Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Multiobjective evolutionary optimization of water distribution systems : exploiting diversity with infeasible solutions

This article investigates the computational efficiency of constraint handling in multi-objective evolutionary optimization algorithms for water distribution systems. The methodology investigated here encourages the co-existence and simultaneous development including crossbreeding of subpopulations of cost-effective feasible and infeasible solutions based on Pareto dominance. This yields a boundary search approach that also promotes diversity in the gene pool throughout the progress of the optimization by exploiting the full spectrum of non-dominated infeasible solutions. The relative effectiveness of small and moderate population sizes with respect to the number of decision variables is investigated also. The results reveal the optimization algorithm to be efficient, stable and robust. It found optimal and near-optimal solutions reliably and efficiently. The real-world system based optimisation problem involved multiple variable head supply nodes, 29 fire-fighting flows, extended period simulation and multiple demand categories including water loss. The least cost solutions found satisfied the flow and pressure requirements consistently. The cheapest feasible solutions achieved represent savings of 48.1% and 48.2%, for populations of 200 and 1000, respectively, and the population of 1000 achieved slightly better results overall

Additional file 4: of Case management to increase quality of life after cancer treatment: a randomized controlled trial

Table S4. Patients taking pain psychoactive drugs. (PDF 428 kb

Additional file 1: of Case management to increase quality of life after cancer treatment: a randomized controlled trial

Table S1. Patients’ reported lifestyle changes (PDF 792 kb

Neutrino masses and cosmology with Lyman-alpha forest power spectrum

We present constraints on neutrino masses, the primordial fluctuation spectrum from inflation, and other parameters of the \u39bCDM model, using the one-dimensional Ly\u3b1-forest power spectrum measured by [1] from the Baryon Oscillation Spectroscopic Survey (BOSS) of the Sloan Digital Sky Survey (SDSS-III), complemented by Planck 2015 cosmic microwave background (CMB) data and other cosmological probes. This paper improves on the previous analysis by [2] by using a more powerful set of calibrating hydrodynamical simulations that reduces uncertainties associated with resolution and box size, by adopting a more flexible set of nuisance parameters for describing the evolution of the intergalactic medium, by including additional freedom to account for systematic uncertainties, and by using Planck 2015 constraints in place of Planck 2013. Fitting Ly\u3b1 data alone leads to cosmological parameters in excellent agreement with the values derived independently from CMB data, except for a weak tension on the scalar index ns. Combining BOSS Ly\u3b1 with Planck CMB constrains the sum of neutrino masses to 11 m\u3bd < 0.12 eV (95% C.L.) including all identified systematic uncertainties, tighter than our previous limit (0.15 eV) and more robust. Adding Ly\u3b1 data to CMB data reduces the uncertainties on the optical depth to reionization \u3c4, through the correlation of \u3c4 with \u3c38. Similarly, correlations between cosmological parameters help in constraining the tensor-to-scalar ratio of primordial fluctuations r. The tension on ns can be accommodated by allowing for a running dns/d ln k. Allowing running as a free parameter in the fits does not change the limit on 11 m\u3bd. We discuss possible interpretations of these results in the context of slow-roll inflation

Lyman-alpha forests cool warm dark matter

The free-streaming of keV-scale particles impacts structure growth on scales that are probed by the Lyman-alpha forest of distant quasars. Using an unprecedentedly large sample of medium-resolution QSO spectra from the ninth data release of SDSS, along with a state-of-the-art set of hydrodynamical simulations to model the Lyman-alpha forest in the non-linear regime, we issue one of the tightest bounds to date, from Ly-alpha data alone, on pure dark matter particles: mX > 4.09 keV (95% CL) for early decoupled thermal relics such as a hypothetical gravitino, and correspondingly m(s) > 24.4 keV (95% CL) for a non-resonantly produced right-handed neutrino. This limit depends on the value on n(s), and Planck measures a higher value of ns than SDSS-III/BOSS. Our bounds thus change slightly when Ly-alpha data are combined with CMB data from Planck 2016. The limits shift to mX > 2.96 keV (95% CL) and m(s) > 16.0 keV (95% CL). Thanks to SDSS-III data featuring smaller uncertainties and covering a larger redshift range than SDSS-I data, our bounds confirm the most stringent results established by previous works and are further at odds with a purely non-resonantly produced sterile neutrino as dark matter