PLASMA-lab: A Flexible, Distributable Statistical Model Checking Library

International audienceWe present PLASMA-lab, a statistical model checking (SMC) library that provides the functionality to create custom statistical model checkers based on arbitrary discrete event modelling languages. PLASMA-lab is written in Java for maximum cross-platform compatibility and has already been incorporated in various performance-critical software and embedded hardware platforms. Users need only implement a few simple methods in a simulator class to take advantage of our efficient SMC algorithms. PLASMA-lab may be instantiated from the command line or from within other software. We have constructed a graphical user interface (GUI) that exposes the functionality of PLASMA-lab and facilitates its use as a standalone application with multiple 'drop-in' modelling languages. The GUI adds the notion of projects and experiments, and implements a simple, practical means of distributing simulations using remote clients

Ordonnancement, assignation et transformations dynamiques de graphe simultanés pour projeter efficacement des applications sur CGRAs

National audiencePorter une application sur une architecture reconfigurable à gros grain est une tâche complexe qui reste encore souvent réalisée entièrement ou partiellement manuellement. Cet article présente un flot original de synthèse automatisé basé sur des étapes d'ordonnancement et d'assignation simultanées. L'approche proposée parcourt en sens inverse les noeuds du modèle formel extrait à partir du code de l'application compilé pour le transformer dynamiquement uniquement si nécessaire. Les résultats des expériences montrent que l'approche proposée permet une meilleure exploration de l'espace de solution et obtient la meilleure latence dans 90% des cas

Analyse du recyclage par la méthode émergétique

International audienceLe recyclage matière est a priori considéré comme éco-favorable par rapport à l'exploitation de minerais provenant de mines, par nature en quantité finie et donc s'épuisant. Néanmoins, une vision holistique du recyclage requiert l'analyse de l'ensemble des ressources mobilisées pour effectuer cette opération. De plus, en suivant le déplacement/cheminement de la matière dans le temps, il devient alors nécessaire de connaître l'ensemble de l'historique de la matière considérée. Les auteurs établissent une équation théorique décrivant l'évolution à temps discret de l'émergie d'un produit : le pas d'échantillonnage est le temps du cycle. L'équation peut se réduire à une suite géométrique de raison, la fraction à recycler, sous certaines hypothèses. L'aluminium est ensuite proposé comme exemple d'application

Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

The growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes

Asteroid Ryugu before the Hayabusa2 encounter

Asteroid (162173) Ryugu is the target object of Hayabusa2, an asteroid exploration and sample return mission led by Japan Aerospace Exploration Agency (JAXA). Ground-based observations indicate that Ryugu is a C-type near-Earth asteroid with a diameter of less than 1 km, but the knowledge of its detailed properties is very limited prior to Hayabusa2 observation. This paper summarizes our best understanding of the physical and dynamical properties of Ryugu based on ground-based remote sensing and theoretical modeling before the Hayabusa2’s arrival at the asteroid. This information is used to construct a design reference model of the asteroid that is used for the formulation of mission operation plans in advance of asteroid arrival. Particular attention is given to the surface properties of Ryugu that are relevant to sample acquisition. This reference model helps readers to appropriately interpret the data that will be directly obtained by Hayabusa2 and promotes scientific studies not only for Ryugu itself and other small bodies but also for the solar system evolution that small bodies shed light on.Additional co-authors: Guy Libourel, Roy Lichtenheldt, Alessandro Maturilli, Scott R. Messenger, Tatsuhiro Michikami, Hideaki Miyamoto, Stefano Mottola, Thomas Müller, Akiko M. Nakamura, Larry R. Nittler, Kazunori Ogawa, Tatsuaki Okada, Ernesto Palomba, Naoya Sakatani, Stefan E. Schröder, Hiroki Senshu, Driss Takir, Michael E. Zolensky and International Regolith Science Group (IRSG) in Hayabusa2 projec

Functional Imaging of Numerical Processing in Adults and 4-y-Old Children

Adult humans, infants, pre-school children, and non-human animals appear to share a system of approximate numerical processing for non-symbolic stimuli such as arrays of dots or sequences of tones. Behavioral studies of adult humans implicate a link between these non-symbolic numerical abilities and symbolic numerical processing (e.g., similar distance effects in accuracy and reaction-time for arrays of dots and Arabic numerals). However, neuroimaging studies have remained inconclusive on the neural basis of this link. The intraparietal sulcus (IPS) is known to respond selectively to symbolic numerical stimuli such as Arabic numerals. Recent studies, however, have arrived at conflicting conclusions regarding the role of the IPS in processing non-symbolic, numerosity arrays in adulthood, and very little is known about the brain basis of numerical processing early in development. Addressing the question of whether there is an early-developing neural basis for abstract numerical processing is essential for understanding the cognitive origins of our uniquely human capacity for math and science. Using functional magnetic resonance imaging (fMRI) at 4-Tesla and an event-related fMRI adaptation paradigm, we found that adults showed a greater IPS response to visual arrays that deviated from standard stimuli in their number of elements, than to stimuli that deviated in local element shape. These results support previous claims that there is a neurophysiological link between non-symbolic and symbolic numerical processing in adulthood. In parallel, we tested 4-y-old children with the same fMRI adaptation paradigm as adults to determine whether the neural locus of non-symbolic numerical activity in adults shows continuity in function over development. We found that the IPS responded to numerical deviants similarly in 4-y-old children and adults. To our knowledge, this is the first evidence that the neural locus of adult numerical cognition takes form early in development, prior to sophisticated symbolic numerical experience. More broadly, this is also, to our knowledge, the first cognitive fMRI study to test healthy children as young as 4 y, providing new insights into the neurophysiology of human cognitive development

OSIRIS-REx Encounters Bennu: Initial Assessment from the Approach Phase

The OSIRIS-REx spacecraft launched on September 8, 2016, on a seven-year journey to return samples from asteroid (101955) Bennu. This presentation summarizes the scientific results from the Approach and Preliminary Survey phases. Bennu observations are set to begin on August 17, 2018,when the asteroid is bright enough for detection by the PolyCam. PolyCam and MapCam collect data to survey the asteroid environment for any hazards and characterize the asteroid point-source photometric properties. Resolved images acquired during final approach, starting in late October 2018, allow the creation of a shape model using stereophotoclinometry (SPC), needed by both the navigation team and science planners. The OVIRS and OTES spectrometers characterize the point- source spectral properties over a full rotation period, providing a first look at any features and thermophysical properties. TAGSAM is released from the launch container and deployed into the sampling configuration then returned to the stow position.Preliminary Survey follows the Approach Phase in early December 2018. This phase consists of a series of hyperbolic trajectories that cross over the North and South poles and the equator of Bennu at a close-approach distance of 7 km. Images from these Preliminary Survey passes provide data to complete the 75-cm resolution SPC global shape model and solve for the rotation state. Once the shape model is complete, the asteroid coordinate system is defined for co-registration of all data products. These higher-resolution images also constrain the photometric properties and allow for an initial assessment of the geology. In Preliminary Survey the team also obtains the first OLA data, providing a measure of the surface topography. OVIRS and OTES collect data as "ride-along" instruments, with the spacecraft pointing driven by imaging constraints. These data provide a first look at the spectral variation across the surface of Bennu. Radio science measurements, combined with altimetry and imagery, determine Bennu's mass, a prerequisite to placing the spacecraft into orbit in late December 2018. Together, data from the Approach and Preliminary Survey phases set the stage for the extensive mapping planned for 2019. These dates are the baseline plan. Any contingency or unexpected discovery may change this mission profile

Reducing Fertilizer and Avoiding Herbicides in Oil Palm Plantations—Ecological and Economic Valuations

Oil palm plantations are intensively managed agricultural systems that increasingly dominate certain tropical regions. Oil palm monocultures have been criticized because of their reduced biodiversity compared to the forests they historically replaced, and because of their negative impact on soils, water, and climate. We experimentally test whether less intensive management schemes may enhance biodiversity and lessen detrimental effects on the environment while maintaining high yields. We compare reduced vs. conventional fertilization, as well as mechanical vs. chemical weed control (with herbicides) in a long-term, full-factorial, multidisciplinary experiment. We conducted the experiment in an oil palm company estate in Sumatra, Indonesia, and report the results of the first 2 years. We measured soil nutrients and functions, surveyed above- and below-ground organisms, tracked oil palm condition and productivity, and calculated plantation gross margins. Plants, aboveground arthropods, and belowground animals were positively affected by mechanical vs. chemical weed control, but we could not detect effects on birds and bats. There were no detectable negative effects of reduced fertilization or mechanical weeding on oil palm yields, fine roots, or leaf area index. Also, we could not detect detrimental effects of the reduced fertilization and mechanical weeding on soil nutrients and functions (mineral nitrogen, bulk density, and litter decomposition), but water infiltration and base saturation tended to be higher under mechanical weeding, while soil moisture, and microbial biomass varied with treatment. Economic performance, measured as gross margins, was higher under reduced fertilization. There might be a delayed response of oil palm to the different management schemes applied, so results of future years may confirm whether this is a sustainable management strategy. Nevertheless, the initial effects of the experiment are encouraging to consider less intensive management practices as economically and ecologically viable options for oil palm plantations

Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria

Abstract: Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n = 564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n = 192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species