ENSEMBLES: a new multi-model ensemble for seasonal-to-annual predictions: Skill and progress beyond DEMETER in forecasting tropical Pacific SSTs

A new 46-year hindcast dataset for seasonal-to-annual ensemble predictions has been created using a multi-model ensemble of 5 state-of-the-art coupled atmosphere-ocean circulation models. The multi-model outperforms any of the single-models in forecasting tropical Pacific SSTs because of reduced RMS errors and enhanced ensemble dispersion at all lead-times. Systematic errors are considerably reduced over the previous generation (DEMETER). Probabilistic skill scores show higher skill for the new multi-model ensemble than for DEMETER in the 4–6 month forecast range. However, substantially improved models would be required to achieve strongly statistical significant skill increases. The combination of ENSEMBLES and DEMETER into a grand multi-model ensemble does not improve the forecast skill further. Annual-range hindcasts show anomaly correlation skill of ∼0.5 up to 14 months ahead. A wide range of output from the multi-model simulations is becoming publicly available and the international community is invited to explore the full scientific potential of these data

Evolutionary Toggling of Vpx/Vpr Specificity Results in Divergent Recognition of the Restriction Factor SAMHD1

SAMHD1 is a host restriction factor that blocks the ability of lentiviruses such as HIV-1 to undergo reverse transcription in myeloid cells and resting T-cells. This restriction is alleviated by expression of the lentiviral accessory proteins Vpx and Vpr (Vpx/Vpr), which target SAMHD1 for proteasome-mediated degradation. However, the precise determinants within SAMHD1 for recognition by Vpx/Vpr remain unclear. Here we show that evolution of Vpx/Vpr in primate lentiviruses has caused the interface between SAMHD1 and Vpx/Vpr to alter during primate lentiviral evolution. Using multiple HIV-2 and SIV Vpx proteins, we show that Vpx from the HIV-2 and SIVmac lineage, but not Vpx from the SIVmnd2 and SIVrcm lineage, require the C-terminus of SAMHD1 for interaction, ubiquitylation, and degradation. On the other hand, the N-terminus of SAMHD1 governs interactions with Vpx from SIVmnd2 and SIVrcm, but has little effect on Vpx from HIV-2 and SIVmac. Furthermore, we show here that this difference in SAMHD1 recognition is evolutionarily dynamic, with the importance of the N- and C-terminus for interaction of SAMHD1 with Vpx and Vpr toggling during lentiviral evolution. We present a model to explain how the head-to-tail conformation of SAMHD1 proteins favors toggling of the interaction sites by Vpx/Vpr during this virus-host arms race. Such drastic functional divergence within a lentiviral protein highlights a novel plasticity in the evolutionary dynamics of viral antagonists for restriction factors during lentiviral adaptation to its hosts. © 2013 Fregoso et al

Cross-correlation of the 2XMMi catalogue with Data Release 7 of the Sloan Digital Sky Survey

The Survey Science Centre of the XMM-Newton satellite released the first incremental version of the 2XMM catalogue in August 2008 . With more than 220,000 X-ray sources, the 2XMMi was at that time the largest catalogue of X-ray sources ever published and thus constitutes an unprecedented resource for studying the high-energy properties of various classes of X-ray emitters such as AGN and stars. The advent of the 7th release of the Sloan Digital Sky Survey offers the opportunity to cross-match two major surveys and extend the spectral energy distribution of many 2XMMi sources towards the optical bands. We here present a cross-matching algorithm based on the classical likelihood ratio estimator. The method developed has the advantage of providing true probabilities of identifications without resorting to Monte-Carlo simulations. Over 30,000 2XMMi sources have SDSS counterparts with individual probabilities of identification higher than 90%. Using spectroscopic identifications from the SDSS DR7 catalogue supplemented by extraction from other catalogues, we build an identified sample from which the way the various classes of X-ray emitters gather in the multi dimensional parameter space can be analysed. We investigate two scientific use cases. In the first example we show how these multi-wavelength data can be used to search for new QSO2s. Although no specific range of observed properties allows us to identify Compton Thick QSO2s, we show that the prospects are much better for Compton Thin AGN2 and discuss several possible multi-parameter selection strategies. In a second example, we confirm the hardening of the mean X-ray spectrum with increasing X-ray luminosity on a sample of over 500 X-ray active stars and reveal that on average X-ray active M stars display bluer $g-r$ colour indexes than less active ones (abridged).Comment: Accepted for publication in A&A. The corresponding fits file can be downloaded from the XCat-DB home page (http://xcatdb.u-strasbg.fr/) (tools and data). The file also contains line information for all SDSS spectroscopic entries matching a 2XMM source. Results from the cross-correlation with the 2XMM DR3 are also available at the same location. 22 pages and 14 figure

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change

Early Universe Quantum Processes in BEC Collapse Experiments

We show that in the collapse of a Bose-Einstein condensate (BEC) {For an excellent introduction to BEC theory, see C. Pethick and H. Smith, Bose-Einstein condensation in dilute gases (Cambridge University Press, Cambridge, England, 2002)} certain processes involved and mechanisms at work share a common origin with corresponding quantum field processes in the early universe such as particle creation, structure formation and spinodal instability. Phenomena associated with the controlled BEC collapse observed in the experiment of Donley et al E. Donley et. al., Nature 412, 295 (2001)(they call it `Bose-Nova', see also J. Chin, J. Vogels and W. Ketterle, Phys. Rev. Lett. 90, 160405 (2003)) such as the appearance of bursts and jets can be explained as a consequence of the squeezing and amplification of quantum fluctuations above the condensate by the dynamics of the condensate. Using the physical insight gained in depicting these cosmological processes, our analysis of the changing amplitude and particle contents of quantum excitations in these BEC dynamics provides excellent quantitative fits with the experimental data on the scaling behavior of the collapse time and the amount of particles emitted in the jets. Because of the coherence properties of BEC and the high degree of control and measurement precision in atomic and optical systems, we see great potential in the design of tabletop experiments for testing out general ideas and specific (quantum field) processes in the early universe, thus opening up the possibility for implementing `laboratory cosmology'.Comment: 7 pages, 3 figures. Invited Talk presented at the Peyresq Meetings of Gravitation and Cosmology, 200

Measurement of the permanent electric dipole moment of the neutron

We present the result of an experiment to measure the electric dipole moment EDM) of the neutron at the Paul Scherrer Institute using Ramsey's method of separated oscillating magnetic fields with ultracold neutrons (UCN). Our measurement stands in the long history of EDM experiments probing physics violating time reversal invariance. The salient features of this experiment were the use of a Hg-199 co-magnetometer and an array of optically pumped cesium vapor magnetometers to cancel and correct for magnetic field changes. The statistical analysis was performed on blinded datasets by two separate groups while the estimation of systematic effects profited from an unprecedented knowledge of the magnetic field. The measured value of the neutron EDM is d_{\rm n} = (0.0\pm1.1_{\rm stat}\pm0.2_{\rmsys})\times10^{-26}e\,{\rm cm}

Finite Temperature Models of Bose-Einstein Condensation

The theoretical description of trapped weakly-interacting Bose-Einstein condensates is characterized by a large number of seemingly very different approaches which have been developed over the course of time by researchers with very distinct backgrounds. Newcomers to this field, experimentalists and young researchers all face a considerable challenge in navigating through the `maze' of abundant theoretical models, and simple correspondences between existing approaches are not always very transparent. This Tutorial provides a generic introduction to such theories, in an attempt to single out common features and deficiencies of certain `classes of approaches' identified by their physical content, rather than their particular mathematical implementation. This Tutorial is structured in a manner accessible to a non-specialist with a good working knowledge of quantum mechanics. Although some familiarity with concepts of quantum field theory would be an advantage, key notions such as the occupation number representation of second quantization are nonetheless briefly reviewed. Following a general introduction, the complexity of models is gradually built up, starting from the basic zero-temperature formalism of the Gross-Pitaevskii equation. This structure enables readers to probe different levels of theoretical developments (mean-field, number-conserving and stochastic) according to their particular needs. In addition to its `training element', we hope that this Tutorial will prove useful to active researchers in this field, both in terms of the correspondences made between different theoretical models, and as a source of reference for existing and developing finite-temperature theoretical models.Comment: Detailed Review Article on finite temperature theoretical techniques for studying weakly-interacting atomic Bose-Einstein condensates written at an elementary level suitable for non-experts in this area (e.g. starting PhD students). Now includes table of content