Detailed TELEMAC modelling to evaluate the effectiveness of sediment recycling

Hydrodynamic

Validation of a TELEMAC-3D model of a seamount

Water Qualit

Detailed modelling to evaluate the effectiveness of sediment recycling on coastal habitat

In many parts of the world, ports and harbours lie adjacent to ecologically important areas of coastal habitat. In such areas port authorities, coastal managers and regulators are required to negotiate the tension between the demands of making ports ever more efficient, with wider and deeper approaches to accommodate vessels of deeper draft and larger handling areas, and the preservation of coastal habitats which are vitally important for bird and fish populations and which help protect the coast from flooding and erosion. The deepening of approach channels and berths usually results in an increased rate of sedimentation and maintenance dredging. There is an increasing recognition that such dredged sediment is a resource which should be utilised beneficially for human development activities and/or enhancement of ecological habitats. One form of beneficial use of dredged material, is termed “sediment recycling” or “strategic placement”. This form of beneficial use consists of the placement of cohesive sediment into the water column or onto the bed in such a way so that currents and waves then transport the released sediment onto the desired habitats. Sediment recycling is less widely practiced because the changes in bed level resulting from placement are generally of the order of a few centimetres/year or less and it is difficult to demonstrate whether such recycling is successful. This paper describes a methodology for the assessment of the effectiveness sediment recycling, implementing the methodology on a case study of a large-scale sediment recycling scheme in the Stour/Orwell Estuary system in the United Kingdom, designed to offset the identified adverse effects of an approach channel deepening on the estuary system. The study represents a major contribution to the consideration of non-direct beneficial use of cohesive sediment. For the first time a methodology for reliably evaluating the effects of sediment recycling, separating the effects of natural changes in morphology from the beneficial use, has been shown to be effective. This method, which is applicable anywhere where there are sufficient data, allows a robust evaluation of the effectiveness of such methods and crucially enables these methods to be tested and optimised using modelling before implementation

TELEMAC-3D Seamounts

Water Qualit

Characterization and mapping of a deep-sea sponge ground on the Tropic Seamount (northeast tropical Atlantic) : implications for spatial management in the high seas

Ferromanganese crusts occurring on seamounts are a potential resource for rare earth elements that are critical for low-carbon technologies. Seamounts, however, host vulnerable marine ecosystems (VMEs), which means that spatial management is needed to address potential conflicts between mineral extraction and the conservation of deep-sea biodiversity. Exploration of the Tropic Seamount, located in an Area Beyond National Jurisdiction (ABNJ) in the subtropical North Atlantic, revealed large amounts of rare earth elements, as well as numerous VMEs, including high-density octocoral gardens, Solenosmilia variabilis patch reefs, xenophyophores, crinoid fields and deep-sea sponge grounds. This study focuses on the extensive monospecific grounds of the hexactinellid sponge Poliopogon amadou (Thomson, 1878). Deep-sea sponge grounds provide structurally complex habitat, augmenting local biodiversity. To understand the potential extent of these sponge grounds and inform spatial management, we produced the first ensemble species distribution model and local habitat suitability maps for P. amadou in the Atlantic employing Maximum Entropy (Maxent), General Additive Models (GAMs), and Random Forest (RF). The main factors driving the distribution of the sponge were depth and maximum current speed. The sponge grounds occurred in a marked bathymetric belt (2,500 – 3,000 m) within the upper North Atlantic Deep Water mass (2.5∘C, 34.7 psu, O2 6.7–7 mg ml-1), with a preference for areas bathed by moderately strong currents (0.2 – 0.4 ms-1). GAMs, Maxent and RF showed similar performance in terms of evaluation statistics but a different prediction, with RF showing the highest differences. This algorithm only retained depth and maximum currents whereas GAM and Maxent included bathymetric position index, slope, aspect and backscatter. In these latter two models, P. amadou showed a preference for high backscatter values and areas slightly elevated, flat or with gentle slopes and with a NE orientation. The lack of significant differences in model performance permitted to merge all predictions using an ensemble model approach. Our results contribute toward understanding the environmental drivers and biogeography of the species in the Atlantic. Furthermore, we present a case toward designating the Tropic Seamount as an Ecologically or Biologically Significant marine Area (EBSA) as a contribution to address biodiversity conservation in ABNJs

Essential Role of Cyclophilin A for Hepatitis C Virus Replication and Virus Production and Possible Link to Polyprotein Cleavage Kinetics

Viruses are obligate intracellular parasites and therefore their replication completely depends on host cell factors. In case of the hepatitis C virus (HCV), a positive-strand RNA virus that in the majority of infections establishes persistence, cyclophilins are considered to play an important role in RNA replication. Subsequent to the observation that cyclosporines, known to sequester cyclophilins by direct binding, profoundly block HCV replication in cultured human hepatoma cells, conflicting results were obtained as to the particular cyclophilin (Cyp) required for viral RNA replication and the underlying possible mode of action. By using a set of cell lines with stable knock-down of CypA or CypB, we demonstrate in the present work that replication of subgenomic HCV replicons of different genotypes is reduced by CypA depletion up to 1,000-fold whereas knock-down of CypB had no effect. Inhibition of replication was rescued by over-expression of wild type CypA, but not by a mutant lacking isomerase activity. Replication of JFH1-derived full length genomes was even more sensitive to CypA depletion as compared to subgenomic replicons and virus production was completely blocked. These results argue that CypA may target an additional viral factor outside of the minimal replicase contributing to RNA amplification and assembly, presumably nonstructural protein 2. By selecting for resistance against the cyclosporine analogue DEBIO-025 that targets CypA in a dose-dependent manner, we identified two mutations (V2440A and V2440L) close to the cleavage site between nonstructural protein 5A and the RNA-dependent RNA polymerase in nonstructural protein 5B that slow down cleavage kinetics at this site and reduce CypA dependence of viral replication. Further amino acid substitutions at the same cleavage site accelerating processing increase CypA dependence. Our results thus identify an unexpected correlation between HCV polyprotein processing and CypA dependence of HCV replication

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe