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Limited data are available on the prevalence of livestock-associated methicillin-resistant Staphylococcus aureus ( LA- MRSA) in the UK. We tested 124 raw meat samples for MRSA including pork ( n = 63), chicken ( n = 50) and turkey ( n = 11) collected from retail outlets in North West England between March and July 2015. MRSA was recovered from nine (7·3%) samples (four chicken, three pork and two turkey) from different butchers and supermarkets. Four were labelled of UK origin, three were from continental Europe; the origin was not specified for two samples. Whole-genome sequencing ( WGS), spa typing and the presence of lineage-specific canonical single nucleotide polymorphisms confirmed that they belonged to the livestock-associated clade of clonal complex ( CC) 398. Seven (77·8%) isolates were multi-drug resistant. Phylogenetic analyses showed the isolates were diverse, suggesting multiple silent introductions of LA- MRSA into the UK food chain. Two chicken meat isolates belonged to a sub-clade recently reported from human cases in Europe where poultry meat was the probable source. The low levels of MRSA identified (<20 CFU per g) and absence of enterotoxin genes suggest the risk of acquisition of, or food-poisoning due to, LA- MRSA is low. Nevertheless, the MRSA contamination rate is higher than previously estimated; further evaluation of the public health impacts of LA- MRSA is warranted. Significance and Impact of the Study Livestock-associated methicillin-resistant Staphylococcus aureus ( LA- MRSA) is a public health concern worldwide, but has only been reported sporadically in the UK. In the largest UK study to date, samples of raw meat at retail sale were examined for both the presence and levels of MRSA. We report the first isolations of CC398 LA- MRSA from poultry meat in the UK including representatives of a particular sub-clade associated with cases of human infection/colonization in Europe. Although levels were low (<20 CFU per g), the contamination rate was higher than previous UK studies. Moreover, whole-genome sequencing revealed multiple independent introductions of LA- MRSA into the UK food chain. [ABSTRACT FROM AUTHOR]

Summary NanoShaper is a program specifically aiming the construction and analysis of the molecular surface of nanoscopic systems. It uses ray-casting for parallelism and it performs analytical computations whenever possible to maximize robustness and accuracy of the approach. Among the other features, NanoShaper provides volume, surface area, including that of internal cavities, for any considered molecular system. It identifies pockets via a very intuitive definition based on the concept of probe radius, intrinsic to the definition of the solvent excluded surface. We show here that, with a suitable choice of the parameters, the same approach can also permit the visualisation of molecular channels. NanoShaper has now been interfaced with the widely used molecular visualization software VMD, further enriching its already well furnished toolset. Availability and implementation VMD is available at http://www.ks.uiuc.edu/Research/vmd/. NanoShaper, its documentation, tutorials and supporting programs are available at http://concept.iit.it/downloads. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Although recent methodological advances have allowed the incorporation of rate variation in molecular dating analyses, the calibration procedure, performed mainly through fossils, remains resistant to improvements. One source of uncertainty pertains to the assignment of fossils to specific nodes in a phylogeny, especially when alternative possibilities exist that can be equally justified on morphological grounds. Here we expand on a recently developed fossil cross-validation method to evaluate whether alternative nodal assignments of multiple fossils produce calibration sets that differ in their internal consistency. We use an enlarged Crypteroniaceae-centered phylogeny of Myrtales, six fossils, and 72 combinations of calibration points, termed calibration sets, to identify (i) the fossil assignments that produce the most internally consistent calibration sets and (ii) the mean ages, derived from these calibration sets, for the split of the Southeast Asian Crypteroniaceae from their West Gondwanan sister clade (node X). We found that a correlation exists between s values, devised to measure the consistency among the calibration points of a calibration set (Near and Sanderson, 2004), and nodal distances among calibration points. By ranking all sets according to the percent deviation of s from the regression line with nodal distance, we identified the sets with the highest level of corrected calibration-set consistency. These sets generated lower standard deviations associated with the ages of node X than sets characterized by lower corrected consistency. The three calibration sets with the highest corrected consistencies produced mean age estimates for node X of 79.70, 79.14, and 78.15 My. These timeframes are most compatible with the hypothesis that the Crypteroniaceae stem lineage dispersed from Africa to the Deccan plate as it drifted northward during the Late Cretaceous. [ABSTRACT FROM AUTHOR]

The article presents two ontological conceptions of sounds which include the unrepeated event (UE) and the repeatable object (RO). In the EU conception, sounds are considered events happening to and depending on material objects, and have temporal parts. The RO conception shares two principles with the EU conception, which state that sounds are particulars rather than universals and are not ordinary space-occupying objects. Lastly, it suggests that RO conception differs from the EU conception in terms of conceiving sounds to be kinds of objects rather than events.