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Abstract Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Abstract The Tara Pacific expedition (2016–2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Abstract Background Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Algal blooms are hotspots of marine primary production that play central roles in microbial ecology and global elemental cycling. Here, the authors show how bloom termination by viral infection can shift the balance between eukaryotic and prokaryotic recyclers of phytoplankton biomass.

Atmospheric bacterial diversity in spring indicates a strong marine influence over the Pacific and terrestrial influence over the Atlantic Ocean, according to a comparison of microbial community compositions in the north Pacific and Atlantic surface oceans and atmosphere.

The global polarization of Λ hyperons along the total orbital angular momentum of a relativistic heavy-ion collision is presented based on the high statistics data samples collected in Au+Au collisions at sNN=2.4 GeV and Ag+Ag at 2.55 GeV with the High-Acceptance Di-Electron Spectrometer (HADES) at GSI, Darmstadt. This is the first measurement below the strangeness production threshold in nucleon-nucleon collisions. Results are reported as a function of the collision centrality as well as a function of the hyperon's transverse momentum (pT) and rapidity (yCM) for the range of centrality 0–40%. We observe a strong centrality dependence of the polarization with an increasing signal towards peripheral collisions. For mid-central (20 – 40%) collisions the polarization magnitudes are 〈PΛ〉(%)=6.8±1.3(stat.)±2.1(syst.) for Au+Au and 〈PΛ〉(%)=6.2±0.4(stat.)±0.6(syst.) for Ag+Ag, which are the largest values observed so far. This observation thus provides a continuation of the increasing trend previously observed by STAR and contrasts expectations from recent theoretical calculations predicting a maximum in the region of collision energies about 3 GeV. The observed polarization is of a similar magnitude as predicted by 3D-fluid-dynamics and the UrQMD plus thermal vorticity model and significantly above results from the AMPT model.

Sea spray aerosol (SSA) are an important way through which oceans can influence the atmosphere’s radiative properties. Here, the authors present measurements taken over a 42,000 km ship cruise in the Atlantic and Pacific Ocean and show that SSA number concentrations vary over a 24-hour cycle, possibly linked to surface water bubble-bursting dynamics.

In this paper, we investigate the use of machine-learning techniques in order to produce harmonised surface reflectances between Sentinel-2 and Pleiades images, and reduce the impact of the differences in sensors, view conditions, and atmospheric correction differences between them. We demonstrate that if a simple linear regression considering Sentinel-2 surface reflectances as the target domain can overcome this problem when both images are calibrated to Top of Canopy reflectances, the non-linearity brought by a simple Multi-Layer-Perceptron is already useful when Pleiades is corrected to Top of Atmosphere level and contributions of the atmosphere need to be learned. We also demonstrate that learning a Convolution Neural Network instead of a plain MLP can learn undesired spatial effects such as mis-registration or differences in spatial frequency content, that will affect the image quality of the corrected Pleiades product. We overcome this issue by proposing an adhoc input convolutional layer that will capture those effects and can later be unplugged during inference. Last, we also propose an architecture and loss function that is robust to unmasked clouds and produces a confidence prediction during inference.

This paper presents a new Multiview Stereo Pipeline (MVS), called CARS, dedicated to satellite imagery. This pipeline is intended for massive Digital Surface Model (DSM) production and has therefore been designed to maximize scalability robustness and performance. Those two properties have driven the design of the workflow as well as the choice of algorithms and parameter trends, making our pipeline unique with respect to existing solutions in literature. This paper intends to serve as a reference paper for the pipeline implementation, and therefore provides a detailed description of algorithms and workflow. It also demonstrates the pipeline robustness and stability in several use cases, and compares its accuracy with the state-of-the-art pipelines on a reference dataset.

Earth Observation (EO) remote sensing missions are producing an increasing volume of data due to higher spatial and spectral resolutions, and higher frequency of acquisitions. Thus, in order to prepare the future of image processing pipelines, CNES has carried out Research & Development studies related to the use of Big Data and Cloud technologies for image processing chains made. Since mid-2019, CNES in partnership with Airbus Defense & Space, has started a new High Resolution Optical EO mission dedicated to very high resolution 3D observation called CO3D (“Constellation Optique 3D”). To achieve those objectives, a new image processing pipeline prototype is being developed taking in consideration the lessons learned from the previous studies. The paper will introduce this new image processing pipeline, the processing paradigms used to take advantage of big data technologies and the results of production benchmarks at a large scale. The on-going works to optimize the processing pipeline and Cloud cluster will be also discussed.

This paper presents a method to perform automatic vector-to-image registration. The proposed method performs well on different kinds of optical satellite images from Very High Resolution (VHR, sub-meter resolution) to images in the 10/20 m resolution range. It allows to automatically register vector dataset such as urban maps (by using building layers). In contrast with existing methods, our method needs few prior-knowledge on the features to match and can therefore adapt to different landscapes.This paper demonstrates the method robustness in several use-cases and presents the implementation which will soon be available as open-source software.

Several 3D reconstruction pipelines are being developed around the world for satellite imagery. Most of them implement their own versions of Semi-Global Matching, as an option for the matching step. However, deep learning based solutions already outperform every SGM derived algorithms on Kitti and Middlebury stereo datasets. But these deep learning based solutions need huge quantities of ground truths for training. This implies that the generation of ground truth stereo datasets, from satellite imagery and lidar, seems to be of great interest for the scientific community. It will aim at reducing the potential transfer learning difficulties, that could arise from a training done on datasets such as Middlebury or Kitti. In this work, we present a new ground truth generation pipeline. It produces stereo-rectified images and ground truth disparity maps, from satellite imagery and lidar. We also assess the rectification and the disparity accuracies of these outputs. We finally train a deep learning network on our preliminary ground truth dataset.

In this letter we report the first multi-differential measurement of correlated pion-proton pairs from 2 billion Au+Au collisions at sNN=2.42 GeV collected with HADES. In this energy regime the population of Δ(1232) resonances plays an important role in the way energy is distributed between intrinsic excitation energy and kinetic energy of the hadrons in the fireball. The triple differential d3N/dMπ±pdpTdy distributions of correlated π±p pairs have been determined by subtracting the πp combinatorial background using an iterative method. The invariant-mass distributions in the Δ(1232) mass region show strong deviations from a Breit-Wigner function with vacuum width and mass. The yield of correlated pion-proton pairs exhibits a complex isospin, rapidity and transverse-momentum dependence. In the invariant mass range 1.1

Untreated tonsillar phlegmon is a life-threatening condition commonly caused by Streptococcus pyogenes and Fusobacterium necrophorum, among other pathogens. Here, using specific laboratory tools, we detected Methanobrevibacter smithii in addition to S. pyogenes. This unprecedented observation questions the role of methanogens in phlegmon and the optimal treatment of this mixed infection.

We investigate identical pion HBT intensity interferometry in central Au+Au collisions at 1.23A GeV. High-statistics π−π− and π+π+ data are measured with HADES at SIS18/GSI. The radius parameters, derived from the correlation function depending on relative momenta in the longitudinally comoving system and parametrized as three-dimensional Gaussian distribution, are studied as function of transverse momentum. A substantial charge-sign difference of the source radii is found, particularly pronounced at low transverse momentum. The extracted source parameters agree well with a smooth extrapolation of the center-of-mass energy dependence established at higher energies, extending the corresponding excitation functions down towards a very low energy.

We present first data on sub-threshold production of Ks0 mesons and Λ hyperons in Au+Au collisions at sNN=2.4 GeV. We observe an universal 〈Apart〉 scaling of hadrons containing strangeness, independent of their corresponding production thresholds. Comparing the yields, their 〈Apart〉 scaling, and the shapes of the rapidity and the pt spectra to state-of-the-art transport model (UrQMD, HSD, IQMD) predictions, we find that none of them can simultaneously describe these observables with reasonable χ2 values.

The production of Σ0 baryons in the nuclear reaction p (3.5 GeV) + Nb (corresponding to sNN=3.18 GeV) is studied with the detector set-up HADES at GSI, Darmstadt. Σ0s were identified via the decay Σ0→Λγ with subsequent decays Λ→pπ− in coincidence with a e+e− pair from either external (γ→e+e−) or internal (Dalitz decay γ⁎→e+e−) gamma conversions. The differential Σ0 cross section integrated over the detector acceptance, i.e. the rapidity interval 0.5

We present data on charged kaons (K±) and ϕ mesons in Au(1.23A GeV)+Au collisions. It is the first simultaneous measurement of K− and ϕ mesons in central heavy-ion collisions below a kinetic beam energy of 10A GeV. The ϕ/K− multiplicity ratio is found to be surprisingly high with a value of 0.52±0.16 and shows no dependence on the centrality of the collision. Consequently, the different slopes of the K+ and K− transverse-mass spectra can be explained solely by feed-down, which substantially softens the spectra of K− mesons. Hence, in contrast to the commonly adapted argumentation in literature, the different slopes do not necessarily imply diverging freeze-out temperatures of K+ and K− mesons caused by different couplings to baryons.

In the frame of the Copernicus program of the European Commission, Sentinel-2 is a constellation of 2 satellites with a revisit time of 5 days in order to have temporal images stacks and a global coverage over terrestrial surfaces. Satellite 2A was launched in June 2015, and satellite 2B will be launched in March 2017. In cooperation with the European Space Agency (ESA), the French space agency (CNES) is in charge of the image quality of the project, and so ensures the CAL/VAL commissioning phase during the months following the launch. This cooperation is also extended to routine phase as CNES supports European Space Research Institute (ESRIN) and the Sentinel-2 Mission performance Centre (MPC) for validation in geometric and radiometric image quality aspects, and in Sentinel-2 GRI geolocation performance assessment whose results will be presented in this paper. The GRI is a set of S2A images at 10m resolution covering the whole world with a good and consistent geolocation. This ground reference enables accurate multi-temporal registration of refined Sentinel-2 products. While not primarily intended for the generation of DSM, Sentinel-2 swaths overlap between orbits would also allow for the generation of a complete DSM of land and ices over 60° of northern latitudes (expected accuracy: few S2 pixels in altimetry). This DSM would benefit from the very frequent revisit times of Sentinel-2, to monitor ice or snow level in area of frequent changes, or to increase measurement accuracy in areas of little changes.

Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions.

In the frame of its earth observation missions, CNES created a library called QPEC, and one of its launcher called Medicis. QPEC / Medicis is a sub-pixel two-dimensional stereo matching algorithm that works on an image pair. This tool is a block matching algorithm, which means that it is based on a local method. Moreover it does not regularize the results found. It proposes several matching costs, such as the Zero mean Normalised Cross-Correlation or statistical measures (the Mutual Information being one of them), and different match validation flags. QPEC / Medicis is able to compute a two-dimensional dense disparity map with a subpixel precision. Hence, it is more versatile than disparity estimation methods found in computer vision literature, which often assume an epipolar geometry. CNES uses Medicis, among other applications, during the in-orbit image quality commissioning of earth observation satellites. For instance the Pléiades-HR 1A & 1B and the Sentinel-2 geometric calibrations are based on this block matching algorithm. Over the years, it has become a common tool in ground segments for in-flight monitoring purposes. For these two kinds of applications, the two-dimensional search and the local sub-pixel measure without regularization can be essential. This tool is also used to generate automatic digital elevation models, for which it was not initially dedicated. This paper deals with the QPEC / Medicis algorithm. It also presents some of its CNES applications (in-orbit commissioning, in flight monitoring or digital elevation model generation). Medicis software is distributed outside the CNES as well. This paper finally describes some of these external applications using Medicis, such as ground displacement measurement, or intra-oral scanner in the dental domain.

The tagged quasi-free np→npπ+π− reaction has been studied experimentally with the High Acceptance Di-Electron Spectrometer (HADES) at GSI at a deuteron incident beam energy of 1.25 GeV/nucleon (s∼2.42 GeV/c for the quasi-free collision). For the first time, differential distributions of solid statistics for π+π− production in np collisions have been collected in the region corresponding to the large transverse momenta of the secondary particles. The invariant mass and angular distributions for the np→npπ+π− reaction are compared with different models. This comparison confirms the dominance of the t-channel with ΔΔ contribution. It also validates the changes previously introduced in the Valencia model to describe two-pion production data in other isospin channels, although some deviations are observed, especially for the π+π− invariant mass spectrum. The extracted total cross section is also in much better agreement with this model. Our new measurement puts useful constraints for the existence of the conjectured dibaryon resonance at mass M∼2.38 GeV and with width Γ∼70 MeV.

Employing the Bonn–Gatchina partial wave analysis framework (PWA), we have analyzed HADES data of the reaction p(3.5 GeV)+p→pK+Λ. This reaction might contain information about the kaonic cluster “ppK−” (with quantum numbers JP=0− and total isospin I=1/2) via its decay into pΛ. Due to interference effects in our coherent description of the data, a hypothetical K‾NN (or, specifically “ppK−”) cluster signal need not necessarily show up as a pronounced feature (e.g. a peak) in an invariant mass spectrum like pΛ. Our PWA analysis includes a variety of resonant and non-resonant intermediate states and delivers a good description of our data (various angular distributions and two-hadron invariant mass spectra) without a contribution of a K‾NN cluster. At a confidence level of CLs=95% such a cluster cannot contribute more than 2–12% to the total cross section with a pK+Λ final state, which translates into a production cross-section between 0.7 μb and 4.2 μb, respectively. The range of the upper limit depends on the assumed cluster mass, width and production process. Keywords: Kaonic nuclei, Anti-kaon–nucleon physics, ppK−, Low energy QCD, Partial wave analysis

The increasing availability of high resolution stereo images from Earth observation satellites has boosted the development of tools for producing 3D elevation models. The objective of these tools is to produce digital elevation models of very large areas with minimal human intervention. The development of these tools has been shaped by the constraints of the remote sensing acquisition, for example, using ad hoc stereo matching tools to deal with the pushbroom image geometry. However, this specialization has also created a gap with respect to the fields of computer vision and image processing, where these constraints are usually factored out. In this work we propose a fully automatic and modular stereo pipeline to produce digital elevation models from satellite images. The aim of this new pipeline, called Satellite Stereo Pipeline and abbreviated as s2p, is to use (and test) off-the-shelf computer vision tools while abstracting from the complexity associated to satellite imaging. To this aim, images are cut in small tiles for which we proved that the pushbroom geometry is very accurately approximated by the pinhole model. These tiles are then processed with standard stereo image rectification and stereo matching tools. The specifics of satellite imaging such as pointing accuracy refinement, estimation of the initial elevation from SRTM data, and geodetic coordinate systems are handled transparently by s2p. We demonstrate the robustness of our approach on a large database of satellite images and by providing an online demo of s2p.

One of the major uncertainties in the understanding of Earth's climate system is the interaction between solar radiation and aerosols in the atmosphere. Aerosols exposed to high humidity will change their chemical, physical, and optical properties due to their increased water content. To model hydrated aerosols, atmospheric chemistry and climate models often use the volume weighted mixing rule to predict the complex refractive index (RI) of aerosols when they interact with high relative humidity, and, in general, assume homogeneous mixing. This study explores the validity of these assumptions. A humidified cavity ring down aerosol spectrometer (CRD-AS) and a tandem hygroscopic DMA (differential mobility analyzer) are used to measure the extinction coefficient and hygroscopic growth factors of humidified aerosols, respectively. The measurements are performed at 80% and 90%RH at wavelengths of 532 nm and 355 nm using size-selected aerosols with different degrees of absorption; from purely scattering to highly absorbing particles. The ratio of the humidified to the dry extinction coefficients (fRHext(%RH, Dry)) is measured and compared to theoretical calculations based on Mie theory. Using the measured hygroscopic growth factors and assuming homogeneous mixing, the expected RIs using the volume weighted mixing rule are compared to the RIs derived from the extinction measurements. We found a weak linear dependence or no dependence of fRH(%RH, Dry) with size for hydrated absorbing aerosols in contrast to the non-monotonically decreasing behavior with size for purely scattering aerosols. No discernible difference could be made between the two wavelengths used. Less than 7% differences were found between the real parts of the complex refractive indices derived and those calculated using the volume weighted mixing rule, and the imaginary parts had up to a 20% difference. However, for substances with growth factor less than 1.15 the volume weighted mixing rule assumption needs to be taken with caution as the imaginary part of the complex RI can be underestimated.

Mechanical properties of a steam tube made of CrMo creep resistant steel are analysed in this contribution after up to 2,6•105 hours service life in creep conditions at temperature 530 °C and calculated stress level in the tube wall 46,5 MPa. During service life there were in the steel gradual micro structure changes, fi rst pearlite spheroidization, precipitation, coaugulation and precipitate coarsening. Nevertheless the strength and deformation properties of the steel (Re, Rm, A5, Z), and the resistance to brittle fracture and the creep strength limit, were near to unchanged after 2,1•105 hours in service. The steam tube is now in service more than 2,6•105 h.

The paper analyses the influence of strain rate on the behaviour of un-alloyed steels with Re (yield strength) in the range of 210 … 550 MPa in the deformation process. It analyses the results of the influence of strain rate ranging from 10-3 to 2,5•102s-1 on the yield strength, the ultimate tensile strength (Rm), the elongation (A) and the reduction of area (Z). Achieved results of strain rate in relationship on values of Erichsen number IE are also given. By increasing of strain rate ranging from 10-3 to 2,5•102s-1 the ratio Re/Rm is increased, whereas it was observed more intensively for steels with the lower value of Re. By increasing of strain rate up to 1 s-1 are IE values of tested steels increased, whereas the ratio Re/Rm was equal 0,82. After exceeding of this strain rate was the ratio Re/Rm increased and IE value is remarkable decreased.

Malaria is a public health problem for more than 2 billion people globally. About 219 million cases of malaria occur worldwide and 660,000 people die, mostly (91%) in the African Region despite decades of efforts to control the disease. Although the disease is preventable, it is life-threatening and parasitically transmitted by the bite of the female Anopheles mosquito. A deterministic mathematical model with intervention strategies is developed in order to investigate the effectiveness and optimal control strategies of indoor residual spraying (IRS), insecticide treated nets (ITNs) and treatment on the transmission dynamics of malaria in Karonga District, Malawi. The effective reproduction number is analytically computed, and the existence and stability conditions of the equilibria are explored. The model does not exhibit backward bifurcation. Pontryagin’s Maximum Principle which uses both the Lagrangian and Hamiltonian principles with respect to a time dependent constant is used to derive the necessary conditions for the optimal control of the disease. Numerical simulations indicate that the prevention strategies lead to the reduction of both the mosquito population and infected human individuals. Effective treatment consolidates the prevention strategies. Thus, malaria can be eradicated in Karonga District by concurrently applying vector control via ITNs and IRS complemented with timely treatment of infected people.