The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model

Water motion and vegetation control the pH dynamics in seagrass-dominated bays

info:eu-repo/semantics/publishe

Efficiency and safety of varying the frequency of whole blood donation (INTERVAL): a randomised trial of 45 000 donors

Background: Limits on the frequency of whole blood donation exist primarily to safeguard donor health. However, there is substantial variation across blood services in the maximum frequency of donations allowed. We compared standard practice in the UK with shorter inter-donation intervals used in other countries. Methods: In this parallel group, pragmatic, randomised trial, we recruited whole blood donors aged 18 years or older from 25 centres across England, UK. By use of a computer-based algorithm, men were randomly assigned (1:1:1) to 12-week (standard) versus 10-week versus 8-week inter-donation intervals, and women were randomly assigned (1:1:1) to 16-week (standard) versus 14-week versus 12-week intervals. Participants were not masked to their allocated intervention group. The primary outcome was the number of donations over 2 years. Secondary outcomes related to safety were quality of life, symptoms potentially related to donation, physical activity, cognitive function, haemoglobin and ferritin concentrations, and deferrals because of low haemoglobin. This trial is registered with ISRCTN, number ISRCTN24760606, and is ongoing but no longer recruiting participants. Findings: 45 263 whole blood donors (22 466 men, 22 797 women) were recruited between June 11, 2012, and June 15, 2014. Data were analysed for 45 042 (99·5%) participants. Men were randomly assigned to the 12-week (n=7452) versus 10-week (n=7449) versus 8-week (n=7456) groups; and women to the 16-week (n=7550) versus 14-week (n=7567) versus 12-week (n=7568) groups. In men, compared with the 12-week group, the mean amount of blood collected per donor over 2 years increased by 1·69 units (95% CI 1·59–1·80; approximately 795 mL) in the 8-week group and by 0·79 units (0·69–0·88; approximately 370 mL) in the 10-week group (p<0·0001 for both). In women, compared with the 16-week group, it increased by 0·84 units (95% CI 0·76–0·91; approximately 395 mL) in the 12-week group and by 0·46 units (0·39–0·53; approximately 215 mL) in the 14-week group (p<0·0001 for both). No significant differences were observed in quality of life, physical activity, or cognitive function across randomised groups. However, more frequent donation resulted in more donation-related symptoms (eg, tiredness, breathlessness, feeling faint, dizziness, and restless legs, especially among men [for all listed symptoms]), lower mean haemoglobin and ferritin concentrations, and more deferrals for low haemoglobin (p<0·0001 for each) than those observed in the standard frequency groups. Interpretation: Over 2 years, more frequent donation than is standard practice in the UK collected substantially more blood without having a major effect on donors' quality of life, physical activity, or cognitive function, but resulted in more donation-related symptoms, deferrals, and iron deficiency. Funding: NHS Blood and Transplant, National Institute for Health Research, UK Medical Research Council, and British Heart Foundation

A Population Genetic Approach to Mapping Neurological Disorder Genes Using Deep Resequencing

Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n = 285 patients) study of candidate genes coupled with population genetics and statistical methods to identify rare variants associated with Autism Spectrum Disorder and Schizophrenia. Three genes, MAP1A, GRIN2B, and CACNA1F, were consistently identified by different methods as having significant excess of rare missense mutations in either one or both disease cohorts. In a broader context, we also found that the overall site frequency spectrum of variation in these cases is best explained by population models of both selection and complex demography rather than neutral models or models accounting for complex demography alone. Mutations in the three disease-associated genes explained much of the difference in the overall site frequency spectrum among the cases versus controls. This study demonstrates that genes associated with complex disorders can be mapped using resequencing and analytical methods with sample sizes far smaller than those required by genome-wide association studies. Additionally, our findings support the hypothesis that rare mutations account for a proportion of the phenotypic variance of these complex disorders

Longer-term efficiency and safety of increasing the frequency of whole blood donation (INTERVAL): extension study of a randomised trial of 20 757 blood donors

Background: The INTERVAL trial showed that, over a 2-year period, inter-donation intervals for whole blood donation can be safely reduced to meet blood shortages. We extended the INTERVAL trial for a further 2 years to evaluate the longer-term risks and benefits of varying inter-donation intervals, and to compare routine versus more intensive reminders to help donors keep appointments. Methods: The INTERVAL trial was a parallel group, pragmatic, randomised trial that recruited blood donors aged 18 years or older from 25 static donor centres of NHS Blood and Transplant across England, UK. Here we report on the prespecified analyses after 4 years of follow-up. Participants were whole blood donors who agreed to continue trial participation on their originally allocated inter-donation intervals (men: 12, 10, and 8 weeks; women: 16, 14, and 12 weeks). They were further block-randomised (1:1) to routine versus more intensive reminders using computer-generated random sequences. The prespecified primary outcome was units of blood collected per year analysed in the intention-to-treat population. Secondary outcomes related to safety were quality of life, self-reported symptoms potentially related to donation, haemoglobin and ferritin concentrations, and deferrals because of low haemoglobin and other factors. This trial is registered with ISRCTN, number ISRCTN24760606, and has completed. Findings: Between Oct 19, 2014, and May 3, 2016, 20 757 of the 38 035 invited blood donors (10 843 [58%] men, 9914 [51%] women) participated in the extension study. 10 378 (50%) were randomly assigned to routine reminders and 10 379 (50%) were randomly assigned to more intensive reminders. Median follow-up was 1·1 years (IQR 0·7–1·3). Compared with routine reminders, more intensive reminders increased blood collection by a mean of 0·11 units per year (95% CI 0·04–0·17; p=0·0003) in men and 0·06 units per year (0·01–0·11; p=0·0094) in women. During the extension study, each week shorter inter-donation interval increased blood collection by a mean of 0·23 units per year (0·21–0·25) in men and 0·14 units per year (0·12–0·15) in women (both p<0·0001). More frequent donation resulted in more deferrals for low haemoglobin (odds ratio per week shorter inter-donation interval 1·19 [95% CI 1·15–1·22] in men and 1·10 [1·06–1·14] in women), and lower mean haemoglobin (difference per week shorter inter-donation interval −0·84 g/L [95% CI −0·99 to −0·70] in men and −0·45 g/L [–0·59 to −0·31] in women) and ferritin concentrations (percentage difference per week shorter inter-donation interval −6·5% [95% CI −7·6 to −5·5] in men and −5·3% [–6·5 to −4·2] in women; all p<0·0001). No differences were observed in quality of life, serious adverse events, or self-reported symptoms (p>0.0001 for tests of linear trend by inter-donation intervals) other than a higher reported frequency of doctor-diagnosed low iron concentrations and prescription of iron supplements in men (p<0·0001). Interpretation: During a period of up to 4 years, shorter inter-donation intervals and more intensive reminders resulted in more blood being collected without a detectable effect on donors' mental and physical wellbeing. However, donors had decreased haemoglobin concentrations and more self-reported symptoms compared with the initial 2 years of the trial. Our findings suggest that blood collection services could safely use shorter donation intervals and more intensive reminders to meet shortages, for donors who maintain adequate haemoglobin concentrations and iron stores. Funding: NHS Blood and Transplant, UK National Institute for Health Research, UK Medical Research Council, and British Heart Foundation

Neptune Odyssey: A Flagship Concept for the Exploration of the Neptune–Triton System

The Neptune Odyssey mission concept is a Flagship-class orbiter and atmospheric probe to the Neptune-Triton system. This bold mission of exploration would orbit an ice-giant planet to study the planet, its rings, small satellites, space environment, and the planet-sized moon Triton. Triton is a captured dwarf planet from the Kuiper Belt, twin of Pluto, and likely ocean world. Odyssey addresses Neptune system-level science, with equal priorities placed on Neptune, its rings, moons, space environment, and Triton. Between Uranus and Neptune, the latter is unique in providing simultaneous access to both an ice giant and a Kuiper Belt dwarf planet. The spacecraft - in a class equivalent to the NASA/ESA/ASI Cassini spacecraft - would launch by 2031 on a Space Launch System or equivalent launch vehicle and utilize a Jupiter gravity assist for a 12 yr cruise to Neptune and a 4 yr prime orbital mission; alternatively a launch after 2031 would have a 16 yr direct-to-Neptune cruise phase. Our solution provides annual launch opportunities and allows for an easy upgrade to the shorter (12 yr) cruise. Odyssey would orbit Neptune retrograde (prograde with respect to Triton), using the moon's gravity to shape the orbital tour and allow coverage of Triton, Neptune, and the space environment. The atmospheric entry probe would descend in ~37 minutes to the 10 bar pressure level in Neptune's atmosphere just before Odyssey's orbit-insertion engine burn. Odyssey's mission would end by conducting a Cassini-like "Grand Finale,"passing inside the rings and ultimately taking a final great plunge into Neptune's atmosphere

Data from: Warming accelerates mangrove expansion and surface elevation gain in a subtropical wetland

Climatic warming can change how coastal wetland plants grow, thus altering their capacity to build land and keep pace with rising seas. As freeze events decline with climate change, mangroves expand their range to higher latitudes and displace salt marsh vegetation. Warmer air temperatures will likely alter above‐ and below‐ground plant dynamics as this dramatic coastal wetland biome shift proceeds, which in turn may result in changes in ecosystem function such as sediment building. We used a large scale in situ warming experiment in a subtropical wetland to increase both marsh and mangrove ecosystem air temperatures. We assessed how 2 years of continuous warming influenced above‐ and below‐ground plant growth and surface elevation relative to sea level. We found that chronic warming doubled plant height and accelerated the expansion of mangrove into salt marsh vegetation, as indicated by a sixfold greater increase in mangrove cover in warmed plots compared to ambient temperature plots and a corresponding loss in salt marsh cover. Surface elevation gain, a measure of soil‐building capacity, increased due to warming over a 2‐year period and these changes in surface elevation were driven by increased mangrove root production in warmed plots. Synthesis. Our findings suggest that, in some coastal wetlands, warming can facilitate plant community changes from marsh to mangrove, with corresponding increases in growth that help coastal wetlands to keep pace with sea‐level rise

OMUSE

The Oceanographic Multi-purpose Software Environment: a package for multi-physics and multi-scale earth science simulations

Water motion and vegetation control the pH dynamics in seagrass-dominated bays

Global oceanic pH is lowering, which is causing great concern for the natural functioning of marine ecosystems. Current pH predictions are based on open ocean models; however, coastal zones are dynamic systems with seawater pH fluctuating temporally and spatially. To understand how coastal ecosystems will respond in the future, we first need to quantify the extent that local processes influence the pH of coastal zones. With this study, we show that over a single diurnal cycle, the total pH can fluctuate up to 0.2 units in a shallow seagrass-dominated bay, driven by the photosynthesis and respiration of the vegetation. However, these biologically controlled pH fluctuations vary significantly over small distances. Monitoring conducted at neighboring sites with contrasting hydrodynamic regimes highlights how water motion controls the extent that the local pH is altered by the metabolism of vegetation. The interactive effects of hydrodynamics and vegetation were further investigated with an in situ experiment, where the hydrodynamics were constrained and thus the local water residence time was increased, displaying the counteractive effect of hydrodynamics on the pH change caused by vegetation. With this research, we provide detailed in situ evidence of the spatial variation of pH within marine ecosystems, highlighting the need to include hydrodynamic conditions when assessing the pH-effects of vegetation, and identifying potential high-pH refuges in a future low pH ocean