Adaptive Underwater Robotic Sampling of Dispersal Dynamics in the Coastal Ocean

To get a better understanding of the highly nonlinear processes driving the ocean, efficient and informative sampling is critical. By combining robotic sampling with ocean models we are able to choose informative sampling sites and adaptively change our path based on measurements. We present models exploiting prior information from ocean models as well as real-time information from in situ measurements. The method uses compact Gaussian process modeling and objective functions to locate informative sampling sites. Our aim is to get a better understanding of ocean processes and improve real-time monitoring of dispersal dynamics. The case study focuses on a fjord located in Norway containing a seafill for mine tailings. Transportation of the deposited particles are studied, and the sampling method is tested in the area. The results from these sea trials are presented.acceptedVersio

Effect of near‐bed turbulence on chronic detachment of epilithic biofilm: Experimental and modeling approaches.

The biomass dynamics of epilithic biofilm, a collective term for a complex microorganism community that grows on gravel bed rivers, was investigated by coupling experimental and numerical approaches focusing on epilithic biofilm‐flow interactions. The experiment was conducted during 65 days in an artificial rough open‐channel flow, where filtered river water circulated at a constant discharge. To characterize the effect of near‐bed turbulence on the chronic detachment process in the dynamics of epilithic biofilm, local hydrodynamic conditions were measured by laser Doppler anemometry and turbulent boundary layer parameters inferred from double‐averaged quantities. Numerical simulations of the EB biomass dynamics were performed using three different models of chronic detachment based upon three different descriptors for the flow conditions: Discharge Q, friction velocity u*, and roughness Reynolds number k+. Comparisons of numerical simulation results with experimental data revealed chronic detachment to be better simulated by taking the roughness Reynolds number as the external physical variable forcing chronic detachment. Indeed, the loss of epilithic matter through the chronic detachment process is related not only to hydrodynamic conditions, but also to change in bottom roughness. This suggests that changes in the behavior and dimensions of river bed roughness must be considered when checking the dynamics of epilithic biofilm in running waters

Autonomous subsea intervention (SEAVENTION)

This paper presents the main results and latest developments in a 4-year project called autonomous subsea intervention (SEAVENTION). In the project we have developed new methods for autonomous inspection, maintenance and repair (IMR) in subsea oil and gas operations with Unmanned Underwater Vehicles (UUVs). The results are also relevant for offshore wind, aquaculture and other industries. We discuss the trends and status for UUV-based IMR in the oil and gas industry and provide an overview of the state of the art in intervention with UUVs. We also present a 3-level taxonomy for UUV autonomy: mission-level, task-level and vehicle-level. To achieve robust 6D underwater pose estimation of objects for UUV intervention, we have developed marker-less approaches with input from 2D and 3D cameras, as well as marker-based approaches with associated uncertainty. We have carried out experiments with varying turbidity to evaluate full 6D pose estimates in challenging conditions. We have also devised a sensor autocalibration method for UUV localization. For intervention, we have developed methods for autonomous underwater grasping and a novel vision-based distance estimator. For high-level task planning, we have evaluated two frameworks for automated planning and acting (AI planning). We have implemented AI planning for subsea inspection scenarios which have been analyzed and formulated in collaboration with the industry partners. One of the frameworks, called T-REX demonstrates a reactive behavior to the dynamic and potentially uncertain nature of subsea operations. We have also presented an architecture for comparing and choosing between mission plans when new mission goals are introduced.publishedVersio

Species-specific activity of antibacterial drug combinations

International audienceThe spread of antimicrobial resistance has become a serious public health concern, making once treatable diseases deadly again and undermining breakthrough achievements of modern medicine 1,2. Drug combinations can aid in fighting multi-drug resistant (MDR) bacterial infections, yet, are largely unexplored and rarely used in clinics. To identify general principles for antibacterial drug combinations and understand their potential, we profiled ~3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in 6 strains from three Gram-negative pathogens, Escherichia coli, Salmonella Typhimurium and Pseudomonas aeruginosa. Despite their phylogenetic relatedness, more than 70% of the detected drug-drug interactions are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs targeting different cellular processes, whereas synergies are more conserved and enriched in drugs targeting the same process. We elucidate mechanisms underlying this dichotomy and further use our resource to dissect the interactions of the food additive, vanillin. Finally, we demonstrate that several synergies are effective against MDR clinical isolates in vitro and during Galleria mellonella infections with one reverting resistance to the last-resort antibiotic, colistin

Inflammatory Monocytes and Neutrophils Are Licensed to Kill during Memory Responses In Vivo

Immunological memory is a hallmark of B and T lymphocytes that have undergone a previous encounter with a given antigen. It is assumed that memory cells mediate better protection of the host upon re-infection because of improved effector functions such as antibody production, cytotoxic activity and cytokine secretion. In contrast to cells of the adaptive immune system, innate immune cells are believed to exhibit a comparable functional effector response each time the same pathogen is encountered. Here, using mice infected by the intracellular bacterium Listeria monocytogenes, we show that during a recall bacterial infection, the chemokine CCL3 secreted by memory CD8+ T cells drives drastic modifications of the functional properties of several populations of phagocytes. We found that inflammatory ly6C+ monocytes and neutrophils largely mediated memory CD8+ T cell bacteriocidal activity by producing increased levels of reactive oxygen species (ROS), augmenting the pH of their phagosomes and inducing antimicrobial autophagy. These events allowed an extremely rapid control of bacterial growth in vivo and accounted for protective immunity. Therefore, our results provide evidence that cytotoxic memory CD8+ T cells can license distinct antimicrobial effector mechanisms of innate cells to efficiently clear pathogens

The Cyst-Dividing Bacterium Ramlibacter tataouinensis TTB310 Genome Reveals a Well-Stocked Toolbox for Adaptation to a Desert Environment

Ramlibacter tataouinensis TTB310T (strain TTB310), a betaproteobacterium isolated from a semi-arid region of South Tunisia (Tataouine), is characterized by the presence of both spherical and rod-shaped cells in pure culture. Cell division of strain TTB310 occurs by the binary fission of spherical “cyst-like” cells (“cyst-cyst” division). The rod-shaped cells formed at the periphery of a colony (consisting mainly of cysts) are highly motile and colonize a new environment, where they form a new colony by reversion to cyst-like cells. This unique cell cycle of strain TTB310, with desiccation tolerant cyst-like cells capable of division and desiccation sensitive motile rods capable of dissemination, appears to be a novel adaptation for life in a hot and dry desert environment. In order to gain insights into strain TTB310's underlying genetic repertoire and possible mechanisms responsible for its unusual lifestyle, the genome of strain TTB310 was completely sequenced and subsequently annotated. The complete genome consists of a single circular chromosome of 4,070,194 bp with an average G+C content of 70.0%, the highest among the Betaproteobacteria sequenced to date, with total of 3,899 predicted coding sequences covering 92% of the genome. We found that strain TTB310 has developed a highly complex network of two-component systems, which may utilize responses to light and perhaps a rudimentary circadian hourglass to anticipate water availability at the dew time in the middle/end of the desert winter nights and thus direct the growth window to cyclic water availability times. Other interesting features of the strain TTB310 genome that appear to be important for desiccation tolerance, including intermediary metabolism compounds such as trehalose or polyhydroxyalkanoate, and signal transduction pathways, are presented and discussed

Advancing multi-vehicle deployments in oceanographic field experiments

Our research concerns the coordination and control of robotic vehicles for upper water-column oceanographic observations. In such an environment, operating multiple vehicles to observe dynamic oceanographic phenomena, such as ocean processes and marine life, from fronts to cetaceans, has required that we design, implement and operate software, methods and processes which can support opportunistic needs in real-world settings with substantial constraints. In this work, an approach for coordinated measurements using such platforms, which relate directly to task outcomes, is presented. We show the use and operational value of a new Artificial Intelligence based mixed-initiative system for handling multiple platforms along with the networked infrastructure support needed to conduct such operations in the open sea. We articulate the need and use of a range of middleware architectures, critical for such deployments and ground this in the context of a field experiment in open waters of the mid-Atlantic in the summer of 2015.Advancing multi-vehicle deployments in oceanographic field experimentsacceptedVersio

Contacts et acculturations en Méditerranée occidentale

La question des contacts entre les différents peuples qui bordent les rives de la Méditerranée nord occidentale est l’un des sujets phares de la recherche archéologique de ces trente dernières années. Que l’on parle d’époque archaïque et classique ou de Protohistoire et d’âge du Fer, les échanges et les processus d’acculturation de ces peuples qui entrèrent alors en contact les uns avec les autres : Grecs, Celtes, Phéniciens, Ibères, Ligures, Étrusques, ont retenu l’attention des chercheurs travaillant sur l’expansion grecque dans ces régions, sur les trafics commerciaux, sur les échanges culturels. L’œuvre de Michel Bats (Directeur de recherche honoraire du CNRS) traverse toutes ces thématiques : la présence des Phocéens et des Étrusques dans le bassin occidental de la Méditerranée, l’acculturation et les identités ethno-culturelles, les recherches sur la céramique et ses usages dans une perspective anthropologique, l’appropriation de l’écriture par les sociétés protohistoriques. Ses collègues et amis, en organisant ce colloque et en participant à ces actes, entendent lui témoigner leur amitié et leur dette intellectuelle. Ce volume réunit des articles des meilleurs spécialistes, actuels de la question - des chercheurs de toute la Méditerranée - autour des quatre grands thèmes que nous venons d’évoquer afin tout à la fois de dresser un bilan et de définir de nouvelles perspectives. Cet ouvrage présente donc aussi bien des synthèses - sur la présence grecque en Espagne, sur l’origine de l’écriture, sur les pratiques funéraires, sur les identités culturelles et ethniques - que des découvertes récentes concernant la thématique des contacts et de l’acculturation en Méditerranée nord occidentale : l’agglomération du Premier âge du Fer de La Cougourlude (Lattes, Hérault) fouillée durant l’été 2010 ; le sanctuaire hellénistique de Cumes et les fouilles récentes de Fratte en Italie ; les ateliers de potiers de Rosas en Espagne ; les dernières découvertes d’Olbia de Provence

A computational framework for complex disease stratification from multiple large-scale datasets.

BACKGROUND: Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states. METHODS: The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification. RESULTS: We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. CONCLUSIONS: This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine