced sensitivity, species differentiation, and inclusion of an internal control for both DNA extraction and PCR amplification.

  14. Bacterial Genome Adaptation to Niches: Divergence of the Potential Virulence Genes in Three Burkholderia Species of Different Survival Strategies

    Science.gov (United States)

    2005-12-01

    species For comparative genomic analysis with pathogenic Bm and Bp, we produced finished sequence of the closely related nonpathogenic soil bacterium...1999. 11. Godoy D, Randle G, Simpson AJ, Aanensen DM, Pitt TL, Kinoshita R, Spratt BG: Multilocus sequence typing and evolutionary rela- tionships...5223):496-512. 34. Waterman MS: Computer analysis of nucleic acid sequences . Methods Enzymol 1988, 164:765-793. 35. Bateman A, Birney E, Durbin R, Eddy

  15. Autotransporters and their role in the virulence of Burkholderia pseudomallei and Burkholderia mallei.

    Directory of Open Access Journals (Sweden)

    Natalie eLazar Adler

    2011-07-01

    Full Text Available Burkholderia pseudomallei and Burkholderia mallei are closely related Gram-negative bacteria responsible for the infectious diseases melioidosis and glanders, respectively. Autotransporters (ATs comprise a large and diverse family of secreted and outer membrane proteins that includes virulence-associated invasins, adhesins, proteases and actin-nucleating factors. The B. pseudomallei K96243 genome contains eleven predicted ATs, eight of which share homologues in the B. mallei ATCC 23344 genome. This review distils key findings from in silico, in vitro and in vivo studies on the ATs of B. pseudomallei and B. mallei. To date, the best characterized of the predicted ATs of B. pseudomallei and B. mallei is BimA, a predicted trimeric AT mediating actin-based motility which varies in sequence and mode of action between Burkholderia species. Of the remaining eight predicted B. pseudomallei trimeric autotransporters, five of which are also present in B. mallei, two (BoaA and BoaB, have been implicated in bacterial adhesion to epithelial cells. Several predicted Burkholderia ATs are recognized by human humoral and cell-mediated immunity, indicating that they are expressed during infection and may be useful for diagnosis and vaccine-mediated protection. Further studies on the mode of secretion and functions of Burkholderia ATs will facilitate the rational design of control strategies.

  16. Burkholderia Vaccines: Are We Moving Forward?

    Directory of Open Access Journals (Sweden)

    Leang-Chung eChoh

    2013-02-01

    Full Text Available The genus Burkholderia consists of diverse species which includes both ‘friends’ and ‘foes’. Some of the ‘friendly’ Burkholderia spp. are extensively used in the biotechnological and agricultural industry for bioremediation and biocontrol. However, several members of the genus including B. pseudomallei, B. mallei and B. cepacia, are known to cause fatal disease in both humans and animals. B. pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, while B. cepacia infection is lethal to cystic fibrosis patients. Due to the high rate of infectivity and intrinsic resistance to many commonly used antibiotics, together with high mortality rate, B. mallei and B. pseudomallei are considered to be potential biological warfare agents. Treatments of the infections caused by these bacteria are often unsuccessful with frequent relapse of the infection. Thus, we are at a crucial stage of the need for Burkholderia vaccines. Although the search for a prophylactic therapy candidate continues, to date development of vaccines has not advanced beyond research to human clinical trials. In this article, we review the current research on development of safe vaccines with high efficacy against B. pseudomallei, B. mallei and B. cepacia. It can be concluded that further research will enable elucidation of the potential benefits and risks of Burkholderia vaccines.

  17. Burkholderia vaccines: are we moving forward?

    Science.gov (United States)

    Choh, Leang-Chung; Ong, Guang-Han; Vellasamy, Kumutha M; Kalaiselvam, Kaveena; Kang, Wen-Tyng; Al-Maleki, Anis R; Mariappan, Vanitha; Vadivelu, Jamuna

    2013-01-01

    The genus Burkholderia consists of diverse species which includes both "friends" and "foes." Some of the "friendly" Burkholderia spp. are extensively used in the biotechnological and agricultural industry for bioremediation and biocontrol. However, several members of the genus including B. pseudomallei, B. mallei, and B. cepacia, are known to cause fatal disease in both humans and animals. B. pseudomallei and B. mallei are the causative agents of melioidosis and glanders, respectively, while B. cepacia infection is lethal to cystic fibrosis (CF) patients. Due to the high rate of infectivity and intrinsic resistance to many commonly used antibiotics, together with high mortality rate, B. mallei and B. pseudomallei are considered to be potential biological warfare agents. Treatments of the infections caused by these bacteria are often unsuccessful with frequent relapse of the infection. Thus, we are at a crucial stage of the need for Burkholderia vaccines. Although the search for a prophylactic therapy candidate continues, to date development of vaccines has not advanced beyond research to human clinical trials. In this article, we review the current research on development of safe vaccines with high efficacy against B. pseudomallei, B. mallei, and B. cepacia. It can be concluded that further research will enable elucidation of the potential benefits and risks of Burkholderia vaccines.

  18. Stress conditions triggering mucoid morphotype variation in Burkholderia species and effect on virulence in Galleria mellonella and biofilm formation in vitro.

    Directory of Open Access Journals (Sweden)

    Inês N Silva

    Full Text Available Burkholderia cepacia complex (Bcc bacteria are opportunistic pathogens causing chronic respiratory infections particularly among cystic fibrosis patients. During these chronic infections, mucoid-to-nonmucoid morphotype variation occurs, with the two morphotypes exhibiting different phenotypic properties. Here we show that in vitro, the mucoid clinical isolate Burkholderia multivorans D2095 gives rise to stable nonmucoid variants in response to prolonged stationary phase, presence of antibiotics, and osmotic and oxidative stresses. Furthermore, in vitro colony morphotype variation within other members of the Burkholderia genus occurred in Bcc and non-Bcc strains, irrespectively of their clinical or environmental origin. Survival to starvation and iron limitation was comparable for the mucoid parental isolate and the respective nonmucoid variant, while susceptibility to antibiotics and to oxidative stress was increased in the nonmucoid variants. Acute infection of Galleria mellonella larvae showed that, in general, the nonmucoid variants were less virulent than the respective parental mucoid isolate, suggesting a role for the exopolysaccharide in virulence. In addition, most of the tested nonmucoid variants produced more biofilm biomass than their respective mucoid parental isolate. As biofilms are often associated with increased persistence of pathogens in the CF lungs and are an indicative of different cell-to-cell interactions, it is possible that the nonmucoid variants are better adapted to persist in this host environment.

  19. Stress conditions triggering mucoid morphotype variation in Burkholderia species and effect on virulence in Galleria mellonella and biofilm formation in vitro.

    Science.gov (United States)

    Silva, Inês N; Tavares, Andreia C; Ferreira, Ana S; Moreira, Leonilde M

    2013-01-01

    Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens causing chronic respiratory infections particularly among cystic fibrosis patients. During these chronic infections, mucoid-to-nonmucoid morphotype variation occurs, with the two morphotypes exhibiting different phenotypic properties. Here we show that in vitro, the mucoid clinical isolate Burkholderia multivorans D2095 gives rise to stable nonmucoid variants in response to prolonged stationary phase, presence of antibiotics, and osmotic and oxidative stresses. Furthermore, in vitro colony morphotype variation within other members of the Burkholderia genus occurred in Bcc and non-Bcc strains, irrespectively of their clinical or environmental origin. Survival to starvation and iron limitation was comparable for the mucoid parental isolate and the respective nonmucoid variant, while susceptibility to antibiotics and to oxidative stress was increased in the nonmucoid variants. Acute infection of Galleria mellonella larvae showed that, in general, the nonmucoid variants were less virulent than the respective parental mucoid isolate, suggesting a role for the exopolysaccharide in virulence. In addition, most of the tested nonmucoid variants produced more biofilm biomass than their respective mucoid parental isolate. As biofilms are often associated with increased persistence of pathogens in the CF lungs and are an indicative of different cell-to-cell interactions, it is possible that the nonmucoid variants are better adapted to persist in this host environment.

  20. Econometric causality

    OpenAIRE

    Heckman, James J.

    2008-01-01

    This paper presents the econometric approach to causal modeling. It is motivated by policy problems. New causal parameters are defined and identified to address specific policy problems. Economists embrace a scientific approach to causality and model the preferences and choices of agents to infer subjective (agent) evaluations as well as objective outcomes. Anticipated and realized subjective and objective outcomes are distinguished. Models for simultaneous causality are developed. The paper ...

  1. Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods

    NARCIS (Netherlands)

    C. van Pelt (Cindy); C.M. Verduin (Cees); W.H.F. Goessens (Wil); M.C. Vos (Margreet); B. Tummler; C. Segonds; F. Reubsaet; A.F. van Belkum (Alex); H.A. Verbrugh (Henri)

    1999-01-01

    textabstractCystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situat

  2. Symbiotic ß-proteobacteria beyond legumes: Burkholderia in Rubiaceae.

    Directory of Open Access Journals (Sweden)

    Brecht Verstraete

    Full Text Available Symbiotic ß-proteobacteria not only occur in root nodules of legumes but are also found in leaves of certain Rubiaceae. The discovery of bacteria in plants formerly not implicated in endosymbiosis suggests a wider occurrence of plant-microbe interactions. Several ß-proteobacteria of the genus Burkholderia are detected in close association with tropical plants. This interaction has occurred three times independently, which suggest a recent and open plant-bacteria association. The presence or absence of Burkholderia endophytes is consistent on genus level and therefore implies a predictive value for the discovery of bacteria. Only a single Burkholderia species is found in association with a given plant species. However, the endophyte species are promiscuous and can be found in association with several plant species. Most of the endophytes are part of the plant-associated beneficial and environmental group, but others are closely related to B. glathei. This soil bacteria, together with related nodulating and non-nodulating endophytes, is therefore transferred to a newly defined and larger PBE group within the genus Burkholderia.

  3. Development of Galleria mellonella as an Alternative Infection Model for the Burkholderia cepacia Complex▿

    OpenAIRE

    Seed, Kimberley D.; Dennis, Jonathan J.

    2008-01-01

    Burkholderia is an important bacterial genus with a complex taxonomy that contains species of both ecological and pathogenic importance, including nine closely related species collectively termed the Burkholderia cepacia complex (BCC). In order to more thoroughly investigate the virulence of this bacterial complex of microorganisms, alternative infection models would be useful. To this end, we have adapted and developed the use of the Galleria mellonella wax moth larvae as a host for examinin...

  4. The three-species consortium of genetically improved strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120, grows with technical polychlorobiphenyl, Aroclor 1242

    Directory of Open Access Journals (Sweden)

    Regina-Michaela eWittich

    2013-04-01

    Full Text Available Burkholderia xenovorans LB400, Cupriavidus necator H850, and Pseudomonas pseudoalcaligenes KF707 are bacterial strains able to mineralize biphenyl and to co-oxidize many of its halogenated derivatives (PCBs. Only strain LB400 also mineralizes a few mono- and dichlorobiphenyls, due to the presence of a functioning chlorocatechol pathway. Here, we used a Tn5-based minitransposon shuttle system to chromosomically introduce genes tcbRCDEF, encoding the chlorocatechol pathway into KF707, and genes cbdABC encoding a 2-chlorobenzoate 1,2-dioxygenase into KF707 and LB400, as well as transposon Tn4653 from the TOL plasmid providing genes xylXYZL, encoding a broad-range toluate (methylbenzoate dioxygenase and its dihydrodiol dehydrogenase, to extend the range for the mineralization of halogenated benzoates in LB400 and in KF707. The engineered derivatives of LB400, and KF707 thus gained the ability for the mineralization of all isomeric monochloro- and bromobenzoates of the so-called lower pathway which, consequently, also allowed the mineralization of all monochlorobiphenyls and a number of di- and trichlorobiphenyls, thus preventing the accumulation of halobenzoates and of catabolites thereof. LB400 and KF707 also grow with the two commercial PCB formulations, Aroclor 1221 and Aroclor 1232, as the sole carbon and energy sources, but not with higher halogenated PCB mixtures, similar to the already published strain RW112. Repeated exposition of the modified LB400 to short pulses of UV light, over a prolonged period of time, allowed the isolation of a derivative of LB400, termed RW118, capable of growth with Aroclor 1016 still containing only traces of biphenyl, and in co-culture with modified KF707 termed RW120, and modified H850 (RW112 with Aroclor 1242, the commercial mixture already void of biphenyl and monochlorobiphenyls.

  5. K-causality coincides with stable causality

    OpenAIRE

    Minguzzi, E

    2008-01-01

    It is proven that K-causality coincides with stable causality, and that in a K-causal spacetime the relation K^+ coincides with the Seifert's relation. As a consequence the causal relation "the spacetime is strongly causal and the closure of the causal relation is transitive" stays between stable causality and causal continuity.

  6. Exploring the HME and HAE1 efflux systems in the genus Burkholderia

    Directory of Open Access Journals (Sweden)

    Pasca Maria

    2010-06-01

    Full Text Available Abstract Background The genus Burkholderia includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. This study aims to i identify rnd genes in the 21 available completely sequenced Burkholderia genomes, ii analyze their phylogenetic distribution, iii define the putative function(s that RND proteins perform within the Burkholderia genus and iv try tracing the evolutionary history of some of these genes in Burkholderia. Results BLAST analysis of the 21 Burkholderia sequenced genomes, using experimentally characterized ceoB sequence (one of the RND family counterpart in the genus Burkholderia as probe, allowed the assembly of a dataset comprising 254 putative RND proteins. An extensive phylogenetic analysis revealed the occurrence of several independent events of gene loss and duplication across the different lineages of the genus Burkholderia, leading to notable differences in the number of paralogs between different genomes. A putative substrate [antibiotics (HAE1 proteins/heavy-metal (HME proteins] was also assigned to the majority of these proteins. No correlation was found between the ecological niche and the lifestyle of Burkholderia strains and the number/type of efflux pumps they possessed, while a relation can be found with genome size and taxonomy. Remarkably, we observed that only HAE1 proteins are mainly responsible for the different number of proteins observed in strains of the same species. Data concerning both the distribution and the phylogenetic analysis of the HAE1 and HME in the Burkholderia genus allowed depicting a likely evolutionary model accounting for the evolution and spreading of HME and HAE

  7. Causal universe

    CERN Document Server

    Ellis, George FR; Pabjan, Tadeusz

    2013-01-01

    Written by philosophers, cosmologists, and physicists, this collection of essays deals with causality, which is a core issue for both science and philosophy. Readers will learn about different types of causality in complex systems and about new perspectives on this issue based on physical and cosmological considerations. In addition, the book includes essays pertaining to the problem of causality in ancient Greek philosophy, and to the problem of God's relation to the causal structures of nature viewed in the light of contemporary physics and cosmology.

  8. Causal and causally separable processes

    Science.gov (United States)

    Oreshkov, Ognyan; Giarmatzi, Christina

    2016-09-01

    The idea that events are equipped with a partial causal order is central to our understanding of physics in the tested regimes: given two pointlike events A and B, either A is in the causal past of B, B is in the causal past of A, or A and B are space-like separated. Operationally, the meaning of these order relations corresponds to constraints on the possible correlations between experiments performed in the vicinities of the respective events: if A is in the causal past of B, an experimenter at A could signal to an experimenter at B but not the other way around, while if A and B are space-like separated, no signaling is possible in either direction. In the context of a concrete physical theory, the correlations compatible with a given causal configuration may obey further constraints. For instance, space-like correlations in quantum mechanics arise from local measurements on joint quantum states, while time-like correlations are established via quantum channels. Similarly to other variables, however, the causal order of a set of events could be random, and little is understood about the constraints that causality implies in this case. A main difficulty concerns the fact that the order of events can now generally depend on the operations performed at the locations of these events, since, for instance, an operation at A could influence the order in which B and C occur in A’s future. So far, no formal theory of causality compatible with such dynamical causal order has been developed. Apart from being of fundamental interest in the context of inferring causal relations, such a theory is imperative for understanding recent suggestions that the causal order of events in quantum mechanics can be indefinite. Here, we develop such a theory in the general multipartite case. Starting from a background-independent definition of causality, we derive an iteratively formulated canonical decomposition of multipartite causal correlations. For a fixed number of settings and

  9. Type VI Secretion is a Major Virulence Determinant in Burkholderia Mallei

    Science.gov (United States)

    2007-06-01

    infections can also occur in felines , camels and goats. Humans are accidental hosts of B. mallei and the majority of cases have been the result of...occupational contact with infected horses. Whereas equines are generally infected orally , the primary route of infection in humans is contamination of skin...Effects of Burkholderia pseudomallei and other Burkholderia species on eukarotic cells in tissue culture. Microbios 96: 71–93. Holm, M.M., Vanlerberg, S.L

  10. Causal mapping

    DEFF Research Database (Denmark)

    Rasmussen, Lauge Baungaard

    2006-01-01

    The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method......The lecture note explains how to use the causal mapping method as well as the theoretical framework aoosciated to the method...

  11. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interim report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.

  12. Molecular mechanisms underlying the close association between soil Burkholderia and fungi.

    Science.gov (United States)

    Stopnisek, Nejc; Zühlke, Daniela; Carlier, Aurélien; Barberán, Albert; Fierer, Noah; Becher, Dörte; Riedel, Katharina; Eberl, Leo; Weisskopf, Laure

    2016-01-01

    Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungal-secreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.

  13. Causality Networks

    OpenAIRE

    Ishanu Chattopadhyay

    2014-01-01

    While correlation measures are used to discern statistical relationships between observed variables in almost all branches of data-driven scientific inquiry, what we are really interested in is the existence of causal dependence. Designing an efficient causality test, that may be carried out in the absence of restrictive pre-suppositions on the underlying dynamical structure of the data at hand, is non-trivial. Nevertheless, ability to computationally infer statistical prima facie evidence of...

  14. Epidemiological causality.

    Science.gov (United States)

    Morabia, Alfredo

    2005-01-01

    Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

  15. Causality: Physics and Philosophy

    Science.gov (United States)

    Chatterjee, Atanu

    2013-01-01

    Nature is a complex causal network exhibiting diverse forms and species. These forms or rather systems are physically open, structurally complex and naturally adaptive. They interact with the surrounding media by operating a positive-feedback loop through which, they adapt, organize and self-organize themselves in response to the ever-changing…

  16. Draft genome sequence of Burkholderia sordidicola S170, a potential plant growth promoter isolated from coniferous forest soil in the Czech Republic

    DEFF Research Database (Denmark)

    Lladó, Salvador; Xu, Zhuofei; Sørensen, Søren Johannes;

    2014-01-01

    Burkholderia species are key players in the accumulation of carbon from cellulose decomposition in coniferous forest ecosystems. We report here the draft genome of Burkholderia sordidicola strain S170, containing features associated with known genes involved in plant growth promotion, the biologi...

  17. Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available Burkholderia ubonensis is an environmental bacterium belonging to the Burkholderia cepacia complex (Bcc, a group of genetically related organisms that are associated with opportunistic but generally nonfatal infections in healthy individuals. In contrast, the near-neighbour species Burkholderia pseudomallei causes melioidosis, a disease that can be fatal in up to 95% of cases if left untreated. B. ubonensis is frequently misidentified as B. pseudomallei from soil samples using selective culturing on Ashdown's medium, reflecting both the shared environmental niche and morphological similarities of these species. Additionally, B. ubonensis shows potential as an important biocontrol agent in B. pseudomallei-endemic regions as certain strains possess antagonistic properties towards B. pseudomallei. Current methods for characterising B. ubonensis are laborious, time-consuming and costly, and as such this bacterium remains poorly studied. The aim of our study was to develop a rapid and inexpensive real-time PCR-based assay specific for B. ubonensis. We demonstrate that a novel B. ubonensis-specific assay, Bu550, accurately differentiates B. ubonensis from B. pseudomallei and other species that grow on selective Ashdown's agar. We anticipate that Bu550 will catalyse research on B. ubonensis by enabling rapid identification of this organism from Ashdown's-positive colonies that are not B. pseudomallei.

  18. Causality Principle

    OpenAIRE

    Chi, Do Minh

    2001-01-01

    We advance a famous principle - causality principle - but under a new view. This principle is a principium automatically leading to most fundamental laws of the nature. It is the inner origin of variation, rules evolutionary processes of things, and the answer of the quest for ultimate theories of the Universe.

  19. Burkholderia, a Genus Rich in Plant-Associated Nitrogen Fixers with Wide Environmental and Geographic Distribution

    Science.gov (United States)

    Estrada-De Los Santos, Paulina; Bustillos-Cristales, Rocío; Caballero-Mellado, Jesús

    2001-01-01

    The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N2-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N2-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75T. These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75T. Although the ability to fix N2 is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N2-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N2-fixing Burkholderia species different from B. vietnamiensis. In addition, this study shows the wide geographic distribution and substantial capability of N2-fixing Burkholderia spp. for colonizing diverse host plants in distantly separated environments. PMID:11375196

  20. Characterization of integrons in Burkholderia cepacia clinical isolates

    Directory of Open Access Journals (Sweden)

    Linda Furlanis

    2010-03-01

    Full Text Available Burkholderia cepacia is an opportunistic pathogen able to colonize the airways of Cystic Fibrosis (CF patients, frequently developing chronic infections. In 20% of cases these infections cause severe and poorly controlled pathological situations because of the intrinsic antibiotic resistance expressed by the microorganism. CF patients are often subjected to antibiotic therapy: this facilitates the acquisition of antibiotic resistance determinants by the infecting bacteria. Integrons are mobile genetic elements that are widespread in bacterial populations and favor the acquisition of gene cassettes coding for these determinants.The presence of class 1 integrons was investigated by PCR with primers specific for the 5’ and 3’ ends in Burkholderia isolates recovered from patients in treatment at the CF center of Friuli Venezia Giulia. The same integron, carrying an uncommon allelic form (Ib of the aacA4 gene in its cassette array and conferring resistance to some aminoglycosides, was found in two independent isolates (different RAPD profiles infecting two different patients. In both isolates the integron was carried by plasmids and was still present 3 and 6 years later the first finding. Despite the exchange of integrons between bacterial pathogens is fully described, these items were not frequently found in Burkholderia isolates. Although the clinical relevance of the integron we identified is low (a single gene cassette encoding a widespread resistance,we feel concerned that these genetic elements begin to circulate in this bacterial species, as this could make more and more troublesome the treatment of infections notoriously difficult to eradicate.

  1. Isolation and Identification of Burkholderia glumae from Symptomless Rice Seeds

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A survey on isolation and detection of the casual organism of bacterial grain rot of rice was conducted during 1997-2006.In 2006,six pathogenic bacterial strains were isolated from two symptomiess seed samples of rice (Oryza sativa L.) originally produced in Hainan Province and then planted in Zhejiang Province,China.They were identified as Burkholderia glumae which is the causal organism of bacterial grain rot of rice by physiological characteristics,colony morphology,pathogenicity test,Biolog,fatty acid methyl ester (FAME) analysis and RAPD-PCR compared with the four standard reference strains.It is confirmed that there is the infection of B.glumae in so-called 'health looking seeds'.

  2. Prevalence of Burkholderia pseudomallei in Guangxi, China.

    Science.gov (United States)

    Ma, G; Zheng, D; Cai, Q; Yuan, Z

    2010-01-01

    Melioidosis, an infectious disease caused by the Gram-negative bacterium Burkholderia pseudomallei, is now recognized as an important public health problem in Southeast Asia and tropical northern Australia. Although B. pseudomallei has been detected in various water and soil samples in southeast China, the enviromental distribution of B. pseudomallei in China is unclear. In the winter months of 2007, 154 and 130 soil and water samples, respectively, were collected from several locations in Guangxi, China. The samples were screened for B. pseudomallei by bacterial culture and identification and confirmed by PCR for species-specific 16S rDNA and flagellin genes. B. pseudomallei was detected in 8.4% of the soil samples but in none of the water samples. All positive samples were confined to a single low-lying region from rice paddy fields. Counts of B. pseudomallei ranged from 23 to 521 c.f.u./g soil. This is the first geographical distribution survey of B. pseudomallei in soil in Guangxi, China, and the data are of importance for further evaluating the impact of this pathogen on melioidosis in this region.

  3. Causal Effect Estimation Methods

    OpenAIRE

    2014-01-01

    Relationship between two popular modeling frameworks of causal inference from observational data, namely, causal graphical model and potential outcome causal model is discussed. How some popular causal effect estimators found in applications of the potential outcome causal model, such as inverse probability of treatment weighted estimator and doubly robust estimator can be obtained by using the causal graphical model is shown. We confine to the simple case of binary outcome and treatment vari...

  4. 40 CFR 725.1075 - Burkholderia cepacia complex.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Burkholderia cepacia complex. 725.1075... Specific Microorganisms § 725.1075 Burkholderia cepacia complex. (a) Microorganism and significant new uses subject to reporting. (1) The microorganisms identified as the Burkholderia cepacia complex defined...

  5. Circular causality.

    Science.gov (United States)

    Thomas, R

    2006-07-01

    The problem of disentangling complex dynamic systems is addressed, especially with a view to identifying those variables that take part in the essential qualitative behaviour of systems. The author presents a series of reflections about the methods of formalisation together with the principles that govern the global operation of systems. In particular, a section on circuits, nuclei, and circular causality and a rather detailed description of the analytic use of the generalised asynchronous logical description, together with a brief description of its synthetic use (OreverseO logic). Some basic rules are recalled, such as the fact that a positive circuit is a necessary condition of multistationarity. Also, the interest of considering as a model, rather than a well-defined set of differential equations, a variety of systems that differ from each other only by the values of constant terms is emphasised. All these systems have a common Jacobian matrix and for all of them phase space has exactly the same structure. It means that all can be partitioned in the same way as regards the signs of the eigenvalues and thus as regards the precise nature of any steady states that might be present. Which steady states are actually present, depends on the values of terms of order zero in the ordinary differential equations (ODEs), and it is easy to find for which values of these terms a given point in phase space is steady. Models can be synthesised first at the level of the circuits involved in the Jacobian matrix (that determines which types and numbers of steady states are consistent with the model), then only at the level of terms of order zero in the ODE's (that determines which of the steady states actually exist), hence the title 'Circular casuality'.

  6. Causally nonseparable processes admitting a causal model

    Science.gov (United States)

    Feix, Adrien; Araújo, Mateus; Brukner, Časlav

    2016-08-01

    A recent framework of quantum theory with no global causal order predicts the existence of ‘causally nonseparable’ processes. Some of these processes produce correlations incompatible with any causal order (they violate so-called ‘causal inequalities’ analogous to Bell inequalities) while others do not (they admit a ‘causal model’ analogous to a local model). Here we show for the first time that bipartite causally nonseparable processes with a causal model exist, and give evidence that they have no clear physical interpretation. We also provide an algorithm to generate processes of this kind and show that they have nonzero measure in the set of all processes. We demonstrate the existence of processes which stop violating causal inequalities but are still causally nonseparable when mixed with a certain amount of ‘white noise’. This is reminiscent of the behavior of Werner states in the context of entanglement and nonlocality. Finally, we provide numerical evidence for the existence of causally nonseparable processes which have a causal model even when extended with an entangled state shared among the parties.

  7. Insecticide applications to soil contribute to the development of Burkholderia mediating insecticide resistance in stinkbugs.

    Science.gov (United States)

    Tago, Kanako; Kikuchi, Yoshitomo; Nakaoka, Sinji; Katsuyama, Chie; Hayatsu, Masahito

    2015-07-01

    Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e. symbiotic and nonsymbiotic fenitrothion degraders and nondegraders) in fenitrothion-treated soil using microcosms. During the incubation with five applications of pesticide, the density of the degraders increased from less than the detection limit to around 10(6)/g of soil. The number of dominant species among the degraders declined with the increasing density of degraders; eventually, one species predominated. This process can be explained according to the competitive exclusion principle using V(max) and K(m) values for fenitrothion metabolism by the degraders. We performed a phylogenetic analysis of representative strains isolated from the microcosms and evaluated their ability to establish symbiosis with the stinkbug Riptortus pedestris. The strains that established symbiosis with R. pedestris were assigned to a cluster including symbionts commonly isolated from stinkbugs. The strains outside the cluster could not necessarily associate with the host. The degraders in the cluster predominated during the initial phase of degrader dynamics in the soil. Therefore, only a few applications of fenitrothion could allow symbiotic degraders to associate with their hosts and may cause the emergence of symbiont-mediated insecticide resistance.

  8. Theories of Causality

    Science.gov (United States)

    Jones, Robert

    2010-03-01

    There are a wide range of views on causality. To some (e.g. Karl Popper) causality is superfluous. Bertrand Russell said ``In advanced science the word cause never occurs. Causality is a relic of a bygone age.'' At the other extreme Rafael Sorkin and L. Bombelli suggest that space and time do not exist but are only an approximation to a reality that is simply a discrete ordered set, a ``causal set.'' For them causality IS reality. Others, like Judea Pearl and Nancy Cartwright are seaking to build a complex fundamental theory of causality (Causality, Cambridge Univ. Press, 2000) Or perhaps a theory of causality is simply the theory of functions. This is more or less my take on causality.

  9. Causal reasoning in physics

    CERN Document Server

    Frisch, Mathias

    2014-01-01

    Much has been written on the role of causal notions and causal reasoning in the so-called 'special sciences' and in common sense. But does causal reasoning also play a role in physics? Mathias Frisch argues that, contrary to what influential philosophical arguments purport to show, the answer is yes. Time-asymmetric causal structures are as integral a part of the representational toolkit of physics as a theory's dynamical equations. Frisch develops his argument partly through a critique of anti-causal arguments and partly through a detailed examination of actual examples of causal notions in physics, including causal principles invoked in linear response theory and in representations of radiation phenomena. Offering a new perspective on the nature of scientific theories and causal reasoning, this book will be of interest to professional philosophers, graduate students, and anyone interested in the role of causal thinking in science.

  10. Natural Burkholderia mallei infection in Dromedary, Bahrain.

    Science.gov (United States)

    Wernery, Ulrich; Wernery, Renate; Joseph, Marina; Al-Salloom, Fajer; Johnson, Bobby; Kinne, Joerg; Jose, Shanti; Jose, Sherry; Tappendorf, Britta; Hornstra, Heidie; Scholz, Holger C

    2011-07-01

    We confirm a natural infection of dromedaries with glanders. Multilocus variable number tandem repeat analysis of a Burkholderia mallei strain isolated from a diseased dromedary in Bahrain revealed close genetic proximity to strain Dubai 7, which caused an outbreak of glanders in horses in the United Arab Emirates in 2004.

  11. Causality in Science

    Directory of Open Access Journals (Sweden)

    Cristina Puente Águeda

    2011-10-01

    Full Text Available Causality is a fundamental notion in every field of science. Since the times of Aristotle, causal relationships have been a matter of study as a way to generate knowledge and provide for explanations. In this paper I review the notion of causality through different scientific areas such as physics, biology, engineering, etc. In the scientific area, causality is usually seen as a precise relation: the same cause provokes always the same effect. But in the everyday world, the links between cause and effect are frequently imprecise or imperfect in nature. Fuzzy logic offers an adequate framework for dealing with imperfect causality, so a few notions of fuzzy causality are introduced.

  12. Recombinant Salmonella Expressing Burkholderia mallei LPS O Antigen Provides Protection in a Murine Model of Melioidosis and Glanders.

    Science.gov (United States)

    Moustafa, Dina A; Scarff, Jennifer M; Garcia, Preston P; Cassidy, Sara K B; DiGiandomenico, Antonio; Waag, David M; Inzana, Thomas J; Goldberg, Joanna B

    2015-01-01

    Burkholderia pseudomallei and Burkholderia mallei are the etiologic agents of melioidosis and glanders, respectively. These bacteria are highly infectious via the respiratory route and can cause severe and often fatal diseases in humans and animals. Both species are considered potential agents of biological warfare; they are classified as category B priority pathogens. Currently there are no human or veterinary vaccines available against these pathogens. Consequently efforts are directed towards the development of an efficacious and safe vaccine. Lipopolysaccharide (LPS) is an immunodominant antigen and potent stimulator of host immune responses. B. mallei express LPS that is structurally similar to that expressed by B. pseudomallei, suggesting the possibility of constructing a single protective vaccine against melioidosis and glanders. Previous studies of others have shown that antibodies against B. mallei or B. pseudomallei LPS partially protect mice against subsequent lethal virulent Burkholderia challenge. In this study, we evaluated the protective efficacy of recombinant Salmonella enterica serovar Typhimurium SL3261 expressing B. mallei O antigen against lethal intranasal infection with Burkholderia thailandensis, a surrogate for biothreat Burkholderia spp. in a murine model that mimics melioidosis and glanders. All vaccine-immunized mice developed a specific antibody response to B. mallei and B. pseudomallei O antigen and to B. thailandensis and were significantly protected against challenge with a lethal dose of B. thailandensis. These results suggest that live-attenuated SL3261 expressing B. mallei O antigen is a promising platform for developing a safe and effective vaccine.

  13. Recombinant Salmonella Expressing Burkholderia mallei LPS O Antigen Provides Protection in a Murine Model of Melioidosis and Glanders.

    Directory of Open Access Journals (Sweden)

    Dina A Moustafa

    Full Text Available Burkholderia pseudomallei and Burkholderia mallei are the etiologic agents of melioidosis and glanders, respectively. These bacteria are highly infectious via the respiratory route and can cause severe and often fatal diseases in humans and animals. Both species are considered potential agents of biological warfare; they are classified as category B priority pathogens. Currently there are no human or veterinary vaccines available against these pathogens. Consequently efforts are directed towards the development of an efficacious and safe vaccine. Lipopolysaccharide (LPS is an immunodominant antigen and potent stimulator of host immune responses. B. mallei express LPS that is structurally similar to that expressed by B. pseudomallei, suggesting the possibility of constructing a single protective vaccine against melioidosis and glanders. Previous studies of others have shown that antibodies against B. mallei or B. pseudomallei LPS partially protect mice against subsequent lethal virulent Burkholderia challenge. In this study, we evaluated the protective efficacy of recombinant Salmonella enterica serovar Typhimurium SL3261 expressing B. mallei O antigen against lethal intranasal infection with Burkholderia thailandensis, a surrogate for biothreat Burkholderia spp. in a murine model that mimics melioidosis and glanders. All vaccine-immunized mice developed a specific antibody response to B. mallei and B. pseudomallei O antigen and to B. thailandensis and were significantly protected against challenge with a lethal dose of B. thailandensis. These results suggest that live-attenuated SL3261 expressing B. mallei O antigen is a promising platform for developing a safe and effective vaccine.

  14. Bayesian Causal Induction

    CERN Document Server

    Ortega, Pedro A

    2011-01-01

    Discovering causal relationships is a hard task, often hindered by the need for intervention, and often requiring large amounts of data to resolve statistical uncertainty. However, humans quickly arrive at useful causal relationships. One possible reason is that humans use strong prior knowledge; and rather than encoding hard causal relationships, they encode beliefs over causal structures, allowing for sound generalization from the observations they obtain from directly acting in the world. In this work we propose a Bayesian approach to causal induction which allows modeling beliefs over multiple causal hypotheses and predicting the behavior of the world under causal interventions. We then illustrate how this method extracts causal information from data containing interventions and observations.

  15. Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex

    OpenAIRE

    Bartholdson, S. Josefin; Brown, Alan R.; Mewburn, Ben R.; Clarke, David J.; Fry, Stephen C.; Campopiano, Dominic J.; John R W Govan

    2008-01-01

    The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysa...

  16. Burkholderia glumae en el cultivo de arroz en Costa Rica.

    OpenAIRE

    Andrea Quesada-Gonz\\u00E1lez; Fernando Garc\\u00EDa-Santamar\\u00EDa

    2014-01-01

    Burkholderia glumae en el cultivo de arroz en Costa Rica. El objetivo de este trabajo fue determinar la presencia de Burkholderia glumae en arroz en Costa Rica. La bacteria Burkholderia glumae está asociada al cultivo del arroz en el que provoca la enfermedad llamada añublo bacterial. Bajo condiciones ambientales favorables, la densidad bacteriana aumenta, lo que provoca que, bajo un sistema de regulación denominado quorum sensing, se expresen sus mecanismos de virulencia mediante la ...

  17. Aerosol phage therapy efficacy in Burkholderia cepacia complex respiratory infections.

    Science.gov (United States)

    Semler, Diana D; Goudie, Amanda D; Finlay, Warren H; Dennis, Jonathan J

    2014-07-01

    Phage therapy has been suggested as a potential treatment for highly antibiotic-resistant bacteria, such as the species of the Burkholderia cepacia complex (BCC). To address this hypothesis, experimental B. cenocepacia respiratory infections were established in mice using a nebulizer and a nose-only inhalation device. Following infection, the mice were treated with one of five B. cenocepacia-specific phages delivered as either an aerosol or intraperitoneal injection. The bacterial and phage titers within the lungs were assayed 2 days after treatment, and mice that received the aerosolized phage therapy demonstrated significant decreases in bacterial loads. Differences in phage activity were observed in vivo. Mice that received phage treatment by intraperitoneal injection did not demonstrate significantly reduced bacterial loads, although phage particles were isolated from their lung tissue. Based on these data, aerosol phage therapy appears to be an effective method for treating highly antibiotic-resistant bacterial respiratory infections, including those caused by BCC bacteria.

  18. Causality for nonlocal phenomena

    CERN Document Server

    Eckstein, Michał

    2015-01-01

    Drawing from the theory of optimal transport we propose a rigorous notion of a causal relation for Borel probability measures on a given spacetime. To prepare the ground, we explore the borderland between causality, topology and measure theory. We provide various characterisations of the proposed causal relation, which turn out to be equivalent if the underlying spacetime has a sufficiently robust causal structure. We also present the notion of the 'Lorentz-Wasserstein distance' and study its basic properties. Finally, we discuss how various results on causality in quantum theory, aggregated around Hegerfeldt's theorem, fit into our framework.

  19. South african papilionoid legumes are nodulated by diverse burkholderia with unique nodulation and nitrogen-fixation Loci.

    Science.gov (United States)

    Beukes, Chrizelle W; Venter, Stephanus N; Law, Ian J; Phalane, Francina L; Steenkamp, Emma T

    2013-01-01

    The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.

  20. Combining functional and structural genomics to sample the essential Burkholderia structome.

    Directory of Open Access Journals (Sweden)

    Loren Baugh

    Full Text Available The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq. We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail.This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against

  1. Burkholderia kirstenboschensis sp. nov. nodulates papilionoid legumes indigenous to South Africa.

    Science.gov (United States)

    Steenkamp, Emma T; van Zyl, Elritha; Beukes, Chrizelle W; Avontuur, Juanita R; Chan, Wai Yin; Palmer, Marike; Mthombeni, Lunghile S; Phalane, Francina L; Sereme, T Karabo; Venter, Stephanus N

    2015-12-01

    Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native regions, relatively few taxa have been formally described. For example, the Cape Floristic Region of South Africa is thought to represent one of the major centres of diversity for the rhizobial members of Burkholderia, yet only five species have been described from legumes occurring in this region and numerous are still awaiting taxonomic treatment. Here, we investigated the taxonomic status of 12 South African root-nodulating Burkholderia isolates from native papilionoid legumes (Hypocalyptus coluteoides, H. oxalidifolius, H. sophoroides and Virgilia oroboides). Analysis of four gene regions (16S rRNA, recA, atpD and rpoB) revealed that the isolates represent a genealogically unique and exclusive assemblage within the genus. Its distinctness was supported by all other aspects of the polyphasic approach utilized, including the genome-based criteria DNA-DNA hybridization (≥70.9%) and average nucleotide identities (≥96%). We accordingly propose the name B. kirstenboschensis sp. nov. for this taxon with isolate Kb15(T) (=LMG 28727(T); =SARC 695(T)) as its type strain. Our data showed that intraspecific genome size differences (≥0.81 Mb) and the occurrence of large DNA regions that are apparently unique to single individuals (16-23% of an isolate's genome) can significantly limit the value of data obtained from DNA-DNA hybridization experiments. Substitution of DNA-DNA hybridization with whole genome sequencing as a prerequisite for the description of Burkholderia species will undoubtedly speed up the pace at which their diversity are documented, especially in hyperdiverse regions such as the Cape Floristic Region.

  2. Development of Burkholderia mallei and pseudomallei vaccines

    Directory of Open Access Journals (Sweden)

    Ediane Batista Silva

    2013-03-01

    Full Text Available B. mallei and B. pseudomallei are Gram-negative bacteria that cause glanders and melioidosis, respectively. Inhalational infection with either organism can result in severe and rapidly fatal pneumonia. Inoculation by the oral and cutaneous routes can also produce infection. chronic infection develops after recovery from acute infection with both agents, and control of infection with antibiotics requires prolonged treatment. Symptoms for both meliodosis and glanders are non-specific, making diagnosis difficult.B. pseudomallei can be located in the environment, but in the host, B. mallei and B. psedomallei are intracellular organisms. Thefection results in similar immune responses to both agents. Effective early innate immune responses are critical to controlling the early phase of the infection. Innate immune signaling molecules such as TLR, NOD, MyD88 and pro-inflammatory cytokines such as IFN- and TNF-α play key roles in regulating control of infection. Neutrophils and monocytes are critical cells in the early infection for these microorganisms. Both monocytes and macrophages are necessary for limiting dissemination of B. pseudomallei. In contrast, the role of adaptive immune responses in controlling Burkholderia infection is less well understood. However, T cell responses are critical for vaccine protection from Burkholderia infection. At present, effective vaccines for prevention of glanders or meliodosis have not been developed, although recently progress of Burkholderia vaccines has received renewed attention.This review will summarize current and past approaches to develop Burkholderia mallei and pseudomalllei vaccines, with emphasis on immune mechanisms of protection and the challenges facing the field. At present, immunization with live attenuated bacteria provides the most effective and durable immunity, and it is important therefore to understand the immune correlates of protection induced by live attenuated vaccines.

  3. Survival of Burkholderia pseudomallei on Environmental Surfaces.

    Science.gov (United States)

    Shams, Alicia M; Rose, Laura J; Hodges, Lisa; Arduino, Matthew J

    2007-12-01

    The survival of the biothreat agent Burkholderia pseudomallei on the surfaces of four materials was measured by culture and esterase activity analyses. The culture results demonstrated that this organism persisted for <24 h to <7 days depending on the material, bacterial isolate, and suspension medium. The persistence determined by analysis of esterase activity, as measured with a ScanRDI solid-phase cytometer, was always longer than the persistence determined by culture analysis.

  4. Burkholderia mallei and Burkholderia pseudomallei: the causative micro-organisms of glanders and melioidosis.

    Science.gov (United States)

    Gilad, Jacob

    2007-11-01

    Burkholderia mallei and Burkholderia pseudomallei are the causative micro-organisms of Glanders and Melioidosis, respectively. Although now rare in Western countries, both micro-organisms have recently gained much interest because of their unique potential as bioterrorism agents. This paper reviews the epidemiology, pathogenesis, diagnosis and treatment of Melioidosis and Glanders. Recent patents relating to these micro-organisms, especially potential vaccines, are presented. Continued research and development is urgently needed, especially in regard to rapid and accurate diagnosis of melioidosis and glanders, efficacious therapy and primary and secondary prevention.

  5. Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

    Science.gov (United States)

    Sacco, Laís Postai; Castellane, Tereza Cristina Luque; Lopes, Erica Mendes; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

    2016-03-01

    A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities.

  6. Study of class I integron in a Burkholderia cepacia complex strain isolated from blood colture

    Directory of Open Access Journals (Sweden)

    Linda Furlanis

    2011-06-01

    Full Text Available The Burkholderia cepacia complex (Bcc consists of several species that cause lung infections in patients with cystic fibrosis but are also capable to colonize immunocompromised patients. Once established, the infection is usually difficult to eradicate, as Bcc is intrinsically resistant to many antibiotics. Besides, the acquisition of additional resistance determinants by horizontal gene transfer makes very difficult the therapeutic approach to these infections. Among horizontally acquired DNAs, integrons have been frequently reported in many Gramnegative bacteria that affect human health, but they have not been found frequently in Burkholderia isolates until now. In the present work we report on a Bcc isolate, recovered from the blood of an immunocompromised patient, that carries a 2.3 kb class I integron already described in a Salmonella enterica isolate eight years ago, coding for aacA4, aadA1 and catB2 in its cassette array.

  7. Extreme antimicrobial peptide and polymyxin B resistance in the genus Burkholderia

    Directory of Open Access Journals (Sweden)

    Slade A. Loutet

    2011-07-01

    Full Text Available Cationic antimicrobial peptides and polymyxins are a group of naturally occurring antibiotics that can also possess immunomodulatory activities. They are considered a new source of antibiotics for treating infections by bacteria that are resistant to conventional antibiotics. Members of the genus Burkholderia, which includes various human pathogens, are inherently resistant to antimicrobial peptides. The resistance is several orders of magnitude higher than that of other Gram-negative bacteria such as Escherichia coli, Salmonella enterica, or Pseudomonas aeruginosa. This review summarizes our current understanding of antimicrobial peptide and polymyxin B resistance in the genus Burkholderia. These bacteria possess major and minor resistance mechanisms that will be described in detail. Recent studies have revealed that many other emerging Gram-negative opportunistic pathogens may also be inherently resistant to antimicrobial peptides and polymyxins and we propose that Burkholderia species are a model system to investigate the molecular basis of the resistance in extremely resistant bacteria. Understanding resistance in these types of bacteria will be important if antimicrobial peptides come to be used regularly for the treatment of infections by susceptible bacteria because this may lead to increased resistance in the species that are currently susceptible and may also open up new niches for opportunistic pathogens with high inherent resistance.

  8. Development of Burkholderia mallei and pseudomallei vaccines.

    Science.gov (United States)

    Silva, Ediane B; Dow, Steven W

    2013-01-01

    Burkholderia mallei and Burkholderia pseudomallei are Gram-negative bacteria that cause glanders and melioidosis, respectively. Inhalational infection with either organism can result in severe and rapidly fatal pneumonia. Inoculation by the oral and cutaneous routes can also produce infection. Chronic infection may develop after recovery from acute infection with both agents, and control of infection with antibiotics requires prolonged treatment. Symptoms for both meliodosis and glanders are non-specific, making diagnosis difficult. B. pseudomallei can be located in the environment, but in the host, B. mallei and B. psedomallei are intracellular organisms, and infection results in similar immune responses to both agents. Effective early innate immune responses are critical to controlling the early phase of the infection. Innate immune signaling molecules such as TLR, NOD, MyD88, and pro-inflammatory cytokines such as IFN-γ and TNF-α play key roles in regulating control of infection. Neutrophils and monocytes are critical cells in the early infection for both microorganisms. Both monocytes and macrophages are necessary for limiting dissemination of B. pseudomallei. In contrast, the role of adaptive immune responses in controlling Burkholderia infection is less well understood. However, T cell responses are critical for vaccine protection from Burkholderia infection. At present, effective vaccines for prevention of glanders or meliodosis have not been developed, although recently development of Burkholderia vaccines has received renewed attention. This review will summarize current and past approaches to develop B. mallei and B. pseudomalllei vaccines, with emphasis on immune mechanisms of protection and the challenges facing the field. At present, immunization with live attenuated bacteria provides the most effective and durable immunity, and it is important therefore to understand the immune correlates of protection induced by live attenuated vaccines. Subunit

  9. Energetic Causal Sets

    CERN Document Server

    Cortês, Marina

    2013-01-01

    We propose an approach to quantum theory based on the energetic causal sets, introduced in Cort\\^{e}s and Smolin (2013). Fundamental processes are causal sets whose events carry momentum and energy, which are transmitted along causal links and conserved at each event. Fundamentally there are amplitudes for such causal processes, but no space-time. An embedding of the causal processes in an emergent space-time arises only at the semiclassical level. Hence, fundamentally there are no commutation relations, no uncertainty principle and, indeed, no hbar. All that remains of quantum theory is the relationship between the absolute value squared of complex amplitudes and probabilities. Consequently, we find that neither locality, nor non locality, are primary concepts, only causality exists at the fundamental level.

  10. Draft Genomes for Eight Burkholderia mallei Isolates from Turkey

    Science.gov (United States)

    Daligault, H. E.; Davenport, K. W.; Minogue, T. D.; Bishop-Lilly, K. A.; Broomall, S. M.; Bruce, D. C.; Coyne, S. R.; Frey, K. G.; Gibbons, H. S.; Jaissle, J.; Koroleva, G. I.; Ladner, J. T.; Lo, C.-C.; Munk, C.; Wolcott, M. J.; Palacios, G. F.; Redden, C. L.; Rosenzweig, C. N.; Scholz, M. B.; Chain, P. S.

    2016-01-01

    Burkholderia mallei, the etiologic agent of glanders, is a Gram-negative, nonmotile, facultative intracellular pathogen. Although glanders has been eradicated from many parts of the world, the threat of B. mallei being used as a weapon is very real. Here we present draft genome assemblies of 8 Burkholderia mallei strains that were isolated in Turkey. PMID:26744368

  11. Causal Decision Trees

    OpenAIRE

    2015-01-01

    Uncovering causal relationships in data is a major objective of data analytics. Causal relationships are normally discovered with designed experiments, e.g. randomised controlled trials, which, however are expensive or infeasible to be conducted in many cases. Causal relationships can also be found using some well designed observational studies, but they require domain experts' knowledge and the process is normally time consuming. Hence there is a need for scalable and automated methods for c...

  12. How to be causal

    CERN Document Server

    Kinsler, Paul

    2011-01-01

    I explain a simple definition of causality in widespread use, and indicate how it links to the Kramers Kronig relations. The specification of causality in terms of temporal differential eqations then shows us the way to write down dynamical models so that their causal nature in the sense used here should be obvious to all. In particular, I apply this reasoning to Maxwell's equations, which is an instructive example since their casual properties are sometimes debated.

  13. Botrytis cinerea: Causal agent of small fruit grey mould

    OpenAIRE

    Tanović, Brankica

    2012-01-01

    Small fruits growing in Serbia is an important and profitable business. However, disease causal agents, pests and weeds often threaten production profitability. A common problem in production of most important small fruit species is a polyfagous, phytopathogenic fungal species Botrytis cinerea, the causal agent of grey mould disease of fruits. Present knowledge on the causal agent, its morphological, ecological and epidemiological characteristics are systematized in the paper. Infection proce...

  14. Editorial: Causal cognition

    NARCIS (Netherlands)

    Blaisdell, A.P.; Beckers, T.

    2009-01-01

    The article discusses various reports published within the issue, including one on psychological approaches to causal discovery in humans, one on the representational and reasoning capacities that underlie causal cognition in rats and one on the generality of knowledge of Great Ape.

  15. Causality in Classical Electrodynamics

    Science.gov (United States)

    Savage, Craig

    2012-01-01

    Causality in electrodynamics is a subject of some confusion, especially regarding the application of Faraday's law and the Ampere-Maxwell law. This has led to the suggestion that we should not teach students that electric and magnetic fields can cause each other, but rather focus on charges and currents as the causal agents. In this paper I argue…

  16. Causality and Lifshitz Holography

    Energy Technology Data Exchange (ETDEWEB)

    Koroteev, Peter [Department of Physics and Astronomy, University of Minnesota, 116 Church Street S.E., Minneapolis, MN 55455 (United States)

    2011-07-15

    We study signal propagation in theories with Lifshitz scaling using the gravity dual and show that backgrounds with z<1 are incompatible with causality of the strongly coupled theory. We argue that causality violations in z<1 theories show up in boundary correlation functions as superluminal modes.

  17. Burkholderia thailandensis harbors two identical rhl gene clusters responsible for the biosynthesis of rhamnolipids

    Directory of Open Access Journals (Sweden)

    Woods Donald E

    2009-12-01

    Full Text Available Abstract Background Rhamnolipids are surface active molecules composed of rhamnose and β-hydroxydecanoic acid. These biosurfactants are produced mainly by Pseudomonas aeruginosa and have been thoroughly investigated since their early discovery. Recently, they have attracted renewed attention because of their involvement in various multicellular behaviors. Despite this high interest, only very few studies have focused on the production of rhamnolipids by Burkholderia species. Results Orthologs of rhlA, rhlB and rhlC, which are responsible for the biosynthesis of rhamnolipids in P. aeruginosa, have been found in the non-infectious Burkholderia thailandensis, as well as in the genetically similar important pathogen B. pseudomallei. In contrast to P. aeruginosa, both Burkholderia species contain these three genes necessary for rhamnolipid production within a single gene cluster. Furthermore, two identical, paralogous copies of this gene cluster are found on the second chromosome of these bacteria. Both Burkholderia spp. produce rhamnolipids containing 3-hydroxy fatty acid moieties with longer side chains than those described for P. aeruginosa. Additionally, the rhamnolipids produced by B. thailandensis contain a much larger proportion of dirhamnolipids versus monorhamnolipids when compared to P. aeruginosa. The rhamnolipids produced by B. thailandensis reduce the surface tension of water to 42 mN/m while displaying a critical micelle concentration value of 225 mg/L. Separate mutations in both rhlA alleles, which are responsible for the synthesis of the rhamnolipid precursor 3-(3-hydroxyalkanoyloxyalkanoic acid, prove that both copies of the rhl gene cluster are functional, but one contributes more to the total production than the other. Finally, a double ΔrhlA mutant that is completely devoid of rhamnolipid production is incapable of swarming motility, showing that both gene clusters contribute to this phenotype. Conclusions Collectively, these

  18. Causality in Europeanization Research

    DEFF Research Database (Denmark)

    Lynggaard, Kennet

    2012-01-01

    Discourse analysis as a methodology is perhaps not readily associated with substantive causality claims. At the same time the study of discourses is very much the study of conceptions of causal relations among a set, or sets, of agents. Within Europeanization research we have seen endeavours...... to develop discursive institutional analytical frameworks and something that comes close to the formulation of hypothesis on the effects of European Union (EU) policies and institutions on domestic change. Even if these efforts so far do not necessarily amount to substantive theories or claims of causality......, it suggests that discourse analysis and the study of causality are by no means opposites. The study of Europeanization discourses may even be seen as an essential step in the move towards claims of causality in Europeanization research. This chapter deals with the question of how we may move from the study...

  19. Causality in demand

    DEFF Research Database (Denmark)

    Nielsen, Max; Jensen, Frank; Setälä, Jari;

    2011-01-01

    This article focuses on causality in demand. A methodology where causality is imposed and tested within an empirical co-integrated demand model, not prespecified, is suggested. The methodology allows different causality of different products within the same demand system. The methodology is applied...... to fish demand. On the German market for farmed trout and substitutes, it is found that supply sources, i.e. aquaculture and fishery, are not the only determinant of causality. Storing, tightness of management and aggregation level of integrated markets might also be important. The methodological...... implication is that more explicit focus on causality in demand analyses provides improved information. The results suggest that frozen trout forms part of a large European whitefish market, where prices of fresh trout are formed on a relatively separate market. Redfish is a substitute on both markets...

  20. Agency, time and causality

    Directory of Open Access Journals (Sweden)

    Thomas eWidlok

    2014-11-01

    Full Text Available Cognitive Scientists interested in causal cognition increasingly search for evidence from non-WEIRD people but find only very few cross-cultural studies that specifically target causal cognition. This article suggests how information about causality can be retrieved from ethnographic monographs, specifically from ethnographies that discuss agency and concepts of time. Many apparent cultural differences with regard to causal cognition dissolve when cultural extensions of agency and personhood to non-humans are taken into account. At the same time considerable variability remains when we include notions of time, linearity and sequence. The article focuses on ethnographic case studies from Africa but provides a more general perspective on the role of ethnography in research on the diversity and universality of causal cognition.

  1. Regression to Causality

    DEFF Research Database (Denmark)

    Bordacconi, Mats Joe; Larsen, Martin Vinæs

    2014-01-01

    Humans are fundamentally primed for making causal attributions based on correlations. This implies that researchers must be careful to present their results in a manner that inhibits unwarranted causal attribution. In this paper, we present the results of an experiment that suggests regression...... models – one of the primary vehicles for analyzing statistical results in political science – encourage causal interpretation. Specifically, we demonstrate that presenting observational results in a regression model, rather than as a simple comparison of means, makes causal interpretation of the results...... of equivalent results presented as either regression models or as a test of two sample means. Our experiment shows that the subjects who were presented with results as estimates from a regression model were more inclined to interpret these results causally. Our experiment implies that scholars using regression...

  2. Causally symmetric spacetimes

    Energy Technology Data Exchange (ETDEWEB)

    Tipler, F.J.

    1977-08-01

    Causally symmetric spacetimes are spacetimes with J/sup +/(S) isometric to J/sup -/(S) for some set S. We discuss certain properties of these spacetimes, showing for example that, if S is a maximal Cauchy surface with matter everywhere on S, then the spacetime has singularities in both J/sup +/(S) and J/sup -/(S). We also consider totally vicious spacetimes, a class of causally symmetric spacetimes for which I/sup +/(p) =I/sup -/(p) = M for any point p in M. Two different notions of stability in general relativity are discussed, using various types of causally symmetric spacetimes as starting points for perturbations.

  3. Bacteria of the Burkholderia cepacia complex are cyanogenic under biofilm and colonial growth conditions

    Directory of Open Access Journals (Sweden)

    Hoshino Saiko

    2008-06-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (Bcc is a collection of nine genotypically distinct but phenotypically similar species. They show wide ecological diversity and include species that are used for promoting plant growth and bio-control as well species that are opportunistic pathogens of vulnerable patients. Over recent years the Bcc have emerged as problematic pathogens of the CF lung. Pseudomonas aeruginosa is another important CF pathogen. It is able to synthesise hydrogen cyanide (HCN, a potent inhibitor of cellular respiration. We have recently shown that HCN production by P. aeruginosa may have a role in CF pathogenesis. This paper describes an investigation of the ability of bacteria of the Bcc to make HCN. Results The genome of Burkholderia cenocepacia has 3 putative HCN synthase encoding (hcnABC gene clusters. B. cenocepacia and all 9 species of the Bcc complex tested were able to make cyanide at comparable levels to P. aeruginosa, but only when grown surface attached as colonies or during biofilm growth on glass beads. In contrast to P. aeruginosa and other cyanogenic bacteria, cyanide was not detected during planktonic growth of Bcc strains. Conclusion All species in the Bcc are cyanogenic when grown as surface attached colonies or as biofilms.

  4. Causal Newton Gravity Law

    CERN Document Server

    Zinoviev, Yury M

    2012-01-01

    The equations of the relativistic causal Newton gravity law for the planets of the solar system are studied in the approximation when the Sun rests at the coordinates origin and the planets do not iteract between each other.

  5. Causal spin foams

    CERN Document Server

    Immirzi, Giorgio

    2016-01-01

    I discuss how to impose causality on spin-foam models, separating forward and backward propagation, turning a given triangulation to a 'causal set', and giving asymptotically the exponential of the Regge action, not a cosine. I show the equivalence of the prescriptions which have been proposed to achieve this. Essential to the argument is the closure condition for the 4-simplices, all made of space-like tetrahedra.

  6. Quantum Causal Graph Dynamics

    CERN Document Server

    Arrighi, Pablo

    2016-01-01

    Consider a graph having quantum systems lying at each node. Suppose that the whole thing evolves in discrete time steps, according to a global, unitary causal operator. By causal we mean that information can only propagate at a bounded speed, with respect to the distance given by the graph. Suppose, moreover, that the graph itself is subject to the evolution, and may be driven to be in a quantum superposition of graphs---in accordance to the superposition principle. We show that these unitary causal operators must decompose as a finite-depth circuit of local unitary gates. This unifies a result on Quantum Cellular Automata with another on Reversible Causal Graph Dynamics. Along the way we formalize a notion of causality which is valid in the context of quantum superpositions of time-varying graphs, and has a number of good properties. Keywords: Quantum Lattice Gas Automata, Block-representation, Curtis-Hedlund-Lyndon, No-signalling, Localizability, Quantum Gravity, Quantum Graphity, Causal Dynamical Triangula...

  7. Use of a safe, reproducible, and rapid aerosol delivery method to study infection by Burkholderia pseudomallei and Burkholderia mallei in mice.

    Directory of Open Access Journals (Sweden)

    Eric R Lafontaine

    Full Text Available Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most common manifestation is severe pneumonia leading to fatal bacteremia. Glanders and melioidosis are difficult to diagnose and require prolonged antibiotic therapy with low success rates. There are no vaccines available to protect against either Burkholderia species, and there is concern regarding their use as biological warfare agents given that B. mallei has previously been utilized in this manner. Hence, experiments were performed to establish a mouse model of aerosol infection to study the organisms and develop countermeasures. Using a hand-held aerosolizer, BALB/c mice were inoculated intratracheally with strains B. pseudomallei 1026b and B. mallei ATCC23344 and growth of the agents in the lungs, as well as dissemination to the spleen, were examined. Mice infected with 10(2, 10(3 and 10(4 organisms were unable to control growth of B. mallei in the lungs and bacteria rapidly disseminated to the spleen. Though similar results were observed in mice inoculated with 10(3 and 10(4 B. pseudomallei cells, animals infected with 10(2 organisms controlled bacterial replication in the lungs, dissemination to the spleen, and the extent of bacteremia. Analysis of sera from mice surviving acute infection revealed that animals produced antibodies against antigens known to be targets of the immune response in humans. Taken together, these data show that small volume aerosol inoculation of mice results in acute disease, dose-dependent chronic infection, and immune responses

  8. Use of a safe, reproducible, and rapid aerosol delivery method to study infection by Burkholderia pseudomallei and Burkholderia mallei in mice.

    Science.gov (United States)

    Lafontaine, Eric R; Zimmerman, Shawn M; Shaffer, Teresa L; Michel, Frank; Gao, Xiudan; Hogan, Robert J

    2013-01-01

    Burkholderia pseudomallei, the etiologic agent of melioidosis, is a saprophytic bacterium readily isolated from wet soils of countries bordering the equator. Burkholderia mallei is a host-adapted clone of B. pseudomallei that does not persist outside of its equine reservoir and causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by these organisms typically occurs via percutaneous inoculation or inhalation of aerosols, and the most common manifestation is severe pneumonia leading to fatal bacteremia. Glanders and melioidosis are difficult to diagnose and require prolonged antibiotic therapy with low success rates. There are no vaccines available to protect against either Burkholderia species, and there is concern regarding their use as biological warfare agents given that B. mallei has previously been utilized in this manner. Hence, experiments were performed to establish a mouse model of aerosol infection to study the organisms and develop countermeasures. Using a hand-held aerosolizer, BALB/c mice were inoculated intratracheally with strains B. pseudomallei 1026b and B. mallei ATCC23344 and growth of the agents in the lungs, as well as dissemination to the spleen, were examined. Mice infected with 10(2), 10(3) and 10(4) organisms were unable to control growth of B. mallei in the lungs and bacteria rapidly disseminated to the spleen. Though similar results were observed in mice inoculated with 10(3) and 10(4) B. pseudomallei cells, animals infected with 10(2) organisms controlled bacterial replication in the lungs, dissemination to the spleen, and the extent of bacteremia. Analysis of sera from mice surviving acute infection revealed that animals produced antibodies against antigens known to be targets of the immune response in humans. Taken together, these data show that small volume aerosol inoculation of mice results in acute disease, dose-dependent chronic infection, and immune responses that correlate

  9. Polymorphisms within the prnD and pltC genes from pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp

    NARCIS (Netherlands)

    Souza, J.T.; Raaijmakers, J.M.

    2003-01-01

    Pyrrolnitrin (PRN) and pyoluteorin (PLT) are broad-spectrum antibiotics produced by several strains of Pseudomonas and Burkholderia species. Both antibiotics play an important role in the suppression of multiple plant pathogenic fungi. Primers were developed from conserved sequences and amplified pr

  10. Cyanide toxicity to Burkholderia cenocepacia is modulated by polymicrobial communities and environmental factors

    Directory of Open Access Journals (Sweden)

    Steve P. Bernier

    2016-05-01

    Full Text Available Microbes within polymicrobial communities can establish positive and negative interactions that have the potential to influence the overall behaviour of the community. Pseudomonas aeruginosa and species of the Burkholderia cepacia complex (Bcc can co-exist in the lower airways, however several studies have shown that P. aeruginosa can effectively kill the Bcc in vitro, for which hydrogen cyanide was recently proposed to play a critical role. Here we show that modification of the environment (i.e. culture medium, long-term genetic adaptation of P. aeruginosa to the cystic fibrosis (CF lung, or the addition of another bacterial species to the community can alter the sensitivity of Burkholderia cenocepacia to P. aeruginosa toxins. We specifically demonstrate that undefined rich media leads to higher susceptibility of B. cenocepacia to P. aeruginosa toxins like cyanide as compared to a synthetic medium (SCFM, that mimics the CF lung nutritional content. Overall, our study shows that the polymicrobial environment can have profound effects on negative interactions mediated by P. aeruginosa against B. cenocepacia. In fact, evolved P. aeruginosa or the presence of other species such as Staphylococcus aureus can directly abolish the direct competition mediated by cyanide and consequently maintaining a higher level of species diversity within the community.

  11. Endophytic colonization of rice (Oryza sativa L.) by the diazotrophic bacterium Burkholderia kururiensis and its ability to enhance plant growth

    OpenAIRE

    Mattos, Katherine A; Vania L.M. Pádua; Alexandre Romeiro; Hallack,Leticia F.; Bianca C. Neves; Tecia M.U. Ulisses; Claudia F. Barros; Adriane R Todeschini; Previato, José O.; Lucia Mendonça-Previato

    2008-01-01

    Burkholderia kururiensis is a diazotrophic bacterium originally isolated from a polluted aquifer environment and presents a high level of similarity with the rice endophyte "B. brasilensis" species. This work assessed the ability of B. kururiensis to endophytically colonize rice plantlets by monitoring different tissues of root-inoculated plants for the presence of bacterial growth in different media, electron microscopy and by 16S rDNA analysis. Observations of roots, stems and leaves of ino...

  12. Strain Identification of Burkholderia cepacia Palleroni and Holmes and Pseudomonas fluorescens Migula Associated to Maize Crop by Polyphasic Taxonomy

    OpenAIRE

    Annia Hernández Rodríguez; María Esther González Vega; Alberto Caballero Núñez; Ariel Medina Concepción; Madelaine Quiñónez Pantoja; Mayra Heydrich Pérez; Ana Niurka Hernández Lauzardo; Monica Höfte

    2004-01-01

    A polyphasic taxonomic study, which included phenotypic characterization, the indirect immunofluorescence (IIF), and the polymerase chain reaction (PCR) was conducted for the identification of Burkholderia cepacia and Pseudomonas fluorescens strains previously isolated from maize rhizosphere. Conventional methods were used (API 20 NE, BioMeuriux), specific hyper-immune antiserum against the species under study, and specific primers were designed out of subunits 16S of the ribosomal RNA of B....

  13. Exploitation of host cells by Burkholderia pseudomallei.

    Science.gov (United States)

    Stevens, Mark P; Galyov, Edouard E

    2004-04-01

    Intracellular bacterial pathogens have evolved mechanisms to enter and exit eukaryotic cells using the power of actin polymerisation and to subvert the activity of cellular enzymes and signal transduction pathways. The proteins deployed by bacteria to subvert cellular processes often mimic eukaryotic proteins in their structure or function. Studies on the exploitation of host cells by the facultative intracellular pathogen Burkholderia pseudomallei are providing novel insights into the pathogenesis of melioidosis, a serious invasive disease of animals and humans that is endemic in tropical and subtropical areas. B. pseudomallei can invade epithelial cells, survive and proliferate inside phagocytes, escape from endocytic vesicles, form actin-based membrane protrusions and induce host cell fusion. Here we review current understanding of the molecular mechanisms underlying these processes.

  14. Study design in causal models

    OpenAIRE

    2012-01-01

    The causal assumptions, the study design and the data are the elements required for scientific inference in empirical research. The research is adequately communicated only if all of these elements and their relations are described precisely. Causal models with design describe the study design and the missing data mechanism together with the causal structure and allow the direct application of causal calculus in the estimation of the causal effects. The flow of the study is visualized by orde...

  15. Assimetria causal: um estudo

    Directory of Open Access Journals (Sweden)

    Túlio Aguiar

    2003-12-01

    Full Text Available Neste artigo, examinamos o aspecto assimétrico da relação causal, confrontando-o com o ponto de vista humiano e neo-humiano. Seguindo Hausman e Ehring, favorecemos uma abordagem situacional para a assimetria causal. Nós exploramos a análise do famoso exemplo do mastro (Flagpole, esclarecendo as conexões entre causação e explicação. Nosso diagnóstico geral é que a tradição neo-humiana supõe, equivocadamente, que as relações nômicas, com exceção de pequenos detalhes, exaurem as relações causais.This paper examines the asymmetrical aspect of causal relation, confronting it to Humean and Neo-Humean's view. Following Hausman and Ehring, we favor a situational approach to causal asymmetry. We explore the Hausman's analysis of flagpole's example, clearing the connexions between causation and explanation. Our general diagnosis is that the Neo-humean tradition wrongly supposes that nomic relations, with the exception of minor details, exhaust the causal relations.

  16. Biased causal inseparable game

    CERN Document Server

    Bhattacharya, Some Sankar

    2015-01-01

    Here we study the \\emph{causal inseparable} game introduced in [\\href{http://www.nature.com/ncomms/journal/v3/n10/full/ncomms2076.html}{Nat. Commun. {\\bf3}, 1092 (2012)}], but it's biased version. Two separated parties, Alice and Bob, generate biased bits (say input bit) in their respective local laboratories. Bob generates another biased bit (say decision bit) which determines their goal: whether Alice has to guess Bob's bit or vice-verse. Under the assumption that events are ordered with respect to some global causal relation, we show that the success probability of this biased causal game is upper bounded, giving rise to \\emph{biased causal inequality} (BCI). In the \\emph{process matrix} formalism, which is locally in agreement with quantum physics but assume no global causal order, we show that there exist \\emph{inseparable} process matrices that violate the BCI for arbitrary bias in the decision bit. In such scenario we also derive the maximal violation of the BCI under local operations involving tracele...

  17. Causality discovery technology

    Science.gov (United States)

    Chen, M.; Ertl, T.; Jirotka, M.; Trefethen, A.; Schmidt, A.; Coecke, B.; Bañares-Alcántara, R.

    2012-11-01

    Causality is the fabric of our dynamic world. We all make frequent attempts to reason causation relationships of everyday events (e.g., what was the cause of my headache, or what has upset Alice?). We attempt to manage causality all the time through planning and scheduling. The greatest scientific discoveries are usually about causality (e.g., Newton found the cause for an apple to fall, and Darwin discovered natural selection). Meanwhile, we continue to seek a comprehensive understanding about the causes of numerous complex phenomena, such as social divisions, economic crisis, global warming, home-grown terrorism, etc. Humans analyse and reason causality based on observation, experimentation and acquired a priori knowledge. Today's technologies enable us to make observations and carry out experiments in an unprecedented scale that has created data mountains everywhere. Whereas there are exciting opportunities to discover new causation relationships, there are also unparalleled challenges to benefit from such data mountains. In this article, we present a case for developing a new piece of ICT, called Causality Discovery Technology. We reason about the necessity, feasibility and potential impact of such a technology.

  18. Causal inference in econometrics

    CERN Document Server

    Kreinovich, Vladik; Sriboonchitta, Songsak

    2016-01-01

    This book is devoted to the analysis of causal inference which is one of the most difficult tasks in data analysis: when two phenomena are observed to be related, it is often difficult to decide whether one of them causally influences the other one, or whether these two phenomena have a common cause. This analysis is the main focus of this volume. To get a good understanding of the causal inference, it is important to have models of economic phenomena which are as accurate as possible. Because of this need, this volume also contains papers that use non-traditional economic models, such as fuzzy models and models obtained by using neural networks and data mining techniques. It also contains papers that apply different econometric models to analyze real-life economic dependencies.

  19. Causal graph dynamics

    CERN Document Server

    Arrighi, Pablo

    2012-01-01

    We generalize the theory of Cellular Automata to arbitrary, time-varying graphs. In other words we formalize, and prove theorems about, the intuitive idea of a labelled graph which evolves in time - but under the natural constraint that information can only ever be transmitted at a bounded speed, with respect to the distance given by the graph. The notion of translation-invariance is also generalized. The definition we provide for these `causal graph dynamics' is simple and axiomatic. The theorems we provide also show that it is robust. For instance, causal graph dynamics are stable under composition and under restriction to radius one. In the finite case some fundamental facts of Cellular Automata theory carry through: causal graph dynamics admit a characterization as continuous functions and they are stable under inversion. The provided examples suggest a wide range of applications of this mathematical object, from complex systems science to theoretical physics. Keywords: Dynamical networks, Boolean network...

  20. Plant host and sugar alcohol induced exopolysaccharide biosynthesis in the Burkholderia cepacia complex.

    Science.gov (United States)

    Bartholdson, S Josefin; Brown, Alan R; Mewburn, Ben R; Clarke, David J; Fry, Stephen C; Campopiano, Dominic J; Govan, John R W

    2008-08-01

    The species that presently constitute the Burkholderia cepacia complex (Bcc) have multiple roles; they include soil and water saprophytes, bioremediators, and plant, animal and human pathogens. Since the first description of pathogenicity in the Bcc was based on sour skin rot of onion bulbs, this study returned to this plant host to investigate the onion-associated phenotype of the Bcc. Many Bcc isolates, which were previously considered to be non-mucoid, produced copious amounts of exopolysaccharide (EPS) when onion tissue was provided as the sole nutrient. EPS production was not species-specific, was observed in isolates from both clinical and environmental sources, and did not correlate with the ability to cause maceration of onion tissue. Chemical analysis suggested that the onion components responsible for EPS induction were primarily the carbohydrates sucrose, fructose and fructans. Additional sugars were investigated, and all alcohol sugars tested were able to induce EPS production, in particular mannitol and glucitol. To investigate the molecular basis for EPS biosynthesis, we focused on the highly conserved bce gene cluster thought to be involved in cepacian biosynthesis. We demonstrated induction of the bce gene cluster by mannitol, and found a clear correlation between the inability of representatives of the Burkholderia cenocepacia ET12 lineage to produce EPS and the presence of an 11 bp deletion within the bceB gene, which encodes a glycosyltransferase. Insertional inactivation of bceB in Burkholderia ambifaria AMMD results in loss of EPS production on sugar alcohol media. These novel and surprising insights into EPS biosynthesis highlight the metabolic potential of the Bcc and show that a potential virulence factor may not be detected by routine laboratory culture. Our results also highlight a potential hazard in the use of inhaled mannitol as an osmolyte to improve mucociliary clearance in individuals with cystic fibrosis.

  1. Complementarity, causality, and explanation

    CERN Document Server

    Losee, John

    2013-01-01

    Prior to the work of Niels Bohr, discussions on the relationship of cause and effect presupposed that successful causal attribution implies explanation. The success of quantum theory challenged this presupposition. In this succinct review of the history of these discussions, John Losee presents the philosophical background of debates over the cause-effect relation. He reviews the positions of Aristotle, René Descartes, Isaac Newton, David Hume, Immanuel Kant, and John Stuart Mill. He shows how nineteenth-century theories in physics and chemistry were informed by a dominant theory of causality

  2. Causal premise semantics.

    Science.gov (United States)

    Kaufmann, Stefan

    2013-08-01

    The rise of causality and the attendant graph-theoretic modeling tools in the study of counterfactual reasoning has had resounding effects in many areas of cognitive science, but it has thus far not permeated the mainstream in linguistic theory to a comparable degree. In this study I show that a version of the predominant framework for the formal semantic analysis of conditionals, Kratzer-style premise semantics, allows for a straightforward implementation of the crucial ideas and insights of Pearl-style causal networks. I spell out the details of such an implementation, focusing especially on the notions of intervention on a network and backtracking interpretations of counterfactuals.

  3. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei.

    Science.gov (United States)

    Godoy, Daniel; Randle, Gaynor; Simpson, Andrew J; Aanensen, David M; Pitt, Tyrone L; Kinoshita, Reimi; Spratt, Brian G

    2003-05-01

    A collection of 147 isolates of Burkholderia pseudomallei, B. mallei, and B. thailandensis was characterized by multilocus sequence typing (MLST). The 128 isolates of B. pseudomallei, the causative agent of melioidosis, were obtained from diverse geographic locations, from humans and animals with disease, and from the environment and were resolved into 71 sequence types. The utility of the MLST scheme for epidemiological investigations was established by analyzing isolates from captive marine mammals and birds and from humans in Hong Kong with melioidosis. MLST gave a level of resolution similar to that given by pulsed-field gel electrophoresis and identified the same three clones causing disease in animals, each of which was also associated with disease in humans. The average divergence between the alleles of B. thailandensis and B. pseudomallei was 3.2%, and there was no sharing of alleles between these species. Trees constructed from differences in the allelic profiles of the isolates and from the concatenated sequences of the seven loci showed that the B. pseudomallei isolates formed a cluster of closely related lineages that were fully resolved from the cluster of B. thailandensis isolates, confirming their separate species status. However, isolates of B. mallei, the causative agent of glanders, recovered from three continents over a 30-year period had identical allelic profiles, and the B. mallei isolates clustered within the B. pseudomallei group of isolates. Alleles at six of the seven loci in B. mallei were also present within B. pseudomallei isolates, and B. mallei is a clone of B. pseudomallei that, on population genetics grounds, should not be given separate species status.

  4. Burkholderia cepacia XXVI siderophore with biocontrol capacity against Colletotrichum gloeosporioides.

    Science.gov (United States)

    de Los Santos-Villalobos, Sergio; Barrera-Galicia, Guadalupe Coyolxauhqui; Miranda-Salcedo, Mario Alberto; Peña-Cabriales, Juan José

    2012-08-01

    Colletotrichum gloeosporioides is the causal agent of anthracnose in mango. Burkholderia cepacia XXVI, isolated from mango rhizosphere and identified by 16S rDNA sequencing as a member of B. cepacia complex, was more effective than 6 other mango rhizosphere bacteria in inhibiting the model mango pathogen, C. gloeosporioides ATCC MYA 456. Biocontrol of this pathogen was demonstrated on Petri-dishes containing PDA by > 90 % reduction of surface colonization. The nature of the biocontrol metabolite(s) was characterized via a variety of tests. The inhibition was almost exclusively due to production of agar-diffusible, not volatile, metabolite(s). The diffusible metabolite(s) underwent thermal degradation at 70 and 121 °C (1 atm). Tests for indole acetic acid production and lytic enzyme activities (cellulase, glucanase and chitinase) by B. cepacia XXVI were negative, indicating that these metabolites were not involved in the biocontrol effect. Based on halo formation and growth inhibition of the pathogen on the diagnostic medium, CAS-agar, as well as colorimetric tests we surmised that strain XXVI produced a hydroxamate siderophore involved in the biocontrol effect observed. The minimal inhibitory concentration test showed that 0.64 μg ml(-1) of siderophore (Deferoxamine mesylate salt-equivalent) was sufficient to achieve 91.1 % inhibition of the pathogen growth on Petri-dishes containing PDA. The biocontrol capacity against C. gloeosporioides ATCC MYA 456 correlated directly with the siderophore production by B. cepacia XXVI: the highest concentration of siderophore production in PDB on day 7, 1.7 μg ml(-1) (Deferoxamine mesylate salt-equivalent), promoted a pathogen growth inhibition of 94.9 %. The growth of 5 additional strains of C. gloeosporioides (isolated from mango "Ataulfo" orchards located in the municipality of Chahuites, State of Oaxaca in Mexico) was also inhibited when confronted with B. cepacia XXVI. Results indicate that B. cepacia XXVI or its

  5. Understanding Causal Coherence Relations

    NARCIS (Netherlands)

    Mulder, G.

    2008-01-01

    The research reported in this dissertation focuses on the cognitive processes and representations involved in understanding causal coherence relations in text. Coherence relations are the meaning relations between the information units in the text, such as Cause-Consequence. These relations can be m

  6. Influence of neutrophil defects on Burkholderia cepacia complex pathogenesis

    Directory of Open Access Journals (Sweden)

    Laura A. Porter

    2011-11-01

    Full Text Available The Burkholderia cepacia complex (Bcc is a group of Gram-negative bacteria that are ubiquitous in the environment and have emerged as opportunistic pathogens in immunocompromised patients. The primary patient populations infected with Bcc include individuals with cystic fibrosis (CF, as well as those with chronic granulomatous disease (CGD. While Bcc infection in CF is better characterized than in CGD, these two genetic diseases are not obviously similar and it is currently unknown if there is any commonality in host immune defects that is responsible for the susceptibility to Bcc. CF is caused by mutations in the CF transmembrane conductance regulator, resulting in manifestations in various organ systems, however the major cause of morbidity and mortality is currently due to bacterial respiratory infections. CGD, on the other hand, is a genetic disorder that is caused by defects in phagocyte NADPH oxidase. Because of the defect in CGD, phagocytes in these patients are unable to produce reactive oxygen species, which results in increased susceptibility to bacterial and fungal infections. Despite this significant defect in microbial clearance, the spectrum of pathogens frequently implicated in infections in CGD is relatively narrow and includes some bacterial species that are considered almost pathognomonic for this disorder. Very little is known about the cause of the specific susceptibility to Bcc over other potential pathogens more prevalent in the environment, and a better understanding of specific mechanisms required for bacterial virulence has become a high priority. This review will summarize both the current knowledge and future directions related to Bcc virulence in immunocompromised individuals with a focus on the roles of bacterial factors and neutrophil defects in pathogenesis.

  7. Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex

    Science.gov (United States)

    Weber, Carolyn F.; King, Gary M.

    2017-01-01

    Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2T = DSM 28029T = LMG 27952T); Paraburkholderia paradisi sp. nov. (type strain WAT = DSM 28027T = LMG 27949T); Paraburkholderia peleae sp. nov. (type strain PP52-1T = DSM 28028T = LMG 27950T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1T = DSM 28030T = LMG 28140T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38T = DSM 28031T = LMG 28138T

  8. Inhibition of Burkholderia multivorans Adhesion to Lung Epithelial Cells by Bivalent Lactosides

    Directory of Open Access Journals (Sweden)

    Trinidad Velasco-Torrijos

    2012-08-01

    Full Text Available Burkholderia cepacia complex (Bcc is an opportunistic pathogen in cystic fibrosis patients which is inherently resistant to antimicrobial agents. The mechanisms of attachment and pathogenesis of Bcc, a group of 17 species, are poorly understood. The most commonly identified Bcc species in newly colonised patients, Burkholderia multivorans, continues to be acquired from the environment. Development of therapies which can prevent or reduce the risk of colonization on exposure to Bcc in the environment would be a better alternative to antimicrobial agents. Previously, it has been shown that Bcc strains bound to many glycolipid receptors on lung epithelia. Using a real-time PCR method to quantify the levels of binding of B. multivorans to the lung epithelial cells, we have examined glycoconjugate derivatives for their potential to inhibit host cell attachment. Bivalent lactosides previously shown to inhibit galectin binding significantly reduced the attachment of B. multivorans to CF lung epithelial cells at micromolar concentrations. This was in contrast to monosaccharides and lactose, which were only effective in the millimolar range. Development of glycoconjugate therapies such as these, which inhibit attachment to lung epithelial cells, represent an alternative means of preventing infection with inherently antimicrobially resistant pathogens such as B. multivorans.

  9. Genomovars of Burkholderia cepacia Complex from Rice Rhizosphere and Clinic in China

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Burkholderia cepacia is regarded as a genetically distinct but phenotypically similar bacteria group referring to Burkholderia cepacia complex (Bcc), which is found not only in clinic but also in rice growing environment. It is very important in microbial safety of rice for us to understand the genomovar status of Bcc. Genomovar analysis was performed among 87 Bcc isolates by means of Hae Ⅲ-recA RFLP assays and species-specific PCR tests. Three genomovars were found from the rice rhizosphere including Ⅰ, ⅢB and Ⅴ, and genomovar Ⅴ was predominant. Genomovars Ⅰ, ⅢA and ⅢB existed in the clinical samples, and genomovar ⅢA was the most popular. It showed that genomovar composition was different between the Bcc strains from the rice rhizosphere and clinical environment. Simultaneously, the results revealed the genetic diversity of Bcc strains from the rice rhizosphere, and genomovar Ⅲ referred as virulent species in clinic also existed in the rice rhizosphere.

  10. Biofilms produced by Burkholderia cenocepacia: influence of media and solid supports on composition of matrix exopolysaccharides.

    Science.gov (United States)

    Pellizzoni, Elena; Ravalico, Fabio; Scaini, Denis; Delneri, Ambra; Rizzo, Roberto; Cescutti, Paola

    2016-02-01

    Bacteria usually grow forming biofilms, which are communities of cells embedded in a self-produced dynamic polymeric matrix, characterized by a complex three-dimensional structure. The matrix holds cells together and above a surface, and eventually releases them, resulting in colonization of other surfaces. Although exopolysaccharides (EPOLs) are important components of the matrix, determination of their structure is usually performed on samples produced in non-biofilm conditions, or indirectly through genetic studies. Among the Burkholderia cepacia complex species, Burkholderia cenocepacia is an important pathogen in cystic fibrosis (CF) patients and is generally more aggressive than other species. In the present investigation, B. cenocepacia strain BTS2, a CF isolate, was grown in biofilm mode on glass slides and cellulose membranes, using five growth media, one of which mimics the nutritional content of CF sputum. The structure of the matrix EPOLs was determined by 1H-NMR spectroscopy, while visualization of the biofilms on glass slides was obtained by means of confocal laser microscopy, phase-contrast microscopy and atomic force microscopy. The results confirmed that the type of EPOLs biosynthesized depends both on the medium used and on the type of support, and showed that mucoid conditions do not always lead to significant biofilm production, while bacteria in a non-mucoid state can still form biofilm containing EPOLs.

  11. Causal diagrams for physical models

    CERN Document Server

    Kinsler, Paul

    2015-01-01

    I present a scheme of drawing causal diagrams based on physically motivated mathematical models expressed in terms of temporal differential equations. They provide a means of better understanding the processes and causal relationships contained within such systems.

  12. Development and validation of Burkholderia pseudomallei-specific real-time PCR assays for clinical, environmental or forensic detection applications.

    Directory of Open Access Journals (Sweden)

    Erin P Price

    Full Text Available The bacterium Burkholderia pseudomallei causes melioidosis, a rare but serious illness that can be fatal if untreated or misdiagnosed. Species-specific PCR assays provide a technically simple method for differentiating B. pseudomallei from near-neighbor species. However, substantial genetic diversity and high levels of recombination within this species reduce the likelihood that molecular signatures will differentiate all B. pseudomallei from other Burkholderiaceae. Currently available molecular assays for B. pseudomallei detection lack rigorous validation across large in silico datasets and isolate collections to test for specificity, and none have been subjected to stringent quality control criteria (accuracy, precision, selectivity, limit of quantitation (LoQ, limit of detection (LoD, linearity, ruggedness and robustness to determine their suitability for environmental, clinical or forensic investigations. In this study, we developed two novel B. pseudomallei specific assays, 122018 and 266152, using a dual-probe approach to differentiate B. pseudomallei from B. thailandensis, B. oklahomensis and B. thailandensis-like species; other species failed to amplify. Species specificity was validated across a large DNA panel (>2,300 samples comprising Burkholderia spp. and non-Burkholderia bacterial and fungal species of clinical and environmental relevance. Comparison of assay specificity to two previously published B. pseudomallei-specific assays, BurkDiff and TTS1, demonstrated comparable performance of all assays, providing between 99.7 and 100% specificity against our isolate panel. Last, we subjected 122018 and 266152 to rigorous quality control analyses, thus providing quantitative limits of assay performance. Using B. pseudomallei as a model, our study provides a framework for comprehensive quantitative validation of molecular assays and provides additional, highly validated B. pseudomallei assays for the scientific research community.

  13. Information causality and noisy computations

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Li-Yi [Department of Physics, Chung Yuan Christian University, Chung-li 32023, Taiwan (China); Yu, I-Ching; Lin, Feng-Li [Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan (China)

    2011-10-15

    We reformulate the information causality in a more general framework by adopting the results of signal propagation and computation in a noisy circuit. In our framework, the information causality leads to a broad class of Tsirelson inequalities. This fact allows us to subject information causality to experimental scrutiny. A no-go theorem for reliable nonlocal computation is also derived. Information causality prevents any physical circuit from performing reliable computations.

  14. Burkholderia pseudomallei musculoskeletal infections (melioidosis in India

    Directory of Open Access Journals (Sweden)

    Pandey Vivek

    2010-01-01

    Full Text Available Melioidosis, an infection due to gram negative Burkholderia pseudomallei, is an important cause of sepsis in east Asia especially Thailand and northern Australia. It usually causes abscesses in lung, liver, spleen, skeletal muscle and parotids especially in patients with diabetes, chronic renal failure and thalassemia. Musculoskeletal melioidosis is not common in India even though sporadic cases have been reported mostly involving soft tissues. During a two-year-period, we had five patients with musculoskeletal melioidosis. All patients presented with multifocal osteomyelitis, recurrent osteomyelitis or septic arthritis. One patient died early because of septicemia and multi-organ failure. All patients were diagnosed on the basis of positive pus culture. All patients were treated by surgical debridement followed by a combination of antibiotics; (ceftazidime, amoxy-clavulanic acid, co-trimoxazole and doxycycline for six months except for one who died due to fulminant septicemia. All other patients recovered completely with no recurrences. With increasing awareness and better diagnostic facilities, probably musculoskeletal melioidosis will be increasingly diagnosed in future.

  15. Spectral Geometry and Causality

    CERN Document Server

    Kopf, T

    1996-01-01

    For a physical interpretation of a theory of quantum gravity, it is necessary to recover classical spacetime, at least approximately. However, quantum gravity may eventually provide classical spacetimes by giving spectral data similar to those appearing in noncommutative geometry, rather than by giving directly a spacetime manifold. It is shown that a globally hyperbolic Lorentzian manifold can be given by spectral data. A new phenomenon in the context of spectral geometry is observed: causal relationships. The employment of the causal relationships of spectral data is shown to lead to a highly efficient description of Lorentzian manifolds, indicating the possible usefulness of this approach. Connections to free quantum field theory are discussed for both motivation and physical interpretation. It is conjectured that the necessary spectral data can be generically obtained from an effective field theory having the fundamental structures of generalized quantum mechanics: a decoherence functional and a choice of...

  16. Quantum information causality

    OpenAIRE

    Pitalúa-García, Damián

    2012-01-01

    How much information can a transmitted physical system fundamentally communicate? We introduce the principle of quantum information causality, which states the maximum amount of quantum information that a quantum system can communicate as a function of its dimension, independently of any previously shared quantum physical resources. We present a new quantum information task, whose success probability is upper bounded by the new principle, and show that an optimal strategy to perform it combin...

  17. Causality between time series

    CERN Document Server

    Liang, X San

    2014-01-01

    Given two time series, can one tell, in a rigorous and quantitative way, the cause and effect between them? Based on a recently rigorized physical notion namely information flow, we arrive at a concise formula and give this challenging question, which is of wide concern in different disciplines, a positive answer. Here causality is measured by the time rate of change of information flowing from one series, say, X2, to another, X1. The measure is asymmetric between the two parties and, particularly, if the process underlying X1 does not depend on X2, then the resulting causality from X2 to X1 vanishes. The formula is tight in form, involving only the commonly used statistics, sample covariances. It has been validated with touchstone series purportedly generated with one-way causality. It has also been applied to the investigation of real world problems; an example presented here is the cause-effect relation between two climate modes, El Ni\\~no and Indian Ocean Dipole, which have been linked to the hazards in f...

  18. Recent Advances in Burkholderia mallei and B. pseudomallei Research

    Science.gov (United States)

    Hatcher, Christopher L.; Muruato, Laura A.

    2015-01-01

    Burkholderia mallei and Burkholderia pseudomallei are Gram-negative organisms, which are etiological agents of glanders and melioidosis, respectively. Although only B. pseudomallei is responsible for a significant number of human cases, both organisms are classified as Tier 1 Select Agents and their diseases lack effective diagnosis and treatment. Despite a recent resurgence in research pertaining to these organisms, there are still a number of knowledge gaps. This article summarizes the latest research progress in the fields of B. mallei and B. pseudomallei pathogenesis, vaccines, and diagnostics. PMID:25932379

  19. Revisiting Causality in Markov Chains

    CERN Document Server

    Shojaee, Abbas

    2016-01-01

    Identifying causal relationships is a key premise of scientific research. The growth of observational data in different disciplines along with the availability of machine learning methods offers the possibility of using an empirical approach to identifying potential causal relationships, to deepen our understandings of causal behavior and to build theories accordingly. Conventional methods of causality inference from observational data require a considerable length of time series data to capture cause-effect relationship. We find that potential causal relationships can be inferred from the composition of one step transition rates to and from an event. Also known as Markov chain, one step transition rates are a commonly available resource in different scientific disciplines. Here we introduce a simple, effective and computationally efficient method that we termed 'Causality Inference using Composition of Transitions CICT' to reveal causal structure with high accuracy. We characterize the differences in causes,...

  20. A new bacterial disease of carnation in Portugal caused by Burkholderia andropogonis

    Directory of Open Access Journals (Sweden)

    Madalena Eloy

    2008-12-01

    Full Text Available The occurrence of a leaf spot disease of carnation caused by Burkholderia andropogonis is recorded for the first time in Portugal. Symptoms consisted of ‘eyespot’ lesions on all aerial plant parts, often bordered by water-soaked halos on the leaves. As the disease progressed lesions became dark brown and affected areas dried out. Phenotypic studies and Polymerase Chain Reaction using specific primers Pf/Pr targeted to 16S rDNA of B. andropogonis were used to identify the pathogen. Pathogenicity tests on china pink plants, re-isolation of the pathogen from inoculated plants and further PCR testing confirmed the identification of the bacterium. Infected plants came from an open air nursery and the whole production was destroyed to avoid dissemination of the pathogen.A ocorrência da mancha bacteriana do craveiro causada por Burkholderia andropogonis é pela primeira vez assinalada em Portugal. Os sintomas observados consistiam em manchas em forma de olho-de-perdiz em todos os órgãos aéreos das plantas afectadas, frequentemente circundadas por halos hidrópicos nas folhas. À medida que a doença progredia, as lesões adquiriam uma coloração castanha escura, acabando os órgãos afectados por secar. A identificação do agente causal da doença baseou-se no estudo dos seus caracteres fenotípicos e na Reacção em Cadeia da Polimerase (PCR, utilizando os iniciadores específicos Pf/Pr dirigidos à região 16S rDNA de B. andropogonis. A identificação foi confirmada por ensaios de patogenicidade em cravinas, reisolamento do agente causal da doença a partir das plantas inoculadas e novos ensaios PCR. As plantas infectadas provinham de um viveiro ao ar livre e toda a produção foi destruída a fim de evitar a disseminação do patogéneo.

  1. Characterization of the papilionoid-Burkholderia interaction in the Fynbos biome: The diversity and distribution of beta-rhizobia nodulating Podalyria calyptrata (Fabaceae, Podalyrieae).

    Science.gov (United States)

    Lemaire, Benny; Van Cauwenberghe, Jannick; Verstraete, Brecht; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Sprent, Janet; James, Euan K; Muasya, A Muthama

    2016-02-01

    The South African Fynbos soils are renowned for nitrogen-fixing Burkholderia associated with diverse papilionoid legumes of the tribes Crotalarieae, Hypocalypteae, Indigofereae, Phaseoleae and Podalyrieae. However, despite numerous rhizobial studies in the region, the symbiotic diversity of Burkholderia has not been investigated in relation to a specific host legume and its geographical provenance. This study analyzed the diversity of nodulating strains of Burkholderia from the legume species Podalyria calyptrata. Diverse lineages were detected that proved to be closely related to Burkholderia taxa, originating from hosts in other legume tribes. By analyzing the genetic variation of chromosomal (recA) and nodulation (nodA) sequence data in relation to the sampling sites we assessed the geographical distribution patterns of the P. calyptrata symbionts. Although we found a degree of genetically differentiated rhizobial populations, a correlation between genetic (recA and nodA) and geographic distances among populations was not observed, suggesting high rates of dispersal and rhizobial colonization within Fynbos soils.

  2. Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes.

    Science.gov (United States)

    Voronina, Olga L; Kunda, Marina S; Ryzhova, Natalia N; Aksenova, Ekaterina I; Semenov, Andrey N; Romanova, Yulia M; Gintsburg, Alexandr L

    2016-01-01

    Biofilm formation by Burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. A "lacking biofilm production" (LBP) strain B. contaminans GIMC4587:Bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. It has an interrupted transcriptional response regulator (RR) gene. The focus of our investigation was a two-component signal transduction system determination, including this RR. B. contaminans clinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. A four-component operon (BiofilmReg) has a key role in biofilm formation. The relative location (i.e., by being separated by another gene) of RR and histidine kinase genes is unique in BiofilmReg. Orthologs were found in other members of the Burkholderiales order. Phylogenetic analysis of strains containing BiofilmReg operons demonstrated evidence for earlier inheritance of a three-component operon. During further evolution one lineage acquired a fourth gene, whereas others lost the third component of the operon. Mutations in sensor domains have created biodiversity which is advantageous for adaptation to various ecological niches. Different species Burkholderia and Achromobacter strains all demonstrated similar BiofilmReg operon structure. Therefore, there may be an opportunity to develop a common drug which is effective for treating all these causative agents.

  3. Research Status and Prospect ofBurkholderia glumae, the Pathogen Causing Bacterial Panicle Blight

    Institute of Scientific and Technical Information of China (English)

    CUI Zhou-qi; ZHU Bo; XIE Guan-lin; LI Bin; HUANG Shi-wen

    2016-01-01

    Bacterial panicle blight caused by Burkholderia glumae is one of the most severe seed-borne bacterial diseases of rice in the world. Currently, this disease has affected many countries of Asia, Africa, South and North America. It is a typical example of the shifting from minor plant disease to major disease due to the changes of environmental conditions. Some virulent factors of B. glumae have been identified, including toxoflavins and lipases, whose productions are dependent on the TofI/TofR quorum-sensing system, and type III effectors. In spite of its economic significance, neither effective control measure for this disease nor resistant rice variety is currently available. In recent years, genomics, transcriptomics and other molecular methods have provided useful information for better understanding the molecular mechanisms underlyingB. glumaevirulence and the rice defence mechanisms against pathogens. For the prevention of this pathogen, our laboratory has developed a rapid and sensitive multiplex PCR assay for detecting and distinguishingB. glumae from otherBurkholderia species. This improved understanding ofB. glumae will shed new light on bacterial panicle blight disease management.

  4. Burkholderia cepacia complex: Virulence characteristics, importance and relationship with cystic fibrosis

    Directory of Open Access Journals (Sweden)

    Melo Coutinho Henrique

    2007-07-01

    Full Text Available Background : Burkholderia cepacia has been described as a cause of opportunist infections in patients with immune deficiency because of the high transmission rates. Actually the B. cepacia is subdivided in nine different genomic species that show morphological similarity, called genomovars. High mortality rates have been associated with infections caused by genomovars in susceptible patients; antibiotics are not efficient because of the high resistance level and genomic mutability. Little is known about the epidemiological traits of this bacterium; therefore, their isolation remains a relevant technical problem.Aims : The objective of this review is to describe Burkholderia cepacia as a bacterial complex with high pathogenicity and variability of habitats. Materials and Methods : A systematic search was realized using the international bibliographic databanks SCIELO, HIGHWIRE, PUBMED, SCIRUS and LILACS to provide a useful and practical review for the health workers that do not know this microorganism. Conclusions : Today, B. cepacia complex is a very important problem for the acquired immunodeficiency syndrome and cystic fibrosis patients. The immunodeficiency caused by these diseases is a positive factor for this microorganism to infect and kill these patients. Therefore, this opportunistic pathogen should be pointed out as a risk to these patients, and hospitals all over the world must be prepared to detect and combat this bacterium.

  5. Survival of Burkholderia pseudomallei in Water

    Directory of Open Access Journals (Sweden)

    Woods Donald E

    2008-05-01

    Full Text Available Abstract Background The ability of Burkholderia pseudomallei to survive in water likely contributes to its environmental persistence in endemic regions. To determine the physiological adaptations which allow B. pseudomallei to survive in aqueous environments, we performed microarray analyses of B. pseudomallei cultures transferred from Luria broth (LB to distilled water. Findings Increased expression of a gene encoding for a putative membrane protein (BPSL0721 was confirmed using a lux-based transcriptional reporter system, and maximal expression was noted at approximately 6 hrs after shifting cells from LB to water. A BPSL0721 deficient mutant of B. pseudomallei was able to survive in water for at least 90 days indicating that although involved, BPSL0721 was not essential for survival. BPSL2961, a gene encoding a putative phosphatidylglycerol phosphatase (PGP, was also induced when cells were shifted to water. This gene is likely involved in cell membrane biosynthesis. We were unable to construct a PGP mutant suggesting that the gene is not only involved in survival in water but is essential for cell viability. We also examined mutants of polyhydroxybutyrate synthase (phbC, lipopolysaccharide (LPS oligosaccharide and capsule synthesis, and these mutations did not affect survival in water. LPS mutants lacking outer core were found to lose viability in water by 200 days indicating that an intact LPS core provides an outer membrane architecture which allows prolonged survival in water. Conclusion The results from these studies suggest that B. pseudomallei survival in water is a complex process that requires an LPS molecule which contains an intact core region.

  6. Production and characterization of chimeric monoclonal antibodies against Burkholderia pseudomallei and B. mallei using the DHFR expression system.

    Directory of Open Access Journals (Sweden)

    Hyung-Yong Kim

    Full Text Available Burkholderia pseudomallei (BP and B. mallei (BM are closely related gram-negative, facultative anaerobic bacteria which cause life-threatening melioidosis in human and glanders in horse, respectively. Our laboratory has previously generated and characterized more than 100 mouse monoclonal antibodies (MAbs against BP and BM, according to in vitro and in vivo assay. In this study, 3 MAbs (BP7 10B11, BP7 2C6, and BP1 7F7 were selected to develop into chimeric mouse-human monoclonal antibodies (cMAbs against BP and/or BM. For the stable production of cMAbs, we constructed 4 major different vector systems with a dihydrofolate reductase (DHFR amplification marker, and optimized transfection/selection conditions in mammalian host cells with the single-gene and/or double-gene expression system. These 3 cMAbs were stably produced by the DHFR double mutant Chinese hamster ovarian (CHO-DG44 cells. By ELISA and Western blot analysis using whole bacterial antigens treated by heat (65°C/90 min, sodium periodate, and proteinase K, the cMAb BP7 10B11 (cMAb CK1 reacted with glycoproteins (34, 38, 48 kDa in BP; 28, 38, 48 kDa in BM. The cMAb BP7 2C6 (cMAb CK2 recognized surface-capsule antigens with molecular sizes of 38 to 52 kDa, and 200 kDa in BM. The cMAb CK2 was weakly reactive to 14∼28, 200 kDa antigens in BP. The cMAb BP1 7F7 (cMAb CK3 reacted with lipopolysaccharides (38∼52 kDa in BP; 38∼60 kDa in B. thailandensis. Western blot results with the outer surface antigens of the 3 Burkholderia species were consistent with results with the whole Burkholderia cell antigens, suggesting that these immunodominant antigens reacting with the 3 cMAbs were primarily present on the outer surface of the Burkholderia species. These 3 cMAbs would be useful for analyzing the role of the major outer surface antigens in Burkholderia infection.

  7. The Madagascar hissing cockroach as a novel surrogate host for Burkholderia pseudomallei, B. mallei and B. thailandensis

    Directory of Open Access Journals (Sweden)

    Fisher Nathan A

    2012-06-01

    Full Text Available Abstract Background Burkholderia pseudomallei and Burkholderia mallei are gram-negative pathogens responsible for the diseases melioidosis and glanders, respectively. Both species cause disease in humans and animals and have been designated as category B select agents by the Centers for Disease Control and Prevention (CDC. Burkholderia thailandensis is a closely related bacterium that is generally considered avirulent for humans. While it can cause disease in rodents, the B. thailandensis 50% lethal dose (LD50 is typically ≥ 104-fold higher than the B. pseudomallei and B. mallei LD50 in mammalian models of infection. Here we describe an alternative to mammalian hosts in the study of virulence and host-pathogen interactions of these Burkholderia species. Results Madagascar hissing cockroaches (MH cockroaches possess a number of qualities that make them desirable for use as a surrogate host, including ease of breeding, ease of handling, a competent innate immune system, and the ability to survive at 37°C. MH cockroaches were highly susceptible to infection with B. pseudomallei, B. mallei and B. thailandensis and the LD50 was 50 for Escherichia coli in MH cockroaches was >105 cfu. B. pseudomallei, B. mallei, and B. thailandensis cluster 1 type VI secretion system (T6SS-1 mutants were all attenuated in MH cockroaches, which is consistent with previous virulence studies conducted in rodents. B. pseudomallei mutants deficient in the other five T6SS gene clusters, T6SS-2 through T6SS-6, were virulent in both MH cockroaches and hamsters. Hemocytes obtained from MH cockroaches infected with B. pseudomallei harbored numerous intracellular bacteria, suggesting that this facultative intracellular pathogen can survive and replicate inside of MH cockroach phagocytic cells. The hemolymph extracted from these MH cockroaches also contained multinuclear giant cells (MNGCs with intracellular B. pseudomallei, which indicates that infected hemocytes can

  8. Quantum Fields on Causal Sets

    CERN Document Server

    Johnston, Steven

    2010-01-01

    Causal set theory provides a model of discrete spacetime in which spacetime events are represented by elements of a causal set---a locally finite, partially ordered set in which the partial order represents the causal relationships between events. The work presented here describes a model for matter on a causal set, specifically a theory of quantum scalar fields on a causal set spacetime background. The work starts with a discrete path integral model for particles on a causal set. Here quantum mechanical amplitudes are assigned to trajectories within the causal set. By summing these over all trajectories between two spacetime events we obtain a causal set particle propagator. With a suitable choice of amplitudes this is shown to agree (in an appropriate sense) with the retarded propagator for the Klein-Gordon equation in Minkowski spacetime. This causal set propagator is then used to define a causal set analogue of the Pauli-Jordan function that appears in continuum quantum field theories. A quantum scalar fi...

  9. Understanding the Pathogenicity of Burkholderia contaminans, an Emerging Pathogen in Cystic Fibrosis

    Science.gov (United States)

    Nunvar, Jaroslav; Kalferstova, Lucie; Bloodworth, Ruhi A. M.; Kolar, Michal; Degrossi, Jose; Lubovich, Silvina; Cardona, Silvia T.; Drevinek, Pavel

    2016-01-01

    Several bacterial species from the Burkholderia cepacia complex (Bcc) are feared opportunistic pathogens that lead to debilitating lung infections with a high risk of developing fatal septicemia in cystic fibrosis (CF) patients. However, the pathogenic potential of other Bcc species is yet unknown. To elucidate clinical relevance of Burkholderia contaminans, a species frequently isolated from CF respiratory samples in Ibero-American countries, we aimed to identify its key virulence factors possibly linked with an unfavorable clinical outcome. We performed a genome-wide comparative analysis of two isolates of B. contaminans ST872 from sputum and blood culture of a female CF patient in Argentina. RNA-seq data showed significant changes in expression for quorum sensing-regulated virulence factors and motility and chemotaxis. Furthermore, we detected expression changes in a recently described low-oxygen-activated (lxa) locus which encodes stress-related proteins, and for two clusters responsible for the biosynthesis of antifungal and hemolytic compounds pyrrolnitrin and occidiofungin. Based on phenotypic assays that confirmed changes in motility and in proteolytic, hemolytic and antifungal activities, we were able to distinguish two phenotypes of B. contaminans that coexisted in the host and entered her bloodstream. Whole genome sequencing revealed that the sputum and bloodstream isolates (each representing a distinct phenotype) differed by over 1,400 mutations as a result of a mismatch repair-deficient hypermutable state of the sputum isolate. The inferred lack of purifying selection against nonsynonymous mutations and the high rate of pseudogenization in the derived isolate indicated limited evolutionary pressure during evolution in the nutrient-rich, stable CF sputum environment. The present study is the first to examine the genomic and transcriptomic differences between longitudinal isolates of B. contaminans. Detected activity of a number of putative virulence

  10. 柑桔黄龙病的鉴定和柯赫氏定理%"Candidatus Liberibacter Species": Without Koch's Postulates Completed, Can the Bacterium be Considered as the Causal Agent of Citrus Huanglongbing (Yellow Shoot Disease) ?

    Institute of Scientific and Technical Information of China (English)

    Chen J; Deng X; Civerolo E L; Lee R F; Jones J B; Zhou C; Hartung J S; Manjunath K L; Brlansky R H

    2011-01-01

    Huanglongbing (HLB, yellow shoot disease) has been a destructive disease of citrus around the world for over a century, yet the etiology of the disease has not been definitively established. Based mainly on assays for 16S rRNA gene sequences, fastidious bacteria known as "Candidatus Liberibacter species" have been .ssociated with HLB. We are concerned that some current literature frequendy refers to "Ca. Liberibacter spp." as the causal or etiological agent of HLB. However, Koch' s postulates, either sensu stricto or modified, have not yet been completely fulfilled to establish that "Ca. Liberibacter spp." are the cause of HLB.Direct pathological interactions between the bacteria and citrus host have not been conclusively documented.We suggest there is a need for the literature to be precise on this point until the etiology of HLB is firmly established.%黄龙(梢)病被认为是世界柑橘生产上的毁灭性病害已超过一个世纪,但该病害的病原学至今还没有清晰地建立起来.根据16S rRNA基因序列分析,一组被称为"Candidatus Liberibacter species"的难培养细菌被认为与黄龙病相关.然而,要确定"Ca.Liberibacter spp."是黄龙病病原的柯赫氏定理并没有真正完成.令我们担忧的是,近年来有些文献频频指出"Ca.Liberibacter spp."是黄龙病的病原,其实该细菌与柑橘寄主的直接病理反应还没有完全确定.我们建议,在黄龙病病原学清楚之前,文献报道在这方面需要有准确的阐述.

  11. Entropy of Causal Horizons

    CERN Document Server

    Howard, Eric M

    2016-01-01

    We analyze spacetimes with horizons and study the thermodynamic aspects of causal horizons, suggesting that the resemblance between gravitational and thermodynamic systems has a deeper quantum mechanical origin. We find that the observer dependence of such horizons is a direct consequence of associating a temperature and entropy to a spacetime. The geometrical picture of a horizon acting as a one-way membrane for information flow can be accepted as a natural interpretation of assigning a quantum field theory to a spacetime with boundary, ultimately leading to a close connection with thermodynamics.

  12. Quantum information causality.

    Science.gov (United States)

    Pitalúa-García, Damián

    2013-05-24

    How much information can a transmitted physical system fundamentally communicate? We introduce the principle of quantum information causality, which states the maximum amount of quantum information that a quantum system can communicate as a function of its dimension, independently of any previously shared quantum physical resources. We present a new quantum information task, whose success probability is upper bounded by the new principle, and show that an optimal strategy to perform it combines the quantum teleportation and superdense coding protocols with a task that has classical inputs.

  13. Melioidosis caused by Burkholderia pseudomallei in drinking water, Thailand, 2012.

    Science.gov (United States)

    Limmathurotsakul, Direk; Wongsuvan, Gumphol; Aanensen, David; Ngamwilai, Sujittra; Saiprom, Natnaree; Rongkard, Patpong; Thaipadungpanit, Janjira; Kanoksil, Manas; Chantratita, Narisara; Day, Nicholas P J; Peacock, Sharon J

    2014-02-01

    We identified 10 patients in Thailand with culture-confirmed melioidosis who had Burkholderia pseudomallei isolated from their drinking water. The multilocus sequence type of B. pseudomallei from clinical specimens and water samples were identical for 2 patients. This finding suggests that drinking water is a preventable source of B. pseudomallei infection.

  14. Intrinsic Resistance of Burkholderia cepacia Complex to Benzalkonium Chloride

    OpenAIRE

    Youngbeom Ahn; Jeong Myeong Kim; Ohgew Kweon; Seong-Jae Kim; Jones, Richard C.; Kellie Woodling; Goncalo Gamboa da Costa; LiPuma, John J.; David Hussong; Marasa, Bernard S.; Cerniglia, Carl E.

    2016-01-01

    ABSTRACT Pharmaceutical products that are contaminated with Burkholderia cepacia complex (BCC) bacteria may pose serious consequences to vulnerable patients. Benzyldimethylalkylammonium chloride (BZK) cationic surfactants are extensively used in medical applications and have been implicated in the coselection of antimicrobial resistance. The ability of BCC to degrade BZK, tetradecyldimethylbenzylammonium chloride (C14BDMA-Cl), dodecyldimethylbenzylammonium chloride (C12BDMA-Cl), decyldimethyl...

  15. Burkholderia pseudomallei: A potential zoonosis in the southeastern United States

    Science.gov (United States)

    Burkholderia pseudomallei, the causative agent of melioidosis, is an underreported zoonosis in many countries where environmental conditions may be favorable for B. pseudomallei. This soil saprophyte is most often detected in tropical areas such as Southeast Asia and Northern Australia where the cas...

  16. Causality and Micro-Causality in Curved Spacetime

    OpenAIRE

    Hollowood, Timothy J.; Shore, Graham M.

    2007-01-01

    We consider how causality and micro-causality are realised in QED in curved spacetime. The photon propagator is found to exhibit novel non-analytic behaviour due to vacuum polarization, which invalidates the Kramers-Kronig dispersion relation and calls into question the validity of micro-causality in curved spacetime. This non-analyticity is ultimately related to the generic focusing nature of congruences of geodesics in curved spacetime, as implied by the null energy condition, and the exist...

  17. Causal events enter awareness faster than non-causal events

    Science.gov (United States)

    Wagemans, Johan; de-Wit, Lee

    2017-01-01

    Philosophers have long argued that causality cannot be directly observed but requires a conscious inference (Hume, 1967). Albert Michotte however developed numerous visual phenomena in which people seemed to perceive causality akin to primary visual properties like colour or motion (Michotte, 1946). Michotte claimed that the perception of causality did not require a conscious, deliberate inference but, working over 70 years ago, he did not have access to the experimental methods to test this claim. Here we employ Continuous Flash Suppression (CFS)—an interocular suppression technique to render stimuli invisible (Tsuchiya & Koch, 2005)—to test whether causal events enter awareness faster than non-causal events. We presented observers with ‘causal’ and ‘non-causal’ events, and found consistent evidence that participants become aware of causal events more rapidly than non-causal events. Our results suggest that, whilst causality must be inferred from sensory evidence, this inference might be computed at low levels of perceptual processing, and does not depend on a deliberative conscious evaluation of the stimulus. This work therefore supports Michotte’s contention that, like colour or motion, causality is an immediate property of our perception of the world. PMID:28149698

  18. Dynamic causal modelling.

    Science.gov (United States)

    Friston, K J; Harrison, L; Penny, W

    2003-08-01

    In this paper we present an approach to the identification of nonlinear input-state-output systems. By using a bilinear approximation to the dynamics of interactions among states, the parameters of the implicit causal model reduce to three sets. These comprise (1) parameters that mediate the influence of extrinsic inputs on the states, (2) parameters that mediate intrinsic coupling among the states, and (3) [bilinear] parameters that allow the inputs to modulate that coupling. Identification proceeds in a Bayesian framework given known, deterministic inputs and the observed responses of the system. We developed this approach for the analysis of effective connectivity using experimentally designed inputs and fMRI responses. In this context, the coupling parameters correspond to effective connectivity and the bilinear parameters reflect the changes in connectivity induced by inputs. The ensuing framework allows one to characterise fMRI experiments, conceptually, as an experimental manipulation of integration among brain regions (by contextual or trial-free inputs, like time or attentional set) that is revealed using evoked responses (to perturbations or trial-bound inputs, like stimuli). As with previous analyses of effective connectivity, the focus is on experimentally induced changes in coupling (cf., psychophysiologic interactions). However, unlike previous approaches in neuroimaging, the causal model ascribes responses to designed deterministic inputs, as opposed to treating inputs as unknown and stochastic.

  19. Relationship of causal effects in a causal chain and related inference

    Institute of Scientific and Technical Information of China (English)

    GENG Zhi; HE Yangbo; WANG Xueli

    2004-01-01

    This paper discusses the relationship among the total causal effect and local causal effects in a causal chain and identifiability of causal effects. We show a transmission relationship of causal effects in a causal chain. According to the relationship, we give an approach to eliminating confounding bias through controlling for intermediate variables in a causal chain.

  20. Experimental test of nonlocal causality.

    Science.gov (United States)

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G; Fedrizzi, Alessandro

    2016-08-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect.

  1. Experimental test of nonlocal causality

    Science.gov (United States)

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G.; Fedrizzi, Alessandro

    2016-01-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell’s local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect. PMID:27532045

  2. Causal inference based on counterfactuals

    Directory of Open Access Journals (Sweden)

    Höfler M

    2005-09-01

    Full Text Available Abstract Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept.

  3. Causal evolution of wave packets

    CERN Document Server

    Eckstein, Michał

    2016-01-01

    Drawing from the optimal transport theory adapted to the relativistic setting we formulate the principle of a causal flow of probability and apply it in the wave packet formalism. We demonstrate that whereas the Dirac system is causal, the relativistic-Schr\\"odinger Hamiltonian impels a superluminal evolution of probabilities. We quantify the causality breakdown in the latter system and argue that, in contrast to the popular viewpoint, it is not related to the localisation properties of the states.

  4. Granger causality for circular variables

    Energy Technology Data Exchange (ETDEWEB)

    Angelini, Leonardo; Pellicoro, Mario [Istituto Nazionale di Fisica Nucleare, Sezione di Bari (Italy); Dipartimento di Fisica, University of Bari (Italy); Stramaglia, Sebastiano, E-mail: sebastiano.stramaglia@ba.infn.i [Istituto Nazionale di Fisica Nucleare, Sezione di Bari (Italy); Dipartimento di Fisica, University of Bari (Italy)

    2009-06-29

    In this Letter we discuss the use of Granger causality to the analyze systems of coupled circular variables, by modifying a recently proposed method for multivariate analysis of causality. We show the application of the proposed approach on several Kuramoto systems, in particular one living on networks built by preferential attachment and a model for the transition from deeply to lightly anaesthetized states. Granger causalities describe the flow of information among variables.

  5. Causality Statistical Perspectives and Applications

    CERN Document Server

    Berzuini, Carlo; Bernardinell, Luisa

    2012-01-01

    A state of the art volume on statistical causality Causality: Statistical Perspectives and Applications presents a wide-ranging collection of seminal contributions by renowned experts in the field, providing a thorough treatment of all aspects of statistical causality. It covers the various formalisms in current use, methods for applying them to specific problems, and the special requirements of a range of examples from medicine, biology and economics to political science. This book:Provides a clear account and comparison of formal languages, concepts and models for statistical causality. Addr

  6. Screening a mushroom extract library for activity against Acinetobacter baumannii and Burkholderia cepacia and the identification of a compound with anti-Burkholderia activity

    Directory of Open Access Journals (Sweden)

    Rott Marc

    2010-01-01

    Full Text Available Abstract Background Acinetobacter baumannii and species within the Burkholderia cepacia complex (BCC are significant opportunistic bacterial pathogens of humans. These species exhibit a high degree of antibiotic resistance, and some clinical isolates are resistant to all currently available antimicrobial drugs used for treatment. Thus, new drugs are needed to treat infections by these species. Mushrooms could be a potential source for new drugs to treat A. baumannii and BCC infections. Methods The aim of this study was to screen a library of crude extracts from 330 wild mushrooms by disk diffusion assays for antibacterial activity against A. baumannii and Burkholderia cepacia in the hope of identifying a novel natural drug that could be used to treat infections caused by these species. Once positive hits were identified, the extracts were subjected to bioassay-guided separations to isolate and identify the active drug molecules. MICs were performed to gauge the in vitro activity of the purified compounds. Results Only three crude extracts (0.9% had activity against A. baumannii and B. cepacia. Compounds from two of these extracts had MICs greater than 128 μg/ml, and further analyses were not performed. From the third extract, prepared from Leucopaxillus albissimus, 2-aminoquinoline (2-AQ was isolated. This compound exhibited a modest MIC in vitro against strains from nine different BCC species, including multi-drug resistant clinical isolates (MIC = 8-64 μg/ml, and a weak MIC (128 μg/ml against A baumannii. The IC50 against a murine monocyte line was 1.5 mg/ml. Conclusion The small number of positive hits in this study suggests that finding a new drug from mushrooms to treat Gram-negative bacterial infections may be difficult. Although 2-AQ was identified in one mushroom, and it was shown to inhibit the growth of multi-drug resistant BCC isolates, the relatively high MICs (8-128 μg/ml for both A. baumannii and BCC strains suggests that 2-AQ

  7. Structural Equations and Causal Explanations: Some Challenges for Causal SEM

    Science.gov (United States)

    Markus, Keith A.

    2010-01-01

    One common application of structural equation modeling (SEM) involves expressing and empirically investigating causal explanations. Nonetheless, several aspects of causal explanation that have an impact on behavioral science methodology remain poorly understood. It remains unclear whether applications of SEM should attempt to provide complete…

  8. The Cradle of Causal Reasoning: Newborns' Preference for Physical Causality

    Science.gov (United States)

    Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio; Simion, Francesca

    2013-01-01

    Perception of mechanical (i.e. physical) causality, in terms of a cause-effect relationship between two motion events, appears to be a powerful mechanism in our daily experience. In spite of a growing interest in the earliest causal representations, the role of experience in the origin of this sensitivity is still a matter of dispute. Here, we…

  9. Identifiability of causal effect for a simple causal model

    Institute of Scientific and Technical Information of China (English)

    郑忠国; 张艳艳; 童行伟

    2002-01-01

    Counterfactual model is put forward to discuss the causal inference in the directed acyclic graph and its corresponding identifiability is thus studied with the ancillary information based on conditional independence. It is shown that the assumption of ignorability can be expanded to the assumption of replaceability,under which the causal efiects are identifiable.

  10. Inferring deterministic causal relations

    CERN Document Server

    Daniusis, Povilas; Mooij, Joris; Zscheischler, Jakob; Steudel, Bastian; Zhang, Kun; Schoelkopf, Bernhard

    2012-01-01

    We consider two variables that are related to each other by an invertible function. While it has previously been shown that the dependence structure of the noise can provide hints to determine which of the two variables is the cause, we presently show that even in the deterministic (noise-free) case, there are asymmetries that can be exploited for causal inference. Our method is based on the idea that if the function and the probability density of the cause are chosen independently, then the distribution of the effect will, in a certain sense, depend on the function. We provide a theoretical analysis of this method, showing that it also works in the low noise regime, and link it to information geometry. We report strong empirical results on various real-world data sets from different domains.

  11. Neural Correlates of Causal Power Judgments

    Directory of Open Access Journals (Sweden)

    Denise Dellarosa Cummins

    2014-12-01

    Full Text Available Causal inference is a fundamental component of cognition and perception. Probabilistic theories of causal judgment (most notably causal Bayes networks derive causal judgments using metrics that integrate contingency information. But human estimates typically diverge from these normative predictions. This is because human causal power judgments are typically strongly influenced by beliefs concerning underlying causal mechanisms, and because of the way knowledge is retrieved from human memory during the judgment process. Neuroimaging studies indicate that the brain distinguishes causal events from mere covariation, and between perceived and inferred causality. Areas involved in error prediction are also activated, implying automatic activation of possible exception cases during causal decision-making.

  12. Identification of Burkholderia mallei and Burkholderia pseudomallei adhesins for human respiratory epithelial cells

    Directory of Open Access Journals (Sweden)

    Hogan Robert J

    2010-09-01

    Full Text Available Abstract Background Burkholderia pseudomallei and Burkholderia mallei cause the diseases melioidosis and glanders, respectively. A well-studied aspect of pathogenesis by these closely-related bacteria is their ability to invade and multiply within eukaryotic cells. In contrast, the means by which B. pseudomallei and B. mallei adhere to cells are poorly defined. The purpose of this study was to identify adherence factors expressed by these organisms. Results Comparative sequence analyses identified a gene product in the published genome of B. mallei strain ATCC23344 (locus # BMAA0649 that resembles the well-characterized Yersinia enterocolitica autotransporter adhesin YadA. The gene encoding this B. mallei protein, designated boaA, was expressed in Escherichia coli and shown to significantly increase adherence to human epithelial cell lines, specifically HEp2 (laryngeal cells and A549 (type II pneumocytes, as well as to cultures of normal human bronchial epithelium (NHBE. Consistent with these findings, disruption of the boaA gene in B. mallei ATCC23344 reduced adherence to all three cell types by ~50%. The genomes of the B. pseudomallei strains K96243 and DD503 were also found to contain boaA and inactivation of the gene in DD503 considerably decreased binding to monolayers of HEp2 and A549 cells and to NHBE cultures. A second YadA-like gene product highly similar to BoaA (65% identity was identified in the published genomic sequence of B. pseudomallei strain K96243 (locus # BPSL1705. The gene specifying this protein, termed boaB, appears to be B. pseudomallei-specific. Quantitative attachment assays demonstrated that recombinant E. coli expressing BoaB displayed greater binding to A549 pneumocytes, HEp2 cells and NHBE cultures. Moreover, a boaB mutant of B. pseudomallei DD503 showed decreased adherence to these respiratory cells. Additionally, a B. pseudomallei strain lacking expression of both boaA and boaB was impaired in its ability to

  13. Theory-Based Causal Induction

    Science.gov (United States)

    Griffiths, Thomas L.; Tenenbaum, Joshua B.

    2009-01-01

    Inducing causal relationships from observations is a classic problem in scientific inference, statistics, and machine learning. It is also a central part of human learning, and a task that people perform remarkably well given its notorious difficulties. People can learn causal structure in various settings, from diverse forms of data: observations…

  14. Expert Causal Reasoning and Explanation.

    Science.gov (United States)

    Kuipers, Benjamin

    The relationship between cognitive psychologists and researchers in artificial intelligence carries substantial benefits for both. An ongoing investigation in causal reasoning in medical problem solving systems illustrates this interaction. This paper traces a dialectic of sorts in which three different types of causal resaoning for medical…

  15. Introduction to causal dynamical triangulations

    DEFF Research Database (Denmark)

    Görlich, Andrzej

    2013-01-01

    The method of causal dynamical triangulations is a non-perturbative and background-independent approach to quantum theory of gravity. In this review we present recent results obtained within the four dimensional model of causal dynamical triangulations. We describe the phase structure of the mode...

  16. Re-thinking local causality

    NARCIS (Netherlands)

    Friederich, Simon

    2015-01-01

    There is widespread belief in a tension between quantum theory and special relativity, motivated by the idea that quantum theory violates J. S. Bell's criterion of local causality, which is meant to implement the causal structure of relativistic space-time. This paper argues that if one takes the es

  17. Causal Inference and Developmental Psychology

    Science.gov (United States)

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  18. On causality of extreme events

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2016-06-01

    Full Text Available Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available.

  19. On causality of extreme events

    Science.gov (United States)

    2016-01-01

    Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available. PMID:27330866

  20. Pyrrolnitrin from Burkholderia cepacia: antibiotic activity against fungi and novel activities against streptomycetes.

    Science.gov (United States)

    el-Banna, N; Winkelmann, G

    1998-07-01

    A bacterial strain identified as Burkholderia cepacia NB-1 was isolated from water ponds in the botanical garden in Tübingen, Germany, and was found to produce a broad spectrum phenylpyrrole antimicrobial substance active against filamentous fungi, yeasts and Gram-positive bacteria. In batch culture containing glycerol and L-glutamic acid, the isolate NB-1 produced the antibiotic optimally late in the growth phase and accumulated a main portion in their cells. Isolation and purification of the antibiotic from Burkholderia (Pseudomonas) cepacia NB-1 by acetone extraction, gel filtration on Sephadex LH-20 and preparative HPLC yielded 0.54 mg l-1 of a pure substance. Spectroscopic data (HPLC, MS and NMR) confirmed that the compound was pyrrolnitrin [3-chloro-4-(2'-nitro-3'-chloro-phenyl) pyrrole]. Pyrrolnitrin has an inhibitory effect on the electron transport system, as demonstrated by isolated mitochondria from Neurospora crassa 74 A. This inhibition was relieved by N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride (TMPD), indicating that pyrrolnitrin blocked the electron transfer between the dehydrogenases and the cytochrome components of the respiratory chain. Among Gram-positive bacteria, pyrrolnitrin was most active against certain Streptomyces species, especially S. antibioticus, which has not previously been described in the literature. In the presence of pyrrolnitrin, aerial mycelium and spore formation of Strep. antibioticus was suppressed, although growth continued via substrate mycelium. The new findings of inhibition of streptomycetes and their secondary metabolism by pyrrolnitrin may contribute to the fact that Pseudomonas species predominate in soil and compete even with antibiotic-producing Streptomyces.

  1. CausalTrail: Testing hypothesis using causal Bayesian networks.

    Science.gov (United States)

    Stöckel, Daniel; Schmidt, Florian; Trampert, Patrick; Lenhof, Hans-Peter

    2015-01-01

    Summary Causal Bayesian Networks are a special class of Bayesian networks in which the hierarchy directly encodes the causal relationships between the variables. This allows to compute the effect of interventions, which are external changes to the system, caused by e.g. gene knockouts or an administered drug. Whereas numerous packages for constructing causal Bayesian networks are available, hardly any program targeted at downstream analysis exists. In this paper we present CausalTrail, a tool for performing reasoning on causal Bayesian networks using the do-calculus. CausalTrail's features include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface. The program is able to account for missing data and thus can be readily applied in multi-omics settings where it is common that not all measurements are performed for all samples. Availability and Implementation CausalTrail is implemented in C++ using the Boost and Qt5 libraries. It can be obtained from https://github.com/dstoeckel/causaltrail.

  2. Interactions of Burkholderia cenocepacia and other Burkholderia cepacia complex bacteria with epithelial and phagocytic cells.

    Science.gov (United States)

    Saldías, M Soledad; Valvano, Miguel A

    2009-09-01

    Burkholderia cenocepacia is a member of the B. cepacia complex (Bcc), a group of opportunistic bacteria that infect the airways of patients with cystic fibrosis (CF) and are extraordinarily resistant to almost all clinically useful antibiotics. Infections in CF patients with Bcc bacteria generally lead to a more rapid decline in lung function, and in some cases to the 'cepacia syndrome', a virtually deadly exacerbation of the lung infection with systemic manifestations. These characteristics of Bcc bacteria contribute to higher morbidity and mortality in infected CF patients. In the last 10 years considerable progress has been made in understanding the interactions between Bcc bacteria and mammalian host cells. Bcc isolates can survive either intracellularly within eukaryotic cells or extracellularly in host tissues. They survive within phagocytes and respiratory epithelial cells, and they have the ability to breach the respiratory epithelium layer. Survival and persistence of Bcc bacteria within host cells and tissues are believed to play a key role in pulmonary infection and to contribute to the persistent inflammation observed in patients with CF. This review summarizes recent findings concerning the interaction between Bcc bacteria and epithelial and phagocytic cells.

  3. Clear message for causality

    Energy Technology Data Exchange (ETDEWEB)

    Steinberg, Aephraim M. [Institute for Experimental Physics, University of Vienna, Vienna (Austria)

    2003-12-01

    Experiment confirms that information cannot be transmitted faster than the speed of light. Ever since Einstein stated that nothing can travel faster than light, physicists have delighted in finding exceptions. One after another, observations of such 'superluminal' propagation have been made. However, while some image or pattern- such as the motion of a spotlight projected on a distant wall - might have appeared to travel faster than light, it seemed that there was no way to use the superluminal effect to transmit energy or information. In recent years, the superluminal propagation of light pulses through certain media has led to renewed controversy. In 1995, for example, Guenther Nimtz of the University of Cologne encoded Mozart's 40th Symphony on a microwave beam, which he claimed to have transmitted at a speed faster than light. Others maintain that such a violation of Einstein's speed limit would wreak havoc on our most fundamental ideas about causality, allowing an effect to precede its cause. Relativity teaches us that sending a signal faster than light would be equivalent to sending it backwards in time. (U.K.)

  4. History, causality, and sexology.

    Science.gov (United States)

    Money, John

    2003-08-01

    In 1896, Krafft-Ebing published Psychopathia Sexualis. Popularly defined as hereditary weakness or taintedness in the family pedigree, degeneracy was called upon as a causal explanation for perversions of the sexual instinct. Although Krafft-Ebing accepted Karl Ulrichs proposal that homosexuality could be innate and probably located in the brain, he paid little attention to neuropathological sexology. Alfred Binet challenged Krafft-Ebing's orthodoxy by explaining fetishism in terms of associative learning, to which Krafft-Ebing's response was that only those with a hereditary taint would be vulnerable. Thus did the venerable nature-nurture antithesis maintain its rhetoric, even to the present day. Krafft-Ebing died too soon to meet the Freudian challenge of endopsychic determinism, and too soon also to encounter the idea of a developmental multivariate outcome of what I have termed the lovemap. Like other brain maps, for example the languagemap, the lovemap requires an intact human brain in which to develop. The personalized content of the lovemap has access to the brain by way of the special senses.

  5. Causal Selection and Counterfactual Reasoning

    Directory of Open Access Journals (Sweden)

    William Jiménez-Leal

    2013-01-01

    Full Text Available El trabajo defiende la posición según la cual el pensamiento contrafactual depende de nuestra representación causal del mundo y, en este sentido, argumenta que existe una estrecha relación entre el razonamiento causal y el contrafactual. Se lleva a cabo una crítica a la teoría de la disociación de juicios de Mandel (Mandel, 2003b, que defiende la independencia funcional entre el proceso de selección causal y el razonamiento contrafactual en el contexto de la selección causal. En los experimentos realizados se manipularon algunos elementos de la semántica de la tarea con el fin de ilustrar aquellos casos en los que no se da la disociación entre el razonamiento causal y el contrafactual. En el Experimento 1, el nivel de descripción del evento objetivo se manipuló en una tarea de generación de listas y evaluación. El Experimento 2 replicó los hallazgos del Experimento 1 utilizando un sistema de codificación alternativo, mientras que el Experimento 3 realizó lo mismo utilizando un formato de respuesta alternativo. Los resultados de los experimentos apoyan la concepción del entendimiento causal propuesta por los modelos mentales causales.

  6. Classical planning and causal implicatures

    DEFF Research Database (Denmark)

    Blackburn, Patrick Rowan; Benotti, Luciana

    In this paper we motivate and describe a dialogue manager (called Frolog) which uses classical planning to infer causal implicatures. A causal implicature is a type of Gricean relation implicature, a highly context dependent form of inference. As we shall see, causal implicatures are important...... to generate clarification requests"; as a result we can model task-oriented dialogue as an interactive process locally structured by negotiation of the underlying task. We give several examples of Frolog-human dialog, discuss the limitations imposed by the classical planning paradigm, and indicate...

  7. Research progress in quorum sensing and quorum quenching of the rice pathogen Burkholderia plantarii%水稻病原菌 Burkholderia plantarii群体感应和群体淬灭研究进展

    Institute of Scientific and Technical Information of China (English)

    MATSUMOTO Haruna; 王蒙岑; 桂文君; 郭逸蓉; 朱国念

    2016-01-01

    植物伯克霍尔德菌 Burkholderia plantarii 是引起水稻秧苗细菌性立枯病的重要病原菌之一,其侵染性、繁殖力及适应性均很强,严重威胁中国水稻生产。文章围绕 B. plantarii 的发生、危害及致病机理,着重论述了细菌群体感应系统(quorum sensing,QS)的生理功能及其在B. plantarii 致病力调控方面的最新研究进展,并进一步从根际微生物互作角度,综述了种间信号分子对病原菌群体淬灭(quorum quenching)的作用机制,同时结合种间信号分子的独特性,展望了其在新型微生物杀菌剂研发中的重要性和应用潜力。%Burkholderia plantarii is a causal agent of bacterial seedling blight of rice. This pathogen is of strong infectivity, reproductive capacity and adapt ability, and thus poses a serious threat to rice production. Hereby, the occurrence, damage and pathogenic mechanism of B. plantarii are introduced. Research progress of physiological traits and the regulation of pathogenicity controlled by bacterial quorum sensing (QS) in B. plantarii are also discussed. Moreover, from the point of view of microbial interaction in rhizosphere, the mechanisms of quorum quenching by interspecific signaling molecules against bacterial pathogens are summarized. According to the characteristics of the interspecies signaling molecules, their importance and application potential in development of novel bactericides are also previewed.

  8. Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural Soils in Morelos, Mexico.

    Science.gov (United States)

    Martínez-Ocampo, Fernando; Fernández López, Maikel Gilberto; Lozano-Aguirre Beltrán, Luis Fernando; Popoca-Ursino, Elida Carolina; Ortiz-Hernández, M Laura; Sánchez-Salinas, Enrique; Ramos Quintana, Fernando; Villalobos-López, Miguel A; Dantán-González, Edgar

    2016-04-28

    Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was isolated from agricultural soils in Morelos, Mexico, and previously has shown its abilities for bioremediation. In this study, we report the draft genome sequence of Burkholderia cenocepacia strain CEIB S5-2.

  9. Functional Characterization of OXA-57, a Class D β-Lactamase from Burkholderia pseudomallei

    OpenAIRE

    Keith, Karen E.; Oyston, Petra C.; Crossett, Ben; Fairweather, Neil F.; Titball, Richard W.; Walsh, Timothy R.; Brown, Katherine A.

    2005-01-01

    Class D β-lactamase OXA-57 was identified in a range of isolates of Burkholderia pseudomallei and Burkholderia thailandensis. Comparative kinetic analyses of wild-type and mutant forms of B. pseudomallei OXA-57 are reported. Implications of these data for β-lactam resistance and the proposed role of Ser-104 in β-lactam hydrolysis are discussed.

  10. Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria.

    Science.gov (United States)

    DiSalvo, Susanne; Haselkorn, Tamara S; Bashir, Usman; Jimenez, Daniela; Brock, Debra A; Queller, David C; Strassmann, Joan E

    2015-09-01

    Symbiotic associations can allow an organism to acquire novel traits by accessing the genetic repertoire of its partner. In the Dictyostelium discoideum farming symbiosis, certain amoebas (termed "farmers") stably associate with bacterial partners. Farmers can suffer a reproductive cost but also gain beneficial capabilities, such as carriage of bacterial food (proto-farming) and defense against competitors. Farming status previously has been attributed to amoeba genotype, but the role of bacterial partners in its induction has not been examined. Here, we explore the role of bacterial associates in the initiation, maintenance, and phenotypic effects of the farming symbiosis. We demonstrate that two clades of farmer-associated Burkholderia isolates colonize D. discoideum nonfarmers and infectiously endow them with farmer-like characteristics, indicating that Burkholderia symbionts are a major driver of the farming phenomenon. Under food-rich conditions, Burkholderia-colonized amoebas produce fewer spores than uncolonized counterparts, with the severity of this reduction being dependent on the Burkholderia colonizer. However, the induction of food carriage by Burkholderia colonization may be considered a conditionally adaptive trait because it can confer an advantage to the amoeba host when grown in food-limiting conditions. We observed Burkholderia inside and outside colonized D. discoideum spores after fruiting body formation; this observation, together with the ability of Burkholderia to colonize new amoebas, suggests a mixed mode of symbiont transmission. These results change our understanding of the D. discoideum farming symbiosis by establishing that the bacterial partner, Burkholderia, is an important causative agent of the farming phenomenon.

  11. Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing.

    Science.gov (United States)

    Ulrich, Ricky L; Deshazer, David; Kenny, Tara A; Ulrich, Melanie P; Moravusova, Anna; Opperman, Timothy; Bavari, Sina; Bowlin, Terry L; Moir, Donald T; Panchal, Rekha G

    2013-10-01

    The bacterial SOS response is a well-characterized regulatory network encoded by most prokaryotic bacterial species and is involved in DNA repair. In addition to nucleic acid repair, the SOS response is involved in pathogenicity, stress-induced mutagenesis, and the emergence and dissemination of antibiotic resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we analyzed the Burkholderia thailandensis global SOS response to the fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical, mitomycin C (MMC). We demonstrate that a B. thailandensis recA mutant (RU0643) is ∼4-fold more sensitive to CIP in contrast to the parental strain B. thailandensis DW503. Our RNA-Seq results show that CIP and MMC treatment (P SOS response were induced and include lexA, uvrA, dnaE, dinB, recX, and recA. At the genome-wide level, we found an overall decrease in gene expression, especially for genes involved in amino acid and carbohydrate transport and metabolism, following both CIP and MMC exposure. Interestingly, we observed the upregulation of several genes involved in bacterial motility and enhanced transcription of a B. thailandensis genomic island encoding a Siphoviridae bacteriophage designated E264. Using B. thailandensis plaque assays and PCR with B. mallei ATCC 23344 as the host, we demonstrate that CIP and MMC exposure in B. thailandensis DW503 induces the transcription and translation of viable bacteriophage in a RecA-dependent manner. This is the first report of the SOS response in Burkholderia spp. to DNA-damaging agents. We have identified both common and unique adaptive responses of B. thailandensis to chemical stress and DNA damage.

  12. Burkholderia cepacia complex Phage-Antibiotic Synergy (PAS): antibiotics stimulate lytic phage activity.

    Science.gov (United States)

    Kamal, Fatima; Dennis, Jonathan J

    2015-02-01

    The Burkholderia cepacia complex (Bcc) is a group of at least 18 species of Gram-negative opportunistic pathogens that can cause chronic lung infection in cystic fibrosis (CF) patients. Bcc organisms possess high levels of innate antimicrobial resistance, and alternative therapeutic strategies are urgently needed. One proposed alternative treatment is phage therapy, the therapeutic application of bacterial viruses (or bacteriophages). Recently, some phages have been observed to form larger plaques in the presence of sublethal concentrations of certain antibiotics; this effect has been termed phage-antibiotic synergy (PAS). Those reports suggest that some antibiotics stimulate increased production of phages under certain conditions. The aim of this study is to examine PAS in phages that infect Burkholderia cenocepacia strains C6433 and K56-2. Bcc phages KS12 and KS14 were tested for PAS, using 6 antibiotics representing 4 different drug classes. Of the antibiotics tested, the most pronounced effects were observed for meropenem, ciprofloxacin, and tetracycline. When grown with subinhibitory concentrations of these three antibiotics, cells developed a chain-like arrangement, an elongated morphology, and a clustered arrangement, respectively. When treated with progressively higher antibiotic concentrations, both the sizes of plaques and phage titers increased, up to a maximum. B. cenocepacia K56-2-infected Galleria mellonella larvae treated with phage KS12 and low-dose meropenem demonstrated increased survival over controls treated with KS12 or antibiotic alone. These results suggest that antibiotics can be combined with phages to stimulate increased phage production and/or activity and thus improve the efficacy of bacterial killing.

  13. Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex

    Directory of Open Access Journals (Sweden)

    Shrivastava Savita

    2008-12-01

    Full Text Available Abstract Background The Burkholderia cepacia complex (BCC is a versatile group of Gram negative organisms that can be found throughout the environment in sources such as soil, water, and plants. While BCC bacteria can be involved in beneficial interactions with plants, they are also considered opportunistic pathogens, specifically in patients with cystic fibrosis and chronic granulomatous disease. These organisms also exhibit resistance to many antibiotics, making conventional treatment often unsuccessful. KS10 was isolated as a prophage of B. cenocepacia K56-2, a clinically relevant strain of the BCC. Our objective was to sequence the genome of this phage and also determine if this prophage encoded any virulence determinants. Results KS10 is a 37,635 base pairs (bp transposable phage of the opportunistic pathogen Burkholderia cenocepacia. Genome sequence analysis and annotation of this phage reveals that KS10 shows the closest sequence homology to Mu and BcepMu. KS10 was found to be a prophage in three different strains of B. cenocepacia, including strains K56-2, J2315, and C5424, and seven tested clinical isolates of B. cenocepacia, but no other BCC species. A survey of 23 strains and 20 clinical isolates of the BCC revealed that KS10 is able to form plaques on lawns of B. ambifaria LMG 19467, B. cenocepacia PC184, and B. stabilis LMG 18870. Conclusion KS10 is a novel phage with a genomic organization that differs from most phages in that its capsid genes are not aligned into one module but rather separated by approximately 11 kb, giving evidence of one or more prior genetic rearrangements. There were no potential virulence factors identified in KS10, though many hypothetical proteins were identified with no known function.

  14. Burkholderia cenocepacia Differential Gene Expression during Host–Pathogen Interactions and Adaptation to the Host Environment

    Science.gov (United States)

    O’Grady, Eoin P.; Sokol, Pamela A.

    2011-01-01

    Members of the Burkholderia cepacia complex (Bcc) are important in medical, biotechnological, and agricultural disciplines. These bacteria naturally occur in soil and water environments and have adapted to survive in association with plants and animals including humans. All Bcc species are opportunistic pathogens including Burkholderia cenocepacia that causes infections in cystic fibrosis and chronic granulomatous disease patients. The adaptation of B. cenocepacia to the host environment was assessed in a rat chronic respiratory infection model and compared to that of high cell-density in vitro grown cultures using transcriptomics. The distribution of genes differentially expressed on chromosomes 1, 2, and 3 was relatively proportional to the size of each genomic element, whereas the proportion of plasmid-encoded genes differentially expressed was much higher relative to its size and most genes were induced in vivo. The majority of genes encoding known virulence factors, components of types II and III secretion systems and chromosome 2-encoded type IV secretion system were similarly expressed between in vitro and in vivo environments. Lower expression in vivo was detected for genes encoding N-acyl-homoserine lactone synthase CepI, orphan LuxR homolog CepR2, zinc metalloproteases ZmpA and ZmpB, LysR-type transcriptional regulator ShvR, nematocidal protein AidA, and genes associated with flagellar motility, Flp type pilus formation, and type VI secretion. Plasmid-encoded type IV secretion genes were markedly induced in vivo. Additional genes induced in vivo included genes predicted to be involved in osmotic stress adaptation or intracellular survival, metal ion, and nutrient transport, as well as those encoding outer membrane proteins. Genes identified in this study are potentially important for virulence during host–pathogen interactions and may be associated with survival and adaptation to the host environment during chronic lung infections. PMID:22919581

  15. On causality of extreme events

    CERN Document Server

    Zanin, Massimiliano

    2016-01-01

    Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect both linear and non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task.

  16. Fluctuations in Relativistic Causal Hydrodynamics

    CERN Document Server

    Kumar, Avdhesh; Mishra, Ananta P

    2013-01-01

    The formalism to calculate the hydrodynamics fluctuation using the quasi-stationary fluctuation theory of Onsager to the relativistic Navier-Stokes hydrodynamics is already known. In this work we calculate hydrodynamic fluctuations in relativistic causal theory of Muller, Israel and Stewart and other related causal hydrodynamic theories. We show that expressions for the Onsager coefficients and the correlation functions have form similar to the ones obtained by using Navier-Stokes equation. However, temporal evolution of the correlation functions obtained using MIS and the other causal theories can be significantly different than the correlation functions obtained using the Navier-Stokes equation. Finally, as an illustrative example, we explicitly plot the correlation functions obtained using the causal-hydrodynamics theories and compare them with correlation functions obtained by earlier authors using the expanding boost-invariant (Bjorken) flows.

  17. Correlation Measure Equivalence in Dynamic Causal Structures

    CERN Document Server

    Gyongyosi, Laszlo

    2016-01-01

    We prove an equivalence transformation between the correlation measure functions of the causally-unbiased quantum gravity space and the causally-biased standard space. The theory of quantum gravity fuses the dynamic (nonfixed) causal structure of general relativity and the quantum uncertainty of quantum mechanics. In a quantum gravity space, the events are causally nonseparable and all time bias vanishes, which makes it no possible to use the standard causally-biased entropy and the correlation measure functions. Since a corrected causally-unbiased entropy function leads to an undefined, obscure mathematical structure, in our approach the correction is made in the data representation of the causally-unbiased space. We prove that the standard causally-biased entropy function with a data correction can be used to identify correlations in dynamic causal structures. As a corollary, all mathematical properties of the causally-biased correlation measure functions are preserved in the causally-unbiased space. The eq...

  18. Causality constraints on TMD PDF

    CERN Document Server

    Efremov, A V

    2013-01-01

    In this short note, we discuss constraints on the transverse momentum dependent factorization formulae coming from the causality properties for the hadronic tensor. We show that the range of definition of the TMD PDFs in the transverse coordinate plane is wider that it is allowed by the causality. It indicates the presents of the large compensating corrections for the TMD PDF factorization theorem and/or overestimation of the transverse component dependence of TMD PDF.

  19. An introduction to causal inference.

    Science.gov (United States)

    Pearl, Judea

    2010-02-26

    This paper summarizes recent advances in causal inference and underscores the paradigmatic shifts that must be undertaken in moving from traditional statistical analysis to causal analysis of multivariate data. Special emphasis is placed on the assumptions that underlie all causal inferences, the languages used in formulating those assumptions, the conditional nature of all causal and counterfactual claims, and the methods that have been developed for the assessment of such claims. These advances are illustrated using a general theory of causation based on the Structural Causal Model (SCM) described in Pearl (2000a), which subsumes and unifies other approaches to causation, and provides a coherent mathematical foundation for the analysis of causes and counterfactuals. In particular, the paper surveys the development of mathematical tools for inferring (from a combination of data and assumptions) answers to three types of causal queries: those about (1) the effects of potential interventions, (2) probabilities of counterfactuals, and (3) direct and indirect effects (also known as "mediation"). Finally, the paper defines the formal and conceptual relationships between the structural and potential-outcome frameworks and presents tools for a symbiotic analysis that uses the strong features of both. The tools are demonstrated in the analyses of mediation, causes of effects, and probabilities of causation.

  20. Causality and Tense - two temporal structure builders

    NARCIS (Netherlands)

    Oversteegen, E.

    2005-01-01

    By force of causes precede effects, causality contributes to the temporal meaning of discourse. In case of semantic causal relations, this contribution is straightforward, but in case of epistemic causal relations, it is not. In order to gain insight into the semantics of epistemic causal relations,

  1. Causal Stability Conditions for General Relativistic Spacetimes

    CERN Document Server

    Howard, E M

    2016-01-01

    A brief overview of some open questions in general relativity with important consequences for causality theory is presented, aiming to a better understanding of the causal structure of the spacetime. Special attention is accorded to the problem of fundamental causal stability conditions. Several questions are raised and some of the potential consequences of recent results regarding the causality problem in general relativity are presented. A key question is whether causality violating regions are locally allowed. The new concept of almost stable causality is introduced; meanwhile, related conditions and criteria for the stability and almost stability of the causal structure are discussed.

  2. The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage.

    Science.gov (United States)

    Roszniowski, Bartosz; Latka, Agnieszka; Maciejewska, Barbara; Vandenheuvel, Dieter; Olszak, Tomasz; Briers, Yves; Holt, Giles S; Valvano, Miguel A; Lavigne, Rob; Smith, Darren L; Drulis-Kawa, Zuzanna

    2017-02-01

    Burkholderia phage AP3 (vB_BceM_AP3) is a temperate virus of the Myoviridae and the Peduovirinae subfamily (P2likevirus genus). This phage specifically infects multidrug-resistant clinical Burkholderia cenocepacia lineage IIIA strains commonly isolated from cystic fibrosis patients. AP3 exhibits high pairwise nucleotide identity (61.7 %) to Burkholderia phage KS5, specific to the same B. cenocepacia host, and has 46.7-49.5 % identity to phages infecting other species of Burkholderia. The lysis cassette of these related phages has a similar organization (putative antiholin, putative holin, endolysin, and spanins) and shows 29-98 % homology between specific lysis genes, in contrast to Enterobacteria phage P2, the hallmark phage of this genus. The AP3 and KS5 lysis genes have conserved locations and high amino acid sequence similarity. The AP3 bacteriophage particles remain infective up to 5 h at pH 4-10 and are stable at 60 °C for 30 min, but are sensitive to chloroform, with no remaining infective particles after 24 h of treatment. AP3 lysogeny can occur by stable genomic integration and by pseudo-lysogeny. The lysogenic bacterial mutants did not exhibit any significant changes in virulence compared to wild-type host strain when tested in the Galleria mellonella moth wax model. Moreover, AP3 treatment of larvae infected with B. cenocepacia revealed a significant increase (P < 0.0001) in larvae survival in comparison to AP3-untreated infected larvae. AP3 showed robust lytic activity, as evidenced by its broad host range, the absence of increased virulence in lysogenic isolates, the lack of bacterial gene disruption conditioned by bacterial tRNA downstream integration site, and the absence of detected toxin sequences. These data suggest that the AP3 phage is a promising potent agent against bacteria belonging to the most common B. cenocepacia IIIA lineage strains.

  3. Causality in physiological signals.

    Science.gov (United States)

    Müller, Andreas; Kraemer, Jan F; Penzel, Thomas; Bonnemeier, Hendrik; Kurths, Jürgen; Wessel, Niels

    2016-05-01

    Health is one of the most important non-material assets and thus also has an enormous influence on material values, since treating and preventing diseases is expensive. The number one cause of death worldwide today originates in cardiovascular diseases. For these reasons the aim of understanding the functions and the interactions of the cardiovascular system is and has been a major research topic throughout various disciplines for more than a hundred years. The purpose of most of today's research is to get as much information as possible with the lowest possible effort and the least discomfort for the subject or patient, e.g. via non-invasive measurements. A family of tools whose importance has been growing during the last years is known under the headline of coupling measures. The rationale for this kind of analysis is to identify the structure of interactions in a system of multiple components. Important information lies for example in the coupling direction, the coupling strength, and occurring time lags. In this work, we will, after a brief general introduction covering the development of cardiovascular time series analysis, introduce, explain and review some of the most important coupling measures and classify them according to their origin and capabilities in the light of physiological analyses. We will begin with classical correlation measures, go via Granger-causality-based tools, entropy-based techniques (e.g. momentary information transfer), nonlinear prediction measures (e.g. mutual prediction) to symbolic dynamics (e.g. symbolic coupling traces). All these methods have contributed important insights into physiological interactions like cardiorespiratory coupling, neuro-cardio-coupling and many more. Furthermore, we will cover tools to detect and analyze synchronization and coordination (e.g. synchrogram and coordigram). As a last point we will address time dependent couplings as identified using a recent approach employing ensembles of time series. The

  4. Role of lipase in Burkholderia cepacia complex (Bcc) invasion of lung epithelial cells.

    Science.gov (United States)

    Mullen, T; Markey, K; Murphy, P; McClean, S; Callaghan, M

    2007-12-01

    The Burkholderia cepacia complex (Bcc) is a group of ten closely related species associated with life-threatening infection in cystic fibrosis (CF). These bacteria are highly antibiotic resistant, with some strains transmissible, and in a subgroup of patients, they can cause a rapid and fatal necrotising pneumonia. The Bcc organisms produce a range of exoproducts with virulence potential, including exopolysaccharide, proteases and lipases. Many members of the Bcc are also capable of epithelial cell invasion, although the mechanism(s) involved are poorly understood. This study investigates a role for Bcc lipase in epithelial cell invasion by Bcc strains. Lipase activity was measured in eight species of the Bcc. Strains that produced high levels of lipase were predominantly from the B. multivorans and B. cenocepacia species. Pre-treatment of two epithelial cell lines with Bcc lipase significantly increased invasion by two B. multivorans strains and one B. cenocepacia strain and did not affect either plasma membrane or tight junction integrity. Inhibition of Bcc lipase production by the lipase inhibitor Orlistat significantly decreased invasion by both B. multivorans and B. cenocepacia strains in a concentration-dependent manner. This study demonstrates the extent of lipase production across the Bcc and establishes a potential role for lipase in Bcc epithelial cell invasion.

  5. Human causal discovery from observational data.

    OpenAIRE

    1996-01-01

    Utilizing Bayesian belief networks as a model of causality, we examined medical students' ability to discover causal relationships from observational data. Nine sets of patient cases were generated from relatively simple causal belief networks by stochastic simulation. Twenty participants examined the data sets and attempted to discover the underlying causal relationships. Performance was poor in general, except at discovering the absence of a causal relationship. This work supports the poten...

  6. The Geometry of Small Causal Cones

    CERN Document Server

    Jubb, Ian

    2016-01-01

    We derive a formula for the spacetime volume of a small causal cone. We use this formula within the context of causal set theory to construct causal set expressions for certain geometric quantities relating to a spacetime with a spacelike hypersurface. We also consider a scalar field on the causal set, and obtain causal set expressions relating to its normal derivatives with respect to the hypersurface.

  7. Burkholderia Hep_Hag autotransporter (BuHA proteins elicit a strong antibody response during experimental glanders but not human melioidosis

    Directory of Open Access Journals (Sweden)

    Foster Simon J

    2007-03-01

    Full Text Available Abstract Background The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei. Results Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA proteins. A total of 110/207 positive clones (53% of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3% of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis. Conclusion Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study.

  8. Burkholderia glumae EN EL CULTIVO DE ARROZ EN COSTA RICA

    Directory of Open Access Journals (Sweden)

    Andrea Quesada-Gonz\\u00E1lez

    2014-01-01

    Full Text Available Burkholderia glumae en el cultivo de arroz en Costa Rica. El objetivo de este trabajo fue determinar la presencia de Burkholderia glumae en arroz en Costa Rica. La bacteria Burkholderia glumae está asociada al cultivo del arroz en el que provoca la enfermedad llamada añublo bacterial. Bajo condiciones ambientales favorables, la densidad bacteriana aumenta, lo que provoca que, bajo un sistema de regulación denominado quorum sensing, se expresen sus mecanismos de virulencia mediante la activación de genes responsables para la síntesis de la toxoflavina, que bloquea el flujo de nutrientes, para la biogénesis de flagelos y la respuesta quimiotáctica, y la producción de la enzima catalasa. Las plantas desarrollan la sintomatología que finalmente conlleva a un vaneamiento del grano provocando pérdidas económicas importantes. Se investigó la situación referente a la contaminación del grano de arroz causado por esta bacteria en Costa Rica durante los años 2009 y 2010, mediante un convenio entre la Corporación Nacional Arrocera y el Laboratorio de Fitopatología del Centro de Investigación en Protección de Cultivos de la Universidad de Costa Rica. Se usó la metodología de PCR de punto final recomendada por investigadores del Centro Internacional de Agricultura Tropical en Colombia y se reforzó la identificación, por medio de técnicas de microbiología convencional. Se obtuvieron resultados que indican la presencia de la bacteria en Costa Rica, la primera información sobre la prevalencia de un fitopatógeno bacteriano de gran importancia para el sector arrocero.

  9. Causality and Primordial Tensor Modes

    CERN Document Server

    Baumann, Daniel

    2009-01-01

    We introduce the real space correlation function of $B$-mode polarization of the cosmic microwave background (CMB) as a probe of superhorizon tensor perturbations created by inflation. By causality, any non-inflationary mechanism for gravitational wave production after reheating, like global phase transitions or cosmic strings, must have vanishing correlations for angular separations greater than the angle subtended by the particle horizon at recombination, i.e. $\\theta \\gtrsim 2^\\circ$. Since ordinary $B$-modes are defined non-locally in terms of the Stokes parameters $Q$ and $U$ and therefore don't have to respect causality, special care is taken to define `causal $\\tilde B$-modes' for the analysis. We compute the real space $\\tilde B$-mode correlation function for inflation and discuss its detectability on superhorizon scales where it provides an unambiguous test of inflationary gravitational waves. The correct identification of inflationary tensor modes is crucial since it relates directly to the energy s...

  10. Causal reasoning with mental models.

    Science.gov (United States)

    Khemlani, Sangeet S; Barbey, Aron K; Johnson-Laird, Philip N

    2014-01-01

    This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews evidence both to corroborate the theory and to account for phenomena sometimes taken to be incompatible with it. Finally, it reviews neuroscience evidence indicating that mental models for causal inference are implemented within lateral prefrontal cortex.

  11. Causal reasoning with mental models

    Directory of Open Access Journals (Sweden)

    Sangeet eKhemlani

    2014-10-01

    Full Text Available This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews evidence both to corroborate the theory and to account for phenomena sometimes taken to be incompatible with it. Finally, it reviews neuroscience evidence indicating that mental models for causal inference are implemented within lateral prefrontal cortex.

  12. Causal Models for Risk Management

    Directory of Open Access Journals (Sweden)

    Neysis Hernández Díaz

    2013-12-01

    Full Text Available In this work a study about the process of risk management in major schools in the world. The project management tools worldwide highlights the need to redefine risk management processes. From the information obtained it is proposed the use of causal models for risk analysis based on information from the project or company, say risks and the influence thereof on the costs, human capital and project requirements and detect the damages of a number of tasks without tribute to the development of the project. A study on the use of causal models as knowledge representation techniques causal, among which are the Fuzzy Cognitive Maps (DCM and Bayesian networks, with the most favorable MCD technique to use because it allows modeling the risk information witho ut having a knowledge base either itemize.

  13. Gravitation, Causality, and Quantum Consistency

    CERN Document Server

    Hertzberg, Mark P

    2016-01-01

    We examine the role of consistency with causality and quantum mechanics in determining the properties of gravitation. We begin by constructing two different classes of interacting theories of massless spin 2 particles -- gravitons. One involves coupling the graviton with the lowest number of derivatives to matter, the other involves coupling the graviton with higher derivatives to matter, making use of the linearized Riemann tensor. The first class requires an infinite tower of terms for consistency, which is known to lead uniquely to general relativity. The second class only requires a finite number of terms for consistency, which appears as a new class of theories of massless spin 2. We recap the causal consistency of general relativity and show how this fails in the second class for the special case of coupling to photons, exploiting related calculations in the literature. In an upcoming publication [1] this result is generalized to a much broader set of theories. Then, as a causal modification of general ...

  14. Statistics, Causality and Bell's theorem

    CERN Document Server

    Gill, Richard D

    2012-01-01

    Bell's (1964) theorem is popularly supposed to establish the non-locality of quantum physics as a mathematical-physical theory. Building from this, observed violation of Bell's inequality in experiments such as that of Aspect and coworkers (1982) is popularly supposed to provide empirical proof of non-locality in the real world. This paper reviews recent work on Bell's theorem, linking it to issues in causality as understood by statisticians. The paper starts with a new proof of a strong (finite sample) version of Bell's theorem which relies only on elementary arithmetic and (counting) probability. This proof underscores the fact that Bell's theorem tells us that quantum theory is incompatible with the conjunction of three cherished and formerly uncontroversial physical principles, nicknamed here locality, realism, and freedom. The first, locality, is obviously connected to causality: causal influences need time to propagate spatially. Less obviously, the other two principles, realism and freedom, are also fo...

  15. Introductive remarks on causal inference

    Directory of Open Access Journals (Sweden)

    Silvana A. Romio

    2013-05-01

    Full Text Available One of the more challenging issues in epidemiological research is being able to provide an unbiased estimate of the causal exposure-disease effect, to assess the possible etiological mechanisms and the implication for public health. A major source of bias is confounding, which can spuriously create or mask the causal relationship. In the last ten years, methodological research has been developed to better de_ne the concept of causation in epidemiology and some important achievements have resulted in new statistical models. In this review, we aim to show how a technique the well known by statisticians, i.e. standardization, can be seen as a method to estimate causal e_ects, equivalent under certain conditions to the inverse probability treatment weight procedure.

  16. On Causality in Dynamical Systems

    CERN Document Server

    Harnack, Daniel

    2016-01-01

    Identification of causal links is fundamental for the analysis of complex systems. In dynamical systems, however, nonlinear interactions may hamper separability of subsystems which poses a challenge for attempts to determine the directions and strengths of their mutual influences. We found that asymmetric causal influences between parts of a dynamical system lead to characteristic distortions in the mappings between the attractor manifolds reconstructed from respective local observables. These distortions can be measured in a model-free, data-driven manner. This approach extends basic intuitions about cause-effect relations to deterministic dynamical systems and suggests a mathematically well defined explanation of results obtained from previous methods based on state space reconstruction.

  17. Cohomology with causally restricted supports

    CERN Document Server

    Khavkine, Igor

    2014-01-01

    De Rham cohomology with spacelike compact and timelike compact supports has recently been noticed to be of importance for understanding the structure of classical and quantum field theories on curved spacetimes. We compute these cohomology groups for globally hyperbolic spacetimes in terms of their standard de Rham cohomologies. The calculation exploits the fact that the de Rham-d'Alambert wave operator can be extended to a chain map that is homotopic to zero and that its causal Green function fits into a convenient exact sequence. This method extends also to the Calabi (or Killing-Riemann-Bianchi) complex and possibly other differential complexes. We also discuss generalized causal structures and functoriality.

  18. Kolmogorov Complexity, Causality And Spin

    CERN Document Server

    Shayda, Dara O

    2012-01-01

    A novel topological and computational method for 'motion' is described. Motion is constrained by inequalities in terms of Kolmogorov Complexity. Causality is obtained as the output of a high-pass filter, passing through only high values of Kolmogorov Complexity. Motion under the electromagnetic field described with immediate relationship with Subscript[G, 2] Holonomy group and its corresponding dense free 2-subgroup. Similar to Causality, Spin emerges as an immediate and inevitable consequence of high values of Kolmogorov Complexity. Consequently, the physical laws are nothing but a low-pass filter for small values of Kolmogorov Complexity.

  19. Information thermodynamics on causal networks.

    Science.gov (United States)

    Ito, Sosuke; Sagawa, Takahiro

    2013-11-01

    We study nonequilibrium thermodynamics of complex information flows induced by interactions between multiple fluctuating systems. Characterizing nonequilibrium dynamics by causal networks (i.e., Bayesian networks), we obtain novel generalizations of the second law of thermodynamics and the fluctuation theorem, which include an informational quantity characterized by the topology of the causal network. Our result implies that the entropy production in a single system in the presence of multiple other systems is bounded by the information flow between these systems. We demonstrate our general result by a simple model of biochemical adaptation.

  20. Local Causality, Probability and Explanation

    CERN Document Server

    Healey, Richard A

    2016-01-01

    In papers published in the 25 years following his famous 1964 proof John Bell refined and reformulated his views on locality and causality. Although his formulations of local causality were in terms of probability, he had little to say about that notion. But assumptions about probability are implicit in his arguments and conclusions. Probability does not conform to these assumptions when quantum mechanics is applied to account for the particular correlations Bell argues are locally inexplicable. This account involves no superluminal action and there is even a sense in which it is local, but it is in tension with the requirement that the direct causes and effects of events are nearby.

  1. Granger Causality and Unit Roots

    DEFF Research Database (Denmark)

    Rodríguez-Caballero, Carlos Vladimir; Ventosa-Santaulària, Daniel

    2014-01-01

    The asymptotic behavior of the Granger-causality test under stochastic nonstationarity is studied. Our results confirm that the inference drawn from the test is not reliable when the series are integrated to the first order. In the presence of deterministic components, the test statistic diverges......, eventually rejecting the null hypothesis, even when the series are independent of each other. Moreover, controlling for these deterministic elements (in the auxiliary regressions of the test) does not preclude the possibility of drawing erroneous inferences. Granger-causality tests should not be used under...

  2. Causality and micro-causality in curved spacetime

    Energy Technology Data Exchange (ETDEWEB)

    Hollowood, Timothy J. [Department of Physics, University of Wales Swansea, Swansea, SA2 8PP (United Kingdom)], E-mail: t.hollowood@swansea.ac.uk; Shore, Graham M. [Department of Physics, University of Wales Swansea, Swansea, SA2 8PP (United Kingdom)], E-mail: g.m.shore@swansea.ac.uk

    2007-10-25

    We consider how causality and micro-causality are realised in QED in curved spacetime. The photon propagator is found to exhibit novel non-analytic behaviour due to vacuum polarization, which invalidates the Kramers-Kronig dispersion relation and calls into question the validity of micro-causality in curved spacetime. This non-analyticity is ultimately related to the generic focusing nature of congruences of geodesics in curved spacetime, as implied by the null energy condition, and the existence of conjugate points. These results arise from a calculation of the complete non-perturbative frequency dependence of the vacuum polarization tensor in QED, using novel world-line path integral methods together with the Penrose plane-wave limit of spacetime in the neighbourhood of a null geodesic. The refractive index of curved spacetime is shown to exhibit superluminal phase velocities, dispersion, absorption (due to {gamma}{yields}e{sup +}e{sup -}) and bi-refringence, but we demonstrate that the wavefront velocity (the high-frequency limit of the phase velocity) is indeed c, thereby guaranteeing that causality itself is respected.

  3. Investigating Burkholderia cepacia complex populations recovered from Italian maize rhizosphere by multilocus sequence typing.

    Science.gov (United States)

    Dalmastri, Claudia; Baldwin, Adam; Tabacchioni, Silvia; Bevivino, Annamaria; Mahenthiralingam, Eshwar; Chiarini, Luigi; Dowson, Christopher

    2007-07-01

    The Burkholderia cepacia complex (BCC) comprises at least nine closely related species of abundant environmental microorganisms. Some of these species are highly spread in the rhizosphere of several crop plants, particularly of maize; additionally, as opportunistic pathogens, strains of the BCC are capable of colonizing humans. We have developed and validated a multilocus sequence typing (MLST) scheme for the BCC. Although widely applied to understand the epidemiology of bacterial pathogens, MLST has seen limited application to the population analysis of species residing in the natural environment; we describe its novel application to BCC populations within maize rhizospheres. 115 BCC isolates were recovered from the roots of different maize cultivars from three different Italian regions over a 9-year period (1994-2002). A total of 44 sequence types (STs) were found of which 41 were novel when compared with existing MLST data which encompassed a global database of 1000 clinical and environmental strains representing nearly 400 STs. In this study of rhizosphere isolates approximately 2.5 isolates per ST was found, comparable to that found for the whole BCC population. Multilocus sequence typing also resolved inaccuracies associated with previous identification of the maize isolates based on recA gene restriction fragment length polymorphims and species-specific polymerase chain reaction. The 115 maize isolates comprised the following BCC species groups, B. ambifaria (39%), BCC6 (29%), BCC5 (10%), B. pyrrocinia (8%), B. cenocepacia IIIB (7%) and B. cepacia (6%), with BCC5 and BCC6 potentially constituting novel species groups within the complex. Closely related clonal complexes of strains were identified within B. cepacia, B. cenocepacia IIIB, BCC5 and BCC6, with one of the BCC5 clonal complexes being distributed across all three sampling sites. Overall, our analysis demonstrates that the maize rhizosphere harbours a massive diversity of novel BCC STs, so that their

  4. Disinfection of Burkholderia cepacia complex from non-touch taps in a neonatal nursery.

    Science.gov (United States)

    Kotsanas, Despina; Brett, Judith; Kidd, Tim J; Stuart, Rhonda L; Korman, Tony M

    2008-01-01

    Burkholderia cepacia complex (Bcc) comprises nine closely related species or genomovars. It is an important causative agent of opportunistic infections and waterborne nosocomial infections. B. cepacia (formerly genomovar I) was identified from the blood culture of a baby in our neonatal unit (NU) in March 2005. B. cepacia was isolated four times from clinical specimens since the introduction of non-touch taps in the NU from 2000 to 2005 and only once from 1994 to 2000. Environmental samples were collected from the NU, including tap water from non-touch taps. Clinical and environmental isolates of Bcc were characterized using molecular identification and strain typing. A literature review was undertaken to delineate a method for eradication of Bcc. Several variations for hot water eradication of the organism from the taps were attempted. Genotyping and molecular analysis revealed that tap water isolates were B. cenocepacia which was a different species from the B. cepacia isolated from blood cultures of the neonate. However, B. cenocepacia has been known to cause nosocomial outbreaks and it was eventually eradicated from the NU by using repeated thermal shock (hot water at 65 degrees C for 10 min), changing taps and decolonizing sinks with hypochlorite. Molecular typing is useful in assisting the investigation of Bcc nosocomial infections.

  5. The argumentative impact of causal relations

    DEFF Research Database (Denmark)

    Nielsen, Anne Ellerup

    1996-01-01

    such as causality, explanation and justification. In certain types of discourse, causal relations also imply an intentional element. This paper describes the way in which the semantic and pragmatic functions of causal markers can be accounted for in terms of linguistic and rhetorical theories of argumentation.......The semantic relations between and within utterances are marked by the use of connectors and adverbials. One type of semantic relations is causal relations expressed by causal markers such as because, therefore, so, for, etc. Some of these markers cover different types of causal relations...

  6. Causality problem in Economic Science

    Directory of Open Access Journals (Sweden)

    JOSÉ LUIS RETOLAZA

    2007-12-01

    Full Text Available The main point of the paper is the problem of the economy to be consider like a science in the most strict term of the concept. In the first step we are going to tackle a presentation about what we understand by science to subsequently present some of the fallacies which have bring certain scepticism about the scientific character of the investigation in economy, to know: 1 The differences between hard and weak sciences -physics and social; 2 The differences between paradigm, —positivist and phenomenological— 3 The differences between physic causalityand historic causality. In the second step we are going to talk about two fundamental problems which are questioned: 1 the confusion between ontology and gnoseology and, 2 the erroneous concept of causality that commonly is used. In the last step of the paper we are going over the recent models of «causal explanation» and we suggest the probabilistic casualty development next with a more elaborated models of causal explanation, like a way to conjugate the scientific severity with the possibility to tackle complex economic realities.

  7. Causal Categories: Relativistically Interacting Processes

    Science.gov (United States)

    Coecke, Bob; Lal, Raymond

    2013-04-01

    A symmetric monoidal category naturally arises as the mathematical structure that organizes physical systems, processes, and composition thereof, both sequentially and in parallel. This structure admits a purely graphical calculus. This paper is concerned with the encoding of a fixed causal structure within a symmetric monoidal category: causal dependencies will correspond to topological connectedness in the graphical language. We show that correlations, either classical or quantum, force terminality of the tensor unit. We also show that well-definedness of the concept of a global state forces the monoidal product to be only partially defined, which in turn results in a relativistic covariance theorem. Except for these assumptions, at no stage do we assume anything more than purely compositional symmetric-monoidal categorical structure. We cast these two structural results in terms of a mathematical entity, which we call a causal category. We provide methods of constructing causal categories, and we study the consequences of these methods for the general framework of categorical quantum mechanics.

  8. Causal feedbacks in climate change

    NARCIS (Netherlands)

    Nes, van E.H.; Scheffer, M.; Brovkin, V.; Lenton, T.M.; Ye, H.; Deyle, E.; Sugihara, G.

    2015-01-01

    The statistical association between temperature and greenhouse gases over glacial cycles is well documented1, but causality behind this correlation remains difficult to extract directly from the data. A time lag of CO2 behind Antarctic temperature—originally thought to hint at a driving role for tem

  9. An Introduction to Causal Inference

    Science.gov (United States)

    2009-11-02

    legitimize causal inference, has removed causation from its natural habitat, and distorted its face beyond recognition. This exclusivist attitude is...In contrast, when the mediation problem is approached from an exclusivist potential-outcome viewpoint, void of the structural guidance of Eq. (28

  10. Breaking the arrows of causality

    DEFF Research Database (Denmark)

    Valsiner, Jaan

    2014-01-01

    Theoretical models of catalysis have proven to bring with them major breakthroughs in chemistry and biology, from the 1830s onward. It can be argued that the scientific status of chemistry has become established through the move from causal to catalytic models. Likewise, the central explanatory...

  11. Learning a Theory of Causality

    Science.gov (United States)

    Goodman, Noah D.; Ullman, Tomer D.; Tenenbaum, Joshua B.

    2011-01-01

    The very early appearance of abstract knowledge is often taken as evidence for innateness. We explore the relative learning speeds of abstract and specific knowledge within a Bayesian framework and the role for innate structure. We focus on knowledge about causality, seen as a domain-general intuitive theory, and ask whether this knowledge can be…

  12. Free Fermions on causal sets

    CERN Document Server

    Noldus, Johan

    2013-01-01

    We construct a Dirac theory on causal sets; a key element in the construction being that the causet must be regarded as emergent in an appropriate sense too. We further notice that mixed norm spaces appear in the construction allowing for negative norm particles and "ghosts".

  13. Entanglement, holography and causal diamonds

    Science.gov (United States)

    de Boer, Jan; Haehl, Felix M.; Heller, Michal P.; Myers, Robert C.

    2016-08-01

    We argue that the degrees of freedom in a d-dimensional CFT can be reorganized in an insightful way by studying observables on the moduli space of causal diamonds (or equivalently, the space of pairs of timelike separated points). This 2 d-dimensional space naturally captures some of the fundamental nonlocality and causal structure inherent in the entanglement of CFT states. For any primary CFT operator, we construct an observable on this space, which is defined by smearing the associated one-point function over causal diamonds. Known examples of such quantities are the entanglement entropy of vacuum excitations and its higher spin generalizations. We show that in holographic CFTs, these observables are given by suitably defined integrals of dual bulk fields over the corresponding Ryu-Takayanagi minimal surfaces. Furthermore, we explain connections to the operator product expansion and the first law of entanglemententropy from this unifying point of view. We demonstrate that for small perturbations of the vacuum, our observables obey linear two-derivative equations of motion on the space of causal diamonds. In two dimensions, the latter is given by a product of two copies of a two-dimensional de Sitter space. For a class of universal states, we show that the entanglement entropy and its spin-three generalization obey nonlinear equations of motion with local interactions on this moduli space, which can be identified with Liouville and Toda equations, respectively. This suggests the possibility of extending the definition of our new observables beyond the linear level more generally and in such a way that they give rise to new dynamically interacting theories on the moduli space of causal diamonds. Various challenges one has to face in order to implement this idea are discussed.

  14. Causal inference in obesity research.

    Science.gov (United States)

    Franks, P W; Atabaki-Pasdar, N

    2017-03-01

    Obesity is a risk factor for a plethora of severe morbidities and premature death. Most supporting evidence comes from observational studies that are prone to chance, bias and confounding. Even data on the protective effects of weight loss from randomized controlled trials will be susceptible to confounding and bias if treatment assignment cannot be masked, which is usually the case with lifestyle and surgical interventions. Thus, whilst obesity is widely considered the major modifiable risk factor for many chronic diseases, its causes and consequences are often difficult to determine. Addressing this is important, as the prevention and treatment of any disease requires that interventions focus on causal risk factors. Disease prediction, although not dependent on knowing the causes, is nevertheless enhanced by such knowledge. Here, we provide an overview of some of the barriers to causal inference in obesity research and discuss analytical approaches, such as Mendelian randomization, that can help to overcome these obstacles. In a systematic review of the literature in this field, we found: (i) probable causal relationships between adiposity and bone health/disease, cancers (colorectal, lung and kidney cancers), cardiometabolic traits (blood pressure, fasting insulin, inflammatory markers and lipids), uric acid concentrations, coronary heart disease and venous thrombosis (in the presence of pulmonary embolism), (ii) possible causal relationships between adiposity and gray matter volume, depression and common mental disorders, oesophageal cancer, macroalbuminuria, end-stage renal disease, diabetic kidney disease, nuclear cataract and gall stone disease, and (iii) no evidence for causal relationships between adiposity and Alzheimer's disease, pancreatic cancer, venous thrombosis (in the absence of pulmonary embolism), liver function and periodontitis.

  15. BIOAUGMENTATION WITH BURKHOLDERIA CEPACIA PR1301 FOR IN SITU BIOREMEDIATION OF TRICHLOROETHYLENE CONTAMINATED GROUNDWATER (RESEARCH BRIEF)

    Science.gov (United States)

    A pilot field study was conducted at the Moffett Federal Airfield, Mountain View, California, to determine whether effective in-situ aerobic cometabolic biodegradation of TCE could be accomplished through bioaugmentation with a genetically modified strain of Burkholderia cepacia ...

  16. Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina

    Science.gov (United States)

    Draghi, Walter Omar; Mancini Villagra, Ulises M.; Wall, Luis Gabriel

    2015-01-01

    Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments. PMID:26494680

  17. Determining the Biochemical Properties of the Oxalate Biosynthetic Component (Obc)1 from Burkholderia mallei

    OpenAIRE

    Lambert, Peter M.; Nakata, Paul A.

    2016-01-01

    Oxalic acid is produced by a variety of organisms ranging from simple microbes to complex animals. This acid has been proposed to fulfill various physiological and pathological functions which vary between organisms. In bacteria from the Burkholderia genus, oxalate secretion has been shown to be quorum sensing dependent and to support pathogenicity and cell viability. In light of the critical roles of oxalate in Burkholderia as well as other organisms, it is surprising that our understanding ...

  18. Causal inference in economics and marketing.

    Science.gov (United States)

    Varian, Hal R

    2016-07-05

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference.

  19. Exploring Individual Differences in Preschoolers' Causal Stance

    Science.gov (United States)

    Alvarez, Aubry; Booth, Amy E.

    2016-01-01

    Preschoolers, as a group, are highly attuned to causality, and this attunement is known to facilitate memory, learning, and problem solving. However, recent work reveals substantial individual variability in the strength of children's "causal stance," as demonstrated by their curiosity about and preference for new causal information. In…

  20. Representing Personal Determinants in Causal Structures.

    Science.gov (United States)

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  1. Designing Effective Supports for Causal Reasoning

    Science.gov (United States)

    Jonassen, David H.; Ionas, Ioan Gelu

    2008-01-01

    Causal reasoning represents one of the most basic and important cognitive processes that underpin all higher-order activities, such as conceptual understanding and problem solving. Hume called causality the "cement of the universe" [Hume (1739/2000). Causal reasoning is required for making predictions, drawing implications and…

  2. Designing Effective Supports for Causal Reasoning

    Science.gov (United States)

    Jonassen, David H.; Ionas, Ioan Gelu

    2008-01-01

    Causal reasoning represents one of the most basic and important cognitive processes that underpin all higher-order activities, such as conceptual understanding and problem solving. Hume called causality the "cement of the universe" [Hume (1739/2000). Causal reasoning is required for making predictions, drawing implications and inferences, and…

  3. Decomposing Granger Causality over the Spectrum

    NARCIS (Netherlands)

    A. Lemmens (Aurélie); C. Croux (Christophe); M.G. Dekimpe (Marnik)

    2004-01-01

    textabstractWe develop a bivariate spectral Granger-causality test that can be applied at each individual frequency of the spectrum. The spectral approach to Granger causality has the distinct advantage that it allows to disentangle (potentially) di®erent Granger- causality relationships over di®ere

  4. Expectations and Interpretations during Causal Learning

    Science.gov (United States)

    Luhmann, Christian C.; Ahn, Woo-kyoung

    2011-01-01

    In existing models of causal induction, 4 types of covariation information (i.e., presence/absence of an event followed by presence/absence of another event) always exert identical influences on causal strength judgments (e.g., joint presence of events always suggests a generative causal relationship). In contrast, we suggest that, due to…

  5. Velocity requirements for causality violation

    CERN Document Server

    Modanese, Giovanni

    2013-01-01

    It is known that the hypothetical existence of superluminal signals would imply the logical possibility of active causal violation: an observer in relative motion with respect to a primary source could in principle emit secondary superluminal signals (triggered by the primary ones) which go back in time and deactivate the primary source before the initial emission. This is a direct consequence of the structure of the Lorentz transformations, sometimes called "Regge-Tolman paradox". It is straightforward to find a formula for the velocity of the moving observer required to produce the causality violation. When applied to some recent claims of slight superluminal propagation, this formula yields a required velocity very close to the speed of light; this raises some doubts about the real physical observability of such violations. We re-compute this velocity requirement introducing a realistic delay between the reception of the primary signal and the emission of the secondary. It turns out that for -any- delay it...

  6. Painless causality in defect calculations

    CERN Document Server

    Cheung, C; Cheung, Charlotte; Magueijo, Joao

    1997-01-01

    Topological defects must respect causality, a statement leading to restrictive constraints on the power spectrum of the total cosmological perturbations they induce. Causality constraints have for long been known to require the presence of an under-density in the surrounding matter compensating the defect network on large scales. This so-called compensation can never be neglected and significantly complicates calculations in defect scenarios, eg. computing cosmic microwave background fluctuations. A quick and dirty way to implement the compensation are the so-called compensation fudge factors. Here we derive the complete photon-baryon-CDM backreaction effects in defect scenarios. The fudge factor comes out as an algebraic identity and so we drop the negative qualifier ``fudge''. The compensation scale is computed and physically interpreted. Secondary backreaction effects exist, and neglecting them constitutes the well-defined approximation scheme within which one should consider compensation factor calculatio...

  7. Confounding Equivalence in Causal Inference

    CERN Document Server

    Pearl, Judea

    2012-01-01

    The paper provides a simple test for deciding, from a given causal diagram, whether two sets of variables have the same bias-reducing potential under adjustment. The test re- quires that one of the following two condi- tions holds: either (1) both sets are admis- sible (i.e., satisfy the back-door criterion) or (2) the Markov boundaries surrounding the manipulated variable(s) are identical in both sets. Applications to covariate selection and model testing are discussed.

  8. Phenomenology of Causal Dynamical Triangulations

    CERN Document Server

    Mielczarek, Jakub

    2015-01-01

    The four dimensional Causal Dynamical Triangulations (CDT) approach to quantum gravity is already more than ten years old theory with numerous unprecedented predictions such as non-trivial phase structure of gravitational field and dimensional running. Here, we discuss possible empirical consequences of CDT derived based on the two features of the approach mentioned above. A possibility of using both astrophysical and cosmological observations to test CDT is discussed. We show that scenarios which can be ruled out at the empirical level exist.

  9. Causality and primordial tensor modes

    Energy Technology Data Exchange (ETDEWEB)

    Baumann, Daniel; Zaldarriaga, Matias, E-mail: dbaumann@physics.harvard.edu, E-mail: mzaldarriaga@cfa.harvard.edu [Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, U.S.A. and Center for Astrophysics, Harvard University, 60 Garden Street, Cambridge, MA 02138 (United States)

    2009-06-01

    We introduce the real space correlation function of B-mode polarization of the cosmic microwave background (CMB) as a probe of superhorizon tensor perturbations created by inflation. By causality, any non-inflationary mechanism for gravitational wave production after reheating, like global phase transitions or cosmic strings, must have vanishing correlations for angular separations greater than the angle subtended by the particle horizon at recombination, i.e. θ ∼> 2°. Since ordinary B-modes are defined non-locally in terms of the Stokes parameters Q and U and therefore don't have to respect causality, special care is taken to define 'causal B-tilde -modes' for the analysis. We compute the real space B-tilde -mode correlation function for inflation and discuss its detectability on superhorizon scales where it provides an unambiguous test of inflationary gravitational waves. The correct identification of inflationary tensor modes is crucial since it relates directly to the energy scale of inflation. Wrongly associating tensor modes from causal seeds with inflation would imply an incorrect inference of the energy scale of inflation. We find that the superhorizon B-tilde -mode signal is above cosmic variance for the angular range 2° < θ < 4° and is therefore in principle detectable. In practice, the signal will be challenging to measure since it requires accurately resolving the recombination peak of the B-mode power spectrum. However, a future CMB satellite (CMBPol), with noise level Δ{sub P} ≅ 1μK-arcmin and sufficient resolution to efficiently correct for lensing-induced B-modes, should be able to detect the signal at more than 3σ if the tensor-to-scalar ratio isn't smaller than r ≅ 0.01.

  10. Burkholderia cepacia Complex Regulation of Virulence Gene Expression: A Review

    Science.gov (United States)

    Sousa, Sílvia A.; Feliciano, Joana R.; Pita, Tiago; Guerreiro, Soraia I.; Leitão, Jorge H.

    2017-01-01

    Burkholderia cepacia complex (Bcc) bacteria emerged as opportunistic pathogens in cystic fibrosis and immunocompromised patients. Their eradication is very difficult due to the high level of intrinsic resistance to clinically relevant antibiotics. Bcc bacteria have large and complex genomes, composed of two to four replicons, with variable numbers of insertion sequences. The complexity of Bcc genomes confers a high genomic plasticity to these bacteria, allowing their adaptation and survival to diverse habitats, including the human host. In this work, we review results from recent studies using omics approaches to elucidate in vivo adaptive strategies and virulence gene regulation expression of Bcc bacteria when infecting the human host or subject to conditions mimicking the stressful environment of the cystic fibrosis lung. PMID:28106859

  11. Glanders: off to the races with Burkholderia mallei.

    Science.gov (United States)

    Whitlock, Gregory C; Estes, D Mark; Torres, Alfredo G

    2007-12-01

    Burkholderia mallei, the etiologic agent of the disease known as glanders, is primarily a disease affecting horses and is transmitted to humans by direct contact with infected animals. The use of B. mallei as a biological weapon has been reported and currently, there is no vaccine available for either humans or animals. Despite the history and highly infective nature of B. mallei, as well as its potential use as a bio-weapon, B. mallei research to understand the pathogenesis and the host responses to infection remains limited. Therefore, this minireview will focus on current efforts to elucidate B. mallei virulence, the associated host immune responses elicited during infection and discuss the feasibility of vaccine development.

  12. Modeling of causality with metamaterials

    Science.gov (United States)

    Smolyaninov, Igor I.

    2013-02-01

    Hyperbolic metamaterials may be used to model a 2 + 1-dimensional Minkowski space-time in which the role of time is played by one of the spatial coordinates. When a metamaterial is built and illuminated with a coherent extraordinary laser beam, the stationary pattern of light propagation inside the metamaterial may be treated as a collection of particle world lines, which represents a complete ‘history’ of this 2 + 1-dimensional space-time. While this model may be used to build interesting space-time analogs, such as metamaterial ‘black holes’ and a metamaterial ‘big bang’, it lacks causality: since light inside the metamaterial may propagate back and forth along the ‘timelike’ spatial coordinate, events in the ‘future’ may affect events in the ‘past’. Here we demonstrate that a more sophisticated metamaterial model may fix this deficiency via breaking the mirror and temporal (PT) symmetries of the original model and producing one-way propagation along the ‘timelike’ spatial coordinate. The resulting 2 + 1-dimensional Minkowski space-time appears to be causal. This scenario may be considered as a metamaterial model of the Wheeler-Feynman absorber theory of causality.

  13. Entanglement, Holography and Causal Diamonds

    CERN Document Server

    de Boer, Jan; Heller, Michal P; Myers, Robert C

    2016-01-01

    We argue that the degrees of freedom in a d-dimensional CFT can be re-organized in an insightful way by studying observables on the moduli space of causal diamonds (or equivalently, the space of pairs of timelike separated points). This 2d-dimensional space naturally captures some of the fundamental nonlocality and causal structure inherent in the entanglement of CFT states. For any primary CFT operator, we construct an observable on this space, which is defined by smearing the associated one-point function over causal diamonds. Known examples of such quantities are the entanglement entropy of vacuum excitations and its higher spin generalizations. We show that in holographic CFTs, these observables are given by suitably defined integrals of dual bulk fields over the corresponding Ryu-Takayanagi minimal surfaces. Furthermore, we explain connections to the operator product expansion and the first law of entanglement entropy from this unifying point of view. We demonstrate that for small perturbations of the va...

  14. Development of ceftazidime resistance in an acute Burkholderia pseudomallei infection

    Directory of Open Access Journals (Sweden)

    Sarovich DS

    2012-08-01

    Full Text Available Derek S Sarovich,1,2,* Erin P Price,1,2,* Direk Limmathurotsakul,3 James M Cook,1 Alex T Von Schulze,1 Spenser R Wolken,1 Paul Keim,1 Sharon J Peacock,3,4 Talima Pearson1 1Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA; 2Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Darwin, Australia; 3Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; 4Department of Medicine, University of Cambridge, Cambridge, United Kingdom*These authors contributed equally to this workAbstract: Burkholderia pseudomallei, a bacterium that causes the disease melioidosis, is intrinsically resistant to many antibiotics. First-line antibiotic therapy for treating melioidosis is usually the synthetic β-lactam, ceftazidime (CAZ, as almost all B. pseudomallei strains are susceptible to this drug. However, acquired CAZ resistance can develop in vivo during treatment with CAZ, which can lead to mortality if therapy is not switched to a different drug in a timely manner. Serial B. pseudomallei isolates obtained from an acute Thai melioidosis patient infected by a CAZ susceptible strain, who ultimately succumbed to infection despite being on CAZ therapy for the duration of their infection, were analyzed. Isolates that developed CAZ resistance due to a proline to serine change at position 167 in the β-lactamase PenA were identified. Importantly, these CAZ resistant isolates remained sensitive to the alternative melioidosis treatments; namely, amoxicillin-clavulanate, imipenem, and meropenem. Lastly, real-time polymerase chain reaction-based assays capable of rapidly identifying CAZ resistance in B. pseudomallei isolates at the position 167 mutation site were developed. The ability to rapidly identify the emergence of CAZ resistant B. pseudomallei populations in melioidosis patients will allow timely alterations in treatment strategies

  15. Use of the common marmoset to study Burkholderia mallei infection.

    Science.gov (United States)

    Jelesijevic, Tomislav; Zimmerman, Shawn M; Harvey, Stephen B; Mead, Daniel G; Shaffer, Teresa L; Estes, D Mark; Michel, Frank; Quinn, Frederick D; Hogan, Robert J; Lafontaine, Eric R

    2015-01-01

    Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus) were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4) to 2.5 X 10(5) bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3) bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3) organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B. mallei.

  16. Burkholderia glumae en el cultivo de arroz en Costa Rica.

    Directory of Open Access Journals (Sweden)

    Andrea Quesada-González

    2014-07-01

    Full Text Available El objetivo de este trabajo fue determinar la presencia de Burkholderia glumae en arroz en Costa Rica. La bacteria Burkholderia glumae está asociada al cultivo del arroz en el que provoca la enfermedad llamada añublo bacterial. Bajo condiciones ambientales favorables, la densidad bacteriana aumenta, lo que provoca que, bajo un sistema de regulación denominado quorum sensing, se expresen sus mecanismos de virulencia mediante la activación de genes responsables para la síntesis de la toxoflavina, que bloquea el flujo de nutrientes, para la biogénesis de flagelos y la respuesta quimiotáctica, y la producción de la enzima catalasa. Las plantas desarrollan la sintomatología que finalmente conlleva a un vaneamiento del grano provocando pérdidas económicas importantes. Se investigó la situación referente a la contaminación del grano de arroz causado por esta bacteria en Costa Rica durante los años 2009 y 2010, mediante un convenio entre la Corporación Nacional Arrocera y el Laboratorio de Fitopatología del Centro de Investigación en Protección de Cultivos de la Universidad de Costa Rica. Se usó la metodología de PCR de punto final recomendada por investigadores del Centro Internacional de Agricultura Tropical en Colombia y se reforzó la identificación, por medio de técnicas de microbiología convencional. Se obtuvieron resultados que indican la presencia de la bacteria en Costa Rica, la primera información sobre la prevalencia de un fitopatógeno bacteriano de gran importancia para el sector arrocero.

  17. Use of the common marmoset to study Burkholderia mallei infection.

    Directory of Open Access Journals (Sweden)

    Tomislav Jelesijevic

    Full Text Available Burkholderia mallei is a host-adapted bacterium that does not persist outside of its equine reservoir. The organism causes the zoonosis glanders, which is endemic in Asia, Africa, the Middle East and South America. Infection by B. mallei typically occurs via the respiratory or percutaneous route, and the most common manifestations are life-threatening pneumonia and bacteremia. Glanders is difficult to diagnose and requires prolonged antibiotic therapy with low success rates. There is no vaccine to protect against B. mallei and there is concern regarding its use as a biothreat agent. Thus, experiments were performed to establish a non-human primate model of intranasal infection to study the organism and develop countermeasures. Groups of marmosets (Callithrix jacchus were inoculated intranasally with B. mallei strain ATCC 23344 and monitored for clinical signs of illness for up to 13 days. We discovered that 83% of marmosets inoculated with doses of 2.5 X 10(4 to 2.5 X 10(5 bacteria developed acute lethal infection within 3-4 days. Signs of disease were severe and included lethargy, inappetence, conjunctivitis, mucopurulent and hemorrhagic nasal discharges, and increased respiratory effort with abdominal lifts. Burkholderia mallei was cultured from the lungs, spleen and liver of these animals, and pathologic examination of tissues revealed lesions characteristic of glanders. Challenge experiments also revealed that 91% of animals infected with doses ranging from 25 to 2.5 X 10(3 bacteria exhibited mild non-specific signs of illness and were culture negative. One marmoset inoculated with 2.5 X 10(3 organisms developed moderate signs of disease and reached humane end-points 8 days post-infection. The liver and spleen of this animal were colonized with the agent and pathological analysis of tissues showed nasal, splenic and hepatic lesions. Taken together, these data indicate that the marmoset is a suitable model to study respiratory infection by B

  18. 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.

  19. [Bacteria of the Burkholderia cepacia complex: specific features of diagnostics, genome organization and metabolism].

    Science.gov (United States)

    Shaginian, I A; Chernukha, M Iu

    2003-01-01

    Modern data, related with the identification and typing of the complex B. cepacia bacteria, are analyzed in the article by using the poly-phase taxonomic approach. An optimal scheme for identifying and typing the complex B. cepacia bacteria, involving the microbiological and molecular-biological methods of laboratory diagnostics, is presented. The key and assumed factors of pathogenicity of the discussed bacteria are described. The possible phylogenetic relations of the complex B. cepacia bacteria with phytopathgens as well as with pathogenic bacteria of species Burkholderia, Pseudomonas, Escherichia, B. mallei, B. pdeudomallei, P. seruginosa and E. coli are described. A possible role of genome alterations and mutations in the genome of the complex B. cepacia bacteria (with the latter genome having unusual properties, i.e. a big size, and a considerable quantity of insertion sequences) in creating the conditions for the "pulsing" evolution "jerks", i.e. for a rapid change-over from saprophytism in the soil to a pathogenic causative agent of a viral-and-bacteriological infection. Such mechanism can be regarded as a rapid and radical adaptation of a microorganism under the conditions of changing ecological niches.

  20. Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing

    Directory of Open Access Journals (Sweden)

    Karger Axel

    2012-10-01

    Full Text Available Abstract Background Burkholderia (B. pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343 was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS

  1. Experimental verification of an indefinite causal order

    Science.gov (United States)

    Rubino, Giulia; Rozema, Lee A.; Feix, Adrien; Araújo, Mateus; Zeuner, Jonas M.; Procopio, Lorenzo M.; Brukner, Časlav; Walther, Philip

    2017-01-01

    Investigating the role of causal order in quantum mechanics has recently revealed that the causal relations of events may not be a priori well defined in quantum theory. Although this has triggered a growing interest on the theoretical side, creating processes without a causal order is an experimental task. We report the first decisive demonstration of a process with an indefinite causal order. To do this, we quantify how incompatible our setup is with a definite causal order by measuring a “causal witness.” This mathematical object incorporates a series of measurements that are designed to yield a certain outcome only if the process under examination is not consistent with any well-defined causal order. In our experiment, we perform a measurement in a superposition of causal orders—without destroying the coherence—to acquire information both inside and outside of a “causally nonordered process.” Using this information, we experimentally determine a causal witness, demonstrating by almost 7 SDs that the experimentally implemented process does not have a definite causal order.

  2. Norms and customs: causally important or causally impotent?

    Science.gov (United States)

    Jones, Todd

    2010-01-01

    In this article, I argue that norms and customs, despite frequently being described as being causes of behavior in the social sciences and ordinary conversation, cannot really cause behavior. Terms like "norms" and the like seem to refer to philosophically disreputable disjunctive properties. More problematically, even if they do not, or even if there can be disjunctive properties after all, I argue that norms and customs still cannot cause behavior. The social sciences would be better off without referring to properties like norms and customs as if they could be causal.

  3. Burkholderia mallei and Burkholderia pseudomallei stimulate differential inflammatory responses from human alveolar type II cells (ATII and macrophages.

    Directory of Open Access Journals (Sweden)

    Richard eLu

    2012-12-01

    Full Text Available Alveolar type II pneumocytes (ATII and alveolar macrophages (AM play a crucial role in the lung’s innate immune response. Burkholderia pseudomallei (BP and Burkholderia mallei (BM are facultative Gram-negative bacilli that cause melioidosis and glanders, respectively. The inhalation of these pathogens can cause lethal disease and death in humans. We sought to compare the pathogenesis of and host responses to BP and BM through contact with human primary ATII cells and monocytes-derived macrophages (MDM. We hypothesized that because BP and BM induce different disease outcomes, each pathogen would induce distinct, unique host immune responses from resident pulmonary cells. Our findings showed that BP adhered readily to ATII cells compared to BM. BP, but not BM, was rapidly internalized by macrophages where it replicated to high numbers. Further, BP induced significantly higher levels of pro-inflammatory cytokine secretion from ATII cells (IL-6, IL-8 and macrophages (IL-6, TNFα at 6h post-infection compared to BM (p<0.05. Interestingly, BM induced the anti-inflammatory cytokine, IL-10, in ATII cells and macrophages at 6h post-infection, with delayed induction of inflammatory cytokines at 24h post-infection. Because BP is flagellated and produces LPS, we confirmed that it stimulated both Toll-like receptor (TLR 4 and TLR5 via NF-κb activation while the non-flagellated BM stimulated only TLR4. These data show the differences in BP and BM pathogenicity in the lung when infecting human ATII cells and macrophages and demonstrate the ability of these pathogens to elicit distinct immune responses from resident lung cells which may open new targets for therapeutic intervention to fight against these pathogens.

  4. Independence and dependence in human causal reasoning.

    Science.gov (United States)

    Rehder, Bob

    2014-07-01

    Causal graphical models (CGMs) are a popular formalism used to model human causal reasoning and learning. The key property of CGMs is the causal Markov condition, which stipulates patterns of independence and dependence among causally related variables. Five experiments found that while adult's causal inferences exhibited aspects of veridical causal reasoning, they also exhibited a small but tenacious tendency to violate the Markov condition. They also failed to exhibit robust discounting in which the presence of one cause as an explanation of an effect makes the presence of another less likely. Instead, subjects often reasoned "associatively," that is, assumed that the presence of one variable implied the presence of other, causally related variables, even those that were (according to the Markov condition) conditionally independent. This tendency was unaffected by manipulations (e.g., response deadlines) known to influence fast and intuitive reasoning processes, suggesting that an associative response to a causal reasoning question is sometimes the product of careful and deliberate thinking. That about 60% of the erroneous associative inferences were made by about a quarter of the subjects suggests the presence of substantial individual differences in this tendency. There was also evidence that inferences were influenced by subjects' assumptions about factors that disable causal relations and their use of a conjunctive reasoning strategy. Theories that strive to provide high fidelity accounts of human causal reasoning will need to relax the independence constraints imposed by CGMs.

  5. Space and time in perceptual causality

    Directory of Open Access Journals (Sweden)

    Benjamin Straube

    2010-04-01

    Full Text Available Inferring causality is a fundamental feature of human cognition that allows us to theorize about and predict future states of the world. Michotte suggested that humans automatically perceive causality based on certain perceptual features of events. However, individual differences in judgments of perceptual causality cast doubt on Michotte’s view. To gain insights in the neural basis of individual difference in the perception of causality, our participants judged causal relationships in animations of a blue ball colliding with a red ball (a launching event while fMRI-data were acquired. Spatial continuity and temporal contiguity were varied parametrically in these stimuli. We did not find consistent brain activation differences between trials judged as caused and those judged as non-caused, making it unlikely that humans have universal instantiation of perceptual causality in the brain. However, participants were slower to respond to and showed greater neural activity for violations of causality, suggesting that humans are biased to expect causal relationships when moving objects appear to interact. Our participants demonstrated considerable individual differences in their sensitivity to spatial and temporal characteristics in perceiving causality. These qualitative differences in sensitivity to time or space in perceiving causality were instantiated in individual differences in activation of the left basal ganglia or right parietal lobe, respectively. Thus, the perception that the movement of one object causes the movement of another is triggered by elemental spatial and temporal sensitivities, which themselves are instantiated in specific distinct neural networks.

  6. How prescriptive norms influence causal inferences.

    Science.gov (United States)

    Samland, Jana; Waldmann, Michael R

    2016-11-01

    Recent experimental findings suggest that prescriptive norms influence causal inferences. The cognitive mechanism underlying this finding is still under debate. We compare three competing theories: The culpable control model of blame argues that reasoners tend to exaggerate the causal influence of norm-violating agents, which should lead to relatively higher causal strength estimates for these agents. By contrast, the counterfactual reasoning account of causal selection assumes that norms do not alter the representation of the causal model, but rather later causal selection stages. According to this view, reasoners tend to preferentially consider counterfactual states of abnormal rather than normal factors, which leads to the choice of the abnormal factor in a causal selection task. A third view, the accountability hypothesis, claims that the effects of prescriptive norms are generated by the ambiguity of the causal test question. Asking whether an agent is a cause can be understood as a request to assess her causal contribution but also her moral accountability. According to this theory norm effects on causal selection are mediated by accountability judgments that are not only sensitive to the abnormality of behavior but also to mitigating factors, such as intentionality and knowledge of norms. Five experiments are presented that favor the accountability account over the two alternative theories.

  7. Primordial Magnetic Fields and Causality

    CERN Document Server

    Durrer, R; Durrer, Ruth; Caprini, Chiara

    2003-01-01

    In this letter we discuss the implications of causality on a primordial magnetic field. We show that the residual field on large scales is much stronger suppressed than usually assumed and that a helical component is even suppressed even more than the parity even part. We show that due to this strong suppression, even maximal primordial fields generated at the electroweak phase transition can just marginally seed the fields in galaxies and clusters, but they cannot leave any detectable imprint on the cosmic microwave background.

  8. Random number generators and causality

    Energy Technology Data Exchange (ETDEWEB)

    Larrondo, H.A. [Facultad de Ingenieria, Universidad Nacional de Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata (Argentina)]. E-mail: larrondo@fi.mdp.edu.ar; Martin, M.T. [Instituto de Fisica (IFLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata and Argentina' s National Council (CONICET), C.C. 727, 1900 La Plata (Argentina)]. E-mail: mtmartin@venus.unlp.edu.ar; Gonzalez, C.M. [Facultad de Ingenieria, Universidad Nacional de Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata (Argentina)]. E-mail: cmgonzal@fi.mdp.edu.ar; Plastino, A. [Instituto de Fisica (IFLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata and Argentina' s National Council (CONICET), C.C. 727, 1900 La Plata (Argentina)]. E-mail: plastino@venus.unlp.edu.ar; Rosso, O.A. [Chaos and Biology Group, Instituto de Calculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellon II, Ciudad Universitaria, 1428 Ciudad de Buenos Aires (Argentina)]. E-mail: oarosso@fibertel.com.ar

    2006-04-03

    We advance a prescription to randomize physical or algorithmic Random Number Generators (RNG's) that do not pass Marsaglia's DIEHARD test suite and discuss a special physical quantifier, based on an intensive statistical complexity measure, that is able to adequately assess the improvements produced thereby. Eight RNG's are evaluated and the associated results are compared to those obtained by recourse to Marsaglia's DIEHARD test suite. Our quantifier, which is evaluated using causality arguments, can forecast whether a given RNG will pass the above mentioned test.

  9. Random number generators and causality

    Science.gov (United States)

    Larrondo, H. A.; Martín, M. T.; González, C. M.; Plastino, A.; Rosso, O. A.

    2006-04-01

    We advance a prescription to randomize physical or algorithmic Random Number Generators (RNG's) that do not pass Marsaglia's DIEHARD test suite and discuss a special physical quantifier, based on an intensive statistical complexity measure, that is able to adequately assess the improvements produced thereby. Eight RNG's are evaluated and the associated results are compared to those obtained by recourse to Marsaglia's DIEHARD test suite. Our quantifier, which is evaluated using causality arguments, can forecast whether a given RNG will pass the above mentioned test.

  10. Induction of immune response to the 17 kDa OMPA Burkholderia cenocepacia polypeptide and protection against pulmonary infection in mice after nasal vaccination with an OMP nanoemulsion-based vaccine.

    Science.gov (United States)

    Makidon, P E; Knowlton, J; Groom, J V; Blanco, L P; LiPuma, J J; Bielinska, A U; Baker, J R

    2010-05-01

    Burkholderia cepacia complex (Bcc) are opportunistic bacteria associated with life-threatening illness in persons with cystic fibrosis. Once Bcc colonization is established, these antimicrobial-resistant and biofilm-forming bacteria are difficult to eradicate and are associated with increased rates of morbidity and mortality. At present, no vaccines are available to prevent the Bcc infection. There is currently a paucity of published information regarding the development of vaccines designed to prevent Burkholderia colonization. This work expands on the recent studies published by Bertot et al. [Infect Immun 75(6):2740-2752, 2007], where successful protective immune responses were generated in mice using a B. multivorans OMP-based vaccine. Here, we evaluate an experimental mucosal vaccine against Bcc using a novel mucosal adjuvant (nanoemulsion) and a novel B. cenocepacia-based OMP antigen. The OMP antigen derived from B. cenocepacia was mixed with either nanoemulsion or with PBS and delivered intranasally to CD-1 mice. Serum analysis showed robust IgG and mucosal secretory IgA immune responses in vaccinated versus control mice. The antibodies had cross-neutralizing activity against both B. cenocepacia and B. multivorans species. We found that immunized mice were protected against pulmonary colonization with B. cenocepacia. We have also identified that a 17 kDa OmpA-like protein highly conserved between Burkholderia and Ralstonia species as a new immunodominant epitope in mucosal immunization.

  11. Modeling of causality with metamaterials

    CERN Document Server

    Smolyaninov, Igor I

    2012-01-01

    Hyperbolic metamaterials may be used to model a 2+1 dimensional Minkowski spacetime in which the role of time is played by one of the spatial coordinates. When a metamaterial is built and illuminated with a coherent extraordinary laser beam, the stationary pattern of light propagation inside the metamaterial may be treated as a collection of particle world lines, which represents a complete history of this 2+1 dimensional spacetime. While this model may be used to build interesting spacetime analogs, such as metamaterial black holes and big bang, it lacks causality: since light inside the metamaterial may propagate back and force along the timelike spatial coordinate, events in the future may affect events in the past. Here we demonstrate that a more sophisticated metamaterial model may fix this deficiency via breaking the mirror and temporal (PT) symmetries of the original model and producing one-way propagation along the timelike spatial coordinate. Resulting 2+1 Minkowski spacetime appears to be causal. Th...

  12. Causal viscous cosmology without singularities

    CERN Document Server

    Laciana, Carlos E

    2016-01-01

    An isotropic and homogeneous cosmological model with a source of dark energy is studied. That source is simulated with a viscous relativistic fluid with minimal causal correction. In this model the restrictions on the parameters coming from the following conditions are analized: a) energy density without singularities along time, b) scale factor increasing with time, c) universe accelerated at present time, d) state equation for dark energy with "w" bounded and close to -1. It is found that those conditions are satified for the following two cases. i) When the transport coefficient ({\\tau}_{{\\Pi}}), associated to the causal correction, is negative, with the aditional restriction {\\zeta}|{\\tau}_{{\\Pi}}|>2/3, where {\\zeta} is the relativistic bulk viscosity coefficient. The state equation is in the "phantom" energy sector. ii) For {\\tau}_{{\\Pi}} positive, in the "k-essence" sector. It is performed an exact calculation for the case where the equation of state is constant, finding that option (ii) is favored in r...

  13. Survey of Bartonella spp. in U.S. bed bugs detects Burkholderia multivorans but not Bartonella.

    Directory of Open Access Journals (Sweden)

    Virna L Saenz

    Full Text Available Bed bugs (Cimex lectularius L. have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S-23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector.

  14. Copper as an antibacterial agent for human pathogenic multidrug resistant Burkholderia cepacia complex bacteria.

    Science.gov (United States)

    Ibrahim, Muhammad; Wang, Fang; Lou, Miao-miao; Xie, Guan-lin; Li, Bin; Bo, Zhu; Zhang, Gou-qing; Liu, He; Wareth, Abdul

    2011-12-01

    The Burkholderia cepacia complex (Bcc) consists of 17 closely related multidrug resistant bacterial species that are difficult to eradicate. Copper has recently gained attention as an antimicrobial agent because of its inhibitory effects on bacteria, yeast, and viruses. The objective of this study was to evaluate the antibacterial activity of copper surfaces and copper powder against members of the B. cepacia complex. The antibacterial activity of different copper surfaces was evaluated by incubating them with Bcc strain suspensions (5×10(7)cfu/ml). The bacterial survival counts were calculated and the data for various copper surfaces were compared to the data for stainless steel and polyvinylchloride, which were used as control surfaces. The antibacterial activity of copper powder was determined with the diffusimetrical technique and the zone of inhibition was evaluated with paper disks. A single cell gel electrophoresis assay, staining assays, and inductively coupled plasma mass spectroscopy were performed to determine the mechanism responsible for the bactericidal activity. The results showed a significant decrease in the viable bacterial count after exposure to copper surfaces. Moreover, the copper powder produced a large zone of inhibition and there was a significantly higher influx of copper ions into the bacterial cells that were exposed to copper surfaces compared to the controls. The present study demonstrates that metallic copper has an antibacterial effect against Bcc bacteria and that copper adversely affects the bacterial cellular structure, thus resulting in cell death. These findings suggest that copper could be utilized in health care facilities to reduce the bioburden of Bcc species, which may protect susceptible members of the community from bacterial infection.

  15. Survey of Bartonella spp. in U.S. bed bugs detects Burkholderia multivorans but not Bartonella.

    Science.gov (United States)

    Saenz, Virna L; Maggi, Ricardo G; Breitschwerdt, Edward B; Kim, Jung; Vargo, Edward L; Schal, Coby

    2013-01-01

    Bed bugs (Cimex lectularius L.) have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S-23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector.

  16. Botrytis species on bulb crops

    NARCIS (Netherlands)

    Lorbeer, J.W.; Seyb, A.M.; Boer, de M.; Ende, van den J.E.

    2007-01-01

    Abstract. A number of Botrytis species are pathogens of bulb crops. Botrytis squamosa (teleomorph= Botrytotinia squamosa) causal agent of botrytis leaf blight and B. allii the causal agent of botrytis neck rot are two of the most important fungal diseases of onion. The taxonomics of several of the n

  17. Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil

    OpenAIRE

    Pawitwar, Shashank S.; Utturkar, Sagar M.; Brown, Steven D.; Yoshinaga, Masafumi; Rosen, Barry P.

    2015-01-01

    To elucidate the environmental organoarsenical biocycle, we isolated a soil organism, Burkholderia sp. MR1, which reduces relatively nontoxic pentavalent methylarsenate to the more toxic trivalent methylarsenite, with the goal of identifying the gene for the reductase. Here, we report the draft genome sequence of Burkholderia sp. MR1.

  18. Draft Genome Sequence of Burkholderia sp. MR1, a Methylarsenate-Reducing Bacterial Isolate from Florida Golf Course Soil

    Science.gov (United States)

    Pawitwar, Shashank S.; Utturkar, Sagar M.; Brown, Steven D.; Yoshinaga, Masafumi

    2015-01-01

    To elucidate the environmental organoarsenical biocycle, we isolated a soil organism, Burkholderia sp. MR1, which reduces relatively nontoxic pentavalent methylarsenate to the more toxic trivalent methylarsenite, with the goal of identifying the gene for the reductase. Here, we report the draft genome sequence of Burkholderia sp. MR1. PMID:26044439

  19. Spin foam models as energetic causal sets

    CERN Document Server

    Cortês, Marina

    2014-01-01

    Energetic causal sets are causal sets endowed by a flow of energy-momentum between causally related events. These incorporate a novel mechanism for the emergence of space-time from causal relations. Here we construct a spin foam model which is also an energetic causal set model. This model is closely related to the model introduced by Wieland, and this construction makes use of results used there. What makes a spin foam model also an energetic causal set is Wieland's identification of new momenta, conserved at events (or four-simplices), whose norms are not mass, but the volume of tetrahedra. This realizes the torsion constraints, which are missing in previous spin foam models, and are needed to relate the connection dynamics to those of the metric, as in general relativity. This identification makes it possible to apply the new mechanism for the emergence of space-time to a spin foam model.

  20. φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity

    Directory of Open Access Journals (Sweden)

    Kvitko Brian H

    2012-12-01

    Full Text Available Abstract Background Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. Results We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. Conclusions The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.

  1. A Possible Link between Infection with Burkholderia Bacteria and Systemic Lupus Erythematosus Based on Epitope Mimicry

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2008-01-01

    Full Text Available We previously demonstrated that purified polyclonal and monoclonal anti-dsDNA antibodies bind a 15-mer peptide ASPVTARVLWKASHV in ELISA and Dot blot. This 15-mer peptide partial sequence ARVLWKASH shares similarity with burkholderia bacterial cytochrome B 561 partial sequence ARVLWRATH. In this study, we show that purified anti-dsDNA antibodies react with burkholderia fungorum bacterial cell lysates in Western blot. We used anti-dsDNA antibodies to make an anti-dsDNA antibodies affinity column and used this column to purify the burkholderia fungorum bacterial protein. Purified anti-dsDNA antibodies bind specifically to purified bacterial antigen and purified bacterial antigen blocked the anti-dsDNA antibodies binding to dsDNA antigen. Sera with anti-dsDNA antibodies bind specifically to purified bacterial antigen. We obtained protein partial sequence of RAGTDEGFG which is shared with burkholderia bacterial transcription regulator protein sequence. Sera with anti-dsDNA antibodies bind to RAGTDEGFG peptide better than control groups. These data support our hypothesis that the origin of anti-dsDNA antibodies in SLE may be associated with burkholderia bacterial infection.

  2. Causal inference in economics and marketing

    Science.gov (United States)

    Varian, Hal R.

    2016-01-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  3. Linear causal modeling with structural equations

    CERN Document Server

    Mulaik, Stanley A

    2009-01-01

    Emphasizing causation as a functional relationship between variables that describe objects, Linear Causal Modeling with Structural Equations integrates a general philosophical theory of causation with structural equation modeling (SEM) that concerns the special case of linear causal relations. In addition to describing how the functional relation concept may be generalized to treat probabilistic causation, the book reviews historical treatments of causation and explores recent developments in experimental psychology on studies of the perception of causation. It looks at how to perceive causal

  4. Identifying Causal Effects with Computer Algebra

    CERN Document Server

    García-Puente, Luis David; Sullivant, Seth

    2010-01-01

    The long-standing identification problem for causal effects in graphical models has many partial results but lacks a systematic study. We show how computer algebra can be used to either prove that a causal effect can be identified, generically identified, or show that the effect is not generically identifiable. We report on the results of our computations for linear structural equation models, where we determine precisely which causal effects are generically identifiable for all graphs on three and four vertices.

  5. Capsule influences the deposition of critical complement C3 levels required for the killing of Burkholderia pseudomallei via NADPH-oxidase induction by human neutrophils.

    Science.gov (United States)

    Woodman, Michael E; Worth, Randall G; Wooten, R Mark

    2012-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis and is a major mediator of sepsis in its endemic areas. Because of the low LD(50) via aerosols and resistance to multiple antibiotics, it is considered a Tier 1 select agent by the CDC and APHIS. B. pseudomallei is an encapsulated bacterium that can infect, multiply, and persist within a variety of host cell types. In vivo studies suggest that macrophages and neutrophils are important for controlling B. pseudomallei infections, however few details are known regarding how neutrophils respond to these bacteria. Our goal is to describe the capacity of human neutrophils to control highly virulent B. pseudomallei compared to the relatively avirulent, acapsular B. thailandensis using in vitro analyses. B. thailandensis was more readily phagocytosed than B. pseudomallei, but both displayed similar rates of persistence within neutrophils, indicating they possess similar inherent abilities to escape neutrophil clearance. Serum opsonization studies showed that both were resistant to direct killing by complement, although B. thailandensis acquired significantly more C3 on its surface than B. pseudomallei, whose polysaccharide capsule significantly decreased the levels of complement deposition on the bacterial surface. Both Burkholderia species showed significantly enhanced uptake and killing by neutrophils after critical levels of C3 were deposited. Serum-opsonized Burkholderia induced a significant respiratory burst by neutrophils compared to unopsonized bacteria, and neutrophil killing was prevented by inhibiting NADPH-oxidase. In summary, neutrophils can efficiently kill B. pseudomallei and B. thailandensis that possess a critical threshold of complement deposition, and the relative differences in their ability to resist surface opsonization may contribute to the distinct virulence phenotypes observed in vivo.

  6. Capsule influences the deposition of critical complement C3 levels required for the killing of Burkholderia pseudomallei via NADPH-oxidase induction by human neutrophils.

    Directory of Open Access Journals (Sweden)

    Michael E Woodman

    Full Text Available Burkholderia pseudomallei is the causative agent of melioidosis and is a major mediator of sepsis in its endemic areas. Because of the low LD(50 via aerosols and resistance to multiple antibiotics, it is considered a Tier 1 select agent by the CDC and APHIS. B. pseudomallei is an encapsulated bacterium that can infect, multiply, and persist within a variety of host cell types. In vivo studies suggest that macrophages and neutrophils are important for controlling B. pseudomallei infections, however few details are known regarding how neutrophils respond to these bacteria. Our goal is to describe the capacity of human neutrophils to control highly virulent B. pseudomallei compared to the relatively avirulent, acapsular B. thailandensis using in vitro analyses. B. thailandensis was more readily phagocytosed than B. pseudomallei, but both displayed similar rates of persistence within neutrophils, indicating they possess similar inherent abilities to escape neutrophil clearance. Serum opsonization studies showed that both were resistant to direct killing by complement, although B. thailandensis acquired significantly more C3 on its surface than B. pseudomallei, whose polysaccharide capsule significantly decreased the levels of complement deposition on the bacterial surface. Both Burkholderia species showed significantly enhanced uptake and killing by neutrophils after critical levels of C3 were deposited. Serum-opsonized Burkholderia induced a significant respiratory burst by neutrophils compared to unopsonized bacteria, and neutrophil killing was prevented by inhibiting NADPH-oxidase. In summary, neutrophils can efficiently kill B. pseudomallei and B. thailandensis that possess a critical threshold of complement deposition, and the relative differences in their ability to resist surface opsonization may contribute to the distinct virulence phenotypes observed in vivo.

  7. ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

    Science.gov (United States)

    Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

  8. Scalar Curvature of a Causal Set

    Science.gov (United States)

    Benincasa, Dionigi M. T.; Dowker, Fay

    2010-05-01

    A one parameter family of retarded linear operators on scalar fields on causal sets is introduced. When the causal set is well approximated by 4 dimensional Minkowski spacetime, the operators are Lorentz invariant but nonlocal, are parametrized by the scale of the nonlocality, and approximate the continuum scalar D’Alembertian □ when acting on fields that vary slowly on the nonlocality scale. The same operators can be applied to scalar fields on causal sets which are well approximated by curved spacetimes in which case they approximate □-(1)/(2)R where R is the Ricci scalar curvature. This can used to define an approximately local action functional for causal sets.

  9. Causal ubiquity in quantum physics. A superluminal and local-causal physical ontology

    Energy Technology Data Exchange (ETDEWEB)

    Neelamkavil, Raphael

    2014-07-01

    A fixed highest criterial velocity (of light) in STR (special theory of relativity) is a convention for a layer of physical inquiry. QM (Quantum Mechanics) avoids action-at-a-distance using this concept, but accepts non-causality and action-at-a-distance in EPR (Einstein-Podolsky-Rosen-Paradox) entanglement experiments. Even in such allegedly [non-causal] processes, something exists processually in extension-motion, between the causal and the [non-causal]. If STR theoretically allows real-valued superluminal communication between EPR entangled particles, quantum processes become fully causal. That is, the QM world is sub-luminally, luminally and superluminally local-causal throughout, and the Law of Causality is ubiquitous in the micro-world. Thus, ''probabilistic causality'' is a merely epistemic term.

  10. Burkholderia pseudomallei: First case of melioidosis in Portugal

    Directory of Open Access Journals (Sweden)

    Ana Pelerito

    2016-01-01

    Full Text Available Burkholderia pseudomallei is a Gram-negative bacillus and the causative agent of melioidosis, a serious infection associated with high mortality rate in humans. It can be naturally found as an environmental saprophyte in soil or stagnant water, and rice paddies that predominate in regions of endemicity such as Northeast Thailand. B. pseudomallei is a Biosafety Level 3 organism due to risks of aerosolization and severe disease and is now included in formal emergency preparedness plans and guidelines issued by various authorities in the United States and Europe. Here, we report the first case of imported melioidosis in Portugal. B. pseudomallei was isolated from the patient's blood as well as from a left gluteal abscess pus. The isolate strain showed the unusual resistance profile to first-line eradication therapy trimethroprim/sulfamethoxazole. Whole genome sequencing revealed its similarity with isolates from Southeast Asia, suggesting the Thai origin of this Portuguese isolate, which is in agreement with a recent patient's travel to Thailand.

  11. Genetic diversity and microevolution of Burkholderia pseudomallei in the environment.

    Directory of Open Access Journals (Sweden)

    Narisara Chantratita

    Full Text Available BACKGROUND: The soil dwelling Gram-negative pathogen Burkholderia pseudomallei is the cause of melioidosis. The diversity and population structure of this organism in the environment is poorly defined. METHODS AND FINDINGS: We undertook a study of B. pseudomallei in soil sampled from 100 equally spaced points within 237.5 m(2 of disused land in northeast Thailand. B. pseudomallei was present on direct culture of 77/100 sampling points. Genotyping of 200 primary plate colonies from three independent sampling points was performed using a combination of pulsed field gel electrophoresis (PFGE and multilocus sequence typing (MLST. Twelve PFGE types and nine sequence types (STs were identified, the majority of which were present at only a single sampling point. Two sampling points contained four STs and the third point contained three STs. Although the distance between the three sampling points was low (7.6, 7.9, and 13.3 meters, respectively, only two STs were present in more than one sampling point. Each of the three samples was characterized by the localized expansion of a single B. pseudomallei clone (corresponding to STs 185, 163, and 93. Comparison of PFGE and MLST results demonstrated that two STs contained strains with variable PFGE banding pattern types, indicating geographic structuring even within a single MLST-defined clone. CONCLUSIONS: We discuss the implications of this extreme structuring of genotype and genotypic frequency in terms of micro-evolutionary dynamics and ecology, and how our results may inform future sampling strategies.

  12. Mouse model of sublethal and lethal intraperitoneal glanders (Burkholderia mallei).

    Science.gov (United States)

    Fritz, D L; Vogel, P; Brown, D R; Deshazer, D; Waag, D M

    2000-11-01

    Sixty male BALB/c mice were inoculated intraperitoneally with either a sublethal or a lethal dose of Burkholderia mallei China 7 strain, then killed at multiple time points postinoculation. Histopathologic changes were qualitatively similar in both groups and consisted of pyogranulomatous inflammation. In sublethal study mice, changes were first seen at 6 hours in mediastinal lymph nodes, then in spleen, liver, peripheral lymph nodes, and bone marrow at day 3. These changes generally reached maximal incidence and severity by day 4 but decreased by comparison in all tissues except the liver. Changes were first seen in lethal study mice also at 6 hours in mediastinal lymph nodes and in spleens. At day 1, changes were present in liver, peripheral lymph nodes, and bone marrow. The incidence and severity of these changes were maximal at day 2. In contrast to sublethal study mice, the incidence and severity of the changes did not decrease through the remainder of the study. The most significant difference between the two groups was the rapid involvement of the spleen in the lethal study mice. Changes indicative of impaired vascular perfusion were more frequently seen in the sublethal study mice. Our findings indicate that mice are susceptible to B. mallei infection and may serve as an appropriate model for glanders infection in a resistant host such as human beings. Additionally, by immunoelectron microscopy, we showed the presence of type I O-antigenic polysaccharide (capsular) antigen surrounding B. mallei.

  13. Incidence of Burkholderia mallei infection among indigenous equines in India

    Science.gov (United States)

    Malik, Praveen; Singha, Harisankar; Goyal, Sachin K; Khurana, Sandip K; Tripathi, Badri Naryan; Dutt, Abha; Singh, Dabal; Sharma, Neeraj; Jain, Sanjay

    2015-01-01

    Burkholderia mallei is the causative agent of glanders which is a highly contagious and fatal disease of equines. Considering the nature and severity of the disease in equines, and potential of transmission to human beings, glanders is recognised as a ‘notifiable’ disease in many countries. An increasing number of glanders outbreaks throughout the Asian continents, including India, have been noticed recently. In view of the recent re-emergence of the disease, the present study was undertaken to estimate the prevalence of glanders among indigenous equines from different parts of India. Serum samples were analysed by complement fixation test (CFT) and ELISA for the detection of B mallei specific antibodies. A total of 7794 equines, which included 4720 horses, 1881 donkeys and 1193 mules were sampled from April 2011 to December 2014 from 10 states of India. Serologically, 36 equines (pony=7, mules=10, horses=19) were found to be positive for glanders by CFT and indirect-ELISA. The highest number of cases were detected in Uttar Pradesh (n=31) followed by Himachal Pradesh (n=4) and Chhattisgarh (n=1). Isolation of B mallei was attempted from nasal and abscess swabs collected from seropositive equines. Four isolates of B mallei were cultured from nasal swabs of two mules and two ponies. Identity of the isolates was confirmed by PCR and sequencing of fliP gene fragment. The study revealed circulation of B mallei in northern India and the need for continued surveillance to support the eradication. PMID:26457190

  14. Monitoring Therapeutic Treatments against Burkholderia Infections Using Imaging Techniques

    Directory of Open Access Journals (Sweden)

    Tiffany M. Mott

    2013-05-01

    Full Text Available Burkholderia mallei, the etiologic agent of glanders, are Category B select agents with biothreat potential, and yet effective therapeutic treatments are lacking. In this study, we showed that CpG administration increased survival, demonstrating protection in the murine glanders model. Bacterial recovery from infected lungs, liver and spleen was significantly reduced in CpG-treated animals as compared with non-treated mice. Reciprocally, lungs of CpG-treated infected animals were infiltrated with higher levels of neutrophils and inflammatory monocytes, as compared to control animals. Employing the B. mallei bioluminescent strain CSM001 and the Neutrophil-Specific Fluorescent Imaging Agent, bacterial dissemination and neutrophil trafficking were monitored in real-time using multimodal in vivo whole body imaging techniques. CpG-treatment increased recruitment of neutrophils to the lungs and reduced bioluminescent bacteria, correlating with decreased bacterial burden and increased protection against acute murine glanders. Our results indicate that protection of CpG-treated animals was associated with recruitment of neutrophils prior to infection and demonstrated, for the first time, simultaneous real time in vivo imaging of neutrophils and bacteria. This study provides experimental evidence supporting the importance of incorporating optimized in vivo imaging methods to monitor disease progression and to evaluate the efficacy of therapeutic treatment during bacterial infections.

  15. Intrinsic Resistance of Burkholderia cepacia Complex to Benzalkonium Chloride.

    Science.gov (United States)

    Ahn, Youngbeom; Kim, Jeong Myeong; Kweon, Ohgew; Kim, Seong-Jae; Jones, Richard C; Woodling, Kellie; Gamboa da Costa, Gonçalo; LiPuma, John J; Hussong, David; Marasa, Bernard S; Cerniglia, Carl E

    2016-11-22

    Pharmaceutical products that are contaminated with Burkholderia cepacia complex (BCC) bacteria may pose serious consequences to vulnerable patients. Benzyldimethylalkylammonium chloride (BZK) cationic surfactants are extensively used in medical applications and have been implicated in the coselection of antimicrobial resistance. The ability of BCC to degrade BZK, tetradecyldimethylbenzylammonium chloride (C14BDMA-Cl), dodecyldimethylbenzylammonium chloride (C12BDMA-Cl), decyldimethylbenzylammonium chloride (C10BDMA-Cl), hexyldimethylbenzylammonium chloride, and benzyltrimethylammonium chloride was determined by incubation in 1/10-diluted tryptic soy broth (TSB) to determine if BCC bacteria have the ability to survive and inactivate these disinfectants. With BZK, C14BDMA-Cl, and C12BDMA-Cl, inhibition of the growth of 20 BCC strains was observed in disinfectant solutions that ranged from 64 to 256 µg/ml. The efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone increased the sensitivity of bacteria to 64 µg/ml BZK. The 20 BCC strains grew well in 1/10-diluted TSB medium with BZK, C12BDMA-Cl, and C10BDMA-Cl; they absorbed and degraded the compounds in 7 days. Formation of benzyldimethylamine and benzylmethylamine as the initial metabolites suggested that the cleavage of the C alkyl-N bond occurred as the first step of BZK degradation by BCC bacteria. Proteomic data confirmed the observed efflux activity and metabolic inactivation via biodegradation in terms of BZK resistance of BCC bacteria, which suggests that the two main resistance mechanisms are intrinsic and widespread.

  16. Degradation of parabens by Pseudomonas beteli and Burkholderia latens.

    Science.gov (United States)

    Amin, Aeshna; Chauhan, Sateesh; Dare, Manish; Bansal, Arvind Kumar

    2010-06-01

    p-Hydroxybenzoic acid esters (parabens) are commonly used antimicrobial preservatives in pharmaceutical formulations. Two microorganisms, isolated from non-sterile methyl paraben (MP) and propyl paraben (PP) solutions, were found to degrade the respective parabens. Identification by 16S rRNA partial gene sequencing revealed them to be Pseudomonas beteli and Burkholderia latens, respectively. The present work describes a previously unreported interaction of the parabens with P. beteli and B. latens. Degradation of MP at various concentrations by P. beteli, followed a logarithmic pattern, while that of PP by B. latens was found to be linear. It was subsequently observed that P. beteli could degrade only MP, while B. latens could degrade both the parabens. Absence of HPLC chromatogram peaks of expected degradation products indicated that the parabens were used up as a carbon source. The behaviour of pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans and Aspergillus niger) of the pharmacopoeial preservative effectiveness test (PET), towards MP, showed that none had the ability to degrade the paraben. It was concluded that, for a paraben-preserved multi-dose ophthalmic formulation, the sole use of the four pathogens that are recommended by the pharmacopoeia for PET can falsely indicate the formulation to be effective against 'in-use' contamination.

  17. Burkholderia cenocepacia zinc metalloproteases influence resistance to antimicrobial peptides.

    Science.gov (United States)

    Kooi, Cora; Sokol, Pamela A

    2009-09-01

    Burkholderia cenocepacia secretes two zinc-dependent metalloproteases, designated ZmpA and ZmpB. Previously, ZmpA and ZmpB have been shown to cleave several proteins important in host defence. In this study, the ability of ZmpA and ZmpB to digest and inactivate antimicrobial peptides involved in innate immunity was examined. ZmpB but not ZmpA cleaved beta-defensin-1. ZmpA but not ZmpB cleaved the cathelicidin LL-37. Both enzymes cleaved elafin and secretory leukocyte inhibitor, which are antimicrobial peptides as well as neutrophil elastase inhibitors. Both ZmpA and ZmpB cleaved protamine, a fish antimicrobial peptide, and a zmpA zmpB mutant was more sensitive to protamine killing than the parental strain. ZmpA or ZmpB cleavage of elafin inactivated its anti-protease activity. The effect of ZmpA and ZmpB on the neutrophil proteases elastase and cathepsin G was also examined but neither enzyme was active against these host proteases. These studies suggest that ZmpA and ZmpB may influence the resistance of B. cenocepacia to host antimicrobial peptides as well as alter the host protease/anti-protease balance in chronic respiratory infections.

  18. Evolving serodiagnostics by rationally designed peptide arrays: the Burkholderia paradigm in Cystic Fibrosis

    Science.gov (United States)

    Peri, Claudio; Gori, Alessandro; Gagni, Paola; Sola, Laura; Girelli, Daniela; Sottotetti, Samantha; Cariani, Lisa; Chiari, Marcella; Cretich, Marina; Colombo, Giorgio

    2016-09-01

    Efficient diagnosis of emerging and novel bacterial infections is fundamental to guide decisions on therapeutic treatments. Here, we engineered a novel rational strategy to design peptide microarray platforms, which combines structural and genomic analyses to predict the binding interfaces between diverse protein antigens and antibodies against Burkholderia cepacia complex infections present in the sera of Cystic Fibrosis (CF) patients. The predicted binding interfaces on the antigens are synthesized in the form of isolated peptides and chemically optimized for controlled orientation on the surface. Our platform displays multiple Burkholderia-related epitopes and is shown to diagnose infected individuals even in presence of superinfections caused by other prevalent CF pathogens, with limited cost and time requirements. Moreover, our data point out that the specific patterns determined by combined probe responses might provide a characterization of Burkholderia infections even at the subtype level (genomovars). The method is general and immediately applicable to other bacteria.

  19. Comparison theorems for causal diamonds

    CERN Document Server

    Berthiere, Clement; Solodukhin, Sergey N

    2015-01-01

    We formulate certain inequalities for the geometric quantities characterizing causal diamonds in curved and Minkowski spacetimes. These inequalities involve the red-shift factor which, as we show explicitly in the spherically symmetric case, is monotonic in the radial direction and it takes its maximal value at the centre. As a byproduct of our discussion we re-derive Bishop's inequality without assuming the positivity of the spatial Ricci tensor. We then generalize our considerations to arbitrary, static and not necessarily spherically symmetric, asymptotically flat spacetimes. In the case of spacetimes with a horizon our generalization involves the so-called {\\it domain of dependence}. The respective volume, expressed in terms of the duration measured by a distant observer compared with the volume of the domain in Minkowski spacetime, exhibits behaviours which differ if $d=4$ or $d>4$. This peculiarity of four dimensions is due to the logarithmic subleading term in the asymptotic expansion of the metric nea...

  20. Further properties of causal relationship: causal structure stability, new criteria for isocausality and counterexamples

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Parrado, Alfonso [Departamento de Fisica Teorica, Universidad del Pais Vasco, Apartado 644, 48080 Bilbao (Spain); Sanchez, Miguel [Departamento de Geometria y Topologia, Facultad de Ciencias, Universidad de Granada, Avenida Fuentenueva s/n, 18071 Granada (Spain)

    2005-11-07

    Recently (Garcia-Parrado and Senovilla 2003 Class. Quantum Grav. 20 625-64) the concept of causal mapping between spacetimes, essentially equivalent in this context to the chronological map defined in abstract chronological spaces, and the related notion of causal structure, have been introduced as new tools to study causality in Lorentzian geometry. In the present paper, these tools are further developed in several directions such as (i) causal mappings-and, thus, abstract chronological ones-do not preserve two levels of the standard hierarchy of causality conditions (however, they preserve the remaining levels as shown in the above reference), (ii) even though global hyperbolicity is a stable property (in the set of all time-oriented Lorentzian metrics on a fixed manifold), the causal structure of a globally hyperbolic spacetime can be unstable against perturbations; in fact, we show that the causal structures of Minkowski and Einstein static spacetimes remain stable, whereas that of de Sitter becomes unstable, (iii) general criteria allow us to discriminate different causal structures in some general spacetimes (e.g. globally hyperbolic, stationary standard); in particular, there are infinitely many different globally hyperbolic causal structures (and thus, different conformal ones) on R{sup 2} (iv) plane waves with the same number of positive eigenvalues in the frequency matrix share the same causal structure and, thus, they have equal causal extensions and causal boundaries.

  1. The Power of Causal Beliefs and Conflicting Evidence on Causal Judgments and Decision Making

    Science.gov (United States)

    Garcia-Retamero, Rocio; Muller, Stephanie M.; Catena, Andres; Maldonado, Antonio

    2009-01-01

    In two experiments, we investigated the relative impact of causal beliefs and empirical evidence on both decision making and causal judgments, and whether this relative impact could be altered by previous experience. 2. Selected groups of participants in both experiments received pre-training with either causal or neutral cues, or no pre-training…

  2. Real-Time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei

    Science.gov (United States)

    2005-10-01

    1 Real - time PCR (RT-PCR) Assays for Burkholderia mallei and B. pseudomallei Vipin K. Rastogi1, Tu-chen Cheng1, Lisa Collins1 and Jennifer Bagley2 1...A 3. DATES COVERED - 4. TITLE AND SUBTITLE Real - time PCR (RT-PCR) Assays for Burkholderia mallei and B.pseudomallei 5a. CONTRACT NUMBER 5b...risk. There is currently no real - time PCR assay for detection of both of these pathogens. Primers and probes corresponding to specific genomic regions

  3. "Comments on Slavin": Synthesizing Causal Inferences

    Science.gov (United States)

    Briggs, Derek C.

    2008-01-01

    When causal inferences are to be synthesized across multiple studies, efforts to establish the magnitude of a causal effect should be balanced by an effort to evaluate the generalizability of the effect. The evaluation of generalizability depends on two factors that are given little attention in current syntheses: construct validity and external…

  4. Structural intervention distance for evaluating causal graphs

    DEFF Research Database (Denmark)

    Peters, Jonas; Bühlmann, Peter

    2015-01-01

    Causal inference relies on the structure of a graph, often a directed acyclic graph (DAG). Different graphs may result in different causal inference statements and different intervention distributions. To quantify such differences, we propose a (pre-)metric between DAGs, the structural interventi...... implementation with software code available on the first author's home page....

  5. On the spectral formulation of Granger causality.

    Science.gov (United States)

    Chicharro, D

    2011-12-01

    Spectral measures of causality are used to explore the role of different rhythms in the causal connectivity between brain regions. We study several spectral measures related to Granger causality, comprising the bivariate and conditional Geweke measures, the directed transfer function, and the partial directed coherence. We derive the formulation of dependence and causality in the spectral domain from the more general formulation in the information-theory framework. We argue that the transfer entropy, the most general measure derived from the concept of Granger causality, lacks a spectral representation in terms of only the processes associated with the recorded signals. For all the spectral measures we show how they are related to mutual information rates when explicitly considering the parametric autoregressive representation of the processes. In this way we express the conditional Geweke spectral measure in terms of a multiple coherence involving innovation variables inherent to the autoregressive representation. We also link partial directed coherence with Sims' criterion of causality. Given our results, we discuss the causal interpretation of the spectral measures related to Granger causality and stress the necessity to explicitly consider their specific formulation based on modeling the signals as linear Gaussian stationary autoregressive processes.

  6. Causal Moderation Analysis Using Propensity Score Methods

    Science.gov (United States)

    Dong, Nianbo

    2012-01-01

    This paper is based on previous studies in applying propensity score methods to study multiple treatment variables to examine the causal moderator effect. The propensity score methods will be demonstrated in a case study to examine the causal moderator effect, where the moderators are categorical and continuous variables. Moderation analysis is an…

  7. Quasi-Experimental Designs for Causal Inference

    Science.gov (United States)

    Kim, Yongnam; Steiner, Peter

    2016-01-01

    When randomized experiments are infeasible, quasi-experimental designs can be exploited to evaluate causal treatment effects. The strongest quasi-experimental designs for causal inference are regression discontinuity designs, instrumental variable designs, matching and propensity score designs, and comparative interrupted time series designs. This…

  8. Causal Mediation Analysis: Warning! Assumptions Ahead

    Science.gov (United States)

    Keele, Luke

    2015-01-01

    In policy evaluations, interest may focus on why a particular treatment works. One tool for understanding why treatments work is causal mediation analysis. In this essay, I focus on the assumptions needed to estimate mediation effects. I show that there is no "gold standard" method for the identification of causal mediation effects. In…

  9. Campbell's and Rubin's Perspectives on Causal Inference

    Science.gov (United States)

    West, Stephen G.; Thoemmes, Felix

    2010-01-01

    Donald Campbell's approach to causal inference (D. T. Campbell, 1957; W. R. Shadish, T. D. Cook, & D. T. Campbell, 2002) is widely used in psychology and education, whereas Donald Rubin's causal model (P. W. Holland, 1986; D. B. Rubin, 1974, 2005) is widely used in economics, statistics, medicine, and public health. Campbell's approach focuses on…

  10. Essays on Causal Inference for Public Policy

    Science.gov (United States)

    Zajonc, Tristan

    2012-01-01

    Effective policymaking requires understanding the causal effects of competing proposals. Relevant causal quantities include proposals' expected effect on different groups of recipients, the impact of policies over time, the potential trade-offs between competing objectives, and, ultimately, the optimal policy. This dissertation studies causal…

  11. Causal random geometry from stochastic quantization

    DEFF Research Database (Denmark)

    Ambjørn, Jan; Loll, R.; Westra, W.

    2010-01-01

     in this short note we review a recently found formulation of two-dimensional causal quantum gravity defined through Causal Dynamical Triangulations and stochastic quantization. This procedure enables one to extract the nonperturbative quantum Hamiltonian of the random surface model including the...

  12. The causal order on the ambient boundary

    CERN Document Server

    Antoniadis, Ignatios; Papadopoulos, Kyriakos

    2016-01-01

    We analyse the causal structure of the ambient boundary, the conformal infinity of the ambient (Poincar\\'e) metric. Using topological tools we show that the only causal relation compatible with the global topology of the boundary spacetime is the horismos order. This has important consequences for the notion of time in the conformal geometry of the ambient boundary.

  13. mediation: R Package for Causal Mediation Analysis

    Directory of Open Access Journals (Sweden)

    Dustin Tingley

    2014-09-01

    Full Text Available In this paper, we describe the R package mediation for conducting causal mediation analysis in applied empirical research. In many scientific disciplines, the goal of researchers is not only estimating causal effects of a treatment but also understanding the process in which the treatment causally affects the outcome. Causal mediation analysis is frequently used to assess potential causal mechanisms. The mediation package implements a comprehensive suite of statistical tools for conducting such an analysis. The package is organized into two distinct approaches. Using the model-based approach, researchers can estimate causal mediation effects and conduct sensitivity analysis under the standard research design. Furthermore, the design-based approach provides several analysis tools that are applicable under different experimental designs. This approach requires weaker assumptions than the model-based approach. We also implement a statistical method for dealing with multiple (causally dependent mediators, which are often encountered in practice. Finally, the package also offers a methodology for assessing causal mediation in the presence of treatment noncompliance, a common problem in randomized trials.

  14. Causal Indicators Can Help to Interpret Factors

    Science.gov (United States)

    Bentler, Peter M.

    2016-01-01

    The latent factor in a causal indicator model is no more than the latent factor of the factor part of the model. However, if the causal indicator variables are well-understood and help to improve the prediction of individuals' factor scores, they can help to interpret the meaning of the latent factor. Aguirre-Urreta, Rönkkö, and Marakas (2016)…

  15. Environmental Free-Living Amoebae Isolated from Soil in Khon Kaen, Thailand, Antagonize Burkholderia pseudomallei

    Science.gov (United States)

    Noinarin, Parumon; Chareonsudjai, Pisit; Wangsomnuk, Pinich; Wongratanacheewin, Surasak

    2016-01-01

    Presence of Burkholderia pseudomallei in soil and water is correlated with endemicity of melioidosis in Southeast Asia and northern Australia. Several biological and physico-chemical factors have been shown to influence persistence of B. pseudomallei in the environment of endemic areas. This study was the first to evaluate the interaction of B. pseudomallei with soil amoebae isolated from B. pseudomallei-positive soil site in Khon Kaen, Thailand. Four species of amoebae, Paravahlkampfia ustiana, Acanthamoeba sp., Naegleria pagei, and isolate A-ST39-E1, were isolated, cultured and identified based on morphology, movement and 18S rRNA gene sequence. Co-cultivation combined with a kanamycin-protection assay of B. pseudomallei with these amoebae at MOI 20 at 30°C were evaluated during 0–6 h using the plate count technique on Ashdown’s agar. The fate of intracellular B. pseudomallei in these amoebae was also monitored by confocal laser scanning microscopy (CLSM) observation of the CellTracker™ Orange-B. pseudomallei stained cells. The results demonstrated the ability of P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 to graze B. pseudomallei. However, the number of internalized B. pseudomallei substantially decreased and the bacterial cells disappeared during the observation period, suggesting they had been digested. We found that B. pseudomallei promoted the growth of Acanthamoeba sp. and isolate A-ST39-E1 in co-cultures at MOI 100 at 30°C, 24 h. These findings indicated that P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 may prey upon B. pseudomallei rather than representing potential environmental reservoirs in which the bacteria can persist. PMID:27898739

  16. Inactivation of [Fe-S] metalloproteins mediates nitric oxide-dependent killing of Burkholderia mallei.

    Directory of Open Access Journals (Sweden)

    Jessica Jones-Carson

    Full Text Available BACKGROUND: Much remains to be known about the mechanisms by which O(2-dependent host defenses mediate broad antimicrobial activity. METHODOLOGY/PRINCIPAL FINDINGS: We show herein that reactive nitrogen species (RNS generated by inducible nitric oxide (NO synthase (iNOS account for the anti-Burkholderia mallei activity of IFNgamma-primed macrophages. Inducible NOS-mediated intracellular killing may represent direct bactericidal activity, because B. mallei showed an exquisite sensitivity to NO generated chemically. Exposure of B. mallei to sublethal concentrations of NO upregulated transcription of [Fe-S] cluster repair genes, while damaging the enzymatic activity of the [Fe-S] protein aconitase. To test whether [Fe-S] clusters are critical targets for RNS-dependent killing of B. mallei, a mutation was constructed in the NO-induced, [Fe-S] cluster repair regulator iscR. Not only was the iscR mutant hypersusceptible to iNOS-mediated killing, but its aconitase pool was readily oxidized by NO donors as compared to wild-type controls. Although killed by authentic H(2O(2, which also oxidizes [Fe-S] clusters, B. mallei appear to be resilient to NADPH oxidase-mediated cytotoxicity. The poor respiratory burst elicited by this bacterium likely explains why the NADPH oxidase is nonessential to the killing of B. mallei while it is still confined within phagosomes. CONCLUSIONS/SIGNIFICANCE: Collectively, these findings have revealed a disparate role for NADPH oxidase and iNOS in the innate macrophage response against the strict aerobe B. mallei. To the best of our knowledge, this is the first instance in which disruption of [Fe-S] clusters is demonstrated as cause of the bactericidal activity of NO congeners.

  17. Garlic revisited: antimicrobial activity of allicin-containing garlic extracts against Burkholderia cepacia complex.

    Directory of Open Access Journals (Sweden)

    Daynea Wallock-Richards

    Full Text Available The antimicrobial activities of garlic and other plant alliums are primarily based on allicin, a thiosulphinate present in crushed garlic bulbs. We set out to determine if pure allicin and aqueous garlic extracts (AGE exhibit antimicrobial properties against the Burkholderia cepacia complex (Bcc, the major bacterial phytopathogen for alliums and an intrinsically multiresistant and life-threatening human pathogen. We prepared an AGE from commercial garlic bulbs and used HPLC to quantify the amount of allicin therein using an aqueous allicin standard (AAS. Initially we determined the minimum inhibitory concentrations (MICs of the AGE against 38 Bcc isolates; these MICs ranged from 0.5 to 3% (v/v. The antimicrobial activity of pure allicin (AAS was confirmed by MIC and minimum bactericidal concentration (MBC assays against a smaller panel of five Bcc isolates; these included three representative strains of the most clinically important species, B. cenocepacia. Time kill assays, in the presence of ten times MIC, showed that the bactericidal activity of AGE and AAS against B. cenocepacia C6433 correlated with the concentration of allicin. We also used protein mass spectrometry analysis to begin to investigate the possible molecular mechanisms of allicin with a recombinant form of a thiol-dependent peroxiredoxin (BCP, Prx from B. cenocepacia. This revealed that AAS and AGE modifies an essential BCP catalytic cysteine residue and suggests a role for allicin as a general electrophilic reagent that targets protein thiols. To our knowledge, we report the first evidence that allicin and allicin-containing garlic extracts possess inhibitory and bactericidal activities against the Bcc. Present therapeutic options against these life-threatening pathogens are limited; thus, allicin-containing compounds merit investigation as adjuncts to existing antibiotics.

  18. Garlic revisited: antimicrobial activity of allicin-containing garlic extracts against Burkholderia cepacia complex.

    Science.gov (United States)

    Wallock-Richards, Daynea; Doherty, Catherine J; Doherty, Lynsey; Clarke, David J; Place, Marc; Govan, John R W; Campopiano, Dominic J

    2014-01-01

    The antimicrobial activities of garlic and other plant alliums are primarily based on allicin, a thiosulphinate present in crushed garlic bulbs. We set out to determine if pure allicin and aqueous garlic extracts (AGE) exhibit antimicrobial properties against the Burkholderia cepacia complex (Bcc), the major bacterial phytopathogen for alliums and an intrinsically multiresistant and life-threatening human pathogen. We prepared an AGE from commercial garlic bulbs and used HPLC to quantify the amount of allicin therein using an aqueous allicin standard (AAS). Initially we determined the minimum inhibitory concentrations (MICs) of the AGE against 38 Bcc isolates; these MICs ranged from 0.5 to 3% (v/v). The antimicrobial activity of pure allicin (AAS) was confirmed by MIC and minimum bactericidal concentration (MBC) assays against a smaller panel of five Bcc isolates; these included three representative strains of the most clinically important species, B. cenocepacia. Time kill assays, in the presence of ten times MIC, showed that the bactericidal activity of AGE and AAS against B. cenocepacia C6433 correlated with the concentration of allicin. We also used protein mass spectrometry analysis to begin to investigate the possible molecular mechanisms of allicin with a recombinant form of a thiol-dependent peroxiredoxin (BCP, Prx) from B. cenocepacia. This revealed that AAS and AGE modifies an essential BCP catalytic cysteine residue and suggests a role for allicin as a general electrophilic reagent that targets protein thiols. To our knowledge, we report the first evidence that allicin and allicin-containing garlic extracts possess inhibitory and bactericidal activities against the Bcc. Present therapeutic options against these life-threatening pathogens are limited; thus, allicin-containing compounds merit investigation as adjuncts to existing antibiotics.

  19. Quantum-coherent mixtures of causal relations

    CERN Document Server

    MacLean, Jean-Philippe W; Spekkens, Robert W; Resch, Kevin J

    2016-01-01

    Understanding the causal influences that hold among the parts of a system is critical both to explaining that system's natural behaviour and to controlling it through targeted interventions. In a quantum world, understanding causal relations is equally important, but the set of possibilities is far richer. The two basic ways in which a pair of time-ordered quantum systems may be causally related are by a cause-effect mechanism or by a common cause acting on both. Here, we show that it is possible to have a coherent mixture of these two possibilities. We realize such a nonclassical causal relation in a quantum optics experiment and derive a set of criteria for witnessing the coherence based on a quantum version of Berkson's paradox. The interplay of causality and quantum theory lies at the heart of challenging foundational puzzles, such as Bell's theorem and the search for quantum gravity, but could also provide a resource for novel quantum technologies.

  20. A Causal Alternative to Feynman's Propagator

    CERN Document Server

    Koksma, Jurjen F

    2010-01-01

    The Feynman propagator used in the conventional in-out formalism in quantum field theory is not a causal propagator as wave packets are propagated virtually instantaneously outside the causal region of the initial state. We formulate a causal in-out formalism in quantum field theory by making use of the Wheeler propagator, the time ordered commutator propagator, which is manifestly causal. Only free scalar field theories and their first quantization are considered. We identify the real Klein Gordon field itself as the wave function of a neutral spinless relativistic particle. Furthermore, we derive a probability density for our relativistic wave packet using the inner product between states that live on a suitably defined Hilbert space of real quantum fields. We show that the time evolution of our probability density is governed by the Wheeler propagator, such that it behaves causally too.

  1. Causality, Bell's theorem, and Ontic Definiteness

    CERN Document Server

    Henson, Joe

    2011-01-01

    Bell's theorem shows that the reasonable relativistic causal principle known as "local causality" is not compatible with the predictions of quantum mechanics. It is not possible maintain a satisfying causal principle of this type while dropping any of the better-known assumptions of Bell's theorem. However, another assumption of Bell's theorem is the use of classical logic. One part of this assumption is the principle of "ontic definiteness", that is, that it must in principle be possible to assign definite truth values to all propositions treated in the theory. Once the logical setting is clarified somewhat, it can be seen that rejecting this principle does not in any way undermine the type of causal principle used by Bell. Without ontic definiteness, the deterministic causal condition known as Einstein Locality succeeds in banning superluminal influence (including signalling) whilst allowing correlations that violate Bell's inequalities. Objections to altering logic, and the consequences for operational and...

  2. A Brief Introduction to Temporality and Causality

    CERN Document Server

    Karimi, Kamran

    2010-01-01

    Causality is a non-obvious concept that is often considered to be related to temporality. In this paper we present a number of past and present approaches to the definition of temporality and causality from philosophical, physical, and computational points of view. We note that time is an important ingredient in many relationships and phenomena. The topic is then divided into the two main areas of temporal discovery, which is concerned with finding relations that are stretched over time, and causal discovery, where a claim is made as to the causal influence of certain events on others. We present a number of computational tools used for attempting to automatically discover temporal and causal relations in data.

  3. Towards Spectral Geometry for Causal Sets

    CERN Document Server

    Yazdi, Yasaman K

    2016-01-01

    We show that the Feynman propagator (or the d'Alembertian) of a causal set contains the complete information about the causal set. Intuitively, this is because the Feynman propagator, being a correlator that decays with distance, provides a measure for the invariant distance between pairs of events. Further, we show that even the spectra alone (of the self-adjoint and anti-self-adjoint parts) of the propagator(s) and d'Alembertian already carry large amounts of geometric information about their causal set. This geometric information is basis independent and also gauge invariant in the sense that it is relabeling invariant (which is analogue to diffeomorphism invariance). We provide numerical evidence that the associated spectral distance between causal sets can serve as a measure for the geometric similarity between causal sets.

  4. Causality Violation, Gravitational Shockwaves and UV Completion

    CERN Document Server

    Hollowood, Timothy J

    2015-01-01

    The effective actions describing the low-energy dynamics of QFTs involving gravity generically exhibit causality violations. These may take the form of superluminal propagation or Shapiro time advances and allow the construction of "time machines", i.e. spacetimes admitting closed non-spacelike curves. Here, we discuss critically whether such causality violations may be used as a criterion to identify unphysical effective actions or whether, and how, causality problems may be resolved by embedding the action in a fundamental, UV complete QFT. We study in detail the case of photon scattering in an Aichelburg-Sexl gravitational shockwave background and calculate the phase shifts in QED for all energies, demonstrating their smooth interpolation from the causality-violating effective action values at low-energy to their manifestly causal high-energy limits. At low energies, these phase shifts may be interpreted as backwards-in-time coordinate jumps as the photon encounters the shock wavefront, and we illustrate h...

  5. Causal ubiquity in quantum physics a superluminal and local-causal physical ontology

    CERN Document Server

    Neelamkavil, Raphael

    2014-01-01

    A fixed highest criterial velocity (of light) in STR (special theory of relativity) is a convention for a layer of physical inquiry. QM (Quantum Mechanics) avoids action-at-a-distance using this concept, but accepts non-causality and action-at-a-distance in EPR (Einstein-Podolsky-Rosen-Paradox) entanglement experiments. Even in such allegedly non-causal processes, something exists processually in extension-motion, between the causal and the non-causal. If STR theoretically allows real-valued superluminal communication between EPR entangled particles, quantum processes become fully causal. That

  6. Causal Cones, Cone Preserving Transformations and Causal Structure in Special and General Theory of Relativity

    CERN Document Server

    Janardhan, Sujatha

    2012-01-01

    We present a short review of geometric and algebraic approach to causal cones and describe cone preserving transformations and their relationship with causal structure related to special and general theory of relativity. We describe Lie groups, especially matrix Lie groups, homogeneous and symmetric spaces and causal cones and certain implications of these concepts in special and general theory of relativity related to causal structure and topology of space-time. We compare and contrast the results on causal relations with those in the literature for general space-times and compare these relations with K-causal maps. We also describe causal orientations and their implications for space-time topology and discuss some more topologies on space-time which arise as an application of domain theory.

  7. Causal systems categories: differences in novice and expert categorization of causal phenomena.

    Science.gov (United States)

    Rottman, Benjamin M; Gentner, Dedre; Goldwater, Micah B

    2012-07-01

    We investigated the understanding of causal systems categories--categories defined by common causal structure rather than by common domain content--among college students. We asked students who were either novices or experts in the physical sciences to sort descriptions of real-world phenomena that varied in their causal structure (e.g., negative feedback vs. causal chain) and in their content domain (e.g., economics vs. biology). Our hypothesis was that there would be a shift from domain-based sorting to causal sorting with increasing expertise in the relevant domains. This prediction was borne out: the novice groups sorted primarily by domain and the expert group sorted by causal category. These results suggest that science training facilitates insight about causal structures.

  8. Potential of Burkholderia seminalis TC3.4.2R3 as Biocontrol Agent Against Fusarium oxysporum Evaluated by Mass Spectrometry Imaging

    Science.gov (United States)

    Araújo, Francisca Diana da Silva; Araújo, Welington Luiz; Eberlin, Marcos Nogueira

    2017-02-01

    Species of genus Burkholderia display different interaction profiles in the environment, causing either several diseases in plants and animals or being beneficial to some plants, promoting their growth, and suppressing phytopathogens. Burkholderia spp. also produce many types of biomolecules with antimicrobial activity, which may be commercially used to protect crops of economic interest, mainly against fungal diseases. Herein we have applied matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate secondary metabolites produced by B. seminalis TC3.4.2R3 in monoculture and coculture with plant pathogen Fusarium oxysporum. The siderophore pyochelin and the rhamnolipid Rha-Rha-C15-C14 were detected in wild-type B. seminalis strain, and their productions were found to vary in mutant strains carrying disruptions in gene clusters associated with antimicrobial compounds. Two mycotoxins were detected in F. oxysporum. During coculture with B. seminalis, metabolites probably related to defense mechanisms of these microorganisms were observed in the interspecies interaction zone. Our findings demonstrate the effective application of MALDI-MSI in the detection of bioactive molecules involved in the defense mechanism of B. seminalis, and these findings suggest the potential use of this bacterium in the biocontrol of plant diseases caused by F. oxysporum.

  9. Burkholderia pseudomallei is spatially distributed in soil in northeast Thailand.

    Directory of Open Access Journals (Sweden)

    Direk Limmathurotsakul

    Full Text Available BACKGROUND: Melioidosis is a frequently fatal infectious disease caused by the soil dwelling Gram-negative bacterium Burkholderia pseudomallei. Environmental sampling is important to identify geographical distribution of the organism and related risk of infection to humans and livestock. The aim of this study was to evaluate spatial distribution of B. pseudomallei in soil and consider the implications of this for soil sampling strategies. METHODS AND FINDINGS: A fixed-interval sampling strategy was used as the basis for detection and quantitation by culture of B. pseudomallei in soil in two environmental sites (disused land covered with low-lying scrub and rice field in northeast Thailand. Semivariogram and indicator semivariogram were used to evaluate the distribution of B. pseudomallei and its relationship with range between sampling points. B. pseudomallei was present on culture of 80/100 sampling points taken from the disused land and 28/100 sampling points from the rice field. The median B. pseudomallei cfu/gram from positive sampling points was 378 and 700 for the disused land and the rice field, respectively (p = 0.17. Spatial autocorrelation of B. pseudomallei was present, in that samples taken from areas adjacent to sampling points that were culture positive (negative for B. pseudomallei were also likely to be culture positive (negative, and samples taken from areas adjacent to sampling points with a high (low B. pseudomallei count were also likely to yield a high (low count. Ranges of spatial autocorrelation in quantitative B. pseudomallei count were 11.4 meters in the disused land and 7.6 meters in the rice field. CONCLUSIONS: We discuss the implications of the uneven distribution of B. pseudomallei in soil for future environmental studies, and describe a range of established geostatistical sampling approaches that would be suitable for the study of B. pseudomallei that take account of our findings.

  10. Intrinsic Resistance of Burkholderia cepacia Complex to Benzalkonium Chloride

    Directory of Open Access Journals (Sweden)

    Youngbeom Ahn

    2016-11-01

    Full Text Available Pharmaceutical products that are contaminated with Burkholderia cepacia complex (BCC bacteria may pose serious consequences to vulnerable patients. Benzyldimethylalkylammonium chloride (BZK cationic surfactants are extensively used in medical applications and have been implicated in the coselection of antimicrobial resistance. The ability of BCC to degrade BZK, tetradecyldimethylbenzylammonium chloride (C14BDMA-Cl, dodecyldimethylbenzylammonium chloride (C12BDMA-Cl, decyldimethylbenzylammonium chloride (C10BDMA-Cl, hexyldimethylbenzylammonium chloride, and benzyltrimethylammonium chloride was determined by incubation in 1/10-diluted tryptic soy broth (TSB to determine if BCC bacteria have the ability to survive and inactivate these disinfectants. With BZK, C14BDMA-Cl, and C12BDMA-Cl, inhibition of the growth of 20 BCC strains was observed in disinfectant solutions that ranged from 64 to 256 µg/ml. The efflux pump inhibitor carbonyl cyanide m-chlorophenylhydrazone increased the sensitivity of bacteria to 64 µg/ml BZK. The 20 BCC strains grew well in 1/10-diluted TSB medium with BZK, C12BDMA-Cl, and C10BDMA-Cl; they absorbed and degraded the compounds in 7 days. Formation of benzyldimethylamine and benzylmethylamine as the initial metabolites suggested that the cleavage of the C alkyl-N bond occurred as the first step of BZK degradation by BCC bacteria. Proteomic data confirmed the observed efflux activity and metabolic inactivation via biodegradation in terms of BZK resistance of BCC bacteria, which suggests that the two main resistance mechanisms are intrinsic and widespread.

  11. Recovery efficiencies for Burkholderia thailandensis from various aerosol sampling media

    Directory of Open Access Journals (Sweden)

    Paul eDabisch

    2012-06-01

    Full Text Available Burkholderia thailandensis is used in the laboratory as a surrogate of the more virulent B. pseudomallei. Since inhalation is believed to be a natural route of infection for B. pseudomallei, many animal studies with B. pseudomallei and B. thailandensis utilize the inhalation route of exposure. The aim of the present study was to quantify the recovery efficiency of culturable B. thailandensis from several common aerosol sampling devices to ensure that collected microorganisms could be reliably recovered post-collection. The sampling devices tested included 25-mm gelatin filters, 25-mm stainless steel disks used in Mercer cascade impactors, and two types of glass impingers. The results demonstrate that while several processing methods tested resulted in significantly lower physical recovery efficiencies than other methods, it was possible to obtain culturable recovery efficiencies for B. thailandensis and physical recovery efficiencies for 1 μm fluorescent spheres of at least 0.95 from all of the sampling media tested given an appropriate sample processing procedure. The results of the present study also demonstrated that the bubbling action of liquid media in all-glass impingers (AGIs can result in physical loss of material from the collection medium, although additional studies are needed to verify the exact mechanisms involved. Overall, the results of this study demonstrate that the collection mechanism as well as the post-collection processing method can significantly affect the recovery from and retention of culturable microorganisms in sampling media, potentially affecting the calculated airborne concentration and any subsequent estimations of risk or dose derived from such data.

  12. Investigation of the multifaceted iron acquisition strategies of Burkholderia cenocepacia.

    Science.gov (United States)

    Tyrrell, J; Whelan, N; Wright, C; Sá-Correia, I; McClean, S; Thomas, M; Callaghan, Máire

    2015-04-01

    Burkholderia cenocepacia is a bacterial pathogen which causes severe respiratory infections in cystic fibrosis (CF). These studies were aimed at gaining an insight into the iron acquisition strategies of B. cenocepacia. In iron restricted conditions, genes associated with the synthesis and utilisation of ornibactin (pvdA, orbA, orb F) were significantly upregulated compared to the expression of pyochelin associated genes (pchD, fptA). In the absence of alternative iron sources, B. cenocepacia J2315 and 715j utilised ferritin and haemin, but not transferrin or lactoferrin for growth. Significantly, mutants unable to produce ornibactin, (715j-orbI) or ornibactin and pyochelin, (715j-pobA), utilised haemin and ferritin more efficiently than the wild-type. Moreover, both mutants were also able to utilise lactoferrin for growth (P ≤ 0.01) and additionally 715j-pobA utilised transferrin (P ≤ 0.01), potentially facilitating adaptation to the host environment. Furthermore, B. cenocepacia increased ornibactin gene expression in response to pyoverdine from Pseudomonas aeruginosa (P ≤ 0.01), demonstrating the capacity to compete for iron in co-colonised niches. Pyoverdine also significantly diminished the growth of B. cenocepacia (P < 0.001) which was related to its iron chelating activity. In a study of three B. cenocepacia sequential clonal isolates obtained from a CF patient over a 3.5 year period, ornibactin upregulation in response to pyoverdine was less pronounced in the last isolate compared to the earlier isolates, as was growth in the presence of haemin and ferritin, indicating alternative iron acquisition mechanism(s) may dominate as chronic infection progresses. These data demonstrate the multifaceted iron acquisition strategies of B. cenocepacia and their capacity to be differentially activated in the presence of P. aeruginosa and during chronic infection.

  13. Burkholderia pseudomallei virulence: definition, stability and association with clonality.

    Science.gov (United States)

    Ulett, G C; Currie, B J; Clair, T W; Mayo, M; Ketheesan, N; Labrooy, J; Gal, D; Norton, R; Smith, C A; Barnes, J; Warner, J; Hirst, R G

    2001-07-01

    Clinical presentations of melioidosis, caused by Burkholderia pseudomallei are protean, but the mechanisms underlying development of the different forms of disease remain poorly understood. In murine melioidosis, the level of virulence of B. pseudomallei is important in disease pathogenesis and progression. In this study, we used B. pseudomallei-susceptible BALB/c mice to determine the virulence of a library of clinical and environmental B. pseudomallei isolates from Australia and Papua New Guinea. Among 42 non-arabinose-assimilating (ara(-)) isolates, LD(50) ranged from 10 to > 10(6) CFU. There were numerous correlations between virulence and disease presentation in patients; however, this was not a consistent observation. Virulence did not correlate with isolate origin (i.e. clinical vs environmental), since numerous ara(-) environmental isolates were highly virulent. The least virulent isolate was a soil isolate from Papua New Guinea, which was arabinose assimilating (ara(+)). Stability of B. pseudomallei virulence was investigated by in vivo passage of isolates through mice and repetitive in vitro subculture. Virulence increased following in vivo exposure in only one of eight isolates tested. In vitro subculture on ferric citrate-containing medium caused attenuation of virulence, and this correlated with changes in colony morphology. Pulsed-field gel electrophoresis and randomly amplified polymorphic DNA typing demonstrated that selected epidemiologically related isolates that had variable clinical outcomes and different in vivo virulence were clonal strains. No molecular changes were observed in isolates after in vivo or in vitro exposure despite changes in virulence. These results indicate that virulence of selected B. pseudomallei isolates is variable, being dependent on factors such as iron bioavailability. They also support the importance of other variables such as inoculum size and host risk factors in determining the clinical severity of melioidosis.

  14. Spread of entanglement and causality

    CERN Document Server

    Casini, Horacio; Mezei, Márk

    2015-01-01

    We investigate causality constraints on the time evolution of entanglement entropy after a global quench in relativistic theories. We first provide a general proof that the so-called tsunami velocity is bounded by the speed of light. We then generalize the free particle streaming model of arXiv:cond-mat/0503393 to general dimensions and to an arbitrary entanglement pattern of the initial state. In more than two spacetime dimensions the spread of entanglement in these models is highly sensitive to the initial entanglement pattern, but we are able to prove an upper bound on the normalized rate of growth of entanglement entropy, and hence the tsunami velocity. The bound is smaller than what one gets for quenches in holographic theories, which highlights the importance of interactions in the spread of entanglement in many-body systems. We propose an interacting model which we believe provides an upper bound on the spread of entanglement for interacting relativistic theories. In two spacetime dimensions with multi...

  15. Spread of entanglement and causality

    Science.gov (United States)

    Casini, Horacio; Liu, Hong; Mezei, Márk

    2016-07-01

    We investigate causality constraints on the time evolution of entanglement entropy after a global quench in relativistic theories. We first provide a general proof that the so-called tsunami velocity is bounded by the speed of light. We then generalize the free particle streaming model of [1] to general dimensions and to an arbitrary entanglement pattern of the initial state. In more than two spacetime dimensions the spread of entanglement in these models is highly sensitive to the initial entanglement pattern, but we are able to prove an upper bound on the normalized rate of growth of entanglement entropy, and hence the tsunami velocity. The bound is smaller than what one gets for quenches in holographic theories, which highlights the importance of interactions in the spread of entanglement in many-body systems. We propose an interacting model which we believe provides an upper bound on the spread of entanglement for interacting relativistic theories. In two spacetime dimensions with multiple intervals, this model and its variations are able to reproduce intricate results exhibited by holographic theories for a significant part of the parameter space. For higher dimensions, the model bounds the tsunami velocity at the speed of light. Finally, we construct a geometric model for entanglement propagation based on a tensor network construction for global quenches.

  16. Entanglement Entropy in Causal Set Theory

    CERN Document Server

    Sorkin, Rafael D

    2016-01-01

    Entanglement entropy is now widely accepted as having deep connections with quantum gravity. It is therefore desirable to understand it in the context of causal sets, especially since they provide in a natural manner the UV cutoff needed to render entanglement entropy finite. Defining entropy in a causal set is not straightforward because the type of canonical hypersurface-data on which definitions of entanglement typically rely is not available in a causal set. Instead, we will appeal to a more global expression given in arXiv:1205.2953 which, for a gaussian scalar field, expresses the entropy of a spacetime region in terms of the field's correlation function within that region. Carrying this formula over to the causal set, one obtains an entanglement entropy which is both finite and of a Lorentz invariant nature. Herein we evaluate this entropy for causal sets of 1+1 dimensions, and specifically for order-intervals ("causal diamonds") within the causal set, finding in the first instance an entropy that obey...

  17. Causal localizations in relativistic quantum mechanics

    Energy Technology Data Exchange (ETDEWEB)

    Castrigiano, Domenico P. L., E-mail: castrig@ma.tum.de; Leiseifer, Andreas D., E-mail: andreas.leiseifer@tum.de [Fakultät für Mathematik, TU München, Boltzmannstraße 3, 85747 Garching (Germany)

    2015-07-15

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac’s localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states.

  18. Mining Causality for Explanation Knowledge from Text

    Institute of Scientific and Technical Information of China (English)

    Chaveevan Pechsiri; Asanee Kawtrakul

    2007-01-01

    Mining causality is essential to provide a diagnosis. This research aims at extracting the causality existing within multiple sentences or EDUs (Elementary Discourse Unit). The research emphasizes the use of causality verbs because they make explicit in a certain way the consequent events of a cause, e.g., "Aphids suck the sap from rice leaves. Then leaves will shrink. Later, they will become yellow and dry.". A verb can also be the causal-verb link between cause and effect within EDU(s), e.g., "Aphids suck the sap from rice leaves causing leaves to be shrunk" ("causing" is equivalent to a causal-verb link in Thai). The research confronts two main problems: identifying the interesting causality events from documents and identifying their boundaries. Then, we propose mining on verbs by using two different machine learning techniques, Naive Bayes classifier and Support Vector Machine. The resulted mining rules will be used for the identification and the causality extraction of the multiple EDUs from text. Our multiple EDUs extraction shows 0.88 precision with 0.75 recall from Na'ive Bayes classifier and 0.89 precision with 0.76 recall from Support Vector Machine.

  19. A Simple Test for Causality in Volatility

    Directory of Open Access Journals (Sweden)

    Chia-Lin Chang

    2017-03-01

    Full Text Available An early development in testing for causality (technically, Granger non-causality in the conditional variance (or volatility associated with financial returns was the portmanteau statistic for non-causality in the variance of Cheng and Ng (1996. A subsequent development was the Lagrange Multiplier (LM test of non-causality in the conditional variance by Hafner and Herwartz (2006, who provided simulation results to show that their LM test was more powerful than the portmanteau statistic for sample sizes of 1000 and 4000 observations. While the LM test for causality proposed by Hafner and Herwartz (2006 is an interesting and useful development, it is nonetheless arbitrary. In particular, the specification on which the LM test is based does not rely on an underlying stochastic process, so the alternative hypothesis is also arbitrary, which can affect the power of the test. The purpose of the paper is to derive a simple test for causality in volatility that provides regularity conditions arising from the underlying stochastic process, namely a random coefficient autoregressive process, and a test for which the (quasi- maximum likelihood estimates have valid asymptotic properties under the null hypothesis of non-causality. The simple test is intuitively appealing as it is based on an underlying stochastic process, is sympathetic to Granger’s (1969, 1988 notion of time series predictability, is easy to implement, and has a regularity condition that is not available in the LM test.

  20. Causal inference, probability theory, and graphical insights.

    Science.gov (United States)

    Baker, Stuart G

    2013-11-10

    Causal inference from observational studies is a fundamental topic in biostatistics. The causal graph literature typically views probability theory as insufficient to express causal concepts in observational studies. In contrast, the view here is that probability theory is a desirable and sufficient basis for many topics in causal inference for the following two reasons. First, probability theory is generally more flexible than causal graphs: Besides explaining such causal graph topics as M-bias (adjusting for a collider) and bias amplification and attenuation (when adjusting for instrumental variable), probability theory is also the foundation of the paired availability design for historical controls, which does not fit into a causal graph framework. Second, probability theory is the basis for insightful graphical displays including the BK-Plot for understanding Simpson's paradox with a binary confounder, the BK2-Plot for understanding bias amplification and attenuation in the presence of an unobserved binary confounder, and the PAD-Plot for understanding the principal stratification component of the paired availability design.

  1. Diagnosis and causal explanation in psychiatry.

    Science.gov (United States)

    Maung, Hane Htut

    2016-12-01

    In clinical medicine, a diagnosis can offer an explanation of a patient's symptoms by specifying the pathology that is causing them. Diagnoses in psychiatry are also sometimes presented in clinical texts as if they pick out pathological processes that cause sets of symptoms. However, current evidence suggests the possibility that many diagnostic categories in psychiatry are highly causally heterogeneous. For example, major depressive disorder may not be associated with a single type of underlying pathological process, but with a range of different causal pathways, each involving complex interactions of various biological, psychological, and social factors. This paper explores the implications of causal heterogeneity for whether psychiatric diagnoses can be said to serve causal explanatory roles in clinical practice. I argue that while they may fall short of picking out a specific cause of the patient's symptoms, they can nonetheless supply different sorts of clinically relevant causal information. In particular, I suggest that some psychiatric diagnoses provide negative information that rules out certain causes, some provide approximate or disjunctive information about the range of possible causal processes, and some provide causal information about the relations between the symptoms themselves.

  2. Construction and characterization of stable, constitutively expressed, chromosomal green and red fluorescent transcriptional fusions in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei.

    Science.gov (United States)

    Su, Shengchang; Bangar, Hansraj; Saldanha, Roland; Pemberton, Adin; Aronow, Bruce; Dean, Gary E; Lamkin, Thomas J; Hassett, Daniel J

    2014-10-01

    Here, we constructed stable, chromosomal, constitutively expressed, green and red fluorescent protein (GFP and RFP) as reporters in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei. Using bioinformatic approaches and other experimental analyses, we identified P0253 and P1 as potent promoters that drive the optimal expression of fluorescent reporters in single copy in B. anthracis and Burkholderia spp. as well as their surrogate strains, respectively. In comparison, Y. pestis and its surrogate strain need two chromosomal copies of cysZK promoter (P2cysZK) for optimal fluorescence. The P0253-, P2cysZK-, and P1-driven GFP and RFP fusions were first cloned into the vectors pRP1028, pUC18R6KT-mini-Tn7T-Km, pmini-Tn7-gat, or their derivatives. The resultant constructs were delivered into the respective surrogates and subsequently into the select agent strains. The chromosomal GFP- and RFP-tagged strains exhibited bright fluorescence at an exposure time of less than 200 msec and displayed the same virulence traits as their wild-type parental strains. The utility of the tagged strains was proven by the macrophage infection assays and lactate dehydrogenase release analysis. Such strains will be extremely useful in high-throughput screens for novel compounds that could either kill these organisms, or interfere with critical virulence processes in these important bioweapon agents and during infection of alveolar macrophages.

  3. Enhanced biodegradation of anthracene in acidic soil by inoculated Burkholderia sp. VUN10013.

    Science.gov (United States)

    Somtrakoon, Khanitta; Suanjit, Sudarat; Pokethitiyook, Prayad; Kruatrachue, Maleeya; Lee, Hung; Upatham, Suchart

    2008-08-01

    The ability of Burkholderia sp. VUN10013 to degrade anthracene in microcosms of two acidic Thai soils was studied. The addition of Burkholderia sp. VUN10013 (initial concentration of 10(5) cells g(-1) dry soil) to autoclaved soil collected from the Plew District, Chanthaburi Province, Thailand, supplemented with anthracene (50 mg kg(-1) dry soil) resulted in complete degradation of the added anthracene within 20 days. In contrast, under the same test conditions but using autoclaved soil collected from the Kitchagude District, Chanthaburi Province, Thailand, only approximately 46.3% of the added anthracene was degraded after 60 days of incubation. In nonautoclaved soils, without adding the VUN10013 inocula, 22.8 and 19.1% of the anthracene in Plew and Kitchagude soils, respectively, were degraded by indigenous bacteria after 60 days. In nonautoclaved soil inoculated with Burkholderia sp. VUN10013, the rate and extent of anthracene degradation were considerably better than those seen in autoclaved soils or in uninoculated nonautoclaved soils in that only 8.2 and 9.1% of anthracene remained in nonautoclaved Plew and Kitchagude soils, respectively, after 10 days of incubation. The results showed that the indigenous microorganisms in the pristine acidic soils have limited ability to degrade anthracene. Inoculation with the anthracene-degrading Burkholderia sp. VUN10013 significantly enhanced anthracene degradation in such acidic soils. The indigenous microorganisms greatly assisted the VUN10013 inoculum in anthracene degradation, especially in the more acidic Kitchagude soil.

  4. N-acylhomoserine-lactone-mediated communication between Pseudomonas aeruginosa and Burkholderia cepacia in mixed biofilms

    DEFF Research Database (Denmark)

    Riedel, K.; Hentzer, Morten; Geisenberger, O.;

    2001-01-01

    Pseudomonas aeruginosa and Burkholderia cepacia are capable of forming mixed biofilms in the lungs of cystic fibrosis patients. Both bacteria employ quorum-sensing systems, which rely on N-acylhomoserine lactone (AHL) signal molecules, to co- ordinate expression of virulence factors with the form...

  5. The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

    DEFF Research Database (Denmark)

    Holden, Matthew T G; Seth-Smith, Helena M B; Crossman, Lisa C;

    2009-01-01

    Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradica...

  6. Molecular Characterization of Genetic Loci Required for Secretion of Exoproducts in Burkholderia pseudomallei

    OpenAIRE

    DeShazer, David; Brett, Paul J.; Mary N Burtnick; Woods, Donald E.

    1999-01-01

    Previous studies have demonstrated that Burkholderia pseudomallei secretes protease, lipase, and phospholipase C (PLC) into the extracellular milieu, but their mechanisms of secretion and roles in pathogenesis have not been elucidated. In this study, we isolated and characterized 29 transposon mutants unable to secrete protease, lipase, and PLC.

  7. Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria)

    Science.gov (United States)

    Ettinger, Cassandra L.; Shehata, Hanan R.; Johnston-Monje, David; Raizada, Manish N.

    2015-01-01

    Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds. PMID:25614570

  8. Susceptibility of Caenorhabditis elegans to Burkholderia infection depends on prior diet and secreted bacterial attractants.

    Directory of Open Access Journals (Sweden)

    Vaughn S Cooper

    Full Text Available The nematode Caenorhabditis elegans may be killed by certain pathogenic bacteria and thus is a model organism for studying interactions between bacteria and animal hosts. However, growing nematodes on prey bacteria may influence their susceptibility to potential pathogens. A method of axenic nematode culture was developed to isolate and quantify interactions between C. elegans and potentially pathogenic strains of the Burkholderia cepacia complex. Studying these dynamics in liquid solution rather than on agar surfaces minimized nematode avoidance behavior and resolved more differences among isolates. Most isolates of B. cenocepacia, B. ambifaria and B. cepacia caused 60-80% mortality of nematodes after 7 days, whereas isolates of B. multivorans caused less mortality (<25% and supported nematode reproduction. However, some B. cenocepacia isolates recovered from chronic infections were much less virulent (5-28% mortality. As predicted, prior diet altered the outcome of interactions between nematodes and bacteria. When given the choice between Burkholderia and E. coli as prey on agar, axenically raised nematodes initially preferred most lethal Burkholderia isolates to E. coli as a food source, but this was not the case for nematodes fed E. coli, which avoided toxic Burkholderia. This food preference was associated with the cell-free supernatant and thus secreted compounds likely mediated bacterial-nematode interactions. This model, which isolates interactions between bacteria and nematodes from the effects of prior feeding, demonstrates that bacteria can influence nematode behavior and their susceptibility to pathogens.

  9. The symbiotic role of O-antigen of Burkholderia symbiont in association with host Riptortus pedestris.

    Science.gov (United States)

    Kim, Jiyeun Kate; Park, Ha Young; Lee, Bok Luel

    2016-07-01

    Riptortus pedestris harboring Burkholderia symbiont is a useful symbiosis model to study the molecular interactions between insects and bacteria. We recently reported that the lipopolysaccharide O-antigen is absent in the Burkholderia symbionts isolated from Riptortus guts. Here, we investigated the symbiotic role of O-antigen comprehensively in the Riptortus-Burkholderia model. Firstly, Burkholderia mutant strains deficient of O-antigen biosynthesis genes were generated and confirmed for their different patterns of the lipopolysaccharide by electrophoretic analysis. The O-antigen-deficient mutant strains initially exhibited a reduction of infectivity, having significantly lower level of symbiont population at the second-instar stage. However, both the wild-type and O-antigen mutant symbionts exhibited a similar level of symbiont population from the third-instar stage, indicating that the O-antigen deficiency did not affect the bacterial persistence in the host midgut. Taken together, we showed that the lipopolysaccharide O-antigen of gut symbiont plays an exclusive role in the initial symbiotic association.

  10. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.

    Science.gov (United States)

    Ho, Ying-Ning; Huang, Chieh-Chen

    2015-11-12

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia.

  11. A heterodimer comprised of two bovine lactoferrin antimicrobial peptides exhibits powerful bactericidal activity against Burkholderia pseudomallei

    NARCIS (Netherlands)

    Puknun, A.; Bolscher, J.G.M.; Nazmi, K.; Veerman, E.C.I.; Tungpradabkul, S.; Wongratanacheewin, S.; Kanthawong, S.; Taweechaisupapong, S.

    2013-01-01

    Melioidosis is a severe infectious disease that is endemic in Southeast Asia and Northern Australia. Burkholderia pseudomallei, the causative agent of this disease, has developed resistance to an increasing list of antibiotics, demanding a search for novel agents. Lactoferricin and lactoferrampin ar

  12. Scalar Field Green Functions on Causal Sets

    OpenAIRE

    Ahmed, S. Nomaan; Dowker, Fay; Surya, Sumati

    2017-01-01

    We examine the validity and scope of Johnston's models for scalar field retarded Green functions on causal sets in 2 and 4 dimensions. As in the continuum, the massive Green function can be obtained from the massless one, and hence the key task in causal set theory is to first identify the massless Green function. We propose that the 2-d model provides a Green function for the massive scalar field on causal sets approximated by any topologically trivial 2 dimensional spacetime. We explicitly ...

  13. On the origin of Hill's causal criteria.

    Science.gov (United States)

    Morabia, A

    1991-09-01

    The rules to assess causation formulated by the eighteenth century Scottish philosopher David Hume are compared to Sir Austin Bradford Hill's causal criteria. The strength of the analogy between Hume's rules and Hill's causal criteria suggests that, irrespective of whether Hume's work was known to Hill or Hill's predecessors, Hume's thinking expresses a point of view still widely shared by contemporary epidemiologists. The lack of systematic experimental proof to causal inferences in epidemiology may explain the analogy of Hume's and Hill's, as opposed to Popper's, logic.

  14. Intrinsic Universality of Causal Graph Dynamics

    Directory of Open Access Journals (Sweden)

    Simon Martiel

    2013-09-01

    Full Text Available Causal graph dynamics are transformations over graphs that capture two important symmetries of physics, namely causality and homogeneity. They can be equivalently defined as continuous and translation invariant transformations or functions induced by a local rule applied simultaneously on every vertex of the graph. Intrinsic universality is the ability of an instance of a model to simulate every other instance of the model while preserving the structure of the computation at every step of the simulation. In this work we present the construction of a family of intrinsically universal instances of causal graphs dynamics, each instance being able to simulate a subset of instances.

  15. Causal structures of pp-waves

    CERN Document Server

    Hubeny, V E; Hubeny, Veronika E.; Rangamani, Mukund

    2002-01-01

    We discuss the causal structure of pp-wave spacetimes using the ideal point construction outlined by Geroch, Kronheimer, and Penrose. This generalizes the recent work of Marolf and Ross, who considered similar issues for plane wave spacetimes. We address the question regarding the dimension of the causal boundary for certain specific pp-wave backgrounds. In particular, we demonstrate that the pp-wave spacetime which gives rise to the N = 2 sine-Gordon string world-sheet theory is geodesically complete and has a one-dimensional causal boundary.

  16. Dual Causality and the Autonomy of Biology.

    Science.gov (United States)

    Bock, Walter J

    2017-03-01

    Ernst Mayr's concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical sciences.

  17. Causality in 3D Massive Gravity Theories

    CERN Document Server

    Edelstein, Jose D; Kilicarslan, Ercan; Leoni, Matias; Tekin, Bayram

    2016-01-01

    We study the constraints coming from local causality requirement in various 2+1 dimensional dynamical theories of gravity. In Topologically Massive Gravity, with a single parity noninvariant massive degree of freedom, and in New Massive Gravity, with two massive spin-$2$ degrees of freedom, causality and unitarity are compatible with each other and they both require the Newton's constant to be negative. In their extensions, such as the Born-Infeld gravity and the minimal massive gravity the situation is similar and quite different from their higher dimensional counterparts, such as quadratic (e.g., Einstein-Gauss-Bonnet) or cubic theories, where causality and unitarity are in conflict.

  18. Granger causality and contiguity between stochastic processes

    Energy Technology Data Exchange (ETDEWEB)

    Triacca, Umberto [Universita di L' Aquila, Roio Poggio, I-67040 L' Aquila (Italy)]. E-mail: triacca@ec.univaq.it

    2007-03-05

    Although according to many econometricians the definition of causality proposed by Granger differs from other definitions of causation in the philosophy of science, in this Letter we argue that it is not completely lacking in philosophical legitimacy. We attempt to shed new light on the nexus between Granger causality and the concept of contiguity. In particular, we prove that the existence of a Granger causal link between two stochastic processes requires that these be 'contiguous' or that there exist a chain of processes, one contiguous to the next, which link the two processes.

  19. Causality and Time in Historical Institutionalism

    DEFF Research Database (Denmark)

    Mahoney, James; Mohamedali, Khairunnisa; Nguyen, Christoph

    2016-01-01

    This chapter explores the dual concern with causality and time in historical institutionalism using a graphical approach. The analysis focuses on three concepts that are central to this field: critical junctures, gradual change, and path dependence. The analysis makes explicit and formal the logic...... underlying studies that use these “causal-temporal” concepts. The chapter shows visually how causality and temporality are linked to one another in varying ways depending on the particular pattern of change. The chapter provides new tools for describing and understanding change in historical- institutional...

  20. Burkholderia mallei and Burkholderia pseudomallei cluster 1 type VI secretion system gene expression is negatively regulated by iron and zinc.

    Directory of Open Access Journals (Sweden)

    Mary N Burtnick

    Full Text Available Burkholderia mallei is a facultative intracellular pathogen that causes glanders in humans and animals. Previous studies have demonstrated that the cluster 1 type VI secretion system (T6SS-1 expressed by this organism is essential for virulence in hamsters and is positively regulated by the VirAG two-component system. Recently, we have shown that T6SS-1 gene expression is up-regulated following internalization of this pathogen into phagocytic cells and that this system promotes multinucleated giant cell formation in infected tissue culture monolayers. In the present study, we further investigated the complex regulation of this important virulence factor. To assess T6SS-1 expression, B. mallei strains were cultured in various media conditions and Hcp1 production was analyzed by Western immunoblotting. Transcript levels of several VirAG-regulated genes (bimA, tssA, hcp1 and tssM were also determined using quantitative real time PCR. Consistent with previous observations, T6SS-1 was not expressed during growth of B. mallei in rich media. Curiously, growth of the organism in minimal media (M9G or minimal media plus casamino acids (M9CG facilitated robust expression of T6SS-1 genes whereas growth in minimal media plus tryptone (M9TG did not. Investigation of this phenomenon confirmed a regulatory role for VirAG in this process. Additionally, T6SS-1 gene expression was significantly down-regulated by the addition of iron and zinc to M9CG. Other genes under the control of VirAG did not appear to be as tightly regulated by these divalent metals. Similar results were observed for B. pseudomallei, but not for B. thailandensis. Collectively, our findings indicate that in addition to being positively regulated by VirAG, B. mallei and B. pseudomallei T6SS-1 gene expression is negatively regulated by iron and zinc.

  1. POLYCLONAL OUTBREAK OF BLOODSTREAM INFECTIONS CAUSED BY Burkholderia cepacia COMPLEX IN HEMATOLOGY AND BONE MARROW TRANSPLANT OUTPATIENT UNITS

    Directory of Open Access Journals (Sweden)

    Icaro Boszczowski

    2014-01-01

    Full Text Available Aim: The objective was to describe an outbreak of bloodstream infections by Burkholderia cepacia complex (Bcc in bone marrow transplant and hematology outpatients. Methods: On February 15, 2008 a Bcc outbreak was suspected. 24 cases were identified. Demographic and clinical data were evaluated. Environment and healthcare workers' (HCW hands were cultured. Species were determined and typed. Reinforcement of hand hygiene, central venous catheter (CVC care, infusion therapy, and maintenance of laminar flow cabinet were undertaken. 16 different HCWs had cared for the CVCs. Multi-dose heparin and saline were prepared on counter common to both units. Findings: 14 patients had B. multivorans (one patient had also B. cenopacia, six non-multivorans Bcc and one did not belong to Bcc. Clone A B. multivorans occurred in 12 patients (from Hematology; in 10 their CVC had been used on February 11/12. Environmental and HCW cultures were negative. All patients were treated with meropenem, and ceftazidime lock-therapy. Eight patients (30% were hospitalized. No deaths occurred. After control measures (multidose vial for single patient; CVC lock with ceftazidime; cleaning of laminar flow cabinet; hand hygiene improvement; use of cabinet to store prepared medication, no new cases occurred. Conclusions: This polyclonal outbreak may be explained by a common source containing multiple species of Bcc, maybe the laminar flow cabinet common to both units. There may have been contamination by B. multivorans (clone A of multi-dose vials.

  2. Modified sublimation to isolate phenanthrene-degrading bacteria of the genera Sphingomonas and Burkholderia from Xiamen oil port.

    Science.gov (United States)

    Huang, X; Tian, Y; Luo, Y R; Liu, H J; Zheng, Wei; Zheng, T L

    2008-01-01

    Sublimation was developed by Alley and Brown (2000) in order to isolate bacterial strains that were capable of degrading water insoluble compounds. In this study, sublimation was modified by the use of nutritional agar plates, instead of mineral salt agar, to isolate phenanthrene-degrading bacteria from a mixed culture that had been enriched under the selective pressure of high phenanthrene content. Five strains were obtained with different morphology and degradation ability. Based on the 16S rDNA sequence, two of them were classified as species of the genus Sphingomonas; the others as species of the genus Burkholderia. Denaturing gradient gel electrophoresis (DGGE) was introduced to detect dynamic changes in the bacterial community during enrichment batch culture, and to determine any correlation between the five isolates and the phenanthrene-degrading consortium. The DGGE profile indicated that these five isolates corresponded to four dominant bands of the consortium. Compared to traditional means of isolation, we concluded that modified sublimation is effective and more convenient.

  3. A Causal Model for Diagnostic Reasoning

    Institute of Scientific and Technical Information of China (English)

    PENG Guoqiang; CHENG Hu

    2000-01-01

    Up to now, there have been many methods for knowledge representation and reasoning in causal networks, but few of them include the research on the coactions of nodes. In practice, ignoring these coactions may influence the accuracy of reasoning and even give rise to incorrect reasoning. In this paper, based on multilayer causal networks, the definitions on coaction nodes are given to construct a new causal network called Coaction Causal Network, which serves to construct a model of neural network for diagnosis followed by fuzzy reasoning, and then the activation rules are given and neural computing methods are used to finish the diagnostic reasoning. These methods are proved in theory and a method of computing the number of solutions for the diagnostic reasoning is given. Finally, the experiments and the conclusions are presented.

  4. The Temporal Logic of Causal Structures

    CERN Document Server

    Kleinberg, Samantha

    2012-01-01

    Computational analysis of time-course data with an underlying causal structure is needed in a variety of domains, including neural spike trains, stock price movements, and gene expression levels. However, it can be challenging to determine from just the numerical time course data alone what is coordinating the visible processes, to separate the underlying prima facie causes into genuine and spurious causes and to do so with a feasible computational complexity. For this purpose, we have been developing a novel algorithm based on a framework that combines notions of causality in philosophy with algorithmic approaches built on model checking and statistical techniques for multiple hypotheses testing. The causal relationships are described in terms of temporal logic formulae, reframing the inference problem in terms of model checking. The logic used, PCTL, allows description of both the time between cause and effect and the probability of this relationship being observed. We show that equipped with these causal f...

  5. Identifiability of Causal Graphs using Functional Models

    CERN Document Server

    Peters, Jonas; Janzing, Dominik; Schoelkopf, Bernhard

    2012-01-01

    This work addresses the following question: Under what assumptions on the data generating process can one infer the causal graph from the joint distribution? The approach taken by conditional independence-based causal discovery methods is based on two assumptions: the Markov condition and faithfulness. It has been shown that under these assumptions the causal graph can be identified up to Markov equivalence (some arrows remain undirected) using methods like the PC algorithm. In this work we propose an alternative by defining Identifiable Functional Model Classes (IFMOCs). As our main theorem we prove that if the data generating process belongs to an IFMOC, one can identify the complete causal graph. To the best of our knowledge this is the first identifiability result of this kind that is not limited to linear functional relationships. We discuss how the IFMOC assumption and the Markov and faithfulness assumptions relate to each other and explain why we believe that the IFMOC assumption can be tested more eas...

  6. Selecting appropriate cases when tracing causal mechanisms

    DEFF Research Database (Denmark)

    Beach, Derek; Pedersen, Rasmus Brun

    2016-01-01

    selection guidelines are appropriate for research aimed at making cross-case claims about causal relationships, where case selection is primarily used to control for other causes. However, existing guidelines are not in alignment with case-based research that aims to trace mechanisms, where the goal......The last decade has witnessed resurgence in the interest in studying the causal mechanisms linking causes and outcomes in the social sciences. This article explores the overlooked implications for case selection when tracing mechanisms using in-depth case studies. Our argument is that existing case...... is to unpack the causal mechanism between X and Y, enabling causal inferences to be made because empirical evidence is provided for how the mechanism actually operated in a particular case. The in-depth, within-case tracing of how mechanisms operate in particular cases produces what can be termed mechanistic...

  7. Causality Between Urban Concentration and Environmental Quality

    Directory of Open Access Journals (Sweden)

    Amin Pujiati

    2015-08-01

    Full Text Available Population is concentrated in urban areas can cause the external diseconomies on environment if it exceeds the carrying capacity of the space and the urban economy. Otherwise the quality of the environment is getting better, led to the concentration of population in urban areas are increasingly high. This study aims to analyze the relationship of causality between the urban concentration and environmental quality in urban agglomeration areas. The data used in the study of secondary data obtained from the Central Bureau of statistics and the City Government from 2000 to 2013. The analytical method used is the Granger causality and descriptive. Granger causality study results showed no pattern of reciprocal causality, between urban concentration and the quality of the environment, but there unidirectional relationship between the urban concentration and environmental quality. This means that increasing urban concentration led to decreased environmental quality.

  8. Risk and causality in newspaper reporting.

    Science.gov (United States)

    Boholm, Max

    2009-11-01

    The study addresses the textual representation of risk and causality in news media reporting. The analytical framework combines two theoretical perspectives: media frame analysis and the philosophy of causality. Empirical data derive from selected newspaper articles on risks in the Göta älv river valley in southwest Sweden from 1994 to 2007. News media content was coded and analyzed with respect to causal explanations of risk issues. At the level of individual articles, this study finds that the media provide simple causal explanations of risks such as water pollution, landslides, and flooding. Furthermore, these explanations are constructed, or framed, in various ways, the same risk being attributed to different causes in different articles. However, the study demonstrates that a fairly complex picture of risks in the media emerges when extensive material is analyzed systematically.

  9. The Gravity Dual of Boundary Causality

    CERN Document Server

    Engelhardt, Netta

    2016-01-01

    In gauge/gravity duality, points which are not causally related on the boundary cannot be causally related through the bulk; this is the statement of boundary causality. By the Gao-Wald theorem, the averaged null energy condition in the bulk is sufficient to ensure this property. Here we proceed in the converse direction: we derive a necessary as well as sufficient condition for the preservation of boundary causality under perturbative (quantum or stringy) corrections to the bulk. The condition that we find is a (background-dependent) constraint on the amount by which light cones can "open" over all null bulk geodesics. We show that this constraint is weaker than the averaged null energy condition.

  10. Synergy, redundancy and unnormalized Granger causality

    CERN Document Server

    Stramaglia, Sebastiano; Cortés, Jesus M; Marinazzo, Daniele

    2015-01-01

    We analyze by means of Granger causality the effect of synergy and redundancy in the inference (from time series data) of the information flow between subsystems of a complex network. Whilst fully conditioned Granger causality is not affected by synergy, the pairwise analysis fails to put in evidence synergetic effects. We show that maximization of the total Granger causality to a given target, over all the possible partitions of the set of driving variables, puts in evidence redundant multiplets of variables influencing the target, provided that an {\\it unnormalized} definition of Granger causality is adopted. Along the same lines we also introduce a pairwise index of synergy (w.r.t. to information flow to a third variable) which is zero when two independent sources additively influence a common target, differently from previous definitions of synergy.

  11. The Scalar Curvature of a Causal Set

    CERN Document Server

    Benincasa, Dionigi M T

    2010-01-01

    A one parameter family of retarded linear operators on scalar fields on causal sets is introduced. When the causal set is well-approximated by 4 dimensional Minkowski spacetime, the operators are Lorentz invariant but nonlocal, are parametrised by the scale of the nonlocality and approximate the continuum scalar D'Alembertian, $\\Box$, when acting on fields that vary slowly on the nonlocality scale. The same operators can be applied to scalar fields on causal sets which are well-approximated by curved spacetimes in which case they approximate $\\Box - {{1/2}}R$ where $R$ is the Ricci scalar curvature. This can used to define an approximately local action functional for causal sets.

  12. Vitalistic causality in young children's naive biology.

    Science.gov (United States)

    Inagaki, Kayoko; Hatano, Giyoo

    2004-08-01

    One of the key issues in conceptual development research concerns what kinds of causal devices young children use to understand the biological world. We review evidence that children predict and interpret biological phenomena, especially human bodily processes, on the basis of 'vitalistic causality'. That is, they assume that vital power or life force taken from food and water makes humans active, prevents them from being taken ill, and enables them to grow. These relationships are also extended readily to other animals and even to plants. Recent experimental results show that a majority of preschoolers tend to choose vitalistic explanations as most plausible. Vitalism, together with other forms of intermediate causality, constitute unique causal devices for naive biology as a core domain of thought.

  13. The Causal Foundations of Structural Equation Modeling

    Science.gov (United States)

    2012-02-16

    The Causal Foundations of Structural Equation Modeling Judea Pearl University of California, Los Angeles Computer Science Department Los Angeles, CA...Handbook of Structural Equation Modeling . New York: Guilford Press. TECHNICAL REPORT R-370 February 2012 Report Documentation Page Form...COVERED 00-00-2012 to 00-00-2012 4. TITLE AND SUBTITLE The Causal Foundations of Structural Equation Modeling 5a. CONTRACT NUMBER 5b. GRANT

  14. Locally Causal Dynamical Triangulations in Two Dimensions

    CERN Document Server

    Loll, Renate

    2015-01-01

    We analyze the universal properties of a new two-dimensional quantum gravity model defined in terms of Locally Causal Dynamical Triangulations (LCDT). Measuring the Hausdorff and spectral dimensions of the dynamical geometrical ensemble, we find numerical evidence that the continuum limit of the model lies in a new universality class of two-dimensional quantum gravity theories, inequivalent to both Euclidean and Causal Dynamical Triangulations.

  15. Causales de ausencia de responsabilidad penal

    OpenAIRE

    Jaime Sandoval Fernández

    2003-01-01

    Este trabajo se ocupa de las causales de ausencia de responsabilidad penal, especialmente de aquellas que tienen efecto en el injusto. Como subtemas se delimita el concepto de responsabilidad penal y su ausencia. Se estudian las principales teorias a cerca de la relación tipicidad-antijuridicidad y su incidencia en el derecho penal colombiano. Por último contiene una propuesta acerca de cómo deberian agruparse las causales del arto 32 C. PlOO.

  16. Causales de ausencia de responsabilidad penal

    Directory of Open Access Journals (Sweden)

    Jaime Sandoval Fernández

    2003-01-01

    Full Text Available Este trabajo se ocupa de las causales de ausencia de responsabilidad penal, especialmente de aquellas que tienen efecto en el injusto. Como subtemas se delimita el concepto de responsabilidad penal y su ausencia. Se estudian las principales teorias a cerca de la relación tipicidad-antijuridicidad y su incidencia en el derecho penal colombiano. Por último contiene una propuesta acerca de cómo deberian agruparse las causales del arto 32 C. PlOO.

  17. Illness causal beliefs in Turkish immigrants

    OpenAIRE

    Klimidis Steven; Minas Harry; Tuncer Can

    2007-01-01

    Abstract Background People hold a wide variety of beliefs concerning the causes of illness. Such beliefs vary across cultures and, among immigrants, may be influenced by many factors, including level of acculturation, gender, level of education, and experience of illness and treatment. This study examines illness causal beliefs in Turkish-immigrants in Australia. Methods Causal beliefs about somatic and mental illness were examined in a sample of 444 members of the Turkish population of Melbo...

  18. Porin involvement in cephalosporin and carbapenem resistance of Burkholderia pseudomallei.

    Directory of Open Access Journals (Sweden)

    Anuwat Aunkham

    Full Text Available BACKGROUND: Burkholderia pseudomallei (Bps is a Gram-negative bacterium that causes frequently lethal melioidosis, with a particularly high prevalence in the north and northeast of Thailand. Bps is highly resistant to many antimicrobial agents and this resistance may result from the low drug permeability of outer membrane proteins, known as porins. PRINCIPAL FINDINGS: Microbiological assays showed that the clinical Bps strain was resistant to most antimicrobial agents and sensitive only to ceftazidime and meropenem. An E. coli strain defective in most porins, but expressing BpsOmp38, exhibited considerably lower antimicrobial susceptibility than the control strain. In addition, mutation of Tyr119, the most prominent pore-lining residue in BpsOmp38, markedly altered membrane permeability, substitution with Ala (mutant BpsOmp38Y119A enhanced uptake of the antimicrobial agents, while substitution with Phe (mutant BpsOmp38Y119F inhibited uptake. Channel recordings of BpsOmp38 reconstituted in a planar black lipid membrane (BLM suggested that the higher permeability of BpsOmp38Y119A was caused by widening of the pore interior through removal of the bulky side chain. In contrast, the lower permeability of BpsOmp38Y119F was caused by introduction of the hydrophobic side chain (Phe, increasing the 'greasiness' of the pore lumen. Significantly, liposome swelling assays showed no permeation through the BpsOmp38 channel by antimicrobial agents to which Bps is resistant (cefoxitin, cefepime, and doripenem. In contrast, high permeability to ceftazidime and meropenem was observed, these being agents to which Bps is sensitive. CONCLUSION/SIGNIFICANCE: Our results, from both in vivo and in vitro studies, demonstrate that membrane permeability associated with BpsOmp38 expression correlates well with the antimicrobial susceptibility of the virulent bacterium B. pseudomallei, especially to carbapenems and cephalosporins. In addition, substitution of the residue

  19. Burkholderia pseudomallei genome plasticity associated with genomic island variation

    Directory of Open Access Journals (Sweden)

    Currie Bart J

    2008-04-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. Results Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with micro-evolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9, to 76% for a metabolic island (GI 16. The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p > 0.05 for all five islands. The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3. The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p = 0.27. The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing; these were ST 70 (n = 15 isolates, ST 54 (n = 11, and ST 167 (n = 9. The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained

  20. Causal Structures in Gauss-Bonnet gravity

    CERN Document Server

    Izumi, Keisuke

    2014-01-01

    We analyze causal structures in Gauss-Bonnet gravity. It is known that Gauss-Bonnet gravity potentially has superluminal propagation of gravitons due to its non-canonical kinetic terms. In a theory with superluminal modes, an analysis of causality based on null curves makes no sense, and thus, we need to analyse them in a different way. In this paper, using the method of the characteristics, we analyze the causal structure in Gauss-Bonnet gravity. We have the result that, on a Killing horizon, gravitons can propagate in the null direction tangent to the Killing horizon. Therefore, a Killing horizon can be a causal edge as in the case of general relativity, i.e. a Killing horizon is the "event horizon" in the sense of causality. We also analyze causal structures on dynamical solutions with $(D-2)$-dimensional maximal symmetry, including spherically symmetric and flat spaces. If the geometrical null energy condition, $R_{AB}N^AN^B \\ge 0$ for any null vector $N^A$, is satisfied, the radial velocity of gravitons ...

  1. Kant on causal laws and powers.

    Science.gov (United States)

    Henschen, Tobias

    2014-12-01

    The aim of the paper is threefold. Its first aim is to defend Eric Watkins's claim that for Kant, a cause is not an event but a causal power: a power that is borne by a substance, and that, when active, brings about its effect, i.e. a change of the states of another substance, by generating a continuous flow of intermediate states of that substance. The second aim of the paper is to argue against Watkins that the Kantian concept of causal power is not the pre-critical concept of real ground but the category of causality, and that Kant holds with Hume that causal laws cannot be inferred non-inductively (that he accordingly has no intention to show in the Second analogy or elsewhere that events fall under causal laws). The third aim of the paper is to compare the Kantian position on causality with central tenets of contemporary powers ontology: it argues that unlike the variants endorsed by contemporary powers theorists, the Kantian variants of these tenets are resistant to objections that neo-Humeans raise to these tenets.

  2. An Oxygen-Sensing Two-Component System in the Burkholderia cepacia Complex Regulates Biofilm, Intracellular Invasion, and Pathogenicity

    Science.gov (United States)

    Liao, Tiffany L.; Boisvert, Nicole M.; Priebe, Gregory P.

    2017-01-01

    Burkholderia dolosa is a member of the Burkholderia cepacia complex (BCC), which is a group of bacteria that cause chronic lung infection in patients with cystic fibrosis (CF) and can be associated with outbreaks carrying high morbidity and mortality. While investigating the genomic diversity of B. dolosa strains collected from an outbreak among CF patients, we previously identified fixL as a gene showing signs of strong positive selection. This gene has homology to fixL of the rhizobial FixL/FixJ two-component system. The goals of this study were to determine the functions of FixLJ and their role in virulence in B. dolosa. We generated a fixLJ deletion mutant and complemented controls in B. dolosa strain AU0158. Using a fixK-lacZ reporter we found that FixLJ was activated in low oxygen in multiple BCC species. In a murine pneumonia model, the B. dolosa fixLJ deletion mutant was cleared faster from the lungs and spleen than wild-type B. dolosa strain AU0158 at 7 days post infection. Interestingly, the fixLJ deletion mutant made more biofilm, albeit with altered structure, but was less motile than strain AU0158. Using RNA-seq with in vitro grown bacteria, we found ~11% of the genome was differentially expressed in the fixLJ deletion mutant relative to strain AU0158. Multiple flagella-associated genes were down-regulated in the fixLJ deletion mutant, so we also evaluated virulence of a fliC deletion mutant, which lacks a flagellum. We saw no difference in the ability of the fliC deletion mutant to persist in the murine model relative to strain AU0158, suggesting factors other than flagella caused the phenotype of decreased persistence. We found the fixLJ deletion mutant to be less invasive in human lung epithelial and macrophage-like cells. In conclusion, B. dolosa fixLJ is a global regulator that controls biofilm formation, motility, intracellular invasion/persistence, and virulence. PMID:28046077

  3. PCR-based identification of Burkholderia pseudomallei Identificação de Burkholderia pseudomallei baseada em PCR

    Directory of Open Access Journals (Sweden)

    Adam Merritt

    2006-10-01

    Full Text Available DNA amplification techniques are being used increasingly in clinical laboratories to confirm the identity of medically important bacteria. A PCR-based identification method has been in use in our centre for 10 years for Burkholderia pseudomallei and was used to confirm the identity of bacteria isolated from cases of melioidosis in Ceará since 2003. This particular method has been used as a reference standard for less discriminatory methods. In this study we evaluated three PCR-based methods of B. pseudomallei identification and used DNA sequencing to resolve discrepancies between PCR-based results and phenotypic identification methods. The established semi-nested PCR protocol for B. pseudomallei 16-23s spacer region produced a consistent negative result for one of our 100 test isolates (BCC #99, but correctly identified all 71 other B. pseudomallei isolates tested. Anomalous sequence variation was detected at the inner, reverse primer binding site for this method. PCR methods were developed for detection of two other B. pseudomallei bacterial metabolic genes. The conventional lpxO PCR protocol had a sensitivity of 0.89 and a specificity of 1.00, while a real-time lpxO protocol performed even better with sensitivity and specificity of 1.00, and 1.00. This method identified all B. pseudomallei isolates including the PCR-negative discrepant isolate. The phaC PCR protocol detected the gene in all B. pseudomallei and all but three B. cepacia isolates, making this method unsuitable for PCR-based identification of B. pseudomallei. This experience with PCR-based B. pseudomallei identification methods indicates that single PCR targets should be used with caution for identification of these bacteria, and need to be interpreted alongside phenotypic and alternative molecular methods such as gene sequencing.As técnicas de amplificação de DNA estão sendo cada vez mais utilizadas em laboratórios clínicos para a confirmação da identificação de bact

  4. Detection of Burkholderia pseudomallei toxin-mediated inhibition of protein synthesis using a Caenorhabditis elegans ugt–29 biosensor

    Science.gov (United States)

    Wong, Rui-Rui; Kong, Cin; Lee, Song-Hua; Nathan, Sheila

    2016-01-01

    Toxins are believed to play a crucial role in Burkholderia pseudomallei pathogenicity, however to date, only a few have been identified. The discovery of additional toxic molecules is limited by the lack of a sensitive indicator of B. pseudomallei toxicity. Previously, from a whole genome transcriptome analysis of B. pseudomallei-infected Caenorhabditis elegans, we noted significant overexpression of a number of worm genes encoding detoxification enzymes, indicating the host’s attempt to clear bacterial toxic molecules. One of these genes, ugt–29, a family member of UDP-glucuronosyltransferases, was the most robustly induced phase II detoxification gene. In this study, we show that strong induction of ugt–29 is restricted to infections by the most virulent species among the pathogens tested. We also noted that ugt–29 is activated upon disruption of host protein synthesis. Hence, we propose that UGT–29 could be a promising biosensor to detect B. pseudomallei toxins that compromise host protein synthesis. The identification of bactobolin, a polyketide-peptide hybrid molecule, as a toxic molecule of B. pseudomallei further verifies the utilization of this surveillance system to search for bacterial toxins. Hence, a ugt–29 based reporter should be useful in screening for other molecules that inhibit host protein synthesis. PMID:27273550

  5. Rhamnolipids from non-pathogenic Burkholderia thailandensis E264: Physicochemical characterization, antimicrobial and antibiofilm efficacy against oral hygiene related pathogens.

    Science.gov (United States)

    Elshikh, Mohamed; Funston, Scott; Chebbi, Alif; Ahmed, Syed; Marchant, Roger; Banat, Ibrahim M

    2017-05-25

    Biosurfactants are naturally occurring surface active compounds that have mainly been exploited for environmental applications and consumer products, with their biomedical efficacy an emerging area of research. Rhamnolipids area major group of biosurfactants that have been reported for their antimicrobial and antibiofilm efficacy. One of the main limiting factors for scaled up production and downstream applications of rhamnolipids is the fact that they are predominantly produced from the opportunistic pathogen Pseudomonas aeruginosa. In this article, we have reported the production and characterisation of long chain rhamnolipids from non-pathogenic Burkholderia thailandensis E264 (ATCC 700388). We have also investigated the antibacterial and antibiofilm properties of these rhamnolipids against some oral pathogens (Streptococcus oralis, Actinomyces naeslundii, Neisseria mucosa and Streptococcus sanguinis), important for oral health and hygiene. Treating these bacteria with different concentrations of long chain rhamnolipids resulted in a reduction of 3-4 log of bacterial viability, placing these rhamnolipids close to being classified as biocidal. Investigating long chain rhamnolipid efficacy as antibiofilm agents for prospective oral-related applications revealed good potency against oral-bacteria biofilms in a co-incubation experiments, in a pre-coated surface format, in disrupting immature biofilms and has shown excellent combination effect with Lauryl Sodium Sulphate which resulted in a drastic decrease in its minimal inhibitory concentration against different bacteria. Investigating the rhamnolipid permeabilization effect along with their ability to induce the formation of reactive oxygen species has shed light on the mechanism through which inhibition/killing of bacteria may occur.

  6. Trimeric autotransporter adhesins in members of the Burkholderia cepacia complex: a multifunctional family of proteins implicated in virulence

    Directory of Open Access Journals (Sweden)

    Arsénio Mendes Fialho

    2011-12-01

    Full Text Available Trimeric autotransporter adhesins (TAAs are multimeric surface proteins, involved in various biological traits of pathogenic Gram-negative bacteria including adherence, biofilm formation, invasion, survival within eukaryotic cells, serum resistance and cytotoxicity. TAAs have a modular architecture composed by a conserved membrane-anchored C-terminal domain and a variable number of stalk and head domains. In this study, a bioinformatic approach has been used to analyze the distribution and architecture of TAAs among Burkholderia cepacia complex (Bcc genomes. Fifteen genomes were probed revealing a total of 74 encoding sequences. Compared with other bacterial species, the Bcc genomes contain a disproportionately large number of TAAs (two genes to up to 8 genes, such as in B.cenocepacia. Phylogenetic analysis showed that the TAAs grouped into at least eight distinct clusters. TAAs with serine-rich repeats are clearly well separated from others, thereby representing a different evolutionary lineage. Comparative gene mapping across Bcc genomes reveals that TAA genes are inserted within conserved synteny blocks. We further focused our analysis on the epidemic strain B. cenocepacia J2315 in which 7 TAAs were annotated. Among these, 3 TAA-encoding genes (BCAM019, BCAM0223 and BCAM0224 are organized into a cluster and are candidates for multifunctional virulence factors. Here we review the current insights into the functional role of BCAM0224 as a model locus.

  7. Preschoolers prefer to learn causal information

    Directory of Open Access Journals (Sweden)

    Aubry eAlvarez

    2015-02-01

    Full Text Available Young children, in general, appear to have a strong drive to explore the environment in ways that reveal its underlying causal structure. But are they really attuned specifically to casual information in this quest for understanding, or do they show equal interest in other types of non-obvious information about the world? To answer this question, we introduced 20 three-year-old children to two puppets who were anxious to tell the child about a set of novel artifacts and animals. One puppet consistently described causal properties of the items while the other puppet consistently described carefully matched non-causal properties of the same items. After a familiarization period in which children learned which type of information to expect from each informant, children were given the opportunity to choose which they wanted to hear describe each of eight pictured test items. On average, children chose to hear from the informant that provided causal descriptions on 72% of the trials. This preference for causal information has important implications for explaining the role of conceptual information in supporting early learning and may suggest means for maximizing interest and motivation in young children.

  8. Causal impressions: predicting when, not just whether.

    Science.gov (United States)

    Young, Michael E; Rogers, Ester T; Beckmann, Joshua S

    2005-03-01

    In 1739, David Hume established the so-called cues to causality--environmental cues that are important to the inference of causality. Although this descriptive account has been corroborated experimentally, it has not been established why these cues are useful, except that they may reflect statistical regularities in the environment. One of the cues to causality, covariation, helps predict whether an effect will occur, but not its time of occurrence. In the present study, evidence is provided that spatial and temporal contiguity improve an observer's ability to predict when an effect will occur, thus complementing the utility of covariation as a predictor of whether an effect will occur. While observing Michotte's (1946/1963) launching effect, participants showed greater accuracy and precision in their predictions of the onset of movement by the launched object when there was spatial and temporal contiguity. Furthermore, when auditory cues that bridged a delayed launch were included, causal ratings and predictability were similarly affected. These results suggest that the everyday inference of causality relies on our ability to predict whether and when an effect will occur.

  9. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

    Directory of Open Access Journals (Sweden)

    Harvey Steven P

    2007-03-01

    Full Text Available Abstract Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were

  10. Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315.

    Directory of Open Access Journals (Sweden)

    Wen-Li Du

    2016-07-01

    Full Text Available Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315. It comprises an extra replicon (c2 of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1, another extra replicon(c3 of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the

  11. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions.

    Directory of Open Access Journals (Sweden)

    Sandra Schwarz

    Full Text Available Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs of Burkholderia thailandensis (B. thai in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans-leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.

  12. Selection of nitrogen-fixing deficient Burkholderia vietnamiensis strains by cystic fibrosis patients: involvement of nif gene deletions and auxotrophic mutations.

    Science.gov (United States)

    Menard, Aymeric; Monnez, Claire; Estrada de Los Santos, Paulina; Segonds, Christine; Caballero-Mellado, Jesus; Lipuma, John J; Chabanon, Gerard; Cournoyer, Benoit

    2007-05-01

    Burkholderia vietnamiensis is the third most prevalent species of the Burkholderia cepacia complex (Bcc) found in cystic fibrosis (CF) patients. Its ability at fixing nitrogen makes it one of the main Bcc species showing strong filiations with environmental reservoirs. In this study, 83% (29 over 35) of the B. vietnamiensis CF isolates and 100% of the environmental ones (over 29) were found expressing the dinitrogenase complex (encoded by the nif cluster) which is essential in N(2) fixation. Among the deficient strains, two were found growing with ammonium chloride suggesting that they were defective in N(2) fixation, and four with amino acids supplements suggesting that they were harbouring auxotrophic mutations. To get insights about the genetic events that led to the emergence of the N(2)-fixing defective strains, a genetic analysis of B. vietnamiensis nitrogen-fixing property was undertaken. A 40-kb-long nif cluster and nif regulatory genes were identified within the B. vietnamiensis strain G4 genome sequence, and analysed. Transposon mutagenesis and nifH genetic marker exchanges showed the nif cluster and several other genes like gltB (encoding a subunit of the glutamate synthase) to play a key role in B. vietnamiensis ability at growing in nitrogen-free media. nif cluster DNA probings of restricted genomic DNA blots showed a full deletion of the nif cluster for one of the N(2)-fixing defective strain while the other one showed a genetic organization similar to the one of the G4 strain. For 17% of B. vietnamiensis clinical strains, CF lungs appeared to have favoured the selection of mutations or deletions leading to N(2)-fixing deficiencies.

  13. Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.

    Science.gov (United States)

    Cuong, Nguyen Duc; Nicolaisen, Mette Haubjerg; Sørensen, Jan; Olsson, Stefan

    2011-08-01

    Sheath blight infection of rice by Rhizoctonia solani Kühn AG1-IA often results in serious yield losses in intensive rice cultivation. Biological control agents (BCAs) have previously been isolated but poor efficiency is often observed when applied under field conditions. This study compares a traditional dual-culture plate assay and a new water-surface microcosm assay for isolation of antagonistic soil bacteria. In the water-surface microcosm assay, floating pathogen mycelium is used as a source for isolation of hyphae-colonizing soil bacteria (HCSB), which are subsequently screened for antagonism. Ten antagonistic soil bacteria (ASB) isolated from a variety of Vietnamese rice soils using dual-culture plates were found to be affiliated with Bacillus based on 16S rRNA gene sequencing. However, all the ASB isolates grew poorly and showed no antagonism in the water-surface microcosm assay. In contrast, 11 (out of 13) HCSB isolates affiliated with Burkholderia sp. all grew well by colonizing the hyphae in the microcosms. Two of the Burkholderia sp. isolates, assigned to B. vietnamiensis based on recA gene sequencing, strongly inhibited fungal growth in both the dual-culture and water-surface microcosm assays; HCSB isolates affiliated to other species or species groups showed limited or no inhibition of R. solani in the microcosms. Our results suggest that HCSB obtained from floating pathogen hyphae can be a new source for isolation of efficient BCAs against R. solani, as the isolation assay mimics the natural habitat for fungal-bacterial interaction in the fields.

  14. Reassessment of Phomopsis species on grapevines

    NARCIS (Netherlands)

    Niekerk, van J.M.; Groenewald, J.Z.; Farr, D.F.; Fourie, P.H.; Halleen, F.; Crous, P.W.

    2005-01-01

    Ten species of Phomopsis have previously been identified from grapevines. Of these, P. viticola, the causal agent of Phomopsis cane and leaf spot, and P. vitimegaspora, the causal agent of swelling arm of grapevines, have been confirmed as severe pathogens of this host. Earlier taxonomic treatments

  15. In vitro antibacterial activity of sphaeropsidins and chemical derivatives toward Xanthomonas oryzae pv. oryzae, the causal agent of rice bacterial blight.

    Science.gov (United States)

    Evidente, Antonio; Venturi, Vittorio; Masi, Marco; Degrassi, Giuliano; Cimmino, Alessio; Maddau, Lucia; Andolfi, Anna

    2011-12-27

    Sphaeropsidin A, the main phytotoxin produced by Diplodia cupressi, as well as the two natural analogues sphaeropsidins B and C and 14 derivatives obtained by chemical modifications were assayed for antibacterial activity against Xanthomonas oryzae pv. oryzae, Pseudomonas fuscovaginae, and Burkholderia glumae, the causal agents of severe bacterial rice diseases. The results showed a strong and specific activity of sphaeropsidin A against X. oryzae pv. oryzae, while no activity was observed against the other two pathogens. The results of structure-activity relationship studies showed that structural features important to impart this antibacterial activity are the presence of the C-7 carbonyl group and the hemiketalic lactone functionality. The C-13 vinyl group, the double bond of ring C, and/or the tertiary C-9 hydroxy group, as well as the pimarane arrangement of the tricylic carbon skeleton, were also important for the antibacterial activity. These findings may be useful in designing novel compounds for practical applications in agriculture.

  16. Host range of Phakopsora pachyrhizi, the causal agent of soybean rust

    Science.gov (United States)

    Phakopsora pachyrhizi, the causal organism of soybean rust, was first described in 1903 from leaves of Glycine max subsp. soja, or wild soybean, in Japan. Since that time, there have been numerous reports of the pathogen on various leguminous species around the world, first in Asia, followed by Aust...

  17. Identification and onion pathogenicity of Burkholderia cepacia complex isolates from the onion rhizosphere and onion field soil.

    Science.gov (United States)

    Jacobs, Janette L; Fasi, Anthony C; Ramette, Alban; Smith, James J; Hammerschmidt, Raymond; Sundin, George W

    2008-05-01

    Burkholderia cepacia complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on B. cepacia complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative B. cepacia complex isolates were recovered on Pseudomonas cepacia azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative B. cepacia complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and recA sequences and restriction fragment length polymorphism analysis of the recA sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species B. cepacia (160), B. cenocepacia (480), B. ambifaria (623), and B. pyrrocinia (27). The majority of isolates identified as B. cepacia (85%), B. cenocepacia (90%), and B. ambifaria (76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of recA sequences from representative B. cepacia complex type and panel strains, along with isolates collected in this study, revealed that the B. cenocepacia isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple B. cepacia complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source

  18. Distinct human antibody response to the biological warfare agent Burkholderia mallei.

    Science.gov (United States)

    Varga, John J; Vigil, Adam; DeShazer, David; Waag, David M; Felgner, Philip; Goldberg, Joanna B

    2012-10-01

    The genetic similarity between Burkholderia mallei (glanders) and Burkholderia pseudomallei (melioidosis) had led to the general assumption that pathogenesis of each bacterium would be similar. In 2000, the first human case of glanders in North America since 1945 was reported in a microbiology laboratory worker. Leveraging the availability of pre-exposure sera for this individual and employing the same well-characterized protein array platform that has been previously used to study a large cohort of melioidosis patients in southeast Asia, we describe the antibody response in a human with glanders. Analysis of 156 peptides present on the array revealed antibodies against 17 peptides with a > 2-fold increase in this infection. Unexpectedly, when the glanders data were compared with a previous data set from B. pseudomallei infections, there were only two highly increased antibodies shared between these two infections. These findings have implications in the diagnosis and treatment of B. mallei and B. pseudomallei infections.

  19. Workshop on treatment of and postexposure prophylaxis for Burkholderia pseudomallei and B. mallei Infection, 2010.

    Science.gov (United States)

    Lipsitz, Rebecca; Garges, Susan; Aurigemma, Rosemarie; Baccam, Prasith; Blaney, David D; Cheng, Allen C; Currie, Bart J; Dance, David; Gee, Jay E; Larsen, Joseph; Limmathurotsakul, Direk; Morrow, Meredith G; Norton, Robert; O'Mara, Elizabeth; Peacock, Sharon J; Pesik, Nicki; Rogers, L Paige; Schweizer, Herbert P; Steinmetz, Ivo; Tan, Gladys; Tan, Patrick; Wiersinga, W Joost; Wuthiekanun, Vanaporn; Smith, Theresa L

    2012-12-01

    The US Public Health Emergency Medical Countermeasures Enterprise convened subject matter experts at the 2010 HHS Burkholderia Workshop to develop consensus recommendations for postexposure prophylaxis against and treatment for Burkholderia pseudomallei and B. mallei infections, which cause melioidosis and glanders, respectively. Drugs recommended by consensus of the participants are ceftazidime or meropenem for initial intensive therapy, and trimethoprim/sulfamethoxazole or amoxicillin/clavulanic acid for eradication therapy. For postexposure prophylaxis, recommended drugs are trimethoprim/sulfamethoxazole or co-amoxiclav. To improve the timely diagnosis of melioidosis and glanders, further development and wide distribution of rapid diagnostic assays were also recommended. Standardized animal models and B. pseudomallei strains are needed for further development of therapeutic options. Training for laboratory technicians and physicians would facilitate better diagnosis and treatment options.

  20. Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005(T.).

    Science.gov (United States)

    Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Rui, Tian; Tiwari, Ravi; Howieson, John; Yates, Ron; O'Hara, Graham; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos

    2013-12-20

    "Burkholderia sprentiae" strain WSM5005(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of "Burkholderia sprentiae" strain WSM5005(T), together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

  1. Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005T

    Science.gov (United States)

    Reeve, Wayne; De Meyer, Sofie; Terpolilli, Jason; Melino, Vanessa; Ardley, Julie; Rui, Tian; Tiwari, Ravi; Howieson, John; Yates, Ron; O’Hara, Graham; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, Cliff; Wei, Chia-Lin; Huntemann, Marcel; Han, James; Chen, I-Min; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Pagani, Ioanna; Pati, Amrita; Goodwin, Lynne; Peters, Lin; Pitluck, Sam; Woyke, Tanja; Kyrpides, Nikos

    2013-01-01

    Burkholderia sprentiae” strain WSM5005T is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated in Australia from an effective N2-fixing root nodule of Lebeckia ambigua collected in Klawer, Western Cape of South Africa, in October 2007. Here we describe the features of “Burkholderia sprentiae” strain WSM5005T, together with the genome sequence and its annotation. The 7,761,063 bp high-quality-draft genome is arranged in 8 scaffolds of 236 contigs, contains 7,147 protein-coding genes and 76 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program. PMID:24976894

  2. Enhanced bioconversion of ethylene glycol to glycolic acid by a newly isolated Burkholderia sp. EG13.

    Science.gov (United States)

    Gao, Xiaoxin; Ma, Zhengfei; Yang, Limin; Ma, Jiangquan

    2014-10-01

    Burkholderia sp. EG13 with high ethylene glycol-oxidizing activity was isolated from soil, which could be used for the synthesis of glycolic acid from the oxidation of ethylene glycol. Using the resting cells of Burkholderia sp. EG13 as biocatalysts, the optimum reaction temperature and pH were 30 °C and 6.0, respectively. After 24 h of biotransformation, the yield of glycolic acid from 200 mM ethylene glycol was 98.8 %. Furthermore, an integrated bioprocess for the production of glycolic acid which involved in situ product removal (ISPR) was investigated. Using fed-batch method with ISPR, a total of 793 mM glycolic acid has been accumulated in the reaction mixture after the 4th feed.

  3. Reducing the Bias of Causality Measures

    CERN Document Server

    Papana, A; Larsson, P G

    2011-01-01

    Measures of the direction and strength of the interdependence between two time series are evaluated and modified in order to reduce the bias in the estimation of the measures, so that they give zero values when there is no causal effect. For this, point shuffling is employed as used in the frame of surrogate data. This correction is not specific to a particular measure and it is implemented here on measures based on state space reconstruction and information measures. The performance of the causality measures and their modifications is evaluated on simulated uncoupled and coupled dynamical systems and for different settings of embedding dimension, time series length and noise level. The corrected measures, and particularly the suggested corrected transfer entropy, turn out to stabilize at the zero level in the absence of causal effect and detect correctly the direction of information flow when it is present. The measures are also evaluated on electroencephalograms (EEG) for the detection of the information fl...

  4. Normalizing the causality between time series

    Science.gov (United States)

    Liang, X. San

    2015-08-01

    Recently, a rigorous yet concise formula was derived to evaluate information flow, and hence the causality in a quantitative sense, between time series. To assess the importance of a resulting causality, it needs to be normalized. The normalization is achieved through distinguishing a Lyapunov exponent-like, one-dimensional phase-space stretching rate and a noise-to-signal ratio from the rate of information flow in the balance of the marginal entropy evolution of the flow recipient. It is verified with autoregressive models and applied to a real financial analysis problem. An unusually strong one-way causality is identified from IBM (International Business Machines Corporation) to GE (General Electric Company) in their early era, revealing to us an old story, which has almost faded into oblivion, about "Seven Dwarfs" competing with a giant for the mainframe computer market.

  5. Noncommutative geometry, Lorentzian structures and causality

    CERN Document Server

    Franco, Nicolas

    2014-01-01

    The theory of noncommutative geometry provides an interesting mathematical background for developing new physical models. In particular, it allows one to describe the classical Standard Model coupled to Euclidean gravity. However, noncommutative geometry has mainly been developed using the Euclidean signature, and the typical Lorentzian aspects of space-time, the causal structure in particular, are not taken into account. We present an extension of noncommutative geometry \\`a la Connes suitable the for accommodation of Lorentzian structures. In this context, we show that it is possible to recover the notion of causality from purely algebraic data. We explore the causal structure of a simple toy model based on an almost commutative geometry and we show that the coupling between the space-time and an internal noncommutative space establishes a new `speed of light constraint'.

  6. Causal binding of actions to their effects.

    Science.gov (United States)

    Buehner, Marc J; Humphreys, Gruffydd R

    2009-10-01

    According to widely held views in cognitive science harking back to David Hume, causality cannot be perceived directly, but instead is inferred from patterns of sensory experience, and the quality of these inferences is determined by perceivable quantities such as contingency and contiguity. We report results that suggest a reversal of Hume's conjecture: People's sense of time is warped by the experience of causality. In a stimulus-anticipation task, participants' response behavior reflected a shortened experience of time in the case of target stimuli participants themselves had generated, relative to equidistant, equally predictable stimuli they had not caused. These findings suggest that causality in the mind leads to temporal binding of cause and effect, and extend and generalize beyond earlier claims of intentional binding between action and outcome.

  7. Causal inheritence in plane wave quotients

    Energy Technology Data Exchange (ETDEWEB)

    Hubeny, Veronika E.; Rangamani, Mukund; Ross, Simon F.

    2003-11-24

    We investigate the appearance of closed timelike curves in quotients of plane waves along spacelike isometries. First we formulate a necessary and sufficient condition for a quotient of a general spacetime to preserve stable causality. We explicitly show that the plane waves are stably causal; in passing, we observe that some pp-waves are not even distinguishing. We then consider the classification of all quotients of the maximally supersymmetric ten-dimensional plane wave under a spacelike isometry, and show that the quotient will lead to closed timelike curves iff the isometry involves a translation along the u direction. The appearance of these closed timelike curves is thus connected to the special properties of the light cones in plane wave spacetimes. We show that all other quotients preserve stable causality.

  8. Diabetes: the layperson's theories of causality.

    Science.gov (United States)

    Mercado-Martinez, Francisco J; Ramos-Herrera, Igor Martin

    2002-07-01

    The authors examine laypersons' perspectives of illness: the content of causal explanations of diabetes and differences in explanations according to gender. Qualitative research was carried out in Guadalajara, Mexico. A nonprobabilistic sample of 20 diabetic individuals participated in interviews, and the content of the interviews was analyzed. On the origin of their condition, participants offered explanations that match neither the biomedical model nor any other formal causal theory. Participants attributed the onset of diabetes to socioemotional circumstances linked to their life experiences and practices. Men attributed causality to work and social circumstances outside the home; women attributed it to family life and domestic circumstances. The authors discuss how lay theories can be useful for the reorganization of health services.

  9. [Clinical research III. The causality studies].

    Science.gov (United States)

    Talavera, Juan O; Wacher-Rodarte, Niels H; Rivas-Ruiz, Rodolfo

    2011-01-01

    The need to solve a clinical problem leads us to establish a starting point to address (risk, prognosis or treatment studies), all these cases seek to attribute causality. Clinical reasoning described in the book Clinical Epidemiology. The architecture of clinical research, offers a simple guide to understanding this phenomenon. And proposes three basic components: baseline, maneuver and outcome. In this model, different systematic errors (bias) are described, which may be favored by omitting characteristics of the three basic components. Thus, omissions in the baseline characteristics cause an improper assembly of the population and susceptibility bias, omissions in the application or evaluation of the maneuver provoke performance bias, and omissions in the assessment of out-come cause detection bias and transfer bias. Importantly, if this way of thinking facilitates understanding of the causal phenomenon, the appropriateness of the variables to be selected in the studies to which attribute or not causality, require additional arguments for evaluate clinical relevance.

  10. Causality, initial conditions and inflationary magnetogenesis

    CERN Document Server

    Tsagas, Christos G

    2016-01-01

    The post-inflationary evolution of inflation-produced magnetic fields, conventional or not, can change dramatically when two fundamental issues are accounted for. The first is causality, which demands that local physical processes can never affect superhorizon perturbations. The second is the nature of the transition from inflation to reheating and then to the radiation era, which determine the initial conditions at the start of these epochs. Technically, the latter issue can be addressed by appealing to Israel's junction conditions. Causality implies that inflationary magnetic fields dot not freeze into the matter until they have re-entered the causal horizon. The nature of cosmological transitions and the associated initial conditions, on the other hand, determine the large-scale magnetic evolution after inflation. Put together, the two can slow down the adiabatic decay of superhorizon-sized magnetic fields throughout their post-inflationary life and thus lead to considerably stronger residual strengths. Th...

  11. Metrics and causality on Moyal planes

    CERN Document Server

    Franco, Nicolas

    2015-01-01

    Metrics structures stemming from the Connes distance promote Moyal planes to the status of quantum metric spaces. We discuss this aspect in the light of recent developments, emphasizing the role of Moyal planes as representative examples of a recently introduced notion of quantum (noncommutative) locally compact space. We move then to the framework of Lorentzian noncommutative geometry and we examine the possibility of defining a notion of causality on Moyal plane, which is somewhat controversial in the area of mathematical physics. We show the actual existence of causal relations between the elements of a particular class of pure (coherent) states on Moyal plane with related causal structure similar to the one of the usual Minkowski space, up to the notion of locality.

  12. Inferring causality from noisy time series data

    DEFF Research Database (Denmark)

    Mønster, Dan; Fusaroli, Riccardo; Tylén, Kristian;

    2016-01-01

    Convergent Cross-Mapping (CCM) has shown high potential to perform causal inference in the absence of models. We assess the strengths and weaknesses of the method by varying coupling strength and noise levels in coupled logistic maps. We find that CCM fails to infer accurate coupling strength...... and even causality direction in synchronized time-series and in the presence of intermediate coupling. We find that the presence of noise deterministically reduces the level of cross-mapping fidelity, while the convergence rate exhibits higher levels of robustness. Finally, we propose that controlled noise...... injections in intermediate-to-strongly coupled systems could enable more accurate causal inferences. Given the inherent noisy nature of real-world systems, our findings enable a more accurate evaluation of CCM applicability and advance suggestions on how to overcome its weaknesses....

  13. Causality bounds for neutron-proton scattering

    Energy Technology Data Exchange (ETDEWEB)

    Elhatisari, S.; Lee, D. [North Carolina State University, Department of Physics, Raleigh, NC (United States)

    2012-08-15

    We consider the constraints of causality and unitarity for the low-energy interactions of protons and neutrons. We derive a general theorem that non-vanishing partial-wave mixing cannot be reproduced with zero-range interactions without violating causality or unitarity. We define and calculate interaction length scales which we call the causal range and the Cauchy-Schwarz range for all spin channels up to J=3. For some channels we find that these length scales are as large as 5fm. We investigate the origin of these large lengths and discuss their significance for the choice of momentum cutoff scales in effective field theory and universality in many-body Fermi systems. (orig.)

  14. A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei

    OpenAIRE

    Mohd. Raih,Mohd. Firdaus; Sailan,Ahmad Tarmidi; Zamrod,Zulkeflie; Embi,Mohd. Noor; Mohamed, Rahmah

    2003-01-01

    Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert from a Burkholderia pseudomallei genomic library was subjected to automated DNA sequencing utilizing a primer walking strategy. Analysis of the 2002 bp insert revealed a 1536 bp open reading frame predicted...

  15. Purification and sequence analysis of 4-methyl-5-nitrocatechol oxygenase from Burkholderia sp. strain DNT.

    OpenAIRE

    Haigler, B E; Suen, W C; Spain, J C

    1996-01-01

    4-Methyl-5-nitrocatechol (MNC) is an intermediate in the degradation of 2,4-dinitrotoluene by Burkholderia sp. strain DNT. In the presence of NADPH and oxygen, MNC monooxygenase catalyzes the removal of the nitro group from MNC to form 2-hydroxy-5-methylquinone. The gene (dntB) encoding MNC monooxygenase has been previously cloned and characterized. In order to examine the properties of MNC monooxygenase and to compare it with other enzymes, we sequenced the gene encoding the MNC monooxygenas...

  16. Novel Burkholderia mallei Virulence Factors Linked to Specific Host-Pathogen Protein Interactions

    Science.gov (United States)

    2013-06-23

    Wallqvist‡ Burkholderia mallei is an infectious intracellular pathogen whose virulence and resistance to antibiotics makes it a potential bioterrorism agent...ingestion, inhalation, or skin abrasion. Given their considerable antibiotic resistance, ability to infect via aerosol, and absence of vaccines, these... equine hosts. Thus, the genes retained in B. mallei share a high sequence similarity to genes common to B. pseudomallei (3), and many virulence

  17. Type III Secretion: a Virulence Factor Delivery System Essential for the Pathogenicity of Burkholderia mallei

    OpenAIRE

    Ulrich, Ricky L; DeShazer, David

    2004-01-01

    By creating mutations in the Burkholderia mallei ATCC 23344 animal pathogen-like type III secretion system (TTSS), this study analyzes the correlation between type III secretion and the pathogenicity of ATCC 23344 in vivo. Mutagenesis demonstrated that a functional TTSS was required for the full pathogenicity of ATCC 23344 in the BALB/c mouse and Syrian hamster models of infection. However, vaccination with each mutant failed to elicit a protective immunity against challenge with wild-type AT...

  18. Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

    Science.gov (United States)

    Memišević, Vesna; Zavaljevski, Nela; Rajagopala, Seesandra V.; Kwon, Keehwan; Pieper, Rembert; DeShazer, David; Reifman, Jaques; Wallqvist, Anders

    2015-01-01

    Burkholderia pathogenicity relies on protein virulence factors to control and promote bacterial internalization, survival, and replication within eukaryotic host cells. We recently used yeast two-hybrid (Y2H) screening to identify a small set of novel Burkholderia proteins that were shown to attenuate disease progression in an aerosol infection animal model using the virulent Burkholderia mallei ATCC 23344 strain. Here, we performed an extended analysis of primarily nine B. mallei virulence factors and their interactions with human proteins to map out how the bacteria can influence and alter host processes and pathways. Specifically, we employed topological analyses to assess the connectivity patterns of targeted host proteins, identify modules of pathogen-interacting host proteins linked to processes promoting infectivity, and evaluate the effect of crosstalk among the identified host protein modules. Overall, our analysis showed that the targeted host proteins generally had a large number of interacting partners and interacted with other host proteins that were also targeted by B. mallei proteins. We also introduced a novel Host-Pathogen Interaction Alignment (HPIA) algorithm and used it to explore similarities between host-pathogen interactions of B. mallei, Yersinia pestis, and Salmonella enterica. We inferred putative roles of B. mallei proteins based on the roles of their aligned Y. pestis and S. enterica partners and showed that up to 73% of the predicted roles matched existing annotations. A key insight into Burkholderia pathogenicity derived from these analyses of Y2H host-pathogen interactions is the identification of eukaryotic-specific targeted cellular mechanisms, including the ubiquitination degradation system and the use of the focal adhesion pathway as a fulcrum for transmitting mechanical forces and regulatory signals. This provides the mechanisms to modulate and adapt the host-cell environment for the successful establishment of host infections

  19. Evaluation of six commercial DNA extraction kits for recovery of Burkholderia pseudomallei DNA.

    Science.gov (United States)

    Marques, Maria Angela de Mello; Zimmermann, Pia; Messelhäußer, Ute; Sing, Andreas

    2012-12-01

    Six commercially available DNA extraction kits, as well as thermal lysis and proteinase K DNA extraction were evaluated regarding bacterial inactivation, DNA yield and purity, and their use in a Burkholderia pseudomallei real-time PCR. While all methods successfully inactivated the bacteria, by measuring DNA purity and the level of detection by real-time PCR, the proteinase K method was the most sensitive.

  20. The Twin Arginine Translocation System Is Essential for Aerobic Growth and Full Virulence of Burkholderia thailandensis

    OpenAIRE

    Wagley, Sariqa; Hemsley, Claudia; Thomas, Rachael; Madeleine G Moule; Vanaporn, Muthita; Andreae, Clio; Robinson, Matthew; Goldman, Stan; Brendan W. Wren; Butler, Clive S.; Richard W Titball

    2014-01-01

    The twin arginine translocation (Tat) system in bacteria is responsible for transporting folded proteins across the cytoplasmic membrane, and in some bacteria, Tat-exported substrates have been linked to virulence. We report here that the Tat machinery is present in Burkholderia pseudomallei, B. mallei, and B. thailandensis, and we show that the system is essential for aerobic but not anaerobic growth. Switching off of the Tat system in B. thailandensis grown anaerobically resulted in filamen...

  1. Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms.

    Directory of Open Access Journals (Sweden)

    Vesna Memišević

    2015-03-01

    Full Text Available Burkholderia pathogenicity relies on protein virulence factors to control and promote bacterial internalization, survival, and replication within eukaryotic host cells. We recently used yeast two-hybrid (Y2H screening to identify a small set of novel Burkholderia proteins that were shown to attenuate disease progression in an aerosol infection animal model using the virulent Burkholderia mallei ATCC 23344 strain. Here, we performed an extended analysis of primarily nine B. mallei virulence factors and their interactions with human proteins to map out how the bacteria can influence and alter host processes and pathways. Specifically, we employed topological analyses to assess the connectivity patterns of targeted host proteins, identify modules of pathogen-interacting host proteins linked to processes promoting infectivity, and evaluate the effect of crosstalk among the identified host protein modules. Overall, our analysis showed that the targeted host proteins generally had a large number of interacting partners and interacted with other host proteins that were also targeted by B. mallei proteins. We also introduced a novel Host-Pathogen Interaction Alignment (HPIA algorithm and used it to explore similarities between host-pathogen interactions of B. mallei, Yersinia pestis, and Salmonella enterica. We inferred putative roles of B. mallei proteins based on the roles of their aligned Y. pestis and S. enterica partners and showed that up to 73% of the predicted roles matched existing annotations. A key insight into Burkholderia pathogenicity derived from these analyses of Y2H host-pathogen interactions is the identification of eukaryotic-specific targeted cellular mechanisms, including the ubiquitination degradation system and the use of the focal adhesion pathway as a fulcrum for transmitting mechanical forces and regulatory signals. This provides the mechanisms to modulate and adapt the host-cell environment for the successful establishment of

  2. Causalities of the Taiwan stock market

    Science.gov (United States)

    Ting, Julian Juhi-Lian

    2003-06-01

    Volatility, fitting with first-order Landau expansion, stationarity, and causality of the Taiwan stock market (TAIEX) are investigated based on daily records. Instead of consensuses that consider stock market index change as a random time series we propose the market change as a dual time series consists of the index and the corresponding volume. Therefore, causalities between these two time series are investigated. Our results suggest the volume time series is of second-order importance than the index time series. The index time series receives slightly stronger influence from the previous 67th trading day, while the volume time series is slightly stronger influenced by the previous 62nd trading day.

  3. Dynamics and causality constraints in field theory

    CERN Document Server

    De Souza, M M

    1997-01-01

    We discuss the physical meaning and the geometric interpretation of causality implementation in classical field theories. Causality is normally implemented through kinematical constraints on fields but we show that in a zero-distance limit they also carry a dynamical information, which calls for a revision of our standard concepts of interacting fields. The origin of infinities and other inconsistencies in field theories is traced to fields defined with support on the lightcone; a finite and consistent field theory requires a lightcone generator as the field support.

  4. Cosmic Time Machines: the Causality Issue

    Directory of Open Access Journals (Sweden)

    Felice Fernando de

    2013-09-01

    Full Text Available Continued gravitational collapse gives rise to curvature singularities. If a curvature singularity is globally naked then the space-time may be causally future illbehaved admitting closed time-like or null curves which extend to asymptotic distances and generate a Cosmic Time Machine (de Felice (1995 Lecture Notes in Physics 455, 99 [6]. The existence of Cosmic Time Machines makes it plausible the violation of causality. I conjecture that this circumstance is prevented by some, yet unknown, physical process and show that such a mechanism indeed exists in the Kerr spacetime.

  5. Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon.

    Science.gov (United States)

    Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E Peter

    2014-04-01

    Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei.

  6. Biodegradation of PAHs by Burkholderia sp. VITRSB1 Isolated from Marine Sediments

    Directory of Open Access Journals (Sweden)

    T. Revathy

    2015-01-01

    Full Text Available The polycyclic aromatic hydrocarbons (PAHs pollution to the environment is a major threat to the living organisms, and hence the degradation of these PAHs is necessary. Studies on PAHs degrading bacteria have focussed on terrestrial microbes and the potential of marine derived microbes is undermined. Herein we report the isolation and characterization of PAHs degrading Burkholderia sp. from lagoon sediments collected at the Southern coast of India. The strain was Gram negative, rod-shaped, motile, and ∼2–5 μm in length. Based on the phylogenetic data the strain was identified as Burkholderia and designated as VITRSB1. Initial PAHs degradation ability of the strain was assessed using basal salt medium supplemented with diesel, kerosene, toluene, aniline, naphthalene, and phenol. The strain was found to be effectively degrading kerosene, diesel, toluene, and aniline even at higher concentration (1%. However, naphthalene and aniline were degraded only at lower concentration (0.1% and phenol, camphor, and DAP inhibited the growth of the strain. Furthermore, the degraded end products of the PAHs were determined using FTIR. Notably, none of the end products were found to be toxic to the biosphere. Our results indicate that the isolated Burkholderia sp. could be a prospective candidate for the effective degradation of selective PAHs.

  7. Oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1

    Science.gov (United States)

    Stankevičiūtė, Jonita; Vaitekūnas, Justas; Petkevičius, Vytautas; Gasparavičiūtė, Renata; Tauraitė, Daiva; Meškys, Rolandas

    2016-01-01

    Pyridinols and pyridinamines are important intermediates with many applications in chemical industry. The pyridine derivatives are in great demand as synthons for pharmaceutical products. Moreover, pyridines are used either as biologically active substances or as building blocks for polymers with unique physical properties. Application of enzymes or whole cells is an attractive strategy for preparation of hydroxylated pyridines since the methods for chemical synthesis of pyridinols, particularly aminopyridinols, are usually limited or inefficient. Burkholderia sp. MAK1 (DSM102049), capable of using pyridin-2-ol as the sole carbon and energy source, was isolated from soil. Whole cells of Burkholderia sp. MAK1 were confirmed to possess a good ability to convert different pyridin-2-amines and pyridin-2-ones into their 5-hydroxy derivatives. Moreover, several methylpyridines as well as methylated pyrazines were converted to appropriate N-oxides. In conclusion, regioselective oxyfunctionalization of pyridine derivatives using whole cells of Burkholderia sp. MAK1 is a promising method for the preparation of various pyridin-5-ols and pyridin-N-oxides. PMID:27982075

  8. Effect of gamma irradiation on Burkholderia thailandensis ( Burkholderia pseudomallei surrogate) survival under combinations of pH and NaCl

    Science.gov (United States)

    Yoon, Yohan; Kim, Jae-Hun; Byun, Myung-Woo; Choi, Kyoung-Hee; Lee, Ju-Woon

    2010-04-01

    This study evaluated the effect of gamma irradiation on Burkholderia thailandensis ( Burkholderia pseudomallei surrogate; potential bioterrorism agent) survival under different levels of NaCl and pH. B. thailandensis in Luria Bertani broth supplemented with NaCl (0-3%), and pH-adjusted to 4-7 was treated with gamma irradiation (0-0.5 kGy). Surviving cell counts of bacteria were then enumerated on tryptic soy agar. Data for the cell counts were also used to calculate D10 values (the dose required to reduce 1 log CFU/mL of B. thailandensis). Cell counts of B. thailandensis were decreased ( Pbacteria were observed among different levels of NaCl and pH. D10 values ranged from 0.04 to 0.07 kGy, regardless of NaCl and pH level. These results indicate that low doses of gamma irradiation should be a useful treatment in decreasing the potential bioterrorism bacteria, which may possibly infect humans through foods.

  9. Effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate) survival under combinations of pH and NaCl

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Yohan; Kim, Jae-Hun; Byun, Myung-Woo [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk 580-185 (Korea, Republic of); Choi, Kyoung-Hee [Department of Oral Microbiology, College of Dentistry, Wonkwang University, Iksan, Jeollabuk 570-749 (Korea, Republic of); Lee, Ju-Woon, E-mail: sjwlee@kaeri.re.k [Team for Radiation Food Science and Biotechnology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Jeollabuk 580-185 (Korea, Republic of)

    2010-04-15

    This study evaluated the effect of gamma irradiation on Burkholderia thailandensis (Burkholderia pseudomallei surrogate; potential bioterrorism agent) survival under different levels of NaCl and pH. B. thailandensis in Luria Bertani broth supplemented with NaCl (0-3%), and pH-adjusted to 4-7 was treated with gamma irradiation (0-0.5 kGy). Surviving cell counts of bacteria were then enumerated on tryptic soy agar. Data for the cell counts were also used to calculate D{sub 10} values (the dose required to reduce 1 log CFU/mL of B. thailandensis). Cell counts of B. thailandensis were decreased (P<0.05) as irradiation dose increased, and no differences (P>=0.05) in cell counts of the bacteria were observed among different levels of NaCl and pH. D{sub 10} values ranged from 0.04 to 0.07 kGy, regardless of NaCl and pH level. These results indicate that low doses of gamma irradiation should be a useful treatment in decreasing the potential bioterrorism bacteria, which may possibly infect humans through foods.

  10. Are bruxism and the bite causally related?

    NARCIS (Netherlands)

    Lobbezoo, F.; Ahlberg, J.; Manfredini, D.; Winocur, E.

    2012-01-01

    In the dental profession, the belief that bruxism and dental (mal-)occlusion (‘the bite’) are causally related is widespread. The aim of this review was to critically assess the available literature on this topic. A PubMed search of the English-language literature, using the query ‘Bruxism [Majr] AN

  11. Causal interpretation of stochastic differential equations

    DEFF Research Database (Denmark)

    Sokol, Alexander; Hansen, Niels Richard

    2014-01-01

    structural equation models based on the Euler scheme of the original SDE, thus relating our definition to mainstream causal concepts. We prove that when the driving noise in the SDE is a Lévy process, the postintervention distribution is identifiable from the generator of the SDE....

  12. On Measurement Bias in Causal Inference

    CERN Document Server

    Pearl, Judea

    2012-01-01

    This paper addresses the problem of measurement errors in causal inference and highlights several algebraic and graphical methods for eliminating systematic bias induced by such errors. In particulars, the paper discusses the control of partially observable confounders in parametric and non parametric models and the computational problem of obtaining bias-free effect estimates in such models.

  13. Causal Poisson bracket via deformation quantization

    Science.gov (United States)

    Berra-Montiel, Jasel; Molgado, Alberto; Palacios-García, César D.

    2016-06-01

    Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through an appropriate causal Green’s functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket that has been analyzed in the multisymplectic context. Once our star-product is defined, we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick’s theorem. Finally, we include some examples to explicitly test our method: the real scalar field, the bosonic string and a physically motivated nonlinear particle model. For the field theoretic models, we have encountered causal generalizations of the creation/annihilation relations, and also a causal generalization of the Virasoro algebra for the bosonic string. For the nonlinear particle case, we use the approximate solution in terms of the Green’s function, in order to construct a well-behaved causal bracket.

  14. A quantum probability model of causal reasoning.

    Science.gov (United States)

    Trueblood, Jennifer S; Busemeyer, Jerome R

    2012-01-01

    People can often outperform statistical methods and machine learning algorithms in situations that involve making inferences about the relationship between causes and effects. While people are remarkably good at causal reasoning in many situations, there are several instances where they deviate from expected responses. This paper examines three situations where judgments related to causal inference problems produce unexpected results and describes a quantum inference model based on the axiomatic principles of quantum probability theory that can explain these effects. Two of the three phenomena arise from the comparison of predictive judgments (i.e., the conditional probability of an effect given a cause) with diagnostic judgments (i.e., the conditional probability of a cause given an effect). The third phenomenon is a new finding examining order effects in predictive causal judgments. The quantum inference model uses the notion of incompatibility among different causes to account for all three phenomena. Psychologically, the model assumes that individuals adopt different points of view when thinking about different causes. The model provides good fits to the data and offers a coherent account for all three causal reasoning effects thus proving to be a viable new candidate for modeling human judgment.

  15. Inductive Reasoning about Causally Transmitted Properties

    Science.gov (United States)

    Shafto, Patrick; Kemp, Charles; Bonawitz, Elizabeth Baraff; Coley, John D.; Tenenbaum, Joshua B.

    2008-01-01

    Different intuitive theories constrain and guide inferences in different contexts. Formalizing simple intuitive theories as probabilistic processes operating over structured representations, we present a new computational model of category-based induction about causally transmitted properties. A first experiment demonstrates undergraduates'…

  16. Objective reality, causality and the aspect experiment

    Science.gov (United States)

    Pegg, D. T.

    1980-08-01

    It is argued that, in the framework of Wheeler-Feynman electrodynamics objective reality and causality in the strict sense are consistent with the outcome of atomic cascade photon correlation experiments, provided this outcome is not altered by the Aspect experimental modification.

  17. Introducing Mechanics by Tapping Core Causal Knowledge

    Science.gov (United States)

    Klaassen, Kees; Westra, Axel; Emmett, Katrina; Eijkelhof, Harrie; Lijnse, Piet

    2008-01-01

    This article concerns an outline of an introductory mechanics course. It is based on the argument that various uses of the concept of force (e.g. from Kepler, Newton and everyday life) share an explanatory strategy based on core causal knowledge. The strategy consists of (a) the idea that a force causes a deviation from how an object would move of…

  18. Pride and Prejudice and Causal Indicators

    Science.gov (United States)

    Lee, Nick; Chamberlain, Laura

    2016-01-01

    Aguirre-Urreta, Rönkkö, and Marakas' (2016) paper in "Measurement: Interdisciplinary Research and Perspectives" (hereafter referred to as ARM2016) is an important and timely piece of scholarship, in that it provides strong analytic support to the growing theoretical literature that questions the underlying ideas behind causal and…

  19. Catastrophizing and Causal Beliefs in Whiplash

    NARCIS (Netherlands)

    Buitenhuis, J.; de Jong, P. J.; Jaspers, J. P. C.; Groothoff, J. W.

    2008-01-01

    Study Design. Prospective cohort study. Objective. This study investigates the role of pain catastrophizing and causal beliefs with regard to severity and persistence of neck complaints after motor vehicle accidents. Summary of Background Data. In previous research on low back pain, somatoform disor

  20. Marriage and Anomie: A Causal Argument

    Science.gov (United States)

    Lee, Gary R.

    1974-01-01

    A sample of 394 married couples is employed to test the possibility of an association between marital satisfaction and personal (attitudinal) anomie. The hypothesis is supported. Conclusions are offered relevant to anomie theory, and to utilization of marital and family phenomena as independent variables in causal explanations of nonfamily events.…

  1. Causality and the speed of sound

    CERN Document Server

    Ellis, G; MacCallum, M; Callum, Malcolm Mac; Ellis, George; Maartens, Roy

    2007-01-01

    A usual causal requirement on a viable theory of matter is that the speed of sound be at most the speed of light. In view of various recent papers querying this limit, the question is revisited here. We point to various issues confronting theories that violate the usual constraint.

  2. A Quantum Probability Model of Causal Reasoning

    Science.gov (United States)

    Trueblood, Jennifer S.; Busemeyer, Jerome R.

    2012-01-01

    People can often outperform statistical methods and machine learning algorithms in situations that involve making inferences about the relationship between causes and effects. While people are remarkably good at causal reasoning in many situations, there are several instances where they deviate from expected responses. This paper examines three situations where judgments related to causal inference problems produce unexpected results and describes a quantum inference model based on the axiomatic principles of quantum probability theory that can explain these effects. Two of the three phenomena arise from the comparison of predictive judgments (i.e., the conditional probability of an effect given a cause) with diagnostic judgments (i.e., the conditional probability of a cause given an effect). The third phenomenon is a new finding examining order effects in predictive causal judgments. The quantum inference model uses the notion of incompatibility among different causes to account for all three phenomena. Psychologically, the model assumes that individuals adopt different points of view when thinking about different causes. The model provides good fits to the data and offers a coherent account for all three causal reasoning effects thus proving to be a viable new candidate for modeling human judgment. PMID:22593747

  3. Causality in the Semantics of Esterel: Revisited

    CERN Document Server

    Mousavi, MohammadReza

    2010-01-01

    We re-examine the challenges concerning causality in the semantics of Esterel and show that they pertain to the known issues in the semantics of Structured Operational Semantics with negative premises. We show that the solutions offered for the semantics of SOS also provide answers to the semantic challenges of Esterel and that they satisfy the intuitive requirements set by the language designers.

  4. Causal Meta-Analysis : Methodology and Applications

    NARCIS (Netherlands)

    Bax, L.J.

    2009-01-01

    Meta-analysis is a statistical method to summarize research data from multiple studies in a quantitative manner. This dissertation addresses a number of methodological topics in causal meta-analysis and reports the development and validation of meta-analysis software. In the first (methodological) p

  5. Causal and Teleological Explanations in Biology

    Science.gov (United States)

    Yip, Cheng-Wai

    2009-01-01

    A causal explanation in biology focuses on the mechanism by which a biological process is brought about, whereas a teleological explanation considers the end result, in the context of the survival of the organism, as a reason for certain biological processes or structures. There is a tendency among students to offer a teleological explanation…

  6. The metagenomic approach and causality in virology

    Directory of Open Access Journals (Sweden)

    Silvana Beres Castrignano

    2015-01-01

    Full Text Available Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.

  7. Comments: Causal Interpretations of Mediation Effects

    Science.gov (United States)

    Jo, Booil; Stuart, Elizabeth A.

    2012-01-01

    The authors thank Dr. Lindsay Page for providing a nice illustration of the use of the principal stratification framework to define causal effects, and a Bayesian model for effect estimation. They hope that her well-written article will help expose education researchers to these concepts and methods, and move the field of mediation analysis in…

  8. Geometry of the Infalling Causal Patch

    NARCIS (Netherlands)

    Freivogel, B.; Jefferson, R.A.; Kabir, L.; Yang, I.S.

    2015-01-01

    The firewall paradox states that an observer falling into an old black hole must see a violation of unitarity, locality, or the equivalence principle. Motivated by this remarkable conflict, we analyze the causal structure of black hole spacetimes in order to determine whether all the necessary ingre

  9. Sequential causal learning in humans and rats

    NARCIS (Netherlands)

    H. Lu; R.R. Rojas; T. Beckers; A. Yuille

    2008-01-01

    Recent experiments (Beckers, De Houwer, Pineño, & Miller, 2005;Beckers, Miller, De Houwer, & Urushihara, 2006) have shown that pretraining with unrelated cues can dramatically influence the performance of humans in a causal learning paradigm and rats in a standard Pavlovian conditioning paradigm. Su

  10. Spectral Dimension from Causal Set Nonlocal Dynamics

    CERN Document Server

    Belenchia, Alessio; Marciano, Antonino; Modesto, Leonardo

    2015-01-01

    We investigate the spectral dimension obtained from non-local continuum d'Alembertians derived from causal sets. We find a universal dimensional reduction to 2 dimensions, in all dimensions. We conclude by discussing the validity and relevance of our results within the broader context of quantum field theories based on these nonlocal dynamics.

  11. From causality to time and back

    Energy Technology Data Exchange (ETDEWEB)

    Minguzzi, Ettore, E-mail: ettore.minguzzi@unifi.i [Dipartimento di Matematica Applicata, Universita degli Studi di Firenze, Via S. Marta 3, I-50139 Firenze (Italy)

    2010-05-01

    In this work the problem of the existence of a (semi-)time function on spacetime is investigated together with the problem of recovering the causal structure from the set of time functions allowed by the spacetime. These problems are solved thanks also to a mathematical correspondence with utility theory.

  12. Linear Response Laws and Causality in Electrodynamics

    Science.gov (United States)

    Yuffa, Alex J.; Scales, John A.

    2012-01-01

    Linear response laws and causality (the effect cannot precede the cause) are of fundamental importance in physics. In the context of classical electrodynamics, students often have a difficult time grasping these concepts because the physics is obscured by the intermingling of the time and frequency domains. In this paper, we analyse the linear…

  13. The metagenomic approach and causality in virology

    Science.gov (United States)

    Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

    2015-01-01

    Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease. PMID:25902566

  14. A quantum probability model of causal reasoning

    Directory of Open Access Journals (Sweden)

    Jennifer S Trueblood

    2012-05-01

    Full Text Available People can often outperform statistical methods and machine learning algorithms in situations that involve making inferences about the relationship between causes and effects. While people are remarkably good at causal reasoning in many situations, there are several instances where they deviate from expected responses. This paper examines three situations where judgments related to causal inference problems produce unexpected results and describes a quantum inference model based on the axiomatic principles of quantum probability theory that can explain these effects. Two of the three phenomena arise from the comparison of predictive judgments (i.e., the conditional probability of an effect given a cause with diagnostic judgments (i.e., the conditional probability of a cause given an effect. The third phenomenon is a new finding examining order effects in predictive causal judgments. The quantum inference model uses the notion of incompatibility among different causes to account for all three phenomena. Psychologically, the model assumes that individuals adopt different points of view when thinking about different causes. The model provides good fits to the data and offers a coherent account for all three causal reasoning effects thus proving to be a viable new candidate for modeling human judgment.

  15. Putrescine reduces antibiotic-induced oxidative stress as a mechanism of modulation of antibiotic resistance in Burkholderia cenocepacia.

    Science.gov (United States)

    El-Halfawy, Omar M; Valvano, Miguel A

    2014-07-01

    Communication of antibiotic resistance among bacteria via small molecules is implicated in transient reduction of bacterial susceptibility to antibiotics, which could lead to therapeutic failures aggravating the problem of antibiotic resistance. Released putrescine from the extremely antibiotic-resistant bacterium Burkholderia cenocepacia protects less-resistant cells from different species against the antimicrobial peptide polymyxin B (PmB). Exposure of B. cenocepacia to sublethal concentrations of PmB and other bactericidal antibiotics induces reactive oxygen species (ROS) production and expression of the oxidative stress response regulator OxyR. We evaluated whether putrescine alleviates antibiotic-induced oxidative stress. The accumulation of intracellular ROS, such as superoxide ion and hydrogen peroxide, was assessed fluorometrically with dichlorofluorescein diacetate, while the expression of OxyR and putrescine synthesis enzymes was determined in luciferase assays using chromosomal promoter-lux reporter system fusions. We evaluated wild-type and isogenic deletion mutant strains with defects in putrescine biosynthesis after exposure to sublethal concentrations of PmB and other bactericidal antibiotics. Exogenous putrescine protected against oxidative stress induced by PmB and other antibiotics, whereas reduced putrescine synthesis resulted in increased ROS generation and a parallel increased sensitivity to PmB. Of the 3 B. cenocepacia putrescine-synthesizing enzymes, PmB induced only BCAL2641, an ornithine decarboxylase. This study reveals BCAL2641 as a critical component of the putrescine-mediated communication of antibiotic resistance and as a plausible target for designing inhibitors that would block the communication of such resistance among different bacteria, ultimately reducing the window of therapeutic failure in treating bacterial infections.

  16. Burkholderia ambifaria and B. caribensis promote growth and increase yield in grain amaranth (Amaranthus cruentus and A. hypochondriacus) by improving plant nitrogen uptake.

    Science.gov (United States)

    Parra-Cota, Fannie I; Peña-Cabriales, Juan J; de Los Santos-Villalobos, Sergio; Martínez-Gallardo, Norma A; Délano-Frier, John P

    2014-01-01

    Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism

  17. Causal knowledge and the development of inductive reasoning.

    Science.gov (United States)

    Bright, Aimée K; Feeney, Aidan

    2014-06-01

    We explored the development of sensitivity to causal relations in children's inductive reasoning. Children (5-, 8-, and 12-year-olds) and adults were given trials in which they decided whether a property known to be possessed by members of one category was also possessed by members of (a) a taxonomically related category or (b) a causally related category. The direction of the causal link was either predictive (prey→predator) or diagnostic (predator→prey), and the property that participants reasoned about established either a taxonomic or causal context. There was a causal asymmetry effect across all age groups, with more causal choices when the causal link was predictive than when it was diagnostic. Furthermore, context-sensitive causal reasoning showed a curvilinear development, with causal choices being most frequent for 8-year-olds regardless of context. Causal inductions decreased thereafter because 12-year-olds and adults made more taxonomic choices when reasoning in the taxonomic context. These findings suggest that simple causal relations may often be the default knowledge structure in young children's inductive reasoning, that sensitivity to causal direction is present early on, and that children over-generalize their causal knowledge when reasoning.

  18. Does Causality Matter More Now? Increase in the Proportion of Causal Language in English Texts.

    Science.gov (United States)

    Iliev, Rumen; Axelrod, Robert

    2016-05-01

    The vast majority of the work on culture and cognition has focused on cross-cultural comparisons, largely ignoring the dynamic aspects of culture. In this article, we provide a diachronic analysis of causal cognition over time. We hypothesized that the increased role of education, science, and technology in Western societies should be accompanied by greater attention to causal connections. To test this hypothesis, we compared word frequencies in English texts from different time periods and found an increase in the use of causal language of about 40% over the past two centuries. The observed increase was not attributable to general language effects or to changing semantics of causal words. We also found that there was a consistent difference between the 19th and the 20th centuries, and that the increase happened mainly in the 20th century.

  19. Development of hydrolysis probe-based real-time PCR for identification of virulent gene targets of Burkholderia pseudomallei and B. mallei--a retrospective study on archival cases of service members with melioidosis and glanders.

    Science.gov (United States)

    Zhang, Binxue; Wear, Douglas J; Kim, H S; Weina, Peter; Stojadinovic, Alexander; Izadjoo, Mina

    2012-02-01

    Burkholderia pseudomallei and B. mallei are two highly pathogenic bacteria responsible for melioidosis and glanders, respectively. Our laboratory developed hydrolysis probe-based real-time polymerase chain reaction assays targeting type three secretion system (TTS) and transposase family protein (TFP) of B. pseudomallei and B. malli, respectively. The assays were validated for target specificity, amplification sensitivity, and reproducibility. A bacterial DNA panel, composed of B. pseudomallei (13 strains), B. mallei (11 strains), Burkholderia species close neighbors (5 strains), and other bacterial species (17 strains), was prepared for specificity testing. Reference DNAs from B. pseudomallei and B. mallei bacterial cultures were used as controls for amplification, limit of detection, and reproducibility testing. The two TaqMan assays, Bp-TTS 1 and Bm-TFP, were optimized and applied in a retrospective study of archived cases from the Armed Forces Institute of Pathology. We tested 10 formalin-fixed paraffin-embedded blocks originally from autopsy specimens of patients who died of melioidosis or glanders during or after overseas tours in 1960s. Polymerase chain reaction results confirmed that DNA samples from formalin-fixed paraffin-embedded blocks of eight patients with melioidosis were positive for Bp-TTS 1 target and two patients with glanders were positive for Bm-TFP target.

  20. Diversity of 16S-23S rDNA internal transcribed spacer (ITS reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors.

    Directory of Open Access Journals (Sweden)

    Andrew P Liguori

    Full Text Available Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.

  1. Causal inference algorithms can be useful in life course epidemiology

    NARCIS (Netherlands)

    la Bastide-van Gemert, Sacha; Stolk, Ronald P.; van den Heuvel, Edwin R.; Fidler, Vaclav

    2014-01-01

    Objectives: Life course epidemiology attempts to unravel causal relationships between variables observed over time. Causal relationships can be represented as directed acyclic graphs. This article explains the theoretical concepts of the search algorithms used for finding such representations, discu

  2. Exploratory Causal Analysis in Bivariate Time Series Data

    Science.gov (United States)

    McCracken, James M.

    Many scientific disciplines rely on observational data of systems for which it is difficult (or impossible) to implement controlled experiments and data analysis techniques are required for identifying causal information and relationships directly from observational data. This need has lead to the development of many different time series causality approaches and tools including transfer entropy, convergent cross-mapping (CCM), and Granger causality statistics. In this thesis, the existing time series causality method of CCM is extended by introducing a new method called pairwise asymmetric inference (PAI). It is found that CCM may provide counter-intuitive causal inferences for simple dynamics with strong intuitive notions of causality, and the CCM causal inference can be a function of physical parameters that are seemingly unrelated to the existence of a driving relationship in the system. For example, a CCM causal inference might alternate between ''voltage drives current'' and ''current drives voltage'' as the frequency of the voltage signal is changed in a series circuit with a single resistor and inductor. PAI is introduced to address both of these limitations. Many of the current approaches in the times series causality literature are not computationally straightforward to apply, do not follow directly from assumptions of probabilistic causality, depend on assumed models for the time series generating process, or rely on embedding procedures. A new approach, called causal leaning, is introduced in this work to avoid these issues. The leaning is found to provide causal inferences that agree with intuition for both simple systems and more complicated empirical examples, including space weather data sets. The leaning may provide a clearer interpretation of the results than those from existing time series causality tools. A practicing analyst can explore the literature to find many proposals for identifying drivers and causal connections in times series data

  3. Institutional Investors and Stock Market Development: A Causality Study

    OpenAIRE

    Guler Aras; Alovsat Muslumov

    2008-01-01

    This article examines causality relationships between institutional investors and stock market development based on the panel data compiled from 23 OECD countries for the years 1982 through 2000. In order to test causality relationship, Sims’ causality test based on Granger definition of causality was used in our study. Our empirical results provide evidence that there are statistically significant positive relationship between institutional investors and stock market development. The develop...

  4. Assessing statistical significance in causal graphs

    Directory of Open Access Journals (Sweden)

    Chindelevitch Leonid

    2012-02-01

    Full Text Available Abstract Background Causal graphs are an increasingly popular tool for the analysis of biological datasets. In particular, signed causal graphs--directed graphs whose edges additionally have a sign denoting upregulation or downregulation--can be used to model regulatory networks within a cell. Such models allow prediction of downstream effects of regulation of biological entities; conversely, they also enable inference of causative agents behind observed expression changes. However, due to their complex nature, signed causal graph models present special challenges with respect to assessing statistical significance. In this paper we frame and solve two fundamental computational problems that arise in practice when computing appropriate null distributions for hypothesis testing. Results First, we show how to compute a p-value for agreement between observed and model-predicted classifications of gene transcripts as upregulated, downregulated, or neither. Specifically, how likely are the classifications to agree to the same extent under the null distribution of the observed classification being randomized? This problem, which we call "Ternary Dot Product Distribution" owing to its mathematical form, can be viewed as a generalization of Fisher's exact test to ternary variables. We present two computationally efficient algorithms for computing the Ternary Dot Product Distribution and investigate its combinatorial structure analytically and numerically to establish computational complexity bounds. Second, we develop an algorithm for efficiently performing random sampling of causal graphs. This enables p-value computation under a different, equally important null distribution obtained by randomizing the graph topology but keeping fixed its basic structure: connectedness and the positive and negative in- and out-degrees of each vertex. We provide an algorithm for sampling a graph from this distribution uniformly at random. We also highlight theoretical

  5. Interpretational Confounding or Confounded Interpretations of Causal Indicators?

    Science.gov (United States)

    Bainter, Sierra A.; Bollen, Kenneth A.

    2014-01-01

    In measurement theory, causal indicators are controversial and little understood. Methodological disagreement concerning causal indicators has centered on the question of whether causal indicators are inherently sensitive to interpretational confounding, which occurs when the empirical meaning of a latent construct departs from the meaning…

  6. Causal Relations and Feature Similarity in Children's Inductive Reasoning

    Science.gov (United States)

    Hayes, Brett K.; Thompson, Susan P.

    2007-01-01

    Four experiments examined the development of property induction on the basis of causal relations. In the first 2 studies, 5-year-olds, 8-year-olds, and adults were presented with triads in which a target instance was equally similar to 2 inductive bases but shared a causal antecedent feature with 1 of them. All 3 age groups used causal relations…

  7. The Effect of Causal Diagrams on Text Learning

    Science.gov (United States)

    McCrudden, Matthew T.; Schraw, Gregory; Lehman, Stephen; Poliquin, Anne

    2007-01-01

    We examined the effect of studying a causal diagram on comprehension of causal relationships from an expository science text. A causal diagram is a type of visual display that explicitly represents cause-effect relationships. In Experiment 1, readers between conditions did not differ with respect to memory for main ideas, but the readers who…

  8. Omission of Causal Indicators: Consequences and Implications for Measurement

    Science.gov (United States)

    Aguirre-Urreta, Miguel I.; Rönkkö, Mikko; Marakas, George M.

    2016-01-01

    One of the central assumptions of the causal-indicator literature is that all causal indicators must be included in the research model and that the exclusion of one or more relevant causal indicators would have severe negative consequences by altering the meaning of the latent variable. In this research we show that the omission of a relevant…

  9. Rationales in Children's Causal Learning from Others' Actions

    Science.gov (United States)

    Sobel, David M.; Sommerville, Jessica A.

    2009-01-01

    Shown commensurate actions and information by an adult, preschoolers' causal learning was influenced by the pedagogical context in which these actions occurred. Four-year-olds who were provided with a reason for an experimenter's action relevant to learning causal structure showed more accurate causal learning than children exposed to the same…

  10. Implications of the Changing Conversation about Causality for Evaluators

    Science.gov (United States)

    Gates, Emily; Dyson, Lisa

    2017-01-01

    Making causal claims is central to evaluation practice because we want to know the effects of a program, project, or policy. In the past decade, the conversation about establishing causal claims has become prominent (and problematic). In response to this changing conversation about causality, we argue that evaluators need to take up some new ways…

  11. How to Be Causal: Time, Spacetime and Spectra

    Science.gov (United States)

    Kinsler, Paul

    2011-01-01

    I explain a simple definition of causality in widespread use, and indicate how it links to the Kramers-Kronig relations. The specification of causality in terms of temporal differential equations then shows us the way to write down dynamical models so that their causal nature "in the sense used here" should be obvious to all. To extend existing…

  12. A Quantitative Causal Model Theory of Conditional Reasoning

    Science.gov (United States)

    Fernbach, Philip M.; Erb, Christopher D.

    2013-01-01

    The authors propose and test a causal model theory of reasoning about conditional arguments with causal content. According to the theory, the acceptability of modus ponens (MP) and affirming the consequent (AC) reflect the conditional likelihood of causes and effects based on a probabilistic causal model of the scenario being judged. Acceptability…

  13. Toward an Intersectional Understanding of Process Causality and Social Context

    Science.gov (United States)

    Anderson, Gary L.; Scott, Janelle

    2012-01-01

    Maxwell and Donmoyer both argue in this issue of "Qualitative Inquiry" that narrow definitions of causality in educational research tend to disqualify qualitative research from influence (and funding) among policy makers. They propose a process view of causality that would allow qualitative researchers to make causal claims more grounded in the…

  14. Normalizing the causality between time series

    CERN Document Server

    Liang, X San

    2015-01-01

    Recently, a rigorous yet concise formula has been derived to evaluate the information flow, and hence the causality in a quantitative sense, between time series. To assess the importance of a resulting causality, it needs to be normalized. The normalization is achieved through distinguishing three types of fundamental mechanisms that govern the marginal entropy change of the flow recipient. A normalized or relative flow measures its importance relative to other mechanisms. In analyzing realistic series, both absolute and relative information flows need to be taken into account, since the normalizers for a pair of reverse flows belong to two different entropy balances; it is quite normal that two identical flows may differ a lot in relative importance in their respective balances. We have reproduced these results with several autoregressive models. We have also shown applications to a climate change problem and a financial analysis problem. For the former, reconfirmed is the role of the Indian Ocean Dipole as ...

  15. Finite quantum electrodynamics the causal approach

    CERN Document Server

    Scharf, Günter

    2014-01-01

    In this classic text for advanced undergraduates and graduate students of physics, author Günter Scharf carefully analyzes the role of causality in quantum electrodynamics. His approach offers full proofs and detailed calculations of scattering processes in a mathematically rigorous manner. This third edition contains Scharf's revisions and corrections plus a brief new Epilogue on gauge invariance of quantum electrodynamics to all orders. The book begins with Dirac's theory, followed by the quantum theory of free fields and causal perturbation theory, a powerful method that avoids ultraviolet divergences and solves the infrared problem by means of the adiabatic limit. Successive chapters explore properties of the S-matrix — such as renormalizability, gauge invariance, and unitarity — the renormalization group, and interactive fields. Additional topics include electromagnetic couplings and the extension of the methods to non-abelian gauge theories. Each chapter is supplemented with problems, and four appe...

  16. Consistence beats causality in recommender systems

    CERN Document Server

    Zhu, Xuzhen; Hu, Zheng; Zhang, Ping; Zhou, Tao

    2015-01-01

    The explosive growth of information challenges people's capability in finding out items fitting to their own interests. Recommender systems provide an efficient solution by automatically push possibly relevant items to users according to their past preferences. Recommendation algorithms usually embody the causality from what having been collected to what should be recommended. In this article, we argue that in many cases, a user's interests are stable, and thus the previous and future preferences are highly consistent. The temporal order of collections then does not necessarily imply a causality relationship. We further propose a consistence-based algorithm that outperforms the state-of-the-art recommendation algorithms in disparate real data sets, including \\textit{Netflix}, \\textit{MovieLens}, \\textit{Amazon} and \\textit{Rate Your Music}.

  17. Localizing epileptic seizure onsets with Granger causality

    Science.gov (United States)

    Adhikari, Bhim M.; Epstein, Charles M.; Dhamala, Mukesh

    2013-09-01

    Accurate localization of the epileptic seizure onset zones (SOZs) is crucial for successful surgery, which usually depends on the information obtained from intracranial electroencephalography (IEEG) recordings. The visual criteria and univariate methods of analyzing IEEG recordings have not always produced clarity on the SOZs for resection and ultimate seizure freedom for patients. Here, to contribute to improving the localization of the SOZs and to understanding the mechanism of seizure propagation over the brain, we applied spectral interdependency methods to IEEG time series recorded from patients during seizures. We found that the high-frequency (>80 Hz) Granger causality (GC) occurs before the onset of any visible ictal activity and causal relationships involve the recording electrodes where clinically identifiable seizures later develop. These results suggest that high-frequency oscillatory network activities precede and underlie epileptic seizures, and that GC spectral measures derived from IEEG can assist in precise delineation of seizure onset times and SOZs.

  18. A new spin on causality constraints

    Science.gov (United States)

    Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

    2016-10-01

    Causality in a shockwave state is related to the analytic properties of a four-point correlation function. Extending recent results for scalar probes, we show that this constrains the couplings of the stress tensor to light spinning operators in conformal field theory, and interpret these constraints in terms of the interaction with null energy. For spin-1 and spin-2 conserved currents in four dimensions, the resulting inequalities are a subset of the Hofman-Maldacena conditions for positive energy deposition. It is well known that energy conditions in holographic theories are related to causality on the gravity side; our results make a connection on the CFT side, and extend it to non-holographic theories.

  19. A New Spin on Causality Constraints

    CERN Document Server

    Hartman, Thomas; Kundu, Sandipan

    2016-01-01

    Causality in a shockwave state is related to the analytic properties of a four-point correlation function. Extending recent results for scalar probes, we show that this constrains the couplings of the stress tensor to light spinning operators in conformal field theory, and interpret these constraints in terms of the interaction with null energy. For spin-1 and spin-2 conserved currents in four dimensions, the resulting inequalities are a subset of the Hofman-Maldacena conditions for positive energy deposition. It is well known that energy conditions in holographic theories are related to causality on the gravity side; our results make a connection on the CFT side, and extend it to non-holographic theories.

  20. Confounding and Collapsibility in Causal Inference

    OpenAIRE

    Greenland, Sander; Robins, James M; Pearl, Judea

    1999-01-01

    Consideration of confounding is fundamental to the design and analysis of studies of causal effects. Yet, apart from confounding in experimental designs, the topic is given little or no discussion in most statistics texts. We here provide an overview of confounding and related concepts based on a counterfactual model for causation. Special attention is given to definitions of confounding, problems in control of confounding, the relation of confounding to exchangeability and ...

  1. A Study of Causality in Military Planning

    Science.gov (United States)

    2012-06-08

    Regional and local governance established Establish police forces training Counter organized crime Integrate trained police into operations...richer way to think about causality in military planning and operations. Uncovering an ontology has become an increasingly employed tactic in...political theory.21 In this context, an ontology is simply a way in which the world is viewed, “the most basic conceptualizations of self, other, and

  2. Consistence beats causality in recommender systems

    OpenAIRE

    Zhu, Xuzhen; Tian, Hui; Hu, Zheng; Zhang, Ping; Zhou, Tao

    2015-01-01

    The explosive growth of information challenges people's capability in finding out items fitting to their own interests. Recommender systems provide an efficient solution by automatically push possibly relevant items to users according to their past preferences. Recommendation algorithms usually embody the causality from what having been collected to what should be recommended. In this article, we argue that in many cases, a user's interests are stable, and thus the previous and future prefere...

  3. Isocausal spacetimes may have different causal boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Flores, J L; Herrera, J [Departamento de Algebra, Geometria y Topologia, Facultad de Ciencias, Universidad de Malaga, Campus Teatinos, 29071 Malaga (Spain); Sanchez, M, E-mail: floresj@agt.cie.uma.es, E-mail: jherrera@uma.es, E-mail: sanchezm@ugr.es [Departamento de Geometria y Topologia, Facultad de Ciencias, Universidad de Granada, Avenida Fuentenueva s/n, 18071 Granada (Spain)

    2011-09-07

    We construct an example which shows that two isocausal spacetimes, in the sense introduced recently in GarcIa-Parrado and Senovilla (2003 Class. Quantum Grav. 20 625-64), may have c-boundaries which are not equal (more precisely, not equivalent, as no bijection between the completions can preserve all the binary relations induced by causality). This example also suggests that isocausality can be useful for the understanding and computation of the c-boundary.

  4. Heterogeneous Causal Effects and Sample Selection Bias

    DEFF Research Database (Denmark)

    Breen, Richard; Choi, Seongsoo; Holm, Anders

    2015-01-01

    The role of education in the process of socioeconomic attainment is a topic of long standing interest to sociologists and economists. Recently there has been growing interest not only in estimating the average causal effect of education on outcomes such as earnings, but also in estimating how cau......, and we illustrate our arguments and our method using National Longitudinal Survey of Youth 1979 (NLSY79) data....

  5. Assessing Causality in a Complex Security Environment

    Science.gov (United States)

    2015-01-01

    Fidel Castro popular revolt. Of course, the Bay of Pigs invasion was a disastrous failure, one that humiliated the new President. The NIE went as...and place great reliance on it. The Castro regime is steadily losing popularity. . . . housewives and servants must stand in line for hours to...was evaluating the possibility of an anti- Castro uprising. What is the causal connection between soap lines and a readiness to spontane- ously

  6. Waves and causality in higher dimensions

    CERN Document Server

    Wesson, Paul S

    2015-01-01

    We give a new, wave-like solution of the field equations of five-dimensional relativity. In ordinary three-dimensional space, the waves resemble de Broglie or matter waves, whose puzzling behaviour can be better understood in terms of one or more extra dimensions. Causality is appropriately defined by a null higher-dimensional interval. It may be possible to test the properties of these waves in the laboratory.

  7. Imposing causality on a matrix model

    Energy Technology Data Exchange (ETDEWEB)

    Benedetti, Dario [Perimeter Institute for Theoretical Physics, 31 Caroline St. N, N2L 2Y5, Waterloo ON (Canada)], E-mail: dbenedetti@perimeterinstitute.ca; Henson, Joe [Perimeter Institute for Theoretical Physics, 31 Caroline St. N, N2L 2Y5, Waterloo ON (Canada)

    2009-07-13

    We introduce a new matrix model that describes Causal Dynamical Triangulations (CDT) in two dimensions. In order to do so, we introduce a new, simpler definition of 2D CDT and show it to be equivalent to the old one. The model makes use of ideas from dually weighted matrix models, combined with multi-matrix models, and can be studied by the method of character expansion.

  8. Waves and causality in higher dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Wesson, Paul S., E-mail: psw.papers@yahoo.ca [Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1 (Canada); Overduin, James M., E-mail: joverduin@towson.edu [Department of Physics, Astronomy and Geosciences, Towson University, Towson, MD, 21252 (United States); Department of Physics and Astronomy, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218 (United States)

    2015-11-12

    We give a new, wave-like solution of the field equations of five-dimensional relativity. In ordinary three-dimensional space, the waves resemble de Broglie or matter waves, whose puzzling behaviour can be better understood in terms of one or more extra dimensions. Causality is appropriately defined by a null higher-dimensional interval. It may be possible to test the properties of these waves in the laboratory.

  9. Bayesian Discovery of Linear Acyclic Causal Models

    CERN Document Server

    Hoyer, Patrik O

    2012-01-01

    Methods for automated discovery of causal relationships from non-interventional data have received much attention recently. A widely used and well understood model family is given by linear acyclic causal models (recursive structural equation models). For Gaussian data both constraint-based methods (Spirtes et al., 1993; Pearl, 2000) (which output a single equivalence class) and Bayesian score-based methods (Geiger and Heckerman, 1994) (which assign relative scores to the equivalence classes) are available. On the contrary, all current methods able to utilize non-Gaussianity in the data (Shimizu et al., 2006; Hoyer et al., 2008) always return only a single graph or a single equivalence class, and so are fundamentally unable to express the degree of certainty attached to that output. In this paper we develop a Bayesian score-based approach able to take advantage of non-Gaussianity when estimating linear acyclic causal models, and we empirically demonstrate that, at least on very modest size networks, its accur...

  10. [Causality in cardiology: concepts in evolution].

    Science.gov (United States)

    Méndez, Gustavo F

    2005-01-01

    This paper describes several concepts about causality from Empedocles, Aristoteles and Galeno, to Koch and Hill and the evolution of these concepts related to cardiovascular diseases. Also defines cause and risk, and the philosophical theories about scientific knowledge: inductive versus refutation analysis. On these basis, the study of cardiovascular disease's causality, especially coronary heart disease, allows us the identification of several risk factors involved in its development. However, even with the presently coronary heart disease risk charts (from Framingham and European studies) the higher probability for the development of a cardiovascular ischemic event is around 40%, establishing an important degree of uncertainty. With the improvement in molecular biology techniques, genetics have attempted to analyse several genetic polymorphisms in search of the origin of coronary heart disease. Unfortunately, less than 10% of these polymorphisms have had a positive correlation with coronary heart disease being of minor risk that those obtained for having the diagnosis of type 2 diabetes mellitus or hypercholesterolemia. On these basis, the requirement of new population research projects in which clinical and genetic risk factors are to be studied for the appropriate understanding of the causality process of cardiovascular diseases must be a worldwide priority.

  11. A causal dispositional account of fitness.

    Science.gov (United States)

    Triviño, Vanessa; Nuño de la Rosa, Laura

    2016-09-01

    The notion of fitness is usually equated to reproductive success. However, this actualist approach presents some difficulties, mainly the explanatory circularity problem, which have lead philosophers of biology to offer alternative definitions in which fitness and reproductive success are distinguished. In this paper, we argue  that none of these alternatives is satisfactory and, inspired by Mumford and Anjum's dispositional theory of causation, we offer a definition of fitness as a causal dispositional property. We argue that, under this framework, the distinctiveness that biologists usually attribute to fitness-namely, the fact that fitness is something different from both the physical traits of an organism and the number of offspring it leaves-can be explained, and the main problems associated with the concept of fitness can be solved. Firstly, we introduce Mumford and Anjum's dispositional theory of causation and present our definition of fitness as a causal disposition. We explain in detail each of the elements involved in our definition, namely: the relationship between fitness and the functional dispositions that compose it, the emergent character of fitness, and the context-sensitivity of fitness. Finally, we explain how fitness and realized fitness, as well as expected and realized fitness are distinguished in our approach to fitness as a causal disposition.

  12. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC populations belonging to Burkholderia cenocepacia IIIB and BCC6 group

    Directory of Open Access Journals (Sweden)

    Bevivino Annamaria

    2011-10-01

    Full Text Available Abstract Background A close association between maize roots and Burkholderia cepacia complex (BCC bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico, in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs, respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94% were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA. The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within

  13. Comparative analysis of two phenotypically-similar but genomically-distinct Burkholderia cenocepacia-specific bacteriophages

    Directory of Open Access Journals (Sweden)

    Lynch Karlene H

    2012-06-01

    Full Text Available Abstract Background Genomic analysis of bacteriophages infecting the Burkholderia cepacia complex (BCC is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. The objective of this study was to characterize KL1 (vB_BceS_KL1 and AH2 (vB_BceS_AH2, two novel Burkholderia cenocepacia-specific siphoviruses isolated from environmental samples. Results KL1 and AH2 exhibit several unique phenotypic similarities: they infect the same B. cenocepacia strains, they require prolonged incubation at 30°C for the formation of plaques at low titres, and they do not form plaques at similar titres following incubation at 37°C. However, despite these similarities, we have determined using whole-genome pyrosequencing that these phages show minimal relatedness to one another. The KL1 genome is 42,832 base pairs (bp in length and is most closely related to Pseudomonas phage 73 (PA73. In contrast, the AH2 genome is 58,065 bp in length and is most closely related to Burkholderia phage BcepNazgul. Using both BLASTP and HHpred analysis, we have identified and analyzed the putative virion morphogenesis, lysis, DNA binding, and MazG proteins of these two phages. Notably, MazG homologs identified in cyanophages have been predicted to facilitate infection of stationary phase cells and may contribute to the unique plaque phenotype of KL1 and AH2. Conclusions The nearly indistinguishable phenotypes but distinct genomes of KL1 and AH2 provide further evidence of both vast diversity and convergent evolution in the BCC-specific phage population.

  14. Alteration in cell surface properties of Burkholderia spp. during surfactant-aided biodegradation of petroleum hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Mohanty, Sagarika; Mukherji, Suparna [Indian Institute of Technology Bombay, Mumbai (India). Centre for Environmental Science and Engineering (CESE)

    2012-04-15

    Chemical surfactants may impact microbial cell surface properties, i.e., cell surface hydrophobicity (CSH) and cell surface charge, and may thus affect the uptake of components from non-aqueous phase liquids (NAPLs). This work explored the impact of Triton X-100, Igepal CA 630, and Tween 80 (at twice the critical micelle concentration, CMC) on the cell surface characteristics of Burkholderia cultures, Burkholderia cepacia (ES1, aliphatic degrader) and Burkholderia multivorans (NG1, aromatic degrader), when grown on a six-component model NAPL. In the presence of Triton X-100, NAPL biodegradation was enhanced from 21% to 60% in B. cepacia and from 18% to 53% in B. multivorans. CSH based on water contact angle (50-52 ) was in the same range for both strains while zeta potential at neutral pH was -38 and -31 mV for B. cepacia and B. multivorans, respectively. In the presence of Triton X-100, their CSH increased to greater than 75 and the zeta potential decreased. This induced a change in the mode of uptake and initiated aliphatic hydrocarbon degradation by B. multivorans and increased the rate of aliphatic hydrocarbon degradation in B. cepacia. Igepal CA 630 and Tween 80 also altered the cell surface properties. For B. cepacia grown in the presence of Triton X-100 at two and five times its CMC, CSH increased significantly in the log growth phase. Growth in the presence of the chemical surfactants also affected the abundance of chemical functional groups on the cell surface. Cell surface changes had maximum impact on NAPL degradation in the presence of emulsifying surfactants, Triton X-100 and Igepal CA630.

  15. Information causality from an entropic and a probabilistic perspective

    Energy Technology Data Exchange (ETDEWEB)

    Al-Safi, Sabri W.; Short, Anthony J. [DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA (United Kingdom)

    2011-10-15

    The information causality principle is a generalization of the no-signaling principle which implies some of the known restrictions on quantum correlations. But despite its clear physical motivation, information causality is formulated in terms of a rather specialized game and figure of merit. We explore different perspectives on information causality, discussing the probability of success as the figure of merit, a relation between information causality and the nonlocal ''inner-product game,'' and the derivation of a quadratic bound for these games. We then examine an entropic formulation of information causality with which one can obtain the same results, arguably in a simpler fashion.

  16. Identification and cloning of four riboswitches from Burkholderia pseudomallei strain K96243

    Science.gov (United States)

    Munyati-Othman, Noor; Fatah, Ahmad Luqman Abdul; Piji, Mohd Al Akmarul Fizree Bin Md; Ramlan, Effirul Ikhwan; Raih, Mohd Firdaus

    2015-09-01

    Structured RNAs referred as riboswitches have been predicted to be present in the genome sequence of Burkholderia pseudomallei strain K96243. Four of the riboswitches were identified and analyzed through BLASTN, Rfam search and multiple sequence alignment. The RNA aptamers belong to the following riboswitch classifications: glycine riboswitch, cobalamin riboswitch, S-adenosyl-(L)-homocysteine (SAH) riboswitch and flavin mononucleotide (FMN) riboswitch. The conserved nucleotides for each aptamer were identified and were marked on the secondary structure generated by RNAfold. These riboswitches were successfully amplified and cloned for further study.

  17. N-acylhomoserine-lactone-mediated communication between Pseudomonas aeruginosa and Burkholderia cepacia in mixed biofilms

    DEFF Research Database (Denmark)

    Riedel, K; Hentzer, Morten; Geisenberger, O

    2001-01-01

    were used to visualize AHL-mediated communication in mixed biofilms, which were cultivated either in artificial flow chambers or in alginate beads in mouse lung tissue. In both model systems B. cepacia was capable of perceiving the AHL signals produced by P. aeruginosa, while the latter strain did......Pseudomonas aeruginosa and Burkholderia cepacia are capable of forming mixed biofilms in the lungs of cystic fibrosis patients. Both bacteria employ quorum-sensing systems, which rely on N-acylhomoserine lactone (AHL) signal molecules, to co-ordinate expression of virulence factors...

  18. The promise of bacteriophage therapy for Burkholderia cepacia complex respiratory infections.

    Directory of Open Access Journals (Sweden)

    Diana Dawn Semler

    2012-01-01

    Full Text Available In recent times, increased attention has been given to evaluating the efficacy of phage therapy, especially in scenarios where the bacterial infectious agent of interest is highly antibiotic resistant. In this regard, phage therapy is especially applicable to infections caused by the Burkholderia cepacia complex (BCC since members of the BCC are antibiotic pan-resistant. Current studies in BCC phage therapy are unique from many other avenues of phage therapy research in that the research is not only comprised of phage isolation, in vitro phage characterization and in vivo infection model efficacy, but also adapting aerosol drug delivery techniques to aerosol phage formulation delivery and storage.

  19. A rare case of community acquired Burkholderia cepacia infection presenting as pyopneumothorax in an immunocompetent individual

    Institute of Scientific and Technical Information of China (English)

    Suman S Karanth; Hariharan Regunath; Kiran Chawla; Mukhyaprana Prabhu

    2012-01-01

    Burkholderia cepacia (B. cepacia) infection is rarely reported in an immunocompetent host. It is a well known occurence in patients with cystic fibrosis and chronic granulomatous disease where it increases both morbidity and mortality. It has also been included in the list of organisms causing nosocomial infections in an immunocompetent host, most of them transmitted from the immunocompromised patient in which this organism harbors. We report a rare case of isolation of B. cepacia from the bronchoalveolar lavage fluid of an immunocompetent agriculturist who presented with productive cough and fever associated with a pyopneumothorax. This is the first case of community acquired infection reported in an immunocompetent person in India.

  20. Eradication of Burkholderia cepacia Using Inhaled Aztreonam Lysine in Two Patients with Bronchiectasis

    Directory of Open Access Journals (Sweden)

    A. Iglesias

    2014-01-01

    Full Text Available There are not many articles about the chronic bronchial infection/colonization in patients with underlying lung disease other than cystic fibrosis (CF, especially with non-CF bronchiectasis (NCFBQ. The prevalence of B. cepacia complex is not well known in NCFBQ. The vast majority of published clinical data on Burkholderia infection in individuals with CF is comprised of uncontrolled, anecdotal, and/or single center experiences, and no consensus has emerged regarding treatment. We present two cases diagnosed with bronchiectasis (BQ of different etiology, with early pulmonary infection by B. cepacia complex, which was eradicated with inhaled aztreonam lysine.