The A4 project: physics data processing using the Google protocol buffer library

In this paper, we present the High Energy Physics data format, processing toolset and analysis library a4, providing fast I/O of structured data using the Google protocol buffer library. The overall goal of a4 is to provide physicists with tools to work efficiently with billions of events, providing not only high speeds, but also automatic metadata handling, a set of UNIX-like tools to operate on a4 files, and powerful and fast histogramming capabilities. At present, a4 is an experimental project, but it has already been used by the authors in preparing physics publications. We give an overview of the individual modules of a4, provide examples of use, and supply a set of basic benchmarks. We compare a4 read performance with the common practice of storing unstructured data in ROOT trees. For the common case of storing a variable number of floating-point numbers per event, speedups in read speed of up to a factor of six are observed.Comment: Proceedings of poster shown at the 2012 International Conference on Computing in High Energy and Nuclear Physics (CHEP 2012). 19 pages, 17 figure

AMEG: the new SETAC advisory group on aquatic macrophyte ecotoxicology

Introduction and background Primary producers play critical structural and functional roles in aquatic ecosystems; therefore, it is imperative that the potential risks of toxicants to aquatic plants are adequately assessed in the risk assessment of chemicals. The standard required macrophyte test species is the floating (non-sediment-rooted) duckweed Lemna spp. This macrophyte species might not be representative of all floating, rooted, emergent, and submerged macrophyte species because of differences in the duration and mode of exposure; sensitivity to the specific toxic mode of action of the chemical; and species-specific traits (e.g., duckweed's very short generation time). Discussion and perspectives These topics were addressed during the workshop entitled “Aquatic Macrophyte Risk Assessment for Pesticides” (AMRAP) where a risk assessment scheme for aquatic macrophytes was proposed. Four working groups evolved from this workshop and were charged with the task of developing Tier 1 and higher-tier aquatic macrophyte risk assessment procedures. Subsequently, a SETAC Advisory Group, the Macrophyte Ecotoxicology Group (AMEG) was formed as an umbrella organization for various macrophyte working groups. The purpose of AMEG is to provide scientifically based guidance in all aspects of aquatic macrophyte testing in the laboratory and field, including prospective as well as retrospective risk assessments for chemicals. As AMEG expands, it will begin to address new topics including bioremediation and sustainable management of aquatic macrophytes in the context of ecosystem services

20 years SETAC GLB: increasing realism of pesticide risk assessment

Abstract Pesticides contribute to this reduction of biodiversity in ecosystems. Obviously, environmental risk assessment did not prevent adverse pesticide effects on non-target organisms. This called for an identification of processes that are relevant to extrapolate from simplified investigations to the reality of pesticide effects in the field, one of the prominent research areas at the SETAC GLB since two decades. We identify research areas that are relevant to link toxicant effects from test systems with the ecosystem to increase the realism of pesticide risk assessment

Environmental and structural factors influencing algal communities in small streams and ditches in central Germany

The suspended algal fraction in small lotic waterbodies has rarely been investigated as the ecological importance was questioned due to low abundances. Recent findings suggest, that substantial riverine plankton communities can establish in small lotic waterbodies. The gap of knowledge concerning the composition of suspended algal assemblages and influential factors determining their composition is addressed in this study by monitoring suspended and attached algal communities over a two year period in agriculturally influenced small lotic waterbodies using delayed fluorescence spectroscopy. A quantitative comparison of suspended and attached algae indicated, that suspended algae exceeded attached algal biomass in late summer and early autumn. Redundancy analyses and corresponding generalized linear models indicated that the suspended algal groups were most influenced by nutrients, temperature and velocity, whereas light regime was of minor importance. The attached algal groups were affected by the same factors, however with differing intensity. Regional factors, such as season, were identified as the major gradients along which both algal fractions varied, inducing temporal synchronous algal assemblages. This work represents a contribution towards a better understanding of algal ecology specifically suspended algae in small lotic waterbodies

Uptake and Transfer of Polyamide Microplastics in a Freshwater Mesocosm Study

Steadily increasing inputs of microplastics pose a growing threat to aquatic fauna, but laboratory studies potentially lack realism to properly investigate its effects on populations and ecosystems. Our study investigates the trophic and ontogenetic transfer of microplastics in a near-natural exposure scenario. The controlled outdoor freshwater mesocosms were exposed to polyamide (PA) 5–50 µm in size in concentrations of 15 and 150 mg L−1 and a control without microplastic addition. To verify the uptake of particles via the food chain, larvae and imagines of the midges Chaoborus crystallinus and C. obscuripes were examined, which feed on zooplankton during their larval stage. Larvae were captured after 117 days and imagines were caught in emergence traps that were emptied weekly. To detect the microparticles within the organisms, 200 larvae and 100 imagines per application were macerated and treated with fluorescent dye before investigation under a fluorescent microscope. We could detect up to 12 PA particles per individual larvae, while nearly no plastic was found in the imagines. This shows that, while Chaoborus sp. takes up microplastics via predation, most of the pollutant is egested through regurgitation and remains in the water, where it can further accumulate and potentially harm other organisms

Testing effects of pesticides on macroinvertebrate communities in outdoor stream mesocosms using carbaryl as example test item

Abstract Background In mesocosms, the fate and effects of chemicals can be investigated under more realistic conditions than in laboratory-scale experiments and most mesocosm studies for higher-tier risk assessment are conducted in lentic test systems. However, particularly for the assessment of EPT taxa (Ephemeroptera, Plecoptera, Trichoptera) and gammarids (Amphipoda), which are considered to be ecologically vulnerable macroinvertebrates, lotic systems seem to be more appropriate. Within this pilot study, eight newly constructed stream mesocosms were tested for their suitability in the effect assessment of plant protection products (PPP). By using the insecticide carbaryl as an example test item, five concentrations without replicates were tested under a worst case exposure scenario and three stream mesocosms served as controls. Results 15 out of the 51 invertebrate taxa found during the study belonged to EPT taxa, while the common lotic amphipod Gammarus sp. (G. pulex and G. roesili) was the most dominant taxa. Estimation of minimum detectable differences based on mean abundances and variance of taxa in the eight mesocosms before application indicate that for five arthropoda taxa and two non-arthropoda taxa, an analysis of effects would have probably would have been possible in a typical test design for a higher-tier study with more test units. Five of these taxa were typical stream taxa, i.e. mayflies, caddisflies and gammarids. With respect to the effects of carbaryl, multivariate analysis (principal response curve) indicates long-term effects on the macroinvertebrates community over several weeks for the highest carbaryl concentration (120 µg a.i./L). Potential effects were observed for the amphipod Gammarus sp., the mayfly Ephemera danica and the caddisfly family Limnephilidae. Conclusions Through this study it was shown that the stream mesocosms provided suitable habitats for potential sensitive and vulnerable taxa, including those typical for lotic systems. To enable a reliable statistical analysis of the effects within the higher-tier ecological risk assessment, the number of stream mesocosms needs to be enhanced. In addition, colonisation and sampling should be improved to increase the number of taxa with sufficiently high abundances for evaluation