Critical Assessment of Metagenome Interpretation:A benchmark of metagenomics software

International audienceIn metagenome analysis, computational methods for assembly, taxonomic profilingand binning are key components facilitating downstream biological datainterpretation. However, a lack of consensus about benchmarking datasets andevaluation metrics complicates proper performance assessment. The CriticalAssessment of Metagenome Interpretation (CAMI) challenge has engaged the globaldeveloper community to benchmark their programs on datasets of unprecedentedcomplexity and realism. Benchmark metagenomes were generated from newlysequenced ~700 microorganisms and ~600 novel viruses and plasmids, includinggenomes with varying degrees of relatedness to each other and to publicly availableones and representing common experimental setups. Across all datasets, assemblyand genome binning programs performed well for species represented by individualgenomes, while performance was substantially affected by the presence of relatedstrains. Taxonomic profiling and binning programs were proficient at high taxonomicranks, with a notable performance decrease below the family level. Parametersettings substantially impacted performances, underscoring the importance ofprogram reproducibility. While highlighting current challenges in computationalmetagenomics, the CAMI results provide a roadmap for software selection to answerspecific research questions

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion

Direct observation of stimulated-Brillouin-scattering detuning by a velocity gradient.

We report the first direct evidence of detuning of stimulated Brillouin scattering (SBS) by a velocity gradient, which was achieved by directly measuring the frequency shift of the SBS-driven acoustic wave relative to the local resonant acoustic frequency. We show that in the expanding part of the plasma, ion-acoustic waves are driven off resonance which leads to the saturation of the SBS instability. These measurements are well reproduced by fluid simulations that include the measured flow

X-ray scattering from solid density plasmas

A study on the x-ray scattering from solid density plasmas was presented. By applying spectrally resolved multi-keV scattering, the measurements of the microscopic properties of dense matter were demonstrated. The scattering spectra from solid density beryllium demonstrated the inelastic Compton-down shifted feature that is spectrally broadened when heating the solid density plasmas isochorically and homogeneously to temperatures of several times the Fermi energy

Implementation of a Faraday rotation diagnostic at the OMEGA laser facility

Magnetic field measurements in turbulent plasmas are often difficult to perform. Here we show that for ⩾ kG magnetic fields, a time-resolved Faraday rotation measurement can be made at the OMEGA laser facility. This diagnostic has been implemented using the Thomson scattering probe beam and the resultant path-integrated magnetic field has been compared with that of proton radiography. Accurate measurement of magnetic fields is essential for satisfying the scientific goals of many current laser–plasma experiments

Stimulated Brillouin scattering from helium-hydrogen plasmas

A study of the stimulated Brillouin scattering (SBS) in helium-hydrogen plasmas has been performed using a gas jet at the Janus Laser Facility. We observe three regions of reflectivity by varying the probe intensity from 1014 to 1016: a saturated region, a linear region, and a region near the threshold for SBS. In the linear regime we find that adding small amounts of hydrogen to a helium plasma reduces the SBS reflectivity by a factor of 4

Measurement of radiative shock properties by X-ray Thomson scattering

X-ray Thomson scattering has enabled us to measure the temperature of a shocked layer, produced in the laboratory, that is relevant to shocks emerging from supernovas. High energy lasers are used to create a shock in argon gas which is probed by x-ray scattering. The scattered, inelastic Compton feature allows inference of the electron temperature. It is measured to be 34 eV in the radiative precursor and ∼60eV near the shock. Comparison of energy fluxes implied by the data demonstrates that the shock wave is strongly radiative. © 2012 American Physical Society

Direct observation of the saturation of stimulated Brillouin scattering by ion-trapping-induced frequency shifts

The measurement of the saturation of stimulated Brillouin scattering (SBS) by an ion-trapping-induced frequency shift was investigated. It was achieved by directly measuring the amplitude and absolute frequency of SBS-driven ion-acoustic waves (IAW). A frequency of up to 30% was observed along with a saturation of driven SBS and IAW reflectivity. The fast 30 ps oscillations of the SBS-driven IAW amplitude induced by the frequency shift were also measured

Nonlocal heat wave propagation in a laser produced plasma

We present the observation of a nonlocal heat wave by measuring spatially and temporally resolved electron temperature profiles in a laser produced nitrogen plasma. Absolutely calibrated measurements have been performed by Rayleigh scattering and by resolving the ion-acoustic wave spectra across the plasma volume with Thomson scattering. We find that the experimental electron temperature profiles disagree with flux-limited models, but are consistent with transport models that account for the nonlocal effects in heat conduction by fest electrons