Multi-GPU aggregation-based AMG preconditioner for iterative linear solvers

We present and release in open source format a sparse linear solver which efficiently exploits heterogeneous parallel computers. The solver can be easily integrated into scientific applications that need to solve large and sparse linear systems on modern parallel computers made of hybrid nodes hosting NVIDIA Graphics Processing Unit (GPU) accelerators. The work extends our previous efforts in the exploitation of a single GPU accelerator and proposes an implementation, based on the hybrid MPI-CUDA software environment, of a Krylov-type linear solver relying on an efficient Algebraic MultiGrid (AMG) preconditioner already available in the BootCMatchG library. Our design for the hybrid implementation has been driven by the best practices for minimizing data communication overhead when multiple GPUs are employed, yet preserving the efficiency of the single GPU kernels. Strong and weak scalability results on well-known benchmark test cases of the new version of the library are discussed. Comparisons with the Nvidia AmgX solution show an improvement of up to 2.0x in the solve phase

The Varied Role of Efflux Pumps of the MFS Family in the Interplay of Bacteria with Animal and Plant Cells

Efflux pumps represent an important and large group of transporter proteins found in all organisms. The importance of efflux pumps resides in their ability to extrude a wide range of antibiotics, resulting in the emergence of multidrug resistance in many bacteria. Besides antibiotics, multidrug efflux pumps can also extrude a large variety of compounds: Bacterial metabolites, plant-produced compounds, quorum-sensing molecules, and virulence factors. This versatility makes efflux pumps relevant players in interactions not only with other bacteria, but also with plant or animal cells. The multidrug efflux pumps belonging to the major facilitator superfamily (MFS) are widely distributed in microbial genomes and exhibit a large spectrum of substrate specificities. Multidrug MFS efflux pumps are present either as single-component transporters or as tripartite complexes. In this review, we will summarize how the multidrug MFS efflux pumps contribute to the interplay between bacteria and targeted host cells, with emphasis on their role in bacterial virulence, in the colonization of plant and animal host cells and in biofilm formation. We will also address the complexity of these interactions in the light of the underlying regulatory networks required for the effective activation of efflux pump genes

Variabilità spaziale di una Tanato-Malacocenosi dell’area marina protetta di Torre Guaceto (Adriatico sud-occidentale)

ItI campioni di sedimento raccolti da tre stazioni di una spiaggia dell’Area Marina Protetta di Torre Guaceto contenevano un totale di 7292 conchiglie appartenenti a 114 specie (86 Gastropoda, 27 Bivalvia ed 1 Scafopoda). Le specie più abbondanti erano i Gastropoda Tricolia pullus, Alvania cimex, Bittium latreillii ed i Bivalvia Striarca lactea e Glans trapezia. Sono state riscontrate differenze statisticamente significative fra i sedimenti delle tre stazioni: lungo il gradiente Est-Ovest diminuisce il numero delle specie e la densità delle conchiglie, mentre aumentano le loro dimensione medie. La deposizione differenziale di conchiglie lungo la spiaggia è ascrivibile alla forma della baia, unitamente ai movimenti prevalenti delle acque.EnThe shell assemblage of Mollusca on a beach of the Torre Guaceto Marine Protected Area was examined in three different sites to detect possible differences in the shell composition in terms of species, size, and abundance. Samples collected from the three stations (600 cc of sediment per station) contained a total of 7292 shells belonging to 114 species (86 Gastropoda, 27 Bivalvia and 1 Scafopoda). The most abundant species were the Gastropoda Tricolia pullus, Alvania cimex, Bittium latreillii and the Bivalvia Striarca lactea and Glans trapezia. Statistically significant differences were found between the three station samples: the density of shells and the number of species decrease from East to West, whereas the mean shell size increases along the same direction. The sediment grain size increases from East to West too. Such differences are possibly due to the shape of the bay sheltering the beach and the prevalent water movements. Studies of Mollusca shell assemblages are deemed useful to obtain information on neighbouring living biocoenoses; however this note shows that the fidelity of shell assemblages may fluctuate according to several factors, including the position of the beach

Coupling Depth-Averaged and 3D numerical models to study debris flow: Saint-Vincent event

Debris flows are extremely rapid and unpredictable phenomena whose rheology is poorly understood. Moreover, human settlements are often located in areas prone to debris flows. The combination of these features makes debris flows hazardous phenomena. Barriers are usually installed in debris flow paths to mitigate risk. However, their design is still based on empirical methods. In order to base the design of barriers on a more reliable approach, the understanding of debris flows must be improved. Continuum numerical models have proved to be a helpful tool for studying debris flows. In particular, numerical models can predict the speed and the flow depth in debris flows paths, and roughly estimate the forces and the pressure acting on a mitigation structure. Currently, two main groups of continuum numerical models are available to study debris flows (i) depth-averaged (DA) models and (ii) three-dimensional (3D) models. Although DA models can study a real-scale event, they may over-simplify the flow-structure interaction. On the other hand, 3D models can be very reliable for studying flow-structure interaction but studying a whole phenomenon (from triggering to deposition) would require enormous computational resources. This work aims to show how the coupling of a DA and a 3D model allows an effective and performing analysis of a debris flow dynamics. The study is focused on the 2014 Saint-Vincent event (Aosta Valley, Italy)

Fatty Acids Abolish Shigella Virulence by Inhibiting Its Master Regulator, VirF

The pathogenicity of Shigella, the intracellular pathogen responsible for human bacillary dysentery, depends on a coordinated and tightly regulated expression of its virulence determinants. This is the result of a cascade organization of its positive regulators, with VirF, a transcriptional activator belonging to the AraC-XylS family, in a pivotal position. VirF itself is submitted to several well-known regulations at the transcriptional level. In this work, we present evidence for a novel posttranslational regulatory mechanism of VirF mediated by the inhibitory interaction with specific fatty acids. By homology modeling and molecular docking analyses, we identify a jelly roll motif in the structure of ViF capable of interacting with medium-chain saturated and long-chain unsaturated fatty acids. In vitro and in vivo assays show that capric, lauric, myristoleic, palmitoleic, and sapienic acids interact effectively with the VirF protein, abolishing its transcription-promoting activity. This silences the virulence system of Shigella, leading to a drastic reduction in its ability to invade epithelial cells and proliferate in their cytoplasm. IMPORTANCE In the absence of a valid vaccine, the main therapeutic approach currently used to treat shigellosis is based on the use of antibiotics. The emergence of antibiotic resistance jeopardizes the future effectiveness of this approach. The importance of the present work resides both in the identification of a new level of posttranslational regulation of the Shigella virulence system and in the characterization of a mechanism offering new opportunities for the design of antivirulence compounds, which may change the treatment paradigm of Shigella infections by limiting the emergence of antibiotic-resistant bacteria

Debris flow: Simulating the mitigation properties of vegetation

Natural vegetation impacted by debris flows can act as an energy dissipator. This braking effect is similar to the one exerted by baffle arrays. However, this effect, and its potential for hazard mitigation, has been studied only marginally. In this work, we apply a depth-averaged model to reproduce scaled laboratory experiments of flow-forest interaction

Focused Inversion of Gravimetric and Magnetotelluric Data for Geothermal Investigations

Focused inversion techniques may be applied to geophysical data inversion in order to image complex structures in the subsoil. These algorithms may image complex \u201cblocky\u201d structures giving useful information in geothermal exploration that may be smoothed out by standard inversion algorithms that use stabilizer that penalize sharp transitions. We have tested the modified total variation and the maximum gradient support stabilizers in the inversion of synthetic and field magnetotelluric and gravimetric data. The gravimetric data from the Luhoi geothermal prospect have been used to map the sharp density transition between the sandstone and the overlying claystone layers. The resulting horst structure imaged in 2D and 3D models by the maximum gradient support stabilizer solution allow to trace the main fault system that drives the up-flow of hydrothermal waters. The 1D magnetotelluric \u201cblocky\u201d models with lateral constrain (pseudo-3D) image the lithological contact between the claystone and sandstone far from the horst area and reveal resistivity variations in the claystone layer associated with sand lenses. In the horst area, resistivity models image hydrothermal alteration affecting the sandstone layer

Adipokines as Possible New Predictors of Cardiovascular Diseases: A Case Control Study

Background and Aims. The secretion of several adipocytokines, such as adiponectin, retinol-binding protein 4 (RBP4), adipocyte fatty acid binding protein (aFABP), and visfatin, is altered in subjects with abdominal adiposity; these endocrine alterations could contribute to increased cardiovascular risk. The aim of the study was to assess the relationship among adiponectin, RBP4, aFABP, and visfatin, and incident cardiovascular disease. Methods and Results. A case-control study, nested within a prospective cohort, on 2945 subjects enrolled for a diabetes screening program was performed. We studied 18 patients with incident fatal or nonfatal IHD (Ischemic Heart Disease) or CVD (Cerebrovascular Disease), compared with 18 matched control subjects. Circulating adiponectin levels were significantly lower in cases of IHD with respect to controls. Circulating RBP4 levels were significantly increased in CVD and decreased in IHD with respect to controls. Circulating aFABP4 levels were significantly increased in CVD, while no difference was associated with IHD. Circulating visfatin levels were significantly lower in cases of both CVD and IHD with respect to controls, while no difference was associated with CVD. Conclusions. The present study confirms that low adiponectin is associated with increased incidents of IHD, but not CVD, and suggests, for the first time, a major effect of visfatin, aFABP, and RBP4 in the development of cardiovascular disease