Determination of biogeochemical properties of marine particles using above water measurements of the degree of polarization at the Brewster angle

Retrieval of biogeochemical parameters from remotely sensed data in optically complex waters such as those found in coastal zones is a challenging task due to the effects of various water constituents (biogenic, nonalgal and inorganic particles, dissolved matter) on the radiation exiting the ocean. Since scattering by molecules, aerosols, hydrosols and reflection at the sea surface introduce and modify the polarization state of light, the polarized upward radiation contains embedded information about the intrinsic nature of aerosols and suspended matter in the ocean. In this study, shipborne above water angularly resolved visible/near infrared multiband measurements of the degree of polarization are analysed against their corresponding in-situ biogeochemically characterized water samples for the first time. Water samples and radiometric data were collected in the English Channel along an inshore-offshore transect. Angular variations in the degree of polarization P are found to be consistent with theory. Maximum values of P are observed near the Brewster viewing angle in the specular direction. Variations in the degree of polarization at the Brewster angle (PB) with water content revealed that the suspended particulate matter, which is mainly composed of inorganic particles during the experiment, contributes to depolarise the skylight reflection, thus reducing PB. An empirical polarization-based approach is proposed to determine biogeochemical properties of the particles. The concentration of inorganic particles can be estimated using PB to within ±13% based on the dataset used. Larger sets of polarized measurements are recommended to corroborate the tendency observed in this study

SOFI: A 3D simulator for the generation of underwater optical images

International audienceWe present an original simulator-called SOFI-for the synthetic generation of underwater optical images. The simulator architecture is flexible and relies on flow diagrams in order to allow the integration of various models for image generation which are based on the underwater optical phenomena. The objective is also to ensure real time or quasi real time performance so it takes advantage of the latest technologies, such as GPGPU, and relies on GPU programming under CUDA. Two kinds of models for image generation are presented and should be integrated in SOFI: (1) the OSOA model based on the radiative transfer theory and (2) global image modeling which describes globally how an image is deteriorated under the effects of sea water

The French EO high spatial resolution hyperspectral dual mission - an update

More than 25 years of airborne imaging spectroscopy and spaceborne sensors such as Hyperion [1] or HICO [2] have clearly demonstrated the ability of such a remote sensing technique to produce value added information regarding surface composition and physical properties for a large variety of applications [3]. Scheduled missions such as EnMAP [4], HISUI [5] or PRISMA [6] prove the increased interest of the scientific community for such a type of remote sensing data. In France, after gathering a group of Science and Defence users of imaging spectrometry data (Groupe de Synthèse Hyperspectral, GSH [7]) to establish an up-to-date review of possible applications, define instrument specifications required for accurate, quantitative retrieval of diagnostic parameters, and identify fields of application where imaging spectrometry is a major contribution, CNES (French Space Agency) decided a pre-phase A study for an hyperspectral mission concept called HYPXIM (HYPerspectral-X IMagery), the main fields of applications of which were to be vegetation, coastal and inland waters, geosciences, urban environment, atmospheric sciences, cryosphere and Defence. During this pre-phase A, the feasibility of such a platform was evaluated, based on specific studies supported by Defence and a more accurate definition of reference radiances and instrument characteristics. Results also pointed to applications where high spatial resolution was necessary and would not be covered by the other foreseen hyperspectral missions. For example, in the case of ecosystem studies, it is generally agreed that many model variables and processes are not accurately represented and that upcoming sensors with improved spatial and spectral capabilities, such as higher resolution imaging spectrometers, are needed to further improve the quality and accuracy of model variables [8, 9]. The growing interest for urban environment related applications also emphasized the need for an increased spatial resolution [10, 11]. Finally, short revisit time is an issue for security and Defense as well as crisis monitoring. Table 1 summarizes the Science and Defence mission requirements at the end of pre-phase A. Two instrument designs were proposed by the industry (EADS-Astrium and Thales Alenia Space) based on these new requirements [12]: HYPXIM-Challenging, on a micro-satellite platform, with a 15 m pixel and HYPXIM-Performance, on a mini-satellite platform, with a 8 m pixel, and possible TIR hyperspectral capabilities. Both scenarios included a PAN camera with a 1.85 m pixel. Platform agility would allow for “on-event mode” with a 3-day revisit time. CNES decided to select HYPXIM-Performance, the system providing a higher spatial resolution (pixel ≤ 8 m, [13, 14]), but without TIR capabilities, for a phase A study [15]. This phase A was to start at the beginning of 2013 but is currently stopped due to budget constraints. An important part of the activities has been focusing on getting the French community more involved through various surveys and workshops in preparation for the CNES prospective meeting, an important step for the future of the mission. During this prospective meeting, which took place last March, decision was taken to keep HYPXIM alive as a mid-term (2020-2025) mission. The attendance at the recent workshop organized by the SFPT-GH (Société Française de Photogrammétrie et Télédétection, Groupe Hyperspectral) which gathered more than 90 participants from various field of application, including the industry (see http://www.sfpt.fr/hyperspectral for more details), demonstrates the interest and support of the French scientific community for a high spatial resolution imaging spectrometry mission

GALENE - Understanding coastal and inland ecosystem properties, processes and dynamics

Coastal and inland aquatic ecosystems are of fundamental interest for societal and economical purposes due to a significant part of the population living there. They both highly contribute to carbon cycling and biodiversity. Those ecosystems are continuously impacted by natural processes and human activities. Many of these impacts become more frequent and severe, particularly with increasing population and climate change. Hence, there is a need (i) to generate reliable, robust and timely evidence of how these environments are changing, (ii) to understand processes causing these changes and their societal, health, and economic consequences, and (iii) to identify steps towards conservation, restoration and sustainable use of water and dependent ecosystems, and resources. Systematic, high-quality and global observations, such as those provided by satellite remote sensing techniques, are key to understand complex aquatic systems. While multitudes of remote sensing missions have been specifically designed for studying ocean biology and biogeochemistry as well as for evaluating terrestrial environments, remote sensing missions dedicated to studying critical coastal and inland aquatic ecosystems at global scale are non-existent. Thus, these ecosystems remain among the most understudied habitats on the Earth’s surface. Specific reasons for such an observational gap lie in the dynamic and optical complexity of water ecosystems, in combination with technological challenges to optimize the relevant spatial, spectral, radiometric, and temporal characteristics. Current and forthcoming missions are either not suited to provide a global coverage (e.g., PRISMA, EnMAP) or to obtain reliable data over dark waters (e.g., carbon-rich lakes) due to inadequate radiometric sensitivity (e.g., Sentinel-2/MSI). They are also not adapted for characterizing the biodiversity patchiness of submerged habitats and water column compositions such as phytoplankton assemblages due to their inadequate spectral resolution (e.g., Sentinel-2/MSI, Sentinel-3/OLCI). Wetland ecosystems are insufficiently described as current sensors do not adequately capture their diversity, which compromises their management and protection. A future satellite mission, so-called Global Assessment of Limnological, Estuarine and Neritic Ecosystems (GALENE), has been proposed to the Earth Explorer 11 call (ESA) to respond to the future challenges linked to coastal and inland ecosystems. GALENE will provide optimized measurements of these aquatic ecosystems, and enable an adaptive sampling of dynamic properties and processes in water columns, benthic habitats and associated wetlands. GALENE will thus fill a major gap by comprehensively quantifying the state of Earth’s water bodies and aquatic ecosystems. It will substantially contribute addressing global water challenges, including water pollution and ensuring clean drinking water supply for all and protecting coastal environments and populations. GALENE mission concept consists of a synergy of three innovative instruments, namely a hyperspectral sensor, a panchromatic camera and a polarimeter. The GALENE science objectives and main technological features will be presented

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Large-scale exome-wide association analysis identifies loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

White blood cells play diverse roles in innate and adaptive immunity. Genetic association analyses of phenotypic variation in circulating white blood cell (WBC) counts from large samples of otherwise healthy individuals can provide insights into genes and biologic pathways involved in production, differentiation, or clearance of particular WBC lineages (myeloid, lymphoid) and also potentially inform the genetic basis of autoimmune, allergic, and blood diseases. We performed an exome array-based meta-analysis of total WBC and subtype counts (neutrophils, monocytes, lymphocytes, basophils, and eosinophils) in a multi-ancestry discovery and replication sample of ∼157,622 individuals from 25 studies. We identified 16 common variants (8 of which were coding variants) associated with one or more WBC traits, the majority of which are pleiotropically associated with autoimmune diseases. Based on functional annotation, these loci included genes encoding surface markers of myeloid, lymphoid, or hematopoietic stem cell differentiation (CD69, CD33, CD87), transcription factors regulating lineage specification during hematopoiesis (ASXL1, IRF8, IKZF1, JMJD1C, ETS2-PSMG1), and molecules involved in neutrophil clearance/apoptosis (C10orf54, LTA), adhesion (TNXB), or centrosome and microtubule structure/function (KIF9, TUBD1). Together with recent reports of somatic ASXL1 mutations among individuals with idiopathic cytopenias or clonal hematopoiesis of undetermined significance, the identification of a common regulatory 3 UTR variant of ASXL1 suggests that both germline and somatic ASXL1 mutations contribute to lower blood counts in otherwise asymptomatic individuals. These association results shed light on genetic mechanisms that regulate circulating WBC counts and suggest a prominent shared genetic architecture with inflammatory and autoimmune diseases

Importance of the polarization in the retrieval of oceanic constituents from the remote sensing reflectance

International audience[1] The influence of marine particles on the polarized radiation exiting the ocean is studied, and the implications for the retrieval of particulate concentration from remotely sensed data are investigated. Simulations were carried out using a vector radiative transfer model. Open ocean and coastal waters conditions were examined separately. In phytoplankton dominated waters, the polarized reflectance is virtually insensitive to the variations in chlorophyll concentration when observing at the top of atmosphere. The polarization effects induced by phytoplankton cells are too weak compared to those induced by the air-water interface and the atmospheric particles ( especially molecules) to significantly contribute to the polarized reflectance at this level of atmosphere. The use of the polarized information at short wavelengths is thus proposed to improve the retrieval of the spectral variation of the aerosol model in atmospheric correction algorithms. In coastal zones, the sensitivity of the polarized signal to the water content is much greater. The analysis demonstrates that the measurement of the polarized reflectance just above the sea surface may not be relevant to reduce the skylight reflection effects when the water mass is mainly dominated by highly refractive particles. It is shown that polarization measurements can be of great interest to separate the fraction of inorganic particles from biogenic cells. This study also highlights that an empirical-based inversion approach relying on the polarized reflectance measured in the green and at longer wavelengths could be efficient to retrieve the concentration of inorganic particles regardless of the phytoplankton content in coastal waters

Estimation of daily photosynthetically active radiation (PAR) in presence of low to high aerosol loads: application to OLCI-like satellite data

Estimation of daily photosynthetically active radiation (PAR) is of primary importance for monitoring the ocean primary production and the subsequent production of carbon by phytoplankton at global scale from remote sensing ocean color sensors. On the other hand, aerosol abundance and composition play a critical role in the modulation of PAR. In this study, an original algorithm, so-called OLCIPAR, is proposed for routinely determining the daily PAR from optical satellite sensors such as the OLCI sensor aboard Sentinel-3 (ESA). The OLCIPAR algorithm has been developed to overcome some of the limitations of the current existing methods. In particular, multiple scattering effects induced by the atmospheric layer are taken into account based on exact radiative transfer calculations. Another advantage of OLCIPAR method is to consider a great variety of aerosol models to better account for their optical variability as observed in real world conditions. The OLCIPAR algorithm was applied to the archive of MERIS data, whose sensor is similar to OLCI. The validation of the retrieved daily PAR was carried out based on comparison with the time series acquired by the BOUSSOLE oceanographic buoy moored in the Mediterranean Sea. Results show a regression slope of 1% and an accuracy within 10% which confirms the robustness of the algorithm. The comparison of OLCIPAR retrievals with the products routinely distributed by NASA shows that estimates of PAR differ by up to 20% in the subtropical Atlantic Ocean where important amounts of dust aerosols are present. The improvements brought by OLCIPAR method for deriving the daily PAR could thus permit to better assess the impact of aerosols on reduction of PAR with implications on the estimation of oceanic primary production. (C) 2016 Optical Society of Americ