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  • MEDLINE/PubMed (NLM)  (22)
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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 04 April 2017, Vol.114(14), pp.E2802-E2803
    Description: In their recent article, Coyte et al. (1) use an innovative combination of microfluidic experiments, mechanistic models, and game theory to study the impact of physical microenvironments on the activity of bacteria in porous media. The authors find that hydrodynamics can profoundly affect how bacteria compete and evolve in these systems. They indicate that this conclusion could in principle have important implications for the management of a range of engineered and natural porous media. However, two aspects of the research significantly limit its relevance to practical applications, especially in soils and sediments.The first aspect is the premise that bacterial growth in porous media occurs within biofilms that cover pore walls uniformly. This assumption underlies the model used by Coyte et al. (1), and has clearly motivated the design of their experiments. However, biofilms are far from ubiquitous in natural porous media. In the pore space of unsaturated soils, where many bacteria live, such biofilms are typically not observed (2, 3). In saturated fine- to medium-textured porous media, numerous microscopic observations indicate that biofilms are the exception rather than the rule. Indeed, even when severe bioclogging occurs in such systems, bacterial cells are not located in continuous biofilms but instead aggregate preferentially at pore necks (4, 5). Various modeling efforts have shown conclusively that to describe the occasionally pronounced effects of bacteria on the hydrodynamics of saturated porous media, approaches assuming the presence of continuous biofilms are not satisfactory, even when biofilms are considered to be permeable, and models need to invoke the development of plugs of low permeability, obstructing the lumen of pores (6, 7). It is possible that Coyte et al.’s (1) conclusions would still stand upon consideration of such plugs, but this will need to be checked.The second aspect that decreases the appeal of Coyte et al.’s (1) results in practice is the fact that, even though their research claims to be related to microbial competition, it involves only bacteria. In real porous media, other microorganisms are unavoidably present (8) and may affect not only the competition and evolution of bacteria directly, but also the hydrodynamics of the pore space. Growing fungal hyphae (9) may transport bacteria (and archaea) from one portion of the pore space to another, as well as partially clog pores. Hydrodynamics may have a sizeable effect on the dynamics of protozoan predators (10), predatory bacteria, or viral particles (phages), all ubiquitous in natural porous media and directly influencing the fate of bacterial populations.In this context, Coyte et al.’s (1) research should be viewed as the exploration of one scenario, among several plausible ones, to account for the competition or evolution of bacteria in porous media. Their results, in particular related to the application of game theory, are interesting, but do not settle the many questions associated with what determines the level of microbial biodiversity found in subsurface environments. A complete description will require the development of more realistic models, and additional data associated with the physical, chemical, and microbial characteristics of microenvironments in real porous media.
    Keywords: Biological Evolution ; Environment
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: The journal of physical chemistry. B, 07 June 2012, Vol.116(22), pp.6233-49
    Description: We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.
    Keywords: Molecular Dynamics Simulation
    ISSN: 15206106
    E-ISSN: 1520-5207
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  • 3
    Language: English
    In: International Journal of Nursing Studies, 2011, Vol.48(1), pp.1-2
    Description: Editorial on the peer review process. Methods of encouraging academics to review manuscripts and ensure that they are properly rewarded and acknowledged are discussed and ensuring the quality of reviews is considered. [(BNI unique abstract)] 10 references
    Keywords: Bibliometrics ; Scientific Publishing ; Peer Review ; Research ; Nursing
    ISSN: 0020-7489
    E-ISSN: 1873-491X
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  • 4
    Language: English
    In: Journal of Hazardous Materials, 21 March 2015, Vol.285, pp.137-139
    Description: In recent years, several authors have suggested repeatedly that visible and near-infrared reflectance spectroscopy (VNIRS) could be an advantageous alternative to traditional wet-laboratory methods for the measurement of heavy metal concentrations in soils. In this comment, we argue that, on the contrary, VNIRS is of limited practical use in such a context and should not serve as an excuse to get rid of direly needed laboratory facilities. The key reasons are that VNIRS spectra are irremediably insensitive to the presence of heavy metals, that the effect of soil moisture and surface rugosity on VNIR sensing still has to be satisfactorily accounted for, and finally that VNIRS probes an extremely thin layer of soil at the surface, which is generally irrelevant in terms of plant growth. Given these intrinsic limitations, it seems indicated to put the persistent VNIRS myth to rest, and to explore other measurement techniques that may have more potential.
    Keywords: Engineering ; Law
    ISSN: 0304-3894
    E-ISSN: 1873-3336
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  • 5
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(9), p.e0137205
    Description: There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented in this study can be easily adapted and applied to other types of data such as bacterial or fungal population densities for the 3D characterization of microbial distribution.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Science of the Total Environment, 15 July 2018, Vol.630, pp.146-153
    Description: Thallium (Tl) is a toxic trace metal, whose geochemical behavior and biological effects are closely controlled by its chemical speciation in the environment. However, little tends to be known about this speciation of Tl in soil and plant systems that directly affect the safety of food supplies. In this context, the objective of the present study was to elaborate an efficient method to separate and detect Tl(I) and Tl(III) species for soil and plant samples. This method involves the selective adsorption of Tl(I) on microcolumns filled with immobilized oxine, in the presence of DTPA (diethylenetriaminepentaacetic acid), followed by DTPA-enhanced ultrasonic and heating-induced extraction, coupled with ICP-MS detection. The method was characterized by a LOD of 0.037 μg/L for Tl(I) and 0.18 μg/L for Tl(III) in 10  mL samples. With this method, a second objective of the research was to assess the speciation of Tl in pot and field soils and in green cabbage crops. Experimental results suggest that DTPA extracted Tl was mainly present as Tl(I) in soils (〉95%). Tl in hyperaccumulator plant green cabbage was also mainly present as Tl(I) (〉90%). With respect to Tl uptake in plants, this study provides direct evidence that green cabbage mainly takes up Tl(I) from soil, and transports it into the aboveground organs. In soils, Tl(III) is reduced to Tl(I) even at the surface where the chemical environment promotes oxidation. This observation is conducive to understanding the mechanisms of Tl isotope fractionation in the soil-plant system. Based on geochemical fraction studies, the reducible fraction was the main source of Tl getting accumulated by plants. These results indicate that the improved analytical method presented in this study offers an economical, simple, fast, and sensitive approach for the separation of Tl species present in soils at trace levels.
    Keywords: Tl Speciation ; Extraction ; Soil ; Green Cabbage ; Geochemical Fraction ; Tl Bioavailability ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 7
    Language: English
    In: Environmental science & technology, 2014, Vol.48(3), pp.1370-1
    Keywords: Environmental Policy ; Industry ; Policy Making ; Research ; Commerce -- Legislation & Jurisprudence
    ISSN: 0013936X
    E-ISSN: 1520-5851
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  • 8
    Language: English
    In: Chemistry Central Journal, 01 December 2018, Vol.12(1), pp.1-7
    Description: Abstract In spite of the development of new measurement techniques in recent years, the rapid and accurate speciation of thallium in environmental aqueous samples remains a challenge. In this context, a novel method of solid phase extraction (SPE), involving the anion exchange resin AG1-X8, is proposed to separate Tl(I) and Tl(III). In the presence of diethylene triamine pentacetate acid (DTPA), Tl(III) and Tl(I) can be separated by selective adsorption of Tl(III)-DTPA onto the resin, Tl(III) is then eluted by a solution of HCl with SO2. The validity of this method was confirmed by assays of standard solutions of Tl(I) and Tl(III). The proposed method is shown to have an outstanding performance even in solutions with a high ratio of Tl(I)/Tl(III), and can be applied to aqueous samples with a high concentration of other electrolytes, which could interfere with the measurement. Portable equipment and reagents make it possible to use the proposed method routinely in the field.
    Keywords: Thallium (III) ; Speciation ; Spe ; Ag1-X8 ; Chemistry
    E-ISSN: 1752-153X
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  • 9
    Language: English
    In: Environmental Pollution, July 2018, Vol.238, pp.140-149
    Description: Soil contamination due to atmospheric deposition of metals originating from smelters is a global environmental problem. A common problem associated with this contamination is the discrimination between anthropic and natural contributions to soil metal concentrations: In this context, we investigated the characteristics of soil contamination in the surrounding area of a world class smelter. We attempted to combine several approaches in order to identify sources of metals in soils and to examine contamination characteristics, such as pollution level, range, and spatial distribution. Soil samples were collected at 100 sites during a field survey and total concentrations of As, Cd, Cr, Cu, Fe, Hg, Ni, Pb, and Zn were analyzed. We conducted a multivariate statistical analysis, and also examined the spatial distribution by 1) identifying the horizontal variation of metals according to particular wind directions and distance from the smelter and 2) drawing a distribution map by means of a GIS tool. As, Cd, Cu, Hg, Pb, and Zn in the soil were found to originate from smelter emissions, and As also originated from other sources such as abandoned mines and waste landfill. Among anthropogenic metals, the horizontal distribution of Cd, Hg, Pb, and Zn according to the downwind direction and distance from the smelter showed a typical feature of atmospheric deposition (regression model:  =   + αe ). Lithogenic Fe was used as an indicator, and it revealed the continuous input and accumulation of these four elements in the surrounding soils. Our approach was effective in clearly identifying the sources of metals and analyzing their contamination characteristics. We believe this study will provide useful information to future studies on soil pollution by metals around smelters.
    Keywords: Soil Contamination ; Smelter ; Metal ; Gis ; Atmospheric Deposition ; Engineering ; Environmental Sciences ; Anatomy & Physiology
    ISSN: 0269-7491
    E-ISSN: 1873-6424
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  • 10
    Language: English
    In: Frontiers in Microbiology, 01 July 2018, Vol.9
    Description: There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.
    Keywords: Soil ; Pore Scale ; Organic Matter ; Resource Allocation ; Bacteria ; Biodiversity ; Biology
    E-ISSN: 1664-302X
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