Possible effects of ocean acidification on coral reef biogeochemistry: topics for research

International audienceABSTRACT: This paper is a short review of recent literature on how ocean acidification may influence coral reef organisms and coral reef communities. We argue that it is unclear as to how, and to what extent, ocean acidification will influence calcium carbonate calcification and dissolution, and affect changes in community structure of present-day coral reefs. It is critical to evaluate the extent to which the metabolism of present-day reefs is influenced by mineral saturation states, and to determine a threshold saturation state at which coral communities cease to function as reefs

Forage Preferences of the European Beaver Castor fiber

By the beginning of the twentieth century, hunting and land use change had reduced the European beaver Castor fiber to a relict population of no more than 1200 individuals. In some European states, re introduction has successfully established viable populations, whilst other schemes have failed. Environmental, social and economic issues associated with beaver reintroduction have given rise to a range of information needs in relation to the species«SQ» ecology. In 2005, six European beavers were translocated from Bavaria to a reintroduction site in southern England. The following year, a 6 month study was undertaken to investigate which tree species and size classes were most frequently utilised by the beavers, and to determine if the utilised species and size classes reflected resource availability within the home range. These questions were answered by comparing the use and the availability of foraged tree species in two ways: (1) using a survey of tree stumps; and (2) as a food choice experiment. The results showed that the reintroduced beavers were highly selective in relation to both the species and the size of the trees they used i.e. the reintroduced beavers selected species in significantly different proportions to their availability. However, they selected similar size classes between the preferred tree species, and did not utilise human timber. The relevance of the study is discussed with respect to information needs associated with the reintroduction of a keystone species, overcoming negative perceptions, population viability, welfare and soft release strategies

Uniform acquisition modelling across PET imaging systems: unified scatter modelling

RIN factor of all samples used for Illumina sequencing. (PDF 225 kb

Uniform acquisition modelling across PET imaging systems: Unified scatter modelling

© 2016 IEEE. PET imaging is an important tool commonly used for studying disease by research consortia which implement multi-centre studies to improve the statistical power of findings. The UK government launched the Dementias Platform UK to facilitate one of the world's largest dementia population study involving national centres equipped with state-of-the-art PET/MR scanners from two major vendors. However, the difference in PET detector technology between the two scanners involved makes the standardisation of data acquisition and image reconstruction necessary. We propose a new approach to PET acquisition system modelling across different PET systems and technologies, focusing in particular on unified scatter estimation across TOF (time-of-flight) and non-TOF PET systems. The proposed scatter modelling is fully 3D and voxel based, as opposed to the popular line-of-response driven methods. This means that for each emitting voxel an independent 3D scatter estimate is found, inherently preserving the necessary information for TOF calculations as well as accounting for the large axial field of view. With adequate sampling of the input images, the non-TOF scatter estimate is identical to the summed TOF estimates across TOF bins, without an additional computational cost used for the TOF estimation. The model is implemented using the latest NVIDA GPU CUDA platform, allowing finer sampling of image space which is more essential for accurate TOF modelling. The high accuracy of the proposed scatter model is validated using Monte Carlo simulations. The model is deployed in our stand-alone image reconstruction pipeline for the Biograph mMR scanner, demonstrating accurate 3D scatter estimates resulting in uniform reconstruction for a high statistics phantom scan

Iron oxidation at low temperature (260–500 C) in air and the effect of water vapor

The oxidation of iron has been studied at low temperatures (between 260 and 500 C) in dry air or air with 2 vol% H2O, in the framework of research on dry corrosion of nuclear waste containers during long-term interim storage. Pure iron is regarded as a model material for low-alloyed steel. Oxidation tests were performed in a thermobalance (up to 250 h) or in a laboratory furnace (up to 1000 h). The oxide scales formed were characterized using SEM-EDX, TEM, XRD, SIMS and EBSD techniques. The parabolic rate constants deduced from microbalance experiments were found to be in good agreement with the few existing values of the literature. The presence of water vapor in air was found to strongly influence the transitory stages of the kinetics. The entire structure of the oxide scale was composed of an internal duplex magnetite scale made of columnar grains and an external hematite scale made of equiaxed grains. 18O tracer experiments performed at 400 C allowed to propose a growth mechanism of the scale

Quality of life, treatment satisfaction, and adherence to treatment in patients with vesicular hand eczema:A cross-sectional study

Background Recurrent vesicular hand eczema frequently has a chronic course and needs long-term treatment. Objectives To evaluate health-related quality of life (HRQoL), treatment satisfaction, and adherence in patients with vesicular hand eczema. Methods Patients using one main treatment for at least three months were included. Data on HRQoL (Quality of Life in Hand Eczema Questionnaire [QOLHEQ]), treatment satisfaction (Treatment Satisfaction Questionnaire for Medication, version II), and treatment adherence (4-item Morisky Medication Adherence Scale) were collected. Univariate and multivariate regression analysis were used to predict variables associated with HRQoL. Results HRQoL was moderately impaired, with the highest impact in the QOLHEQ subdomain symptoms. Female sex, more severe hand eczema, and lower treatment satisfaction were associated with more impairment in HRQoL. Patients with severe/very severe hand eczema had significant lower "global satisfaction" scores compared with the other severity groups. The "global satisfaction" and treatment adherence in patients using systemic treatment were significantly higher compared with those with only topical treatment. Conclusions In patients with vesicular hand eczema disease severity affects both HRQoL and treatment satisfaction. Systemic treatment of severe hand eczema could improve the severity and as a result also HRQoL, treatment satisfaction, and medication adherence

On the accuracy of language trees

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical, phonological, syntactic) features or characters for many different languages. From this perspective the reconstruction of language trees is an example of inverse problems: starting from present, incomplete and often noisy, information, one aims at inferring the most likely past evolutionary history. A fundamental issue in inverse problems is the evaluation of the inference made. A standard way of dealing with this question is to generate data with artificial models in order to have full access to the evolutionary process one is going to infer. This procedure presents an intrinsic limitation: when dealing with real data sets, one typically does not know which model of evolution is the most suitable for them. A possible way out is to compare algorithmic inference with expert classifications. This is the point of view we take here by conducting a thorough survey of the accuracy of reconstruction methods as compared with the Ethnologue expert classifications. We focus in particular on state-of-the-art distance-based methods for phylogeny reconstruction using worldwide linguistic databases. In order to assess the accuracy of the inferred trees we introduce and characterize two generalizations of standard definitions of distances between trees. Based on these scores we quantify the relative performances of the distance-based algorithms considered. Further we quantify how the completeness and the coverage of the available databases affect the accuracy of the reconstruction. Finally we draw some conclusions about where the accuracy of the reconstructions in historical linguistics stands and about the leading directions to improve it.Comment: 36 pages, 14 figure

On the benefits of tasking with OpenMP

Tasking promises a model to program parallel applications that provides intuitive semantics. In the case of tasks with dependences, it also promises better load balancing by removing global synchronizations (barriers), and potential for improved locality. Still, the adoption of tasking in production HPC codes has been slow. Despite OpenMP supporting tasks, most codes rely on worksharing-loop constructs alongside MPI primitives. This paper provides insights on the benefits of tasking over the worksharing-loop model by reporting on the experience of taskifying an adaptive mesh refinement proxy application: miniAMR. The performance evaluation shows the taskified implementation being 15–30% faster than the loop-parallel one for certain thread counts across four systems, three architectures and four compilers thanks to better load balancing and system utilization. Dynamic scheduling of loops narrows the gap but still falls short of tasking due to serial sections between loops. Locality improvements are incidental due to the lack of locality-aware scheduling. Overall, the introduction of asynchrony with tasking lives up to its promises, provided that programmers parallelize beyond individual loops and across application phases.Peer ReviewedPostprint (author's final draft

Extending basic principles of measurement models to the design and validation of Patient Reported Outcomes

A recently published article by the Scientific Advisory Committee of the Medical Outcomes Trust presents guidelines for selecting and evaluating health status and health-related quality of life measures used in health outcomes research. In their article, they propose a number of validation and performance criteria with which to evaluate such self-report measures. We provide an alternate, yet complementary, perspective by extending the types of measurement models which are available to the instrument designer. During psychometric development or selection of a Patient Reported Outcome measure it is necessary to determine which, of the five types of measurement models, the measure is based on; 1) a Multiple Effect Indicator model, 2) a Multiple Cause Indicator model, 3) a Single Item Effect Indicator model, 4) a Single Item Cause Indicator model, or 5) a Mixed Multiple Indicator model. Specification of the measurement model has a major influence on decisions about item and scale design, the appropriate application of statistical validation methods, and the suitability of the resulting measure for a particular use in clinical and population-based outcomes research activities