Validation of the NEMO-ERSEM operational ecosystem model for the North West European Continental Shelf

This paper details updates to the Met Office's operational coupled hydrodynamic-ecosystem model from the 7 km Medium-Resolution Continental Shelf – POLCOMS-ERSEM (MRCS-PE) system (Siddorn et al., 2007) to the 7 km Atlantic Margin Model NEMO-ERSEM (AMM7-NE) system. We also provide a validation of the ecosystem component of the new operational system. Comparisons have been made between the model variables and available in situ, satellite and climatological data. The AMM7-NE system has also been benchmarked against the MRCS-PE system. The transition to the new AMM7-NE system was successful and it has been running operationally since March 2012 and has been providing products through MyOcean (<a href="http://www.myocean.eu.org" target="_blank">http://www.myocean.eu.org</a>) since that time. The results presented herein show the AMM7-NE system performs better than the MRCS-PE system with the most improvement in the model nutrient fields. The problem of nutrient accumulation in the MRCS-PE system appears to be solved in the new AMM7-NE system with nutrient fields improved throughout the domain as discussed in Sect. 4. Improvements in model chlorophyll are also seen but are more modest

An ECOOP web portal for visualising and comparing distributed coastal oceanography model and in situ data

As part of a large European coastal operational oceanography project (ECOOP), we have developed a web portal for the display and comparison of model and in situ marine data. The distributed model and in situ datasets are accessed via an Open Geospatial Consortium Web Map Service (WMS) and Web Feature Service (WFS) respectively. These services were developed independently and readily integrated for the purposes of the ECOOP project, illustrating the ease of interoperability resulting from adherence to international standards. The key feature of the portal is the ability to display co-plotted timeseries of the in situ and model data and the quantification of misfits between the two. By using standards-based web technology we allow the user to quickly and easily explore over twenty model data feeds and compare these with dozens of in situ data feeds without being concerned with the low level details of differing file formats or the physical location of the data. Scientific and operational benefits to this work include model validation, quality control of observations, data assimilation and decision support in near real time. In these areas it is essential to be able to bring different data streams together from often disparate locations

What are the prospects for seasonal prediction of the marine environment of the North-west European Shelf?

Sustainable management and utilisation of the North-west European Shelf (NWS) seas could benefit from reliable forecasts of the marine environment on monthly to seasonal timescales. Recent advances in global seasonal forecast systems and regional marine reanalyses for the NWS allow us to investigate the potential for seasonal forecasts of the state of the NWS. We identify three possible approaches to address this issue: (A) basing NWS seasonal forecasts directly on output from the Met Office's GloSea5 global seasonal forecast system; (B) developing empirical downscaling relationships between large-scale climate drivers predicted by GloSea5 and the state of the NWS; and (C) dynamically downscaling GloSea5 using a regional model. We show that the GloSea5 system can be inadequate for simulating the NWS directly (approach A). We explore empirical relationships between the winter North Atlantic Oscillation (NAO) and NWS variables estimated using a regional reanalysis (approach B). We find some statistically significant relationships and present a skillful prototype seasonal forecast for English Channel sea surface temperature. We find large-scale relationships between inter-annual variability in the boundary conditions and inter-annual variability modelled on the shelf, suggesting that dynamic downscaling may be possible (approach C). We also show that for some variables there are opposing mechanisms correlated with the NAO, for which dynamic downscaling may improve on the skill possible with empirical forecasts. We conclude that there is potential for the development of reliable seasonal forecasts for the NWS and consider the research priorities for their development

El Paleolítico Medio en el territorio valenciano y la variabilidad tecno-económica de la Cova del Bolomor

En el presente artículo se exponen las principales características de las industrias líticas del Paleolítico Medio en el territorio valenciano. Se hace especial hincapié en la variabilidad tecno-económica observada en la secuencia estratigráfica de la Cova del Bolomor. Con dicho análisis se pretende contribuir al establecimiento de los rasgos evolutivos de las industrias asociadas a los grupos de neandertales. En este sentido, el estudio pone de manifiesto que en estas sociedades se produjo, en los momentos finales, cierto progreso tecnológico, en un contexto arqueológico en el que es difícil precisar si hubo, o no, influencia externa o aculturación por parte de las poblaciones de cromañones en el territorio valenciano.En el present article s'exposen les principals característiques de les indústries lítiques del Paleolític Mitjà en el territori valencià. Es posa especial atenció a la variabilitat tecno-econòmica observada en la seqüència estratigràfica de la Cova del Bolomor. Amb aquesta anàlisi es pretén contribuir a l'establiment dels trets evolutius de les indústries associades als grups de neandertals. En aquest sentit, l'estudi posa de manifest que en aquestes societats es va produir, en els moments finals, un cert progrés tecnològic, en un context arqueològic en el qual és difícil precisar si va haver-hi, o no, influència externa o aculturació per part de les poblacions de cromanyons en el territori valencià.Dans l'article ci-dessous, s'exposent les principales caractéristiques des industries lithiques du Paléolithique Moyen dans le territoire valencien. On veut mettre en relief la variabilité techno-économique observée dans la séquence stratigraphique de la Cova del Bolomor. Avec cette analyse, on cherche à établir les traits évolutifs des industries associées aux groupes néandertaliens. Dans ce sens, l'étude met en relief que ces sociétés ont probablement connu, dans un dernier temps, un certain progrès technologique, dans un contexte archéologique où il est difficile de préciser s'il y a eu ou pas une influence externe ou une acculturation venue des populations cromagnones dans la région de Valence.In this paper main characteristics of the Middle Palaeolithic lithic industries from the territory of Valencia are presented. Particular attention is paid to the techno-economical variability of the archaeological record in Cova del Bolomor. This study aims to discuss the evolutionary features of Neanderthal industries; our analysis shows that there was some technological progress at the end of the Middle Palaeolithic, in an archaeological context in which it is uncertain whether or not there was external influence or acculturation from Cro-Magnon populations in the valencian territory

Patterns of phytoplankton size structure and productivity in contrasting open-ocean environments

A total of 94 vertical profiles of size-fractionated chlorophyll a concentration and primary production rate were obtained along a meridional transect from the United Kingdom to the Falkland Islands (50°N to 50°S) during 4 cruises carried out in April and October 1996 and in April and October 1997. This data set allowed us to characterize the patterns of phytoplankton size-structure and productivity in temperate, oligotrophic, upwelling and equatorial regions. On average, picophytoplankton (0.2 to 2 µm) accounted for 56 and 71% of the total integrated carbon (C) fixation and autotrophic biomass, respectively. Enhanced biomass and productivity contributions by nano- and microplankton took place in the temperate regions and in the upwelling area off Mauritania. Small (<2 µm in diameter) phytoplankton cells should not be regarded as a background, relatively invariant component of the microbial community, given that most of the latitudinal variability in total photoautotrophic biomass and production was driven by changes in the picophytoplankton. In temperate regions and in the upwelling area off Mauritania, small (<2 µm) and large (>2 µm) phytoplankton accounted for a proportion of total biomass that was similar to their shares of productivity. In the oligotrophic and equatorial regions, in contrast, large phytoplankton tended to account for a fraction of the total production that was significantly higher than their share of the biomass. We found that the equatorial upwelling causes an increase in phytoplankton biomass and productivity without altering the typical size structure found in less productive regions such as the subtropical gyres. In the oligotrophic ocean, significant changes in C fixation rates take place without accompanying variations in the magnitude of the phytoplankton standing stocks or the size structure of the microbial community

Cadmium, manganese, nickel and lead contents in surface sediments of the lower Ulla River and its estuary (northwest Spain)

The authors determined the total contents of cadmium, manganese, nickel and lead in 16 surface sediment samples along the last 7 km of the Ulla River and in its estuary. Prior to chemical analysis, the grain-size fractions below 500, 63 and 2 μm were separated. The metal concentrations were analysed in the fraction below 63 μm, and in selected samples from the clay fraction ( 2 μm). The soil samples were digested with a HF + HNO₃ + HCl mixture and the total concentrations of Cd, Mn, Ni and Pb were analysed with the AAS method. The highest contents of metals were found in the riverine sediments, near the town of Padrón, and in the estuary. The enrichment of metals in the sediments was mainly related to the proximity of the industrial sources, and to the fine particles transported and deposited in the sediments. The Ni and Mn contents found are considered very high, at some points reaching values of up to 357 mg kg⁻¹ and 2 110 mg kg⁻¹, respectively. Lead and Cd were mainly found within the range considered as natural background levels in the sediments of the Galician rias, with concentrations of 25-68 mg kg⁻¹ for Pb and 0.01-0.92 mg kg⁻¹ for Cd. The lower part of the Ulla River and its estuary present: l) moderate to high contamination levels of Mn and Ni; 2) moderate Pb pollution levels; and 3) no Cd contamination. The highest concentrations of metals were obtained in the river, near the wastewater discharges, and in the estuary, associated with fine particles.El contenido total de cadmio, manganeso, níquel y plomo se determinó en 16 muestras de sedimentos superficiales a lo largo de los últimos 7 km del río Ulla y en su estuario. Previamente a los análisis químicos, se realizó la separación granulométrica de los sedimentos en las fracciones inferiores a 500, 63 y 2 μm. La concentración de metales se determinó en la fracción inferior a 63 μm y, para algunas muestras, en la fracción arcilla ( 2 μm). La digestión del sedimento se realizó en una mezcla ácida de HF + HNO₃ + HCl y se analizó la concentración total de Cd, Mn, Ni y Pb por espectroscopia de absorción atómica. Los contenidos más altos en metales se encontraron en los sedimentos del río, en las inmediaciones de Padrón y en los del estuario. El enriquecimiento de los sedimentos en metales se ha relacionado con la proximidad a las zonas industriales y con el material fino transportado y depositado en los sedimentos. Se han encontrado contenidos muy altos de Ni y Mn con valores de 357 mg kg⁻¹ y 2 110 mg kg⁻¹, respectivamente. Las concentraciones de Cd y Pb son comparables a los valores establecidos como niveles naturales en los sedimentos de las rías gallegas: 25-68 mg kg⁻¹ para el Pb y 0.01-0.92 mg kg⁻¹ para el Cd. El sedimento de la parte baja del río Ulla y su estuario presentan niveles moderados-altos de contaminación para Mn y Ni, moderados para Pb y nulos para Cd. Las mayores concentraciones de estos metales en el sedimento fueron medidas asociadas con las fracciones finas ( 63 μm): cerca de Padrón, zona de influencia fluvial y, también, aunque con valores más bajos, en la desembocadura del Ulla, zona de influencia marina.Instituto Español de Oceanografí

Zoonotic Abbreviata caucasica in wild chimpanzees (Pan troglodytes verus) from Senegal

Abbreviata caucasica (syn. Physaloptera mordens) has been reported in human and various non-human primates including great apes. The identification of this nematode is seldom performed and relies on egg characterization at the coproscopy, in the absence of any molecular tool. Following the recovery of two adult females of A. caucasica from the feces of wild Senegalese chimpanzees, morphometric characteristics were reported and new data on the width of the esophagus (0.268-0.287 mm) and on the cuticle structure (0.70-0.122 mm) were provided. The molecular characterization of a set of mitochondrial (cox1, 16S rRNA, 12S rRNA) and nuclear (18S rRNA and ITS2) partial genes was performed. Our phylogenetic analysis indicates for the first time that A. caucasica is monophyletic with Physaloptera species. A novel molecular tool was developed for the routine diagnosis of A. caucasica and the surveillance of Nematoda infestations. An A. caucasica-specific qPCR targeting the 12S gene was assessed. The assay was able to detect up to 1.13 × 10−3 eggs/g of fecal matter irrespective of its consistency, with an efficiency of 101.8% and a perfect adjustment (R2 = 0.99). The infection rate by A. caucasica in the chimpanzee fecal samples was 52.08%. Only 6.19% of the environmental samples were positive for nematode DNA and any for A. caucasica. Our findings indicate the need for further studies to clarify the epidemiology, circulation, life cycle, and possible pathological effects of this infestation using the molecular tool herein developed

Zoonotic abbreviata caucasica in wild chimpanzees (Pan troglodytes verus) from Senegal

Abbreviata caucasica (syn. Physaloptera mordens) has been reported in human and various non-human primates including great apes. The identification of this nematode is seldom performed and relies on egg characterization at the coproscopy, in the absence of any molecular tool. Following the recovery of two adult females of A. caucasica from the feces of wild Senegalese chimpanzees, morphometric characteristics were reported and new data on the width of the esophagus (0.268– 0.287 mm) and on the cuticle structure (0.70–0.122 mm) were provided. The molecular characterization of a set of mitochondrial (cox1, 16S rRNA, 12S rRNA) and nuclear (18S rRNA and ITS2) partial genes was performed. Our phylogenetic analysis indicates for the first time that A. caucasica is monophyletic with Physaloptera species. A novel molecular tool was developed for the routine diagnosis of A. caucasica and the surveillance of Nematoda infestations. An A. caucasica-specific qPCR targeting the 12S gene was assessed. The assay was able to detect up to 1.13 × 10−3 eggs/g of fecal matter irrespective of its consistency, with an efficiency of 101.8% and a perfect adjustment (R2 = 0.99). The infection rate by A. caucasica in the chimpanzee fecal samples was 52.08%. Only 6.19% of the environmental samples were positive for nematode DNA and any for A. caucasica. Our findings indicate the need for further studies to clarify the epidemiology, circulation, life cycle, and possible pathological effects of this infestation using the molecular tool herein developed

Analysis of the oscillations induced by a supersonic jet applied to produce nanofibers

Financiado para publicación en acceso aberto: Universidade de Vigo/CISUGHigh-performance fibers are key components for enhancing the mechanical properties of composite materials. The development of high strength nanofibers augurs the production of new nano-composites with outstanding features. However, the robust production of continuous glass nanofibers that can be feasible processed for efficiently manufacturing nanocomposites is still challenging. Recently, Cofiblas (Continuous Fiberizing by Laser melting and Supersonic dragging) was demonstrated as a technique capable of producing continuous glass nanofibers with unlimited length. Cofiblas process has some similarities with the widely known melt blowing technique for the production of polymeric fibers. In both techniques, the design of the gas nozzle is key to ensure the feasibility of the process since the turbulences of the gas jet may induce strong whipping of the filament. This paper gives novel experimental evidences on the correlation of the supersonic gas jet instabilities with the oscillation of the filament in the melt-blowing and Cofiblas processes, relating these oscillations with the presence of shock waves and unsteadiness in the flow, and gives valuable insight into the use of supersonic jets in the melt blowing process as an effective approach for the formation of nanofibers. A thin 3D-axisymmetric model in OpenFOAM® was put to test by comparing the performance of different solvers which were validated by flow visualization of the exit jet using digital holography (DH). In order to perform a realistic and thorough validation, we simulated the optical measurements of the flow from the CFD simulations of the mass density by Abel transform and numerical differentiation. The application of digital holography as the flow visualization technique makes possible both a precise validation of the density maps obtained from the Abel transformation of the 2D-alike results, and the analysis of the shockwave pattern in the air jet. Conversely, the numerical reconstruction of time-averaged holograms is employed to detect unsteadiness in the flow and to analyze the fiber oscillation, which is essential to assess the stability of the process. Lastly, the analysis and comparison of the vibration of the filament using the basic design and the optimized nozzle demonstrates a clear influence of the shock waves and flow unsteadiness in the stability of the filament.Agencia Estatal de Investigación | Ref. PGC2018-094900-B-I00Xunta de Galicia | Ref. ED431C 2019/23Ministerio de Universidades | Ref. FPU20/0311

Standardized Hepatitis B Virus RNA Quantification in Untreated and Treated Chronic Patients: a Promising Marker of Infection Follow-Up.

The measurement and interpretation of HBV DNA and RNA levels in HBV infected patients treated with antiviral therapy supports the objective of HBV disease management. Here, we quantified circulating HBV RNA through a standardized and sensitive assay in follow-up samples from both naive and treated patients as a marker of infection evolution. HBV DNA (HBV DNA for use in Cobas 6800/8800 Automated Roche Molecular Systems), RNA (Roche HBV RNA Investigational Assay for use in the Cobas 6800/8800; Roche), HBeAg and HBsAg (Elycsys HBsAg chemiluminescence immunoassay by Cobas 8000; Roche), and core-related antigen (Lumipulse G chemiluminescence assay; Fujirebio) levels were measured in cohorts of untreated or nucleos(t)ide treated, HBV-infected subjects in an outpatient hospital setting. HBV DNA levels in untreated people were 3.6 log10 higher than corresponding RNA levels and were stable over 5 years of observation. While only five of 52 treated patients had DNA levels below the lower limit of quantification (10 IU/mL) at the end of follow-up, 13 had HBV RNA levels persistently above this limit, including eight with undetectable DNA. In samples with undetectable core-related antigen we observed a median HBsAg titer 2.7-fold higher than in samples with undetectable RNA (adjusted P = 0.012). Detectable HBV RNA with undetectable HBV DNA was a negative predictor of HBsAg decrease to a level ≤100 IU/mL (P = 0.03). In naive patients the difference between HBV DNA and RNA was higher than previously reported. HBV RNA rapidly decreased during treatment. However, in some cases, it was detectable even after years of effective therapy, being a negative predictor of HBsAg decrease. The investigational RNA assay for use on the Cobas 6800/8800 instruments is a sensitive and standardized method that could be applied in general management of HBV infection. IMPORTANCE This study focused on the quantification of circulating HBV RNA by using a standardized and sensitive assay. Thanks to this system we observed a higher difference between circulating HBV DNA and RNA than previously reported. In treated patients, HBV RNA decreased together with DNA, although some patients presented detectable levels even after years of successful antiviral treatment, suggesting a persistent viral transcription. Of note, the detection of viral RNA when HBV DNA is undetectable was a negative predictor of HBsAg decrease to a level ≤100 IU/mL. This assay could be extremely helpful in HBV patients management to study viral transcription and to identify those treated patients that may achieve sustained viral suppression