1,720,960 research outputs found
Liquid flow in biofilm systems
No full textA model biofilm consisting of Pseudomonas aeruginosa, Pseudomonas fluorescens, and Klebsiella pneumoniae was developed to study the relationships between structural heterogeneity and hydrodynamics. Local fluid velocity in the biofilm system was measured by a noninvasive method of particle image velocimetry, using confocal scanning laser microscopy. Velocity profiles were measured in conduit and porous medium reactors in the presence and absence of biofilm. Liquid flow was observed within biofilm channels; simultaneous imaging of the biofilm allowed the liquid velocity to be related to the physical structure of the biofilm
Nitrate respiration occurs throughout the depth of mucoid and non-mucoid: Pseudomonas aeruginosa submerged agar colony biofilms including the oxic zone.
Get PDFPseudomonas aeruginosa is an opportunistic pathogen and well characterized biofilm former. P. aeruginosa forms strong oxygen gradients inside biofilms due to rapid oxygen respiration in the top layers and the poor solubility of oxygen coupled with diffusion limited transport. Transcriptomic evidence from in vitro and ex vivo sampling suggests that denitrification is occurring in biofilms in ostensibly oxic environments. It is hypothesized that in the presence of nitrate there is stratification with aerobic respiration occurring in the outer oxic layer and denitrification in the lower anoxic zone. We used submerged agar colony biofilms grown from mucoid (FRD1) and non-mucoid (PAO1) strains to simultaneously measure depth microprofiles of oxygen and nitrous oxide in the same colony with microelectrodes. Oxygen respiration occurred at the top of the colony as expected but denitrification occurred throughout the entire depth, even in the oxic region. Local denitrification rates were highly variable suggesting heterogenous metabolic activity within the colony. We also assessed the short-term influence of tobramycin on aerobic respiration within a PAO1 colony. Although there was an immediate reduction in respiration it was never completely arrested over a 2 h period. On tobramycin removal the oxygen gradient steadily reestablished, demonstrating immediate recovery of metabolic activity.</p
Intermediate sulfur oxidation state compounds in the euxinic surface sediments of the Dvurechenskii mud volcano (Black Sea)
No full textThe deep Black Sea is known to be depleted in electron-acceptors for sulfide oxidation. This study on depth distributions of sulfur species (S(II), S(0), View the MathML sourceSn2-, View the MathML sourceS2O32-, View the MathML sourceSO32-, View the MathML sourceSO42-) in the Dvurechenskii mud volcano, a cold seep situated in the permanently anoxic eastern Black Sea basin (Sorokin Trough, 2060 m water depth), showed remarkable concentrations of sulfide oxidation products. Sulfite concentrations of up to 11 μmol L−1, thiosulfate concentrations of up to 22 μmol L−1, zero-valent sulfur concentrations of up to 150 μmol L−1 and up to five polysulfide species were measured in the upper 20 cm of the sediment. Electron-acceptors found to be available in the Dvurechenskii mud volcano (DMV) for the oxidation of hydrogen sulfide to sulfide oxidation intermediates are iron-minerals, and probably also reactive manganese phases. Up to 60 μmol g−1 of reactive iron-minerals and up to 170 μmol L−1 dissolved iron was present in the central summit with the highest fluid upflow and fresh mud outflow. Thus, the source for the oxidative power in the DMV are reactive iron phases extruded with the mud from an ancient source in the deeply buried sediments, leading to the formation of various sulfur intermediates in comparably high concentrations. Another possible source of sulfide oxidation intermediates in DMV sediments could be the formation of zero-valent sulfur by sulfate dependent anaerobic microbial oxidation of methane followed by disproportionation of zero-valent sulfur. Sulfide oxidation intermediates, which are produced by these processes, do not reach thermodynamic equilibrium with rhombic sulfur, especially close to the active center of the DMV due to a short equilibration time. Thus, mud volcano sediments, such as in the DMV, can provide oxidizing niches even in a highly reduced environment like the abyssal part of the Black Sea
Evolving perspectives of biofilm structure
No full textThe application of confocal scanning laser microscopy (CSLM) to biofilm research has provided detailed new information on the structural complexity of fully hydrated living biofilms. Biofilms studied by CSLM are widely reported to be heterogeneous and consist of micro-colonies or cell clusters (aggregates of microbial cells in an extracellular polysaccharide matrix) separated by interstitial voids and channels. CSLM combined with molecular probing can identify the distribution of individual species within biofilms, while CSLM combined with microelectrodes and particle tracking has demonstrated the significance of structural heterogeneity on mass transfer in biofilms. In this review the contribution that CSLM has made towards the development of conceptual and mathematical biofilm models over the last decade is discussed. The significance of biofilm structural heterogeneity to understanding of mass transfer processes in biofilm systems and the fundamental significance of hydrodynamics in shaping biofilm structure are also discussed. Finally, some of the recent findings which suggest that biofilm structure may be controlled in part by cell signalling, quorum sensing mechanisms, are briefly discussed
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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