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

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

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

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

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

Hepatitis B Virus Variants with Multiple Insertions and/or Deletions in the X Open Reading Frame 3 ' End: Common Members of Viral Quasispecies in Chronic Hepatitis B Patients

Hepatitis B virus; Insertions; Next-generation sequencingVirus de l'hepatitis B; Insercions; Seqüenciació de nova generacióVirus de la hepatitis B; Inserciones; Secuenciación de próxima generaciónDeletions in the 3′ end region of the hepatitis B virus (HBV) X open reading frame (HBX) may affect the core promoter (Cp) and have been frequently associated with hepatocellular carcinoma (HCC). The aim of this study was to investigate the presence of variants with deletions and/or insertions (Indels) in this region in the quasispecies of 50 chronic hepatitis B (CHB) patients without HCC. We identified 103 different Indels in 47 (94%) patients, in a median of 3.4% of their reads (IQR, 1.3–8.4%), and 25% (IQR, 13.1–40.7%) of unique sequences identified in each quasispecies (haplotypes). Of those Indels, 101 (98.1%) caused 44 different altered stop codons, the most commonly observed were at positions 128, 129, 135, and 362 (putative position). Moreover, 39 (37.9%) Indels altered the TATA-like box (TA) sequences of Cp; the most commonly observed caused TA2 + TA3 fusion, creating a new putative canonical TATA box. Four (8%) patients developed negative clinical outcomes after a median follow-up of 9.4 (8.7–12) years. In conclusion, we observed variants with Indels in the HBX 3′ end in the vast majority of our CHB patients, some of them encoding alternative versions of HBx with potential functional roles, and/or alterations in the regulation of transcription.This research was funded by Instituto de Salud Carlos III and co-financed by the European Regional Development Fund (ERDF), grant number PI18/01436; PI19/00301; and by the Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297. The APC was funded by the grant PI18/01436

Inhaled Methoxyflurane Provides Greater Analgesia and Faster Onset of Action Versus Standard Analgesia in Patients With Trauma Pain: InMEDIATE: A Randomized Controlled Trial in Emergency Departments

STUDY OBJECTIVE: The objective of the InMEDIATE study was to evaluate the change in intensity of traumatic pain over the first 20 min in adult patients treated with methoxyflurane versus standard analgesic treatment in Spain. This the first randomized, active-controlled, multicenter trial of methoxyflurane in the emergency setting in Europe. METHODS: This was a randomized, controlled study that enrolled adult patients with acute moderate to severe (score >/=4 on the 11-point Numeric Rating Scale) trauma-associated pain in 14 Spanish emergency departments. Patients were randomized 1:1 to methoxyflurane (up to 2x3 mL) or standard analgesic treatment. Coprimary endpoints were the change from baseline in Numeric Rating Scale pain intensity score during the first 20 minutes of treatment and time to first pain relief. RESULTS: Three hundred five patients were randomized (methoxyflurane 156; standard analgesic treatment 149). Most patients in the standard analgesic treatment group (70%) received intravenous first-step analgesics and 9.4% of patients were treated with opioids. Mean decrease from baseline in Numeric Rating Scale pain intensity score was greater for methoxyflurane than standard analgesic treatment at all points, with a significant treatment difference overall up to 20 minutes (repeated-measures model 2.47 versus 1.39; treatment difference 1.00; 95% confidence interval 0.84 to 1.32). Median time to first pain relief was significantly shorter for methoxyflurane than standard analgesic treatment (3 versus 10 minutes). Methoxyflurane achieved better patient and clinician ratings for pain control and comfort of treatment than standard analgesic treatment and exceeded patient and clinician expectations of treatment in, respectively, 77% and 72% of cases compared with 38% and 19% for standard analgesic treatment. CONCLUSION: These results support consideration of methoxyflurane as a nonnarcotic, easy-to-administer, rapid-acting, first-line alternative to currently available analgesic treatments for trauma pain

Effectiveness and safety of sofosbuvir‐based regimens plus an NS5A inhibitor for patients with HCV genotype 3 infection and cirrhosis: results of a multicenter real‐life cohort

[Abstract] Patients with HCV genotype 3 (GT3) infection and cirrhosis are currently the most difficult to cure. We report our experience with sofosbuvir+daclatasvir (SOF+DCV) or sofosbuvir/ledipasvir (SOF/LDV), with or without ribavirin (RBV) in clinical practice in this population. This was a multicenter observational study including cirrhotic patients infected by HCV GT3, treated with sofosbuvir plus an NS5A inhibitor (May 2014‐October 2015). In total, 208 patients were included: 98 (47%) treatment‐experienced, 42 (20%) decompensated and 55 (27%) MELD score >10. In 131 (63%), treatment was SOF+DCV and in 77 (37%), SOF/LDV. Overall, 86% received RBV. RBV addition and extension to 24 weeks was higher in the SOF/LDV group (95% vs 80%, P=.002 and 83% vs 72%, P=.044, respectively). A higher percentage of decompensated patients were treated with DCV than LDV (25% vs 12%, P=.013). Overall, SVR12 was 93.8% (195/208): 94% with SOF+DCV and 93.5% with SOF/LDV. SVR12 was achieved in 90.5% of decompensated patients. Eleven treatment failures: 10 relapses and one breakthrough. RBV addition did not improve SVR (RR: 1.08; P=.919). The single factor associated with failure to achieve SVR was platelet count <75×10E9/mL (RR: 3.50, P=.019). In patients with MELD <10, type of NS5A inhibitor did not impact on SVR12 (94% vs 97%; adjusted RR: 0.49). Thirteen patients (6.3%) had serious adverse events, including three deaths (1.4%) and one therapy discontinuation (0.5%), higher in decompensated patients (16.7% vs 3.6%, P<.006). In patients with GT3 infection and cirrhosis, SVR12 rates were high with both SOF+DCV and SOF/LDV, with few serious adverse events

Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.Introduction Results - Genetic substructure in the Iberian CA - Genetic turnover in the southern Iberian BA and the rise of El Argar - Mediterranean and central European ancestries shaped the genetic profile of southeastern BA groups in Iberia - A late Argar genetic outlier makes links to North Africa and the central Mediterranean - Insights into phenotypic variation, demography, and social correlates of CA and EBA El Argar societies Discussion Material and method