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  • 1
    Language: English
    In: Journal of Hydrology, 17 May 2012, Vol.438-439, pp.1-2
    Keywords: Geography;
    ISSN: 0022-1694
    E-ISSN: 18792707
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  • 2
    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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  • 3
    Language: English
    In: International Journal of Nursing Studies, December 2016, Vol.64, pp.96-97
    Description: Baveye comments on a recent article by Duffy et al (2016) which present a well thought-out list of points to pay attention to in order to maximize the chances that a manuscript, submitted for publication, sail through the review process and eventually get printed. There is no doubt that this thorough roadmap will be extremely useful to individuals in many disciplines, and especially to young researchers who may find the mechanics of the publishing process. Nevertheless, as a more seasoned researcher and long-time editor, Baveye feels that this roadmap would be even more useful if it included an additional ingredient, which in some sense might be considered "the" most important one. Indeed, from my experience, provided of course a manuscript contain novel and technically-sound scholarship, the single most determining factor to speed up acceptance for publication is whether the text presents an appealing story.
    Keywords: Manuscripts ; Publishing ; Researchers ; Publishing ; Publications;
    ISSN: 0020-7489
    E-ISSN: 1873491X
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  • 4
    Language: English
    In: Science (New York, N.Y.), 17 September 2010, Vol.329(5998), pp.1466
    Description: The academic community continues to believe that the formal scholarly publishing process separates sound research from shoddy or biased counterparts. Unfortunately, scholarly publishing may not be able to effectively fulfill its role as a gatekeeper much longer. As soon as the “publish or perish
    Keywords: Bibliometrics ; Publishing
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 5
    Language: English
    In: Journal of Hydrology, 2011, Vol.406(3), pp.137-140
    Keywords: Hydrological Research ; Publishing ; Interdisciplinarity ; Sociological Aspects ; Scholarly Communication
    ISSN: 0022-1694
    E-ISSN: 18792707
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  • 6
    In: Nature, 2000, Vol.404(6776), p.329
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 7
    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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  • 8
    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
    ISSN: 0020-7489
    E-ISSN: 1873491X
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  • 9
    Language: English
    In: Journal of Hazardous Materials, March 21, Vol.285, p.137(3)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.jhazmat.2014.11.043 Byline: Philippe C. Baveye, Magdeline Laba Abstract: 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. Author Affiliation: (a) Soil and Water Laboratory, Department of Civil and Environmental Engineering, Rensselaer Polytechnic Institute, 110 8th street, Troy, NY 12180, USA (b) Department of Natural Resources, Cornell University, Ithaca, NY 14850, USA Article History: Received 22 July 2014; Accepted 2 November 2014
    Keywords: Soil Pollution ; Soil Moisture ; Spectroscopy ; Heavy Metals
    ISSN: 0304-3894
    Source: Cengage Learning, Inc.
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  • 10
    Language: English
    In: Ecological Modelling, Feb 24, Vol.298, p.24(15)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ecolmodel.2014.03.018 Byline: Philippe C. Baveye, Magdeline Laba Abstract: * Reviews background of the application of geostatistics to soils. * Soil spatial heterogeneity does not always have to be accounted for explicitly. * Perception of heterogeneity depends closely on measurement carried out. * For cases related to plants and microbes, different measurements are needed. * Lessons from the geostatistical story are applicable to soil science in general. Author Affiliation: (a) Soil and Water Laboratory, Department of Civil and Environmental Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA (b) SIMBIOS Centre, Abertay University, Kydd Building, 40 Bell Street, Dundee DD1 1HG, Scotland, UK (c) Department of Natural Resources, Cornell University, Ithaca, NY 14850, USA
    Keywords: Soils ; Geostatistics
    ISSN: 0304-3800
    Source: Cengage Learning, Inc.
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