Coupling hydrodynamic and wave models: first step and sensitivity experiments in the Mediterranean Sea

This work describes the first step towards a fully coupled modelling system composed of an ocean circulation and a wind wave model. Sensitivity experiments are presented for the Mediterranean Sea where the hydrodynamic model NEMO is coupled with the third-generation wave model WaveWatchIII (WW3). Both models are implemented at 1/16° horizontal resolution and are forced by ECMWF 1/4° horizontal resolution atmospheric fields. The models are two-way coupled at hourly intervals exchanging the following fields: sea surface currents and temperature are transferred from NEMO to WW3 by modifying the mean momentum transfer of waves and the wind speed stability parameter, respectively. The neutral drag coefficient computed by WW3 is then passed to NEMO, which computes the surface stress. Five-year (2009–2013) numerical experiments were carried out in both uncoupled and coupled mode. In order to validate the modelling system, numerical results were compared with coastal and drifting buoys and remote sensing data. The results show that the coupling of currents with waves improves the representation of the wave spectrum. However, the wave-induced drag coefficient shows only minor improvements in NEMO circulation fields, such as temperature, salinity, and currents

A box model to represent estuarine dynamics in mesoscale resolution ocean models

Representing the net freshwater flux at river mouths is challenging for global and regional scale ocean modelling. Although rivers are well known to affect both the coastal and basin-wide circulation and dynamics, coarse resolution ocean models cannot resolve the estuarine dynamics and are usually forced at river outlets in a simplistic way, with climatological runoff and zero or constant salinity values. The aim of this study is to provide a more realistic representation of the estuarine water inputs to a coarse but eddy-resolving regional model. First, the river volume transport and salinity values at the outlets are modelled with three different Estuary Box Models (EBMs) for stratified estuaries: the Knudsen relations model, a published EBM, called UCONN-NCAR EBM, which parameterizes the tidal inflow and mixing inside the estuary, and a new model, called CMCC-EBM. The CMCC EBM has been conceived to represent the estuarine processes coupled to a mesoscale resolving hydrodynamic model that resolves the entering flow field at the estuary mouth and it offers a new representation of the tidal inflow and a new salinity tidal mixing parameterization via horizontal diffusive processes. The Ofanto and Po rivers flowing into the Adriatic Sea (northern part of the central Mediterranean Sea) are selected as case studies. The coupling of the eddy resolving ocean model to the CMCC EBM is found to outperform the one with the UCONN-NCAR EBM in the region of freshwater influence on the shelf area

Short- and Long-Term, 11–22 Years, Results after Laparoscopic Nissen Fundoplication in Obese versus Nonobese Patients

Background. Some studies suggest that obesity is associated with a poor outcome after Laparoscopic Nissen Fundoplication (LNF), whereas others have not replicated these findings. The effect of body mass index (BMI) on the short- and long-term results of LNF is investigated. Methods. Inclusion criteria were only patients who undergone a LNF with at least 11-year follow-up data available, patients with preoperative weight and height data available for calculation of BMI (Kg/m2), and patients with a BMI up to a maximum of 34.9. Results. 201 patients met the inclusion criteria: 43 (21.4%) had a normal BMI, 89 (44.2%) were overweight, and 69 (34.4%) were obese. The operation was significantly longer in obese patients; the use of drains and graft was less in the normal BMI group (p<0.0001). The hospital stay, conversion (6,4%), and intraoperative and early postoperative complications were not influenced by BMI. Conclusions. BMI does not influence short-term outcomes following LNF, but long-term control of reflux in obese patients is worse than in normal weight subjects

Occurrence of wine yeasts on grapes subjected to different pesticide treatments

As a contribution to the study and preservation of indigenous wine yeast populations, we initiated a programme of isolation and characterization of yeast strains from grapes of the Italian region of Marche. During the 1996 vintage, grape samples were collected from three groups of vineyards differing in the pesticide treatments given. Of the 279 yeasts isolated, thirty-nine were assigned to the species Saccharomyces cerevisiae. The majority of the isolates and all thirty-nine S. cerevisiae came from vineyards which had not been treated with systemic pesticides, indicating that these pesticides may exert a negative effect on the biodiversity of the grape microflora, and in particular on the occurrence of S. cerevisiae on grapes. The thirty-nine S. cerevisiae isolated were subjected to microfermentation mals, in which ten of them showed promising fermentative capabilities

Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols

Background: Notwithstanding the efforts of direct-acting antivirals (DAAs) for the treatment of chronically infected hepatitis C virus (HCV) patients, concerns exist regarding the emergence of resistance-associated substitutions (RAS) related to therapy failure. Sanger sequencing is still the reference technique used for the detection of RAS and it detects viral variants present up to 15%, meaning that minority variants are undetectable, using this technique. To date, many studies are focused on the analysis of the impact of HCV low variants using next-generation sequencing (NGS) techniques, but the importance of these minority variants is still debated, and importantly, a common data analysis method is still not defined. Methods: Serum samples from four patients failing DAAs therapy were collected at baseline and failure, and amplification of NS3, NS5A and NS5B genes was performed on each sample. The genes amplified were sequenced using Sanger and NGS Illumina sequencing and the data generated were analyzed with different approaches. Three different NGS data analysis methods, two homemade in silico pipeline and one commercially available certified user-friendly software, were used to detect low-level variants. Results: The NGS approach allowed to infer also very-low level virus variants. Moreover, data processing allowed to generate high accuracy data which results in reduction in the error rates for each single sequence polymorphism. The results improved the detection of low-level viral variants in the HCV quasispecies of the analyzed patients, and in one patient a low-level RAS related to treatment failure was identified. Importantly, the results obtained from only two out of the three data analysis strategies were in complete agreement in terms of both detection and frequency of RAS. Conclusions: These results highlight the need to find a robust NGS data analysis method to standardize NGS results for a better comprehension of the clinical role of low-level HCV variants. Based on the extreme importance of data analysis approaches for wet-data interpretation, a detailed description of the used pipelines and further standardization of the in silico analysis could allow increasing diagnostic laboratory networking to unleash true potentials of NGS

NMR as evaluation strategy for cellular uptake of nanoparticles

Advanced nanostructured materials, such as gold nanoparticles, magnetic nanoparticles, and multifunctional materials, are nowadays used in many state-of-the-art biomedical application. However, although the engineering in this field is very advanced, there remain some fundamental problems involving the interaction mechanisms between nanostructures and cells or tissues. Here we show the potential of 1H NMR in the investigation of the uptake of two different kinds of nanostructures, that is, maghemite and gold nanoparticles, and of a chemotherapy drug (Temozolomide) in glioblastoma tumor cells. The proposed experimental protocol provides a new way to investigate the general problem of cellular uptake for a variety of biocompatible nanostructures and drugs. © 2014 American Chemical Society

The Mediterranean analysis and forecasting physical system for the Copernicus Marine Service: description and skill assessment

The Mediterranean Analysis and Forecasting System is a numerical ocean prediction system that operationally produces analyses and 10 days forecasts of the main physical parameters for the entire Mediterranean Sea and its Atlantic Ocean adjacent areas. The system is composed by the hydrodynamic model NEMO (Nucleus for European Modelling of the Ocean) 2-way coupled with the third-generation wave model WW3 (WaveWatchIII) and forced by ECMWF (European Centre for Medium-range Weather Forecasts) atmospheric fields. The forecast initial conditions are produced by a 3D variational data assimilation system which considers a daily assimilation cycle of Sea Level Anomaly, vertical profiles of Temperature and Salinity from ARGO and ship CTDs and heat flux corrections with satellite SST. The system has been recently upgraded in the framework of the Copernicus Marine Environment Monitoring Service (CMEMS) by increasing the grid resolution from 1/16 to 1/24 degree in the horizontal, thus becoming fully mesoscale resolving and from 72 to 141 vertical levels, by increasing the number of fresh water river inputs and by updating the data assimilation scheme. The model has a non-linear explicit free surface and the forecast is forced by surface pressure, interactive heat, momentum and water fluxes at the air-sea interface. The focus of this work is to present the latest modeling system upgrades and the related improvements achieved by showing the model skill assessment including comparison with independent (insitu coastal moorings) and quasi-independent (insitu vertical profiles and satellite) datasets.PublishedHalifax, Nova Scotia, Canada4A. Oceanografia e clim

Last improvements in the data assimilation scheme for the Mediterranean Analysis and Forecast system of the Copernicus Marine Service

The Mediterranean Forecasting System (MFS) is a numerical ocean prediction system that produces analyses, reanalyses and short term forecasts for the entire Mediterranean Sea and its Atlantic Ocean adjacent areas. The system is now part of the Copernicus Marine Environment Monitoring Service (CMEMS) providing regular and systematic information about the physical state and dynamics of the Mediterranean Sea through the Med-MFC (Mediterranean Monitoring and Forecasting Center). MFS has been implemented in the Mediterranean Sea with 1/16o horizontal resolution and 72 vertical levels and is composed by the hydrodynamic model NEMO (Nucleus for European Modelling of the Ocean) 2-way online coupled with the third generation wave model WaveWatchIII (Clementi et al., 2017a) and forced by ECMWF atmospheric fields at 1/8° horizontal resolution. The model solutions are corrected by the data assimilation system (3D variational scheme, Dobricic and Pinardi, 2008) with a daily assimilation cycle of along track satellite Sea Level Anomaly (SLA) and vertical profiles of Temperature and Salinity from ARGO and gliders. In this study we present a new estimate of the background error covariance matrix with vertical Empirical Orthogonal Functions (EOFs) that are defined at each grid point of the model domain in order to better account for the error covariance between temperature and salinity in the shelf and open ocean areas. Moreover the Observational error covariance matrix is z-dependent and varies in each month. This new dataset has been tested and validated for more than 2 years against a background error correlation matrix varying only seasonally and in thirteen sub-regions of the Mediterranean Sea (Dobricic et al. 2005).PublishedBergen, Norway3SR. AMBIENTE - Servizi e ricerca per la Societ

Last improvements in the data assimilation scheme for the Mediterranean Analysis and Forecast system of the Copernicus Marine Service

The Mediterranean Forecasting System (MFS) is a numerical ocean prediction system that produces analyses, reanalyses and short term forecasts for the entire Mediterranean Sea and its Atlantic Ocean adjacent areas. The system is now part of the Copernicus Marine Environment Monitoring Service (CMEMS) providing regular and systematic information about the physical state and dynamics of the Mediterranean Sea through the Med-MFC (Mediterranean Monitoring and Forecasting Center). MFS has been implemented in the Mediterranean Sea with 1/16o horizontal resolution and 72 vertical levels and is composed by the hydrodynamic model NEMO (Nucleus for European Modelling of the Ocean) 2-way online coupled with the third generation wave model WW3 (WaveWatchIII) and forced by ECMWF atmospheric fields at 1/8o horizontal resolution. The model solutions are corrected by the data assimilation system (3D variational-3Dvar scheme adapted to the oceanic assimilation problem, Dobricic and Pinardi, 2008) with a daily assimilation cycle of satellite Sea Level Anomaly (SLA) and vertical profiles of Temperature and Salinity. In this study we present a new estimate the of the background error covariance matrix with vertical Empirical Orthogonal Functions (EOFs) that are defined at each grid point of the model domain in order to better account for the error covariance between temperature and salinity in the shelf and open ocean areas. Moreover the Error covariance matrix is z-dependent and varies in each month. This new dataset has been tested and validated for more than 2 years against a background error correlation matrix varying only seasonally and in thirteen sub-regions of the Mediterranean Sea. Latest developments include the implementation of an upgraded 3Dvar (Storto et al. 2012) for a high-resolution model, 1/24o in the horizontal and 141 vertical levelsPublishedBergen, Norway3SR. AMBIENTE - Servizi e ricerca per la Societ