An international, multicentre evaluation and description of Burkholderia pseudomallei infection in cystic fibrosis

BACKGROUND: Several cases of Burkholderia pseudomallei infection in CF have been previously reported. We aimed to identify all cases globally, risk factors for acquisition, clinical consequences, and optimal treatment strategies. METHODS: We performed a literature search to identify all published cases of B. pseudomallei infection in CF. In addition we hand-searched respiratory journals, and contacted experts in infectious diseases and CF around the world. Supervising clinicians for identified cases were contacted and contemporaneous clinical data was requested. RESULTS: 25 culture-confirmed cases were identified. The median age at acquisition was 21 years, mean FEV(1) % predicted was 60 %, and mean BMI was 19.5 kg/m(2). The location of acquisition was northern Australia or south-east Asia for most. 19 patients (76 %) developed chronic infection, which was usually associated with clinical decline. Successful eradication strategies included a minimum of two weeks of intravenous ceftazidime, followed by a consolidation phase with trimethoprim/sulfamethoxazole, and this resulted in a higher chance of success when instituted early. Three cases of lung transplantation have been recorded in the setting of chronic B. pseudomallei infection. CONCLUSION: Chronic carriage of B. pseudomallei in patients with CF appears common after infection, in contrast to the non-CF population. This is often associated with an accelerated clinical decline. Lung transplantation has been performed in select cases of chronic B. pseudomallei infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12890-015-0109-9) contains supplementary material, which is available to authorized users

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution.

MOTIVATION: Many methods have been developed to cluster genes on the basis of their changes in mRNA expression over time, using bulk RNA-seq or microarray data. However, single-cell data may present a particular challenge for these algorithms, since the temporal ordering of cells is not directly observed. One way to address this is to first use pseudotime methods to order the cells, and then apply clustering techniques for time course data. However, pseudotime estimates are subject to high levels of uncertainty, and failing to account for this uncertainty is liable to lead to erroneous and/or over-confident gene clusters. RESULTS: The proposed method, GPseudoClust, is a novel approach that jointly infers pseudotemporal ordering and gene clusters, and quantifies the uncertainty in both. GPseudoClust combines a recent method for pseudotime inference with non-parametric Bayesian clustering methods, efficient Markov Chain Monte Carlo sampling and novel subsampling strategies which aid computation. We consider a broad array of simulated and experimental datasets to demonstrate the effectiveness of GPseudoClust in a range of settings. AVAILABILITY AND IMPLEMENTATION: An implementation is available on GitHub: https://github.com/magStra/nonparametricSummaryPSM and https://github.com/magStra/GPseudoClust. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Quantifying full phenological event distributions reveals simultaneous advances, temporal stability and delays in spring and autumn migration timing in long-distance migratory birds

Acknowledgements We thank all Fair Isle Bird Observatory staff and volunteers for help with data collection and acknowledge the foresight of George Waterston and Ken Williamson in instigating the observatory and census methodology. We thank all current and previous directors of Fair Isle Bird Observatory Trust for their contributions, particularly Dave Okill and Mike Wood for their stalwart support for the long-term data collection and for the current analyses. Dawn Balmer and Ian Newton provided helpful guidance on manuscript drafts. We thank Ally Phillimore and two anonymous referees for helpful comments. This study would have been impossible without the Fair Isle community's invaluable support and patience over many decades, which is very gratefully acknowledged. WTSM and JMR designed and undertook analyses, wrote the paper and contributed to data collection and compilation, MB contributed to analysis and editing, all other authors oversaw and undertook data collection and compilation and contributed to editing.Peer reviewedPostprin

Biofilm formation on bone-anchored hearing aids

AbstractObjective:To investigate microbiological biofilm contamination of retrieved bone-anchored hearing aids.Materials and methods:Nine failed, retrieved bone-anchored hearing aids and 16 internal screws were examined by scanning electron microscopy. A fixture from a failing implant, which had been removed and disassembled under aseptic conditions, was cultured. Finally, an internal screw from a new, unimplanted fixture was examined by scanning electron microscopy.Results:Debris was seen on the fixture and abutment of all bone-anchored hearing aids, and on the heads of the 16 internal screws. On eight screws, biofilm extended down the shaft to the threads, where it was several micrometres thick. Culture of a failing fixture yielded staphylococcus. The new, unimplanted fixture internal screw showed evidence of scratching and metallic debris on the threads, which may interfere with close fitting of the screw and subsequently facilitate microleakage.Conclusion:There may be a link between internal microbial contamination and failure of bone-anchored hearing aids.</jats:sec

The magic nature of 132Sn explored through the single-particle states of 133Sn

Atomic nuclei have a shell structure where nuclei with 'magic numbers' of neutrons and protons are analogous to the noble gases in atomic physics. Only ten nuclei with the standard magic numbers of both neutrons and protons have so far been observed. The nuclear shell model is founded on the precept that neutrons and protons can move as independent particles in orbitals with discrete quantum numbers, subject to a mean field generated by all the other nucleons. Knowledge of the properties of single-particle states outside nuclear shell closures in exotic nuclei is important for a fundamental understanding of nuclear structure and nucleosynthesis (for example the r-process, which is responsible for the production of about half of the heavy elements). However, as a result of their short lifetimes, there is a paucity of knowledge about the nature of single-particle states outside exotic doubly magic nuclei. Here we measure the single-particle character of the levels in 133Sn that lie outside the double shell closure present at the short-lived nucleus 132Sn. We use an inverse kinematics technique that involves the transfer of a single nucleon to the nucleus. The purity of the measured single-particle states clearly illustrates the magic nature of 132Sn.Comment: 19 pages, 5 figures and 4 table

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb

A Step Towards Seascape Scale Conservation: Using Vessel Monitoring Systems (VMS) to Map Fishing Activity

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tBACKGROUND: Conservation of marine ecosystems will require a holistic understanding of fisheries with concurrent spatial patterns of biodiversity. METHODOLOGY/PRINCIPAL FINDINGS: Using data from the UK Government Vessel Monitoring System (VMS) deployed on UK-registered large fishing vessels we investigate patterns of fisheries activity on annual and seasonal scales. Analysis of VMS data shows that regions of the UK European continental shelf (i.e. Western Channel and Celtic Sea, Northern North Sea and the Goban Spur) receive consistently greater fisheries pressure than the rest of the UK continental shelf fishing zone. CONCLUSIONS/SIGNIFICANCE: VMS provides a unique and independent method from which to derive patterns of spatially and temporally explicit fisheries activity. Such information may feed into ecosystem management plans seeking to achieve sustainable fisheries while minimising putative risk to non-target species (e.g. cetaceans, seabirds and elasmobranchs) and habitats of conservation concern. With multilateral collaboration VMS technologies may offer an important solution to quantifying and managing ecosystem disturbance, particularly on the high-seas.MJW is supported by a Natural Environment Research Council PhD studentship (NER/S/A/2004/12980) at the University of Exeter (Cornwall Campus). BJG receives funding from the European Social Fund

Surface features, rotation and atmospheric variability of ultra cool dwarfs

Photometric I band light curves of 21 ultra cool M and L dwarfs are presented. Variability with amplitudes of 0.01 to 0.055 magnitudes (RMS) with typical timescales of an hour to several hours are discovered in half of these objects. Periodic variability is discovered in a few cases, but interestingly several variable objects show no significant periods, even though the observations were almost certainly sensitive to the expected rotation periods. It is argued that in these cases the variability is due to the evolution of the surface features on timescales of a few hours. This is supported in the case of 2M1145 for which no common period is found in two separate light curves. It is speculated that these features are photospheric dust clouds, with their evolution possibly driven by rotation and turbulence. An alternative possibility is magnetically-induced surface features. However, chromospheric activity undergoes a sharp decrease between M7 and L1, whereas a greater occurrence of variability is observed in objects later than M9, lending support to the dust interpretation.Comment: To appear in "Ultracool Dwarf Stars" (Lecture Notes in Physics), H.R.A. Jones, I. Steele (eds), Springer-Verlag, 2001. Also available from http://www.mpia-hd.mpg.de/homes/calj/ultra.htm

The RAVE-on Catalog of Stellar Atmospheric Parameters and Chemical Abundances for Chemo-dynamic Studies in the Gaia Era

The orbits, atmospheric parameters, chemical abundances, and ages of individual stars in the Milky Way provide the most comprehensive illustration of galaxy formation available. The Tycho-Gaia Astrometric Solution (TGAS) will deliver astrometric parameters for the largest ever sample of Milky Way stars, though its full potential cannot be realized without the addition of complementary spectroscopy. Among existing spectroscopic surveys, the RAdial Velocity Experiment (RAVE) has the largest overlap with TGAS ($\gtrsim$200,000 stars). We present a data-driven re-analysis of 520,781 RAVE spectra using The Cannon. For red giants, we build our model using high-fidelity APOGEE stellar parameters and abundances for stars that overlap with RAVE. For main-sequence and sub-giant stars, our model uses stellar parameters from the K2/EPIC. We derive and validate effective temperature $T_{\rm eff}$, surface gravity $\log{g}$, and chemical abundances of up to seven elements (O, Mg, Al, Si, Ca, Fe, Ni). We report a total of 1,685,851 elemental abundances with a typical precision of 0.07 dex, a substantial improvement over previous RAVE data releases. The synthesis of RAVE-on and TGAS is the most powerful data set for chemo-dynamic analyses of the Milky Way ever produced