Thermodynamically constrained averaging theory approach for modeling flow and transport phenomena in porous medium systems: 3. Single-fluid-phase flow

Abstract This work is the third in a series of papers on the thermodynamically constrained averaging theory (TCAT) approach to modeling flow and transport phenomena in multiscale porous medium systems. Building upon the general TCAT framework and the mathematical foundation presented in previous works in this series, we demonstrate the TCAT approach for the case of single-fluid-phase flow. The formulated model is based upon conservation equations for mass, momentum, and energy and a general entropy inequality constraint, which is developed to guide model closure. A specific example of a closed model is derived under limiting assumptions using a linearization approach and these results are compared and contrasted with the traditional single-phase-flow model. Potential extensions to this work are discussed. Specific advancements in this work beyond previous averaging theory approaches to single-phase flow include use of macroscale thermodynamics that is averaged from the microscale, the use of derived equilibrium conditions to guide a flux–force pair approach to simplification, use of a general Lagrange multiplier approach to connect conservation equation constraints to the entropy inequality, and a focus on producing complete, closed models that are solvable

Multilocus sequence typing methods for the emerging Campylobacter species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus

Multilocus sequence typing (MLST) systems have been reported previously for multiple food - and food animal-associated Campylobacter species (e.g., C. jejuni, C. coli, C. lari, and C. fetus) to both differentiate strains and identify clonal lineages. These MLST methods focused primarily on campylobacters of human clinical (e.g., C. jejuni) or veterinary (e.g., C. fetus) relevance. However, other, emerging, Campylobacter species have been isolated increasingly from environmental, food animal, or human clinical samples. We describe herein four MLST methods for five emerging Campylobacter species: C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus. The concisus/curvus method uses the loci aspA, atpA, glnA, gltA, glyA, ilvD, and pgm, whereas the other methods use the seven loci defined for C. jejuni (i.e., aspA, atpA, glnA, gltA, glyA, pgm, and tkt). Multiple food animal and human clinical C. hyointestinalis (n = 48), C. lanienae (n = 34), and C. sputorum (n = 24) isolates were typed, along with 86 human clinical C. concisus and C. curvus isolates. A large number of sequence types were identified using all four MLST methods. Additionally, these methods speciated unequivocally isolates that had been typed ambiguously using other molecular-based speciation methods, such as 16S rDNA sequencing. Finally, the design of degenerate primer pairs for some methods permitted the typing of related species; for example, the C. hyointestinalis primer pairs could be used to type C. fetus strains. Therefore, these novel Campylobacter MLST methods will prove useful in differentiating strains of multiple, emerging Campylobacter species.IS

Phase behavior of repulsive polymer-tethered colloids

We report molecular dynamics simulations of a system of repulsive, polymer-tethered colloidal particles. We use an explicit polymer model to explore how the length and the behavior of the polymer (ideal or self-avoiding) affect the ability of the particles to organize into ordered structures when the system is compressed to moderate volume fractions. We find a variety of different phases whose origin can be explained in terms of the configurational entropy of polymers and colloids. Finally, we discuss and compare our results to those obtained for similar systems using simplified coarse-grained polymer models, and set the limits of their applicability.Comment: 7 pages, 5 figures. Published in the Journal of Chemical Physic

Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

cknowledgements We like to thank Emma Yee (U.S. Department of Agriculture) for the generation of sequence data, we thank James Bono (U.S. Department of Agriculture) for the generation of PacBio RS reads and thank Dr. Brian Brooks and Dr. John Devenish (Canadian Food Inspection Agency) for providing C. fetus strains and for critical review of this manuscript. Funding Publication charges for this article have been funded by Utrecht University, the Netherlands.Peer reviewedPublisher PD

Modeling kicks from the merger of generic black-hole binaries

Recent numerical relativistic results demonstrate that the merger of comparable-mass spinning black holes has a maximum ``recoil kick'' of up to \sim 4000 \kms. However the scaling of these recoil velocities with mass ratio is poorly understood. We present new runs showing that the maximum possible kick perpendicular to the orbital plane does not scale as $\sim\eta^2$ (where $\eta$ is the symmetric mass ratio), as previously proposed, but is more consistent with $\sim\eta^3$, at least for systems with low orbital precession. We discuss the effect of this dependence on galactic ejection scenarios and retention of intermediate-mass black holes in globular clusters.Comment: 5 pages, 1 figure, 3 tables. Version published in Astrophys. J. Let

The Journal of the Friends' Historical Society vol. 1 No. 2

1. Notices 2. Notes and Queries 3. Account of the Illness and Death of George Fox 4. Daniel Quare 5. The Wilkinson-Story Controversy in Reading 6. The Handwriting of George Fox 7. Our Recording Clerks: II - Richard Richardson 8. Notes on Friends in the South of Scotland 9. The Quaker Family of Owne II 10. An Appeal from Ireland 11. Gleanings from Original REgisters at Somerset House 12. Book Notes 13. Friends' Reference Library 14. Second List of Member

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae : Campylobacter, Arcobacter, Helicobacter and Wolinella spp.

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended

Campylobacter fetus Subspecies Contain Conserved Type IV Secretion Systems on Multiple Genomic Islands and Plasmids

Acknowledgments We like to thank Dr. John Devenish and Dr. Brian Brooks (Canadian Food Inspection Agency) for providing strains. We thank Nathaniel Simon and Mary Chapman for the generation of Illumina MiSeq reads and we thank James Bono for the generation of PacBio RS reads. Funding: The authors have no support or funding to report.Peer reviewedPublisher PD