Introducing a novel, broad host range temperate phage family infecting Rhizobium leguminosarum and beyond

Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species

Relationships between traditional and fundamental dough-testing methods

Two fundamental test systems were used to evaluate the visco-elastic properties of doughs from wheat samples of three varieties grown at four distinct sites. For comparison, tests were also performed with traditional equipment, namely the Mixograph, an extension tester and a Farinograph-type small-scale recording mixer. Uniaxial dough elongation (with an Instron) produced results similar to the conventional extension tester, except that results were provided in fundamental units (Pascals), the critical value recorded being the elongational stress at maximum strain. Stress relaxation measurements were performed following a small initial shear strain. With this method, it was possible to distinguish between the viscosity and the elastic components of dough visco-elasticity. In all the tests the extra dough-strength properties were evident for the variety (Guardian) that had the 5 + 10 glutenin subunits, in contrast to the other two with the 2 + 12 combination of subunits

Rms-flux relation in the optical fast variability data of BL Lacertae object S5 0716+714

The possibility that BL Lac S5 0716+714 exhibits a linear root mean square (rms)-flux relation in its IntraDay Variability (IDV) is analysed. The results may be used as an argument in the existing debate regarding the source of optical IDV in Active Galactic Nuclei. 63 time series in different optical bands were used. A linear rms-flux relation at a confidence level higher than 65% was recovered for less than 8% of the cases. We were able to check if the magnitude is log-normally distributed for eight timeseries and found, with a confidence > 95%, that this is not the case.Comment: Accepted by Astrophysics and Space Scienc

Overcoming challenges regarding reference materials and regulations that influence global standardization of medical laboratory testing results

Background: Standardized results for laboratory tests are particularly important when their interpretation depends on fixed medical practice guidelines or common reference intervals. The medical laboratory community has developed a roadmap for an infrastructure to achieve standardized test results described in the International Organization for Standardization standard 17511:2020 In vitro diagnostic medical devices - Requirements for establishing metrological traceability of values assigned to calibrators, trueness control materials and human samples. Among the challenges to implementing metrological traceability are the availability of fit-for-purpose matrix-based certified reference materials (CRMs) and requirements for regulatory review that differ among countries. A workshop in December 2021 focused on these two challenges and developed recommendations for improved practices. Discussion: The participants agreed that prioritization of measurands for standardization should be based on their impact on medical decisions in a clinical pathway. Ensuring that matrix-based CRMs are globally available for more measurands will enable fit-for-purpose calibration hierarchies for more laboratory tests. Regulation of laboratory tests is important to ensure safety and effectiveness for the populations served. Because regulations are country or region specific, manufacturers must submit recalibration changes intended to standardize results for regulatory review to all areas in which a measuring system is marketed. Recommendations: A standardization initiative requires collaboration and planning among all interested stakeholders. Global collaboration should be further developed for prioritization of measurands for standardization, and for coordinating the production and supply of CRMs worldwide. More uniform regulatory submission requirements are desirable when recalibration is implemented to achieve internationally standardized results.Afdeling Klinische Chemie en Laboratoriumgeneeskunde (AKCL

Atomic X-ray Spectroscopy of Accreting Black Holes

Current astrophysical research suggests that the most persistently luminous objects in the Universe are powered by the flow of matter through accretion disks onto black holes. Accretion disk systems are observed to emit copious radiation across the electromagnetic spectrum, each energy band providing access to rather distinct regimes of physical conditions and geometric scale. X-ray emission probes the innermost regions of the accretion disk, where relativistic effects prevail. While this has been known for decades, it also has been acknowledged that inferring physical conditions in the relativistic regime from the behavior of the X-ray continuum is problematic and not satisfactorily constraining. With the discovery in the 1990s of iron X-ray lines bearing signatures of relativistic distortion came the hope that such emission would more firmly constrain models of disk accretion near black holes, as well as provide observational criteria by which to test general relativity in the strong field limit. Here we provide an introduction to this phenomenon. While the presentation is intended to be primarily tutorial in nature, we aim also to acquaint the reader with trends in current research. To achieve these ends, we present the basic applications of general relativity that pertain to X-ray spectroscopic observations of black hole accretion disk systems, focusing on the Schwarzschild and Kerr solutions to the Einstein field equations. To this we add treatments of the fundamental concepts associated with the theoretical and modeling aspects of accretion disks, as well as relevant topics from observational and theoretical X-ray spectroscopy.Comment: 63 pages, 21 figures, Einstein Centennial Review Article, Canadian Journal of Physics, in pres

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

Formation of Large-Scale Semi-Organized Structures in Turbulent Convection

A new mean-field theory of turbulent convection is developed. This theory predicts the convective wind instability in a shear-free turbulent convection which causes formation of large-scale semi-organized fluid motions in the form of cells or rolls. Spatial characteristics of these motions, such as the minimum size of the growing perturbations and the size of perturbations with the maximum growth rate, are determined. This study predicts also the existence of the convective shear instability in a sheared turbulent convection which results in generation of convective shear waves with a nonzero hydrodynamic helicity. Increase of shear promotes excitation of the convective shear instability. Applications of the obtained results to the atmospheric turbulent convection and the laboratory experiments on turbulent convection are discussed. This theory can be applied also for the describing a mesogranular turbulent convection in astrophysics.Comment: 16 pages, 10 figures, REVTEX4, PHYSICAL REVIEW E, v. 67, in press (2003

The π0→e+e−\pi^0\to e^+e^- and η→μ+μ−\eta\to \mu^+ \mu^- Decays Revisited

The rare $\pi^0 \to e^+e^-$ and $\eta \to \mu^+\mu^-$ decays are calculated in different schemes, which are seen to be essentially equivalent to and produce the same results as conventional Vector-Meson Dominance. We obtain the theoretical predictions $B(\pi^0 \to e^+e^-) = (6.41 \pm 0.19)\times 10^{-8}$ and $B(\eta \to \mu^+\mu^-) = (1.14 +0.06 -0.03) \times 10^{-5}$ in agreement with recent experimental data.Comment: 10 pages, LATEX (revised version for recent experimental data

Mediation of foundation ontology based knowledge sources

This is the author’s version of a work that was accepted for publication in the journal Computers in Industry [© Elsevier]. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Computers and Industry: www.elsevier.com/locate/compindOntologies are helpful in giving interoperable structures to sources of knowledge and information. This interoperability, however, is greatly hindered by the heterogeneity of independently developed ontologies which in turn increases the requirements for mediation systems to reconcile the differences. A core concepts ontology for a certain domain contained by a foundation ontology can be used to alleviate this problem and to facilitate the reconciliation efforts. Possible differences in the use of concepts from the core concepts to model entities in domain ontologies can be prevented by binding the domain ontology developers to some rules. These rules can be particularly useful for domain ontologies requiring some kind of traceability of their concepts in the foundation ontology. The mediation system can then use this traceability to establish similarities between two ontologies. Software applications, like the one explained in this paper, can then be developed to perform the mediation task automatically and accurately