Université Pierre-et-Marie-Curie

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection methods in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2 million customers and by analysing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad hoc modular networks.

Abstract. By coordinating the design and distribution of global climate model simulations of the past, current, and future climate, the Coupled Model Intercomparison Project (CMIP) has become one of the foundational elements of climate science. However, the need to address an ever-expanding range of scientific questions arising from more and more research communities has made it necessary to revise the organization of CMIP. After a long and wide community consultation, a new and more federated structure has been put in place. It consists of three major elements: (1) a handful of common experiments, the DECK (Diagnostic, Evaluation and Characterization of Klima) and CMIP historical simulations (1850–near present) that will maintain continuity and help document basic characteristics of models across different phases of CMIP; (2) common standards, coordination, infrastructure, and documentation that will facilitate the distribution of model outputs and the characterization of the model ensemble; and (3) an ensemble of CMIP-Endorsed Model Intercomparison Projects (MIPs) that will be specific to a particular phase of CMIP (now CMIP6) and that will build on the DECK and CMIP historical simulations to address a large range of specific questions and fill the scientific gaps of the previous CMIP phases. The DECK and CMIP historical simulations, together with the use of CMIP data standards, will be the entry cards for models participating in CMIP. Participation in CMIP6-Endorsed MIPs by individual modelling groups will be at their own discretion and will depend on their scientific interests and priorities. With the Grand Science Challenges of the World Climate Research Programme (WCRP) as its scientific backdrop, CMIP6 will address three broad questions: – How does the Earth system respond to forcing? – What are the origins and consequences of systematic model biases? – How can we assess future climate changes given internal climate variability, predictability, and uncertainties in scenarios? This CMIP6 overview paper presents the background and rationale for the new structure of CMIP, provides a detailed description of the DECK and CMIP6 historical simulations, and includes a brief introduction to the 21 CMIP6-Endorsed MIPs.

This paper presents cosmological results based on full-mission Planck observations of temperature and polarization anisotropies of the cosmic microwave background (CMB) radiation.Our results are in very good agreement with the 2013 analysis of the Planck nominal-mission temperature data, but with increased precision.The temperature and polarization power spectra are consistent with the standard spatially-flat 6-parameter ΛCDM cosmology with a power-law spectrum of adiabatic scalar perturbations (denoted "base ΛCDM" in this paper).From the Planck temperature data combined with Planck lensing, for this cosmology we find a Hubble constant, H 0 = (67.8± 0.9) km s -1 Mpc -1 , a matter density parameter Ω m = 0.308 ± 0.012, and a tilted scalar spectral index with n s = 0.968 ± 0.006, consistent with the 2013 analysis.Note that in this abstract we quote 68% confidence limits on measured parameters and 95% upper limits on other parameters.We present the first results of polarization measurements with the Low Frequency Instrument at large angular scales.Combined with the Planck temperature and lensing data, these measurements give a reionization optical depth of τ = 0.066 ± 0.016, corresponding to a reionization redshift of z re = 8.8 +1.7 -1.4 .These results are consistent with those from WMAP polarization measurements cleaned for dust emission using 353-GHz polarization maps from the High Frequency Instrument.We find no evidence for any departure from base ΛCDM in the neutrino sector of the theory; for example, combining Planck observations with other astrophysical data we find N eff = 3.15 ± 0.23 for the effective number of relativistic degrees of freedom, consistent with the value N eff = 3.046 of the Standard Model of particle physics.The sum of neutrino masses is constrained to m ν < 0.23 eV.The spatial curvature of our Universe is found to be very close to zero, with |Ω K | < 0.005.Adding a tensor component as a single-parameter extension to base ΛCDM we find an upper limit on the tensor-to-scalar ratio of r 0.002 < 0.11, consistent with the Planck 2013 results and consistent with the B-mode polarization constraints from a joint analysis of BICEP2, Keck Array, and Planck (BKP) data.Adding the BKP B-mode data to our analysis leads to a tighter constraint of r 0.002 < 0.09 and disfavours inflationary models with a V(φ) ∝ φ 2 potential.The addition of Planck polarization data leads to strong constraints on deviations from a purely adiabatic spectrum of fluctuations.We find no evidence for any contribution from isocurvature perturbations or from cosmic defects.Combining Planck data with other astrophysical data, including Type Ia supernovae, the equation of state of dark energy is constrained to w = -1.006± 0.045, consistent with the expected

Context. We present the second Gaia data release, Gaia DR2, consisting of astrometry, photometry, radial velocities, and information on astrophysical parameters and variability, for sources brighter than magnitude 21. In addition epoch astrometry and photometry are provided for a modest sample of minor planets in the solar system. Aims. A summary of the contents of Gaia DR2 is presented, accompanied by a discussion on the differences with respect to Gaia DR1 and an overview of the main limitations which are still present in the survey. Recommendations are made on the responsible use of Gaia DR2 results. Methods. The raw data collected with the Gaia instruments during the first 22 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into this second data release, which represents a major advance with respect to Gaia DR1 in terms of completeness, performance, and richness of the data products. Results. Gaia DR2 contains celestial positions and the apparent brightness in G for approximately 1.7 billion sources. For 1.3 billion of those sources, parallaxes and proper motions are in addition available. The sample of sources for which variability information is provided is expanded to 0.5 million stars. This data release contains four new elements: broad-band colour information in the form of the apparent brightness in the G BP (330–680 nm) and G RP (630–1050 nm) bands is available for 1.4 billion sources; median radial velocities for some 7 million sources are presented; for between 77 and 161 million sources estimates are provided of the stellar effective temperature, extinction, reddening, and radius and luminosity; and for a pre-selected list of 14 000 minor planets in the solar system epoch astrometry and photometry are presented. Finally, Gaia DR2 also represents a new materialisation of the celestial reference frame in the optical, the Gaia -CRF2, which is the first optical reference frame based solely on extragalactic sources. There are notable changes in the photometric system and the catalogue source list with respect to Gaia DR1, and we stress the need to consider the two data releases as independent. Conclusions. Gaia DR2 represents a major achievement for the Gaia mission, delivering on the long standing promise to provide parallaxes and proper motions for over 1 billion stars, and representing a first step in the availability of complementary radial velocity and source astrophysical information for a sample of stars in the Gaia survey which covers a very substantial fraction of the volume of our galaxy.

International audience

International audience

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

We discuss the theoretical bases that underpin the automation of the computations of tree-level and next-to-leading order cross sections, of their matching to parton shower simulations, and of the merging of matched samples that differ by light-parton multiplicities. We present a computer program, MadGraph5 aMC@NLO, capable of handling all these computations — parton-level fixed order, shower-matched, merged — in a unified framework whose defining features are flexibility, high level of parallelisation, and human intervention limited to input physics quantities. We demonstrate the potential of the program by presenting selected phenomenological applications relevant to the LHC and to a 1-TeV e + e − collider. While next-to-leading order results are restricted to QCD corrections to SM processes in the first public version, we show that from the user viewpoint no changes have to be expected in the case of corrections due to any given renormalisable Lagrangian, and that the implementation of these are well under way.

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,873 new measurements from 758 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 118 reviews are many that are new or heavily revised, including a new review on Neutrinos in Cosmology.Starting with this edition, the Review is divided into two volumes. Volume 1 includes the Summary Tables and all review articles. Volume 2 consists of the Particle Listings. Review articles that were previously part of the Listings are now included in volume 1.The complete Review (both volumes) is published online on the website of the Particle Data Group (http://pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is also available.The 2018 edition of the Review of Particle Physics should be cited as: M. Tanabashi et al. (Particle Data Group), Phys. Rev. D 98, 030001 (2018).

Gaia is a cornerstone mission in the science programme of the EuropeanSpace Agency (ESA). The spacecraft construction was approved in 2006, following a study in which the original interferometric concept was changed to a direct-imaging approach. Both the spacecraft and the payload were built by European industry. The involvement of the scientific community focusses on data processing for which the international Gaia Data Processing and Analysis Consortium (DPAC) was selected in 2007. Gaia was launched on 19 December 2013 and arrived at its operating point, the second Lagrange point of the Sun-Earth-Moon system, a few weeks later. The commissioning of the spacecraft and payload was completed on 19 July 2014. The nominal five-year mission started with four weeks of special, ecliptic-pole scanning and subsequently transferred into full-sky scanning mode. We recall the scientific goals of Gaia and give a description of the as-built spacecraft that is currently (mid-2016) being operated to achieve these goals. We pay special attention to the payload module, the performance of which is closely related to the scientific performance of the mission. We provide a summary of the commissioning activities and findings, followed by a description of the routine operational mode. We summarise scientific performance estimates on the basis of in-orbit operations. Several intermediate Gaia data releases are planned and the data can be retrieved from the Gaia Archive, which is available through the Gaia home page.

Abstract Summary: We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time. ClueGO provides an intuitive representation of the analysis results and can be optionally used in conjunction with the GOlorize plug-in. Availability: http://www.ici.upmc.fr/cluego/cluegoDownload.shtml Contact: jerome.galon@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online.

1. The general discrete inverse problem 2. Monte Carol methods 3. The least-squares criterion 4. Least-absolute values criterion and minimax criterion 5. Functional inverse problems 6. Appendices 7. Problems References Index.

The role of the adaptive immune response in controlling the growth and recurrence of human tumors has been controversial. We characterized the tumor-infiltrating immune cells in large cohorts of human colorectal cancers by gene expression profiling and in situ immunohistochemical staining. Collectively, the immunological data (the type, density, and location of immune cells within the tumor samples) were found to be a better predictor of patient survival than the histopathological methods currently used to stage colorectal cancer. The results were validated in two additional patient populations. These data support the hypothesis that the adaptive immune response influences the behavior of human tumors. In situ analysis of tumor-infiltrating immune cells may therefore be a valuable prognostic tool in the treatment of colorectal cancer and possibly other malignancies.

This paper presents the first cosmological results based on Planck measurements of the cosmic microwave background (CMB) temperature and lensing-potential power spectra.We find that the Planck spectra at high multipoles (ℓ > ∼ 40) are extremely well described by the standard spatiallyflat six-parameter ΛCDM cosmology with a power-law spectrum of adiabatic scalar perturbations.Within the context of this cosmology, the Planck data determine the cosmological parameters to high precision: the angular size of the sound horizon at recombination, the physical densities of baryons and cold dark matter, and the scalar spectral index are estimated to be θ * = (1.04147± 0.00062) × 10 -2 , Ω b h 2 = 0.02205 ± 0.00028, Ω c h 2 = 0.1199 ± 0.0027, and n s = 0.9603 ± 0.0073, respectively (note that in this abstract we quote 68% errors on measured parameters and 95% upper limits on other parameters).For this cosmology, we find a low value of the Hubble constant, H 0 = (67.3± 1.2) km s -1 Mpc -1 , and a high value of the matter density parameter, Ω m = 0.315 ± 0.017.These values are in tension with recent direct measurements of H 0 and the magnituderedshift relation for Type Ia supernovae, but are in excellent agreement with geometrical constraints from baryon acoustic oscillation (BAO) surveys.Including curvature, we find that the Universe is consistent with spatial flatness to percent level precision using Planck CMB data alone.We use high-resolution CMB data together with Planck to provide greater control on extragalactic foreground components in an investigation of extensions to the six-parameter ΛCDM model.We present selected results from a large grid of cosmological models, using a range of additional astrophysical data sets in addition to Planck and high-resolution CMB data.None of these models are favoured over the standard six-parameter ΛCDM cosmology.The deviation of the scalar spectral index from unity is insensitive to the addition of tensor modes and to changes in the matter content of the Universe.We find an upper limit of r 0.002 < 0.11 on the tensor-to-scalar ratio.There is no evidence for additional neutrino-like relativistic particles beyond the three families of neutrinos in the standard model.Using BAO and CMB data, we find N eff = 3.30 ± 0.27 for the effective number of relativistic degrees of freedom, and an upper limit of 0.23 eV for the sum of neutrino masses.Our results are in excellent agreement with big bang nucleosynthesis and the standard value of N eff = 3.046.We find no evidence for dynamical dark energy; using BAO and CMB data, the dark energy equation of state parameter is constrained to be w = -1.13+0.13 -0.10 .We also use the Planck data to set limits on a possible variation of the fine-structure constant, dark matter annihilation and primordial magnetic fields.Despite the success of the six-parameter ΛCDM model in describing the Planck data at high multipoles, we note that this cosmology does not provide a good fit to the temperature power spectrum at low multipoles.The unusual shape of the spectrum in the multipole range 20 < ∼ ℓ < ∼ 40 was seen previously in the WMAP data and is a real feature of the primordial CMB anisotropies.The poor fit to the spectrum at low multipoles is not of decisive significance, but is an "anomaly" in an otherwise self-consistent analysis of the Planck temperature data.

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.

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This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, ${V}_{\mathit{cb}}$ ${V}_{\mathit{ub}}$, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter.A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov/.The 2012 edition of Review of Particle Physics is published for the Particle Data Group as article 010001 in volume 86 of Physical Review D.This edition should be cited as: J. Beringer et al. (Particle Data Group), Phys. Rev. D 86, 010001 (2012).

Good bacteria help fight cancer Resident gut bacteria can affect patient responses to cancer immunotherapy (see the Perspective by Jobin). Routy et al. show that antibiotic consumption is associated with poor response to immunotherapeutic PD-1 blockade. They profiled samples from patients with lung and kidney cancers and found that nonresponding patients had low levels of the bacterium Akkermansia muciniphila . Oral supplementation of the bacteria to antibiotic-treated mice restored the response to immunotherapy. Matson et al. and Gopalakrishnan et al. studied melanoma patients receiving PD-1 blockade and found a greater abundance of “good” bacteria in the guts of responding patients. Nonresponders had an imbalance in gut flora composition, which correlated with impaired immune cell activity. Thus, maintaining healthy gut flora could help patients combat cancer. Science , this issue p. 91 , p. 104 , p. 97 ; see also p. 32

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.