Validation Through Simulations of a Cn2 Profiler for the ESO/VLT Adaptive Optics Facility

The Adaptive Optics Facility (AOF) project envisages transforming one of the VLT units into an adaptive telescope and providing its ESO (European Southern Observatory) second generation instruments with turbulence corrected wavefronts. For MUSE and HAWK-I this correction will be achieved through the GALACSI and GRAAL AO modules working in conjunction with a 1170 actuators Deformable Secondary Mirror (DSM) and the new Laser Guide Star Facility (4LGSF). Multiple wavefront sensors will enable GLAO and LTAO capabilities, whose performance can greatly benefit from a knowledge about the stratification of the turbulence in the atmosphere. This work, totally based on end-to-end simulations, describes the validation tests conducted on a Cn2 profiler adapted for the AOF specifications. Because an absolute profile calibration is strongly dependent on a reliable knowledge of turbulence parameters r0 and L0, the tests presented here refer only to normalized output profiles. Uncertainties in the input parameters inherent to the code are tested as well as the profiler response to different turbulence distributions. It adopts a correction for the unseen turbulence, critical for the GRAAL mode, and highlights the effects of masking out parts of the corrected wavefront on the results. Simulations of data with typical turbulence profiles from Paranal were input to the profiler, showing that it is possible to identify reliably the input features for all the AOF modes.Comment: 15 pages, 12 figures, accepted for publication in the MNRAS Accepted 2015 January 22. Received 2015 January 21; in original form 2014 December

SpikeletFCN: Counting Spikelets from Infield Wheat Crop Images Using Fully Convolutional Networks

Currently, crop management through automatic monitoring is growing momentum, but presents various challenges. One key challenge is to quantify yield traits from images captured automatically. Wheat is one of the three major crops in the world with a total demand expected to exceed 850 million tons by 2050. In this paper we attempt estimation of wheat spikelets from high-definition RGB infield images using a fully convolutional model. We propose also the use of transfer learning and segmentation to improve the model. We report cross validated Mean Absolute Error (MAE) and Mean Square Error (MSE) of 53.0, 71.2 respectively on 15 real field images. We produce visualisations which show the good fit of our model to the task. We also concluded that both transfer learning and segmentation lead to a very positive impact for CNN-based models, reducing error by up to 89%, when extracting key traits such as wheat spikelet counts

NEMO-ICB (v1.0): interactive icebergs in the NEMO ocean model globally configured at eddy-permitting resolution

An established iceberg module, ICB, is used interactively with the Nucleus for European Modelling of the Ocean (NEMO) ocean model in a new implementation, NEMO–ICB (v1.0). A 30-year hindcast (1976–2005) simulation with an eddy-permitting (0.25°) global configuration of NEMO–ICB is undertaken to evaluate the influence of icebergs on sea ice, hydrography, mixed layer depths (MLDs), and ocean currents, through comparison with a control simulation in which the equivalent iceberg mass flux is applied as coastal runoff, a common forcing in ocean models. In the Southern Hemisphere (SH), drift and melting of icebergs are in balance after around 5 years, whereas the equilibration timescale for the Northern Hemisphere (NH) is 15–20 years. Iceberg drift patterns, and Southern Ocean iceberg mass, compare favourably with available observations. Freshwater forcing due to iceberg melting is most pronounced very locally, in the coastal zone around much of Antarctica, where it often exceeds in magnitude and opposes the negative freshwater fluxes associated with sea ice freezing. However, at most locations in the polar Southern Ocean, the annual-mean freshwater flux due to icebergs, if present, is typically an order of magnitude smaller than the contribution of sea ice melting and precipitation. A notable exception is the southwest Atlantic sector of the Southern Ocean, where iceberg melting reaches around 50% of net precipitation over a large area. Including icebergs in place of coastal runoff, sea ice concentration and thickness are notably decreased at most locations around Antarctica, by up to ~ 20% in the eastern Weddell Sea, with more limited increases, of up to ~ 10% in the Bellingshausen Sea. Antarctic sea ice mass decreases by 2.9%, overall. As a consequence of changes in net freshwater forcing and sea ice, salinity and temperature distributions are also substantially altered. Surface salinity increases by ~ 0.1 psu around much of Antarctica, due to suppressed coastal runoff, with extensive freshening at depth, extending to the greatest depths in the polar Southern Ocean where discernible effects on both salinity and temperature reach 2500 m in the Weddell Sea by the last pentad of the simulation. Substantial physical and dynamical responses to icebergs, throughout the global ocean, are explained by rapid propagation of density anomalies from high-to-low latitudes. Complementary to the baseline model used here, three prototype modifications to NEMO–ICB are also introduced and discussed

Characterizing, modelling and understanding the climate variability of the deep water formation in the North-Western Mediterranean Sea

Observing, modelling and understanding the climate-scale variability of the deep water formation (DWF) in the North-Western Mediterranean Sea remains today very challenging. In this study, we first characterize the interannual variability of this phenomenon by a thorough reanalysis of observations in order to establish reference time series. These quantitative indicators include 31 observed years for the yearly maximum mixed layer depth over the period 1980–2013 and a detailed multi-indicator description of the period 2007–2013. Then a 1980–2013 hindcast simulation is performed with a fully-coupled regional climate system model including the high-resolution representation of the regional atmosphere, ocean, land-surface and rivers. The simulation reproduces quantitatively well the mean behaviour and the large interannual variability of the DWF phenomenon. The model shows convection deeper than 1000 m in 2/3 of the modelled winters, a mean DWF rate equal to 0.35 Sv with maximum values of 1.7 (resp. 1.6) Sv in 2013 (resp. 2005). Using the model results, the winter-integrated buoyancy loss over the Gulf of Lions is identified as the primary driving factor of the DWF interannual variability and explains, alone, around 50 % of its variance. It is itself explained by the occurrence of few stormy days during winter. At daily scale, the Atlantic ridge weather regime is identified as favourable to strong buoyancy losses and therefore DWF, whereas the positive phase of the North Atlantic oscillation is unfavourable. The driving role of the vertical stratification in autumn, a measure of the water column inhibition to mixing, has also been analyzed. Combining both driving factors allows to explain more than 70 % of the interannual variance of the phenomenon and in particular the occurrence of the five strongest convective years of the model (1981, 1999, 2005, 2009, 2013). The model simulates qualitatively well the trends in the deep waters (warming, saltening, increase in the dense water volume, increase in the bottom water density) despite an underestimation of the salinity and density trends. These deep trends come from a heat and salt accumulation during the 1980s and the 1990s in the surface and intermediate layers of the Gulf of Lions before being transferred stepwise towards the deep layers when very convective years occur in 1999 and later. The salinity increase in the near Atlantic Ocean surface layers seems to be the external forcing that finally leads to these deep trends. In the future, our results may allow to better understand the behaviour of the DWF phenomenon in Mediterranean Sea simulations in hindcast, forecast, reanalysis or future climate change scenario modes. The robustness of the obtained results must be however confirmed in multi-model studies

A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.

Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle

Post conjunction detection of β\beta Pictoris b with VLT/SPHERE

With an orbital distance comparable to that of Saturn in the solar system, \bpic b is the closest (semi-major axis $\simeq$\,9\,au) exoplanet that has been imaged to orbit a star. Thus it offers unique opportunities for detailed studies of its orbital, physical, and atmospheric properties, and of disk-planet interactions. With the exception of the discovery observations in 2003 with NaCo at the Very Large Telescope (VLT), all following astrometric measurements relative to \bpic have been obtained in the southwestern part of the orbit, which severely limits the determination of the planet's orbital parameters. We aimed at further constraining \bpic b orbital properties using more data, and, in particular, data taken in the northeastern part of the orbit. We used SPHERE at the VLT to precisely monitor the orbital motion of beta \bpic b since first light of the instrument in 2014. We were able to monitor the planet until November 2016, when its angular separation became too small (125 mas, i.e., 1.6\,au) and prevented further detection. We redetected \bpic b on the northeast side of the disk at a separation of 139\,mas and a PA of 30$^{\circ}$ in September 2018. The planetary orbit is now well constrained. With a semi-major axis (sma) of $a = 9.0 \pm 0.5$ au (1 $\sigma$), it definitely excludes previously reported possible long orbital periods, and excludes \bpic b as the origin of photometric variations that took place in 1981. We also refine the eccentricity and inclination of the planet. From an instrumental point of view, these data demonstrate that it is possible to detect, if they exist, young massive Jupiters that orbit at less than 2 au from a star that is 20 pc away.Comment: accepted by A&

SPHERE: the exoplanet imager for the Very Large Telescope

Observations of circumstellar environments to look for the direct signal of exoplanets and the scattered light from disks has significant instrumental implications. In the past 15 years, major developments in adaptive optics, coronagraphy, optical manufacturing, wavefront sensing and data processing, together with a consistent global system analysis have enabled a new generation of high-contrast imagers and spectrographs on large ground-based telescopes with much better performance. One of the most productive is the Spectro-Polarimetic High contrast imager for Exoplanets REsearch (SPHERE) designed and built for the ESO Very Large Telescope (VLT) in Chile. SPHERE includes an extreme adaptive optics system, a highly stable common path interface, several types of coronagraphs and three science instruments. Two of them, the Integral Field Spectrograph (IFS) and the Infra-Red Dual-band Imager and Spectrograph (IRDIS), are designed to efficiently cover the near-infrared (NIR) range in a single observation for efficient young planet search. The third one, ZIMPOL, is designed for visible (VIR) polarimetric observation to look for the reflected light of exoplanets and the light scattered by debris disks. This suite of three science instruments enables to study circumstellar environments at unprecedented angular resolution both in the visible and the near-infrared. In this work, we present the complete instrument and its on-sky performance after 4 years of operations at the VLT.Comment: Final version accepted for publication in A&

Oceanic hindcast simulations at high resolution suggest that the Atlantic MOC is bistable

All climate models predict a freshening of the North Atlantic at high latitude that may induce an abrupt change of the Atlantic Meridional Overturning Circulation (hereafter AMOC) if it resides in the bistable regime, where both a strong and a weak state coexist. The latter remains uncertain as there is no consensus among observations and ocean reanalyses, where the AMOC is bistable, versus most climate models that reproduce a mono-stable strong AMOC. A series of four hindcast simulations of the global ocean at 1/12° resolution, which is presently unique, are used to diagnose freshwater transport by the AMOC in the South Atlantic, an indicator of AMOC bistability. In all simulations, the AMOC resides in the bistable regime: it exports freshwater southward in the South Atlantic, implying a positive salt advection feedback that would act to amplify a decreasing trend in subarctic deep water formation as projected in climate scenarios