The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach

Throughout the 1990s, there was an epidemic of multidrug resistant Salmonella Typhimurium DT104 in both animals and humans in Scotland. The use of antimicrobials in agriculture is often cited as a major source of antimicrobial resistance in pathogenic bacteria of humans, suggesting that DT104 in animals and humans should demonstrate similar prevalences of resistance determinants. Until very recently, only the application of molecular methods would allow such a comparison and our understanding has been hindered by the fact that surveillance data are primarily phenotypic in nature. Here, using large scale surveillance datasets and a novel Bayesian approach, we infer and compare the prevalence of Salmonella Genomic Island 1 (SGI1), SGI1 variants, and resistance determinants independent of SGI1 in animal and human DT104 isolates from such phenotypic data. We demonstrate differences in the prevalences of SGI1, SGI1-B, SGI1-C, absence of SGI1, and tetracycline resistance determinants independent of SGI1 between these human and animal populations, a finding that challenges established tenets that DT104 in domestic animals and humans are from the same well-mixed microbial population

Positive-Buoyancy Rover for Under Ice Mobility

A buoyant rover has been developed to traverse the underside of ice-covered lakes and seas. The rover operates at the ice/water interface and permits direct observation and measurement of processes affecting freeze- over and thaw events in lake and marine environments. Operating along the 2- D ice-water interface simplifies many aspects of underwater exploration, especially when compared to submersibles, which have difficulty in station-keeping and precision mobility. The buoyant rover consists of an all aluminum body with two aluminum sawtooth wheels. The two independent body segments are sandwiched between four actuators that permit isolation of wheel movement from movement of the central tether spool. For normal operations, the wheels move while the tether spool feeds out line and the cameras on each segment maintain a user-controlled fixed position. Typically one camera targets the ice/water interface and one camera looks down to the lake floor to identify seep sources. Each wheel can be operated independently for precision turning and adjustments. The rover is controlled by a touch- tablet interface and wireless goggles enable real-time viewing of video streamed from the rover cameras. The buoyant rover was successfully deployed and tested during an October 2012 field campaign to investigate methane trapped in ice in lakes along the North Slope of Alaska

Decadal variability of the extratropical response to the Madden-Julian Oscillation

The Madden–Julian Oscillation (MJO) is the leading mode of sub-seasonal variability in the tropical atmosphere and is a source of predictability for extratropical weather through its teleconnections. MJO teleconnection patterns can be modulated by the El Niño–Southern Oscillation (ENSO) on seasonal to interannual time scales. However, changes over decadal time scales are less well understood. ERA5 reanalysis data are used to show that the boreal winter MJO teleconnection pattern in the Northern Hemisphere has changed in recent decades in line with changes in the Pacific Decadal Oscillation and Atlantic Multidecadal Variability. Changes are seen in the circulation, temperature and precipitation responses. In particular, from 1997, intraseasonal cold anomalies appear over Europe and the eastern United States due to MJO convection over the western Pacific; these were not present 20 years previously. The decadal variability observed is not the product of aliasing of ENSO modulation of the teleconnection

Detection of Rare Antimicrobial Resistance Profiles by Active and Passive Surveillance Approaches.

Antimicrobial resistance (AMR) surveillance systems are generally not specifically designed to detect emerging resistances and usually focus primarily on resistance to individual drugs. Evaluating the diversity of resistance, using ecological metrics, allows the assessment of sampling protocols with regard to the detection of rare phenotypes, comprising combinations of resistances. Surveillance data of phenotypic AMR of Canadian poultry Salmonella Heidelberg and swine Salmonella Typhimurium var. 5- were used to contrast active (representative isolates derived from healthy animals) and passive (diagnostic isolates) surveillance and assess their suitability for detecting emerging resistance patterns. Although in both datasets the prevalences of resistance to individual antimicrobials were not significantly different between the two surveillance systems, analysis of the diversity of entire resistance phenotypes demonstrated that passive surveillance of diagnostic isolates detected more unique phenotypes. Whilst the most appropriate surveillance method will depend on the relevant objectives, under the conditions of this study, passive surveillance of diagnostic isolates was more effective for the detection of rare and therefore potentially emerging resistance phenotypes.AEM was supported by the William Stewart Fellowship whilst at the University of Glasgow, and is currently supported by Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/ M014088/1; RR is supported by BBSRC grant BB/ E010326/1 and BB/L004070/1; LM is supported by BB/K01126X/1, BB/L004070/1, BB/F015313/1, National Science Foundation DEB1216040 and an EU-funded Marie Curie Initial Training Network (MCITN) program (NEMATODE SYSTEM HEALTH project (FP7-PEOPLE-2010-ITN- ID:264639)).This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pone.015851

Outcomes After Virologic Failure of First-Line ART in South Africa

Article approval pendingTo determine initial 24-week outcomes among prospectively enrolled patients with failure of initial antiretroviral therapy (ART)

Photodissociation dynamics of the iodide-uracil (I-U) complex

Photofragment action spectroscopy and femtosecond time-resolved photoelectron imaging are utilized to probe the dissociation channels in iodide-uracil (I− ⋅ U) binary clusters upon photoexcitation. The photofragment action spectra show strong I− and weak [U- H]− ion signal upon photoexcitation. The action spectra show two bands for I− and [U- H]− production peaking around 4.0 and 4.8 eV. Time-resolved experiments measured the rate of I− production resulting from excitation of the two bands. At 4.03 eV and 4.72 eV, the photoelectron signal from I− exhibits rise times of 86 ± 7 ps and 36 ± 3 ps, respectively. Electronic structure calculations indicate that the lower energy band, which encompasses the vertical detachment energy (4.11 eV) of I−U, corresponds to excitation of a dipole-bound state of the complex, while the higher energy band is primarily a π-π∗ excitation on the uracil moiety. Although the nature of the two excited states is very different, the long lifetimes for I− production suggest that this channel results from internal conversion to the I− ⋅ U ground state followed by evaporation of I−. This hypothesis was tested by comparing the dissociation rates to Rice-Ramsperger-Kassel-Marcus calculations

Direct measurement of stellar angular diameters by the VERITAS Cherenkov Telescopes

The angular size of a star is a critical factor in determining its basic properties. Direct measurement of stellar angular diameters is difficult: at interstellar distances stars are generally too small to resolve by any individual imaging telescope. This fundamental limitation can be overcome by studying the diffraction pattern in the shadow cast when an asteroid occults a star, but only when the photometric uncertainty is smaller than the noise added by atmospheric scintillation. Atmospheric Cherenkov telescopes used for particle astrophysics observations have not generally been exploited for optical astronomy due to the modest optical quality of the mirror surface. However, their large mirror area makes them well suited for such high-time-resolution precision photometry measurements. Here we report two occultations of stars observed by the VERITAS Cherenkov telescopes with millisecond sampling, from which we are able to provide a direct measurement of the occulted stars' angular diameter at the $\leq0.1$ milliarcsecond scale. This is a resolution never achieved before with optical measurements and represents an order of magnitude improvement over the equivalent lunar occultation method. We compare the resulting stellar radius with empirically derived estimates from temperature and brightness measurements, confirming the latter can be biased for stars with ambiguous stellar classifications.Comment: Accepted for publication in Nature Astronom

N2H+ depletion in the massive protostellar cluster AFGL 5142

We aim at investigating with high angular resolution the NH3/N2H+ ratio toward the high-mass star-forming region AFGL 5142 in order to study whether this ratio behaves similarly to the low-mass case, for which the ratio decreases from starless cores to cores associated with YSOs. CARMA was used to observe the 3.2 mm continuum and N2H+(1-0) emission. We used NH3(1,1) and (2,2), HCO+(1-0) and H13CO+(1-0) data from the literature and we performed a time-dependent chemical modeling of the region. The 3.2 mm continuum emission reveals a dust condensation of ~23 Msun associated with the massive YSOs, deeply embedded in the strongest NH3 core (hereafter central core). The N2H+ emission reveals two main cores, the western and eastern core, located to the west and to the east of the mm condensation, and surrounded by a more extended and complex structure of ~0.5 pc. Toward the central core the N2H+ emission drops significantly, indicating a clear chemical differentiation in the region. We found low values of the NH3/N2H+ ratio ~50-100 toward the western/eastern cores, and high values up to 1000 in the central core. The chemical model indicates that density, and in particular temperature, are key parameters in determining the NH3/N2H+ ratio. The high density and temperature reached in the central core allow molecules like CO to evaporate from grain mantles. The CO desorption causes a significant destruction of N2H+, favoring the formation of HCO+. This result is supported by our observations, which show that N2H+ and HCO+ are anticorrelated in the central core. The observed values of the NH3/N2H+ ratio in the central core can be reproduced by our model for times t~4.5-5.3x10^5 yr (central) and t~10^4-3x10^6 yr (western/eastern). The NH3/N2H+ ratio in AFGL 5142 does not follow the same trend as in regions of low-mass star formation mainly due to the high temperature reached in hot cores.Comment: Accepted for publication in A&A. 14 pages, 9 Figures, 5 Table

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html