STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies

The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

A compendium of multi-omics data illuminating host responses to lethal human virus infections

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology

Modified structure of protons and neutrons in correlated pairs

The atomic nucleus is made of protons and neutrons (nucleons), which are themselves composed of quarks and gluons. Understanding how the quark–gluon structure of a nucleon bound in an atomic nucleus is modified by the surrounding nucleons is an outstanding challenge. Although evidence for such modification—known as the EMC effect—was first observed over 35 years ago, there is still no generally accepted explanation for its cause1,2,3. Recent observations suggest that the EMC effect is related to close-proximity short-range correlated (SRC) nucleon pairs in nuclei4,5. Here we report simultaneous, high-precision measurements of the EMC effect and SRC abundances. We show that EMC data can be explained by a universal modification of the structure of nucleons in neutron–proton SRC pairs and present a data-driven extraction of the corresponding universal modification function. This implies that in heavier nuclei with many more neutrons than protons, each proton is more likely than each neutron to belong to an SRC pair and hence to have distorted quark structure. This universal modification function will be useful for determining the structure of the free neutron and thereby testing quantum chromodynamics symmetry-breaking mechanisms and may help to discriminate between nuclear physics effects and beyond-the-standard-model effects in neutrino experiments

Measurement of nuclear transparency ratios for protons and neutrons

This paper presents, for the first time, measurements of neutron transparency ratios for nuclei relative to C measured using the (e,e′n) reaction, spanning measured neutron momenta of 1.4 to 2.4 GeV/c. The transparency ratios were extracted in two kinematical regions, corresponding to knockout of mean-field nucleons and to the breakup of Short-Range Correlated nucleon pairs. The extracted neutron transparency ratios are consistent with each other for the two measured kinematical regions and agree with the proton transparencies extracted from new and previous (e,e′p) measurements, including those from neutron-rich nuclei such as lead. The data also agree with and confirm the Glauber approximation that is commonly used to interpret experimental data. The nuclear-mass-dependence of the extracted transparencies scales as Aα with α=−0.289±0.007, which is consistent with nuclear-surface dominance of the reactions

The performance of the jet trigger for the ATLAS detector during 2011 data taking

The performance of the jet trigger for the ATLAS detector at the LHC during the 2011 data taking period is described. During 2011 the LHC provided proton–proton collisions with a centre-of-mass energy of 7 TeV and heavy ion collisions with a 2.76 TeV per nucleon–nucleon collision energy. The ATLAS trigger is a three level system designed to reduce the rate of events from the 40 MHz nominal maximum bunch crossing rate to the approximate 400 Hz which can be written to offline storage. The ATLAS jet trigger is the primary means for the online selection of events containing jets. Events are accepted by the trigger if they contain one or more jets above some transverse energy threshold. During 2011 data taking the jet trigger was fully efficient for jets with transverse energy above 25 GeV for triggers seeded randomly at Level 1. For triggers which require a jet to be identified at each of the three trigger levels, full efficiency is reached for offline jets with transverse energy above 60 GeV. Jets reconstructed in the final trigger level and corresponding to offline jets with transverse energy greater than 60 GeV, are reconstructed with a resolution in transverse energy with respect to offline jets, of better than 4 % in the central region and better than 2.5 % in the forward direction