Constraint-Guided Workflow Composition Based on the EDAM Ontology

Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain, in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how the ability to flexibly formulate domain-specific and problem-specific constraints supports the workflow development process

Preface

oai:journal.ub.tu-berlin.de:article/120

Direct 2D measurement of time-averaged forces and pressure amplitudes in acoustophoretic devices using optical trapping

Ultrasonic standing waves are increasingly applied in the manipulation and sorting of micrometer-sized particles in microfluidic cells. To optimize the performance of such devices, it is essential to know the exact forces that the particles experience in the acoustic wave. Although much progress has been made via analytical and numerical modeling, the reliability of these methods relies strongly on the assumptions used, e.g. the boundary conditions. Here, we have combined an acoustic flow cell with an optical laser trap to directly measure the force on a single spherical particle in two dimensions. While performing ultrasonic frequency scans, we measured the time-averaged forces on single particles that were moved with the laser trap through the microfluidic cell. The cell including piezoelectric transducers was modeled with finite element methods. We found that the experimentally obtained forces and the derived pressure fields confirm the predictions from theory and modeling. This novel approach can now be readily expanded to other particle, chamber, and fluid regimes and opens up the possibility of studying the effects of the presence of boundaries, acoustic streaming, and non-linear fluids.ISSN:1473-0197ISSN:1473-018

Water-friendly plant protection to conserve grown orchard landscapes in Germany

Ziel des FuE-Vorhabens war es, neue Techniken der Abdriftminderung in Obstbaubetrieben des Alten Landes in Niedersachsen (NS) und des Anbaugebiets Bodensee in Baden-Württemberg (BW) zu erproben und durch begleitende Untersuchungen ihre Eignung für einen gewässerschonenden Pflanzenschutz zu beurteilen. Bei den in NS eingesetzten Sprühgeräten dominierte die zweireihig-übergreifende Arbeitsweise, wohingegen die Geräte in BW aufgrund der großen Verbreitung von Hagelschutznetzen bevorzugt für eine einreihige Behandlung konzipiert waren. Die in neun Ostbaubetrieben eingesetzten Sprühgeräte (NS: 4, BW: 5) waren mit folgenden Einrichtungen zur Abdriftminderung ausgestattet: •ein- und zweireihiger Tunnel mit Rückführung nicht angelagerter Pflanzenschutzmittel (Recycling) •Reflektorsystem mit Umlenkung des aus der behandelten Baumreihe austretenden Sprühstrahles mit integriertem Recyclingsystem •Gebläse mit unterschiedlicher Luftführung, sensorgestützter Düsenschaltung und Luftstromanpassung Die Praxiserprobung hat gezeigt, dass sowohl die einreihigen Sprühgeräte, als auch zweireihige Geräte für den Einsatz in den gewässerreichen Regionen geeignet sind. Hinsichtlich der Anlagerung der Behandlungsflüssigkeit im Bestand wurde deutlich, dass nur die Tunnelsprüh­geräte, die sich durch eine abgeschirmte Applikations­zone auszeichnen, sehr gleichmäßige und kontinuierlich hohe Spritzbeläge von durchschnittlich ca. 20% der Aufwandmenge erzielen. Die einreihigen Sprühgeräte mit Gebläseaufsatz und elektrisch verstellbarer Gebläseab­deckung erzeugten Spritzbeläge von durchschnittlich 16 bis 18%. Die Ergebnisse zur Abdrift zeigten, dass alle Sprüh­geräte eine Abdriftminderung von mehr als 95% erzielen können. Voraussetzung hierfür sind der Einsatz grobtropfiger, verlustmindernder Düsen sowie die Reduzierung des Luftvolumenstromes in den ersten 1 bis 5 Reihen am Gewässer. Sprühgeräte mit Recyclingsystem oder Sensortechnik bringen durch die Einsparung an Pflanzenschutzmittel einen zusätzlichen ökonomischen Vorteil. Das einreihige Tunnelsprühgerät konnte durch seine flexible Anpassung an die Reihenbreiten eine Einsparung von durchschnittlich ca. 50% erreichen. Mit dem zweireihigen Tunnelsprühgerät sowie der Sensortechnik sind im Durchschnitt Einsparungen von lediglich 12 bis 18% erzielt worden. Mit allen Sprühgeräten wurde eine ausreichend gute biologische Wirksamkeit erzielt. Allerdings sind beim Reflektorgerät und den Geräten mit Sensorsteuerung gewisse Unsicherheiten nicht völlig auszuschließen. Aus betriebswirtschaftlicher Sicht ist der Einsatz des einreihigen Tunnelgerätes bereits ab einer Betriebsgröße von 8 bis 10 ha sinnvoll und ist somit vergleichbar mit den einreihigen Geräten. Die zweireihigen Techniken rentierten sich nur auf arrondierten Flächen ab 20 ha. Sie waren im Vergleich zu den einreihigen Sprühgeräten in der Anwendung sehr anspruchsvoll, führen aber zu einer Erhöhung der Schlagkraft um ca. 80%. Grobtropfige Düsen führten zu mehr Spritzflecken. Dieser Aspekt ist heutzutage nur noch bei einer Direktvermarktung und Sortierung ohne Wasserentleerung relevant. Die Ergebnisse des Gewässermonitoring bestätigten im Wesentlichen die hohe Abdriftminderung des geprüften Recyclinggerätes und des Sprühgerätes mit Querstromgebläse und Sensortechnik. Bei den anderen drei geprüften Geräten ergab sich im Gewässermonitoring eine geringere Abdriftminderung. Bei den aus dem Gewässermonitoring errechneten Abdriftminderungsraten unter 99% wurde der Gewässerschutz nicht in jedem Fall eingehalten.    The FuE project aimed at testing new techniques to reduce drift in orchards of the Alten Landes (NS) and the fruit growing area around Lake Constance (BW), and assess their suitability as to water-friendly plant protection by accompanying examinations. The sprayers used in NS were dominated by a double row, overarching mode of operation, whereas the sprayers in BW were designed for single row treatment because of the extensive spread of hail protection nets. In both growing areas a technically identical sprayer with axial flow fan for single row treatment (air exit outlets and sensor controlled nozzle regulation were covered) was used as reference sprayer. The sprayers used on nine fruit farms (NS: 4, BW: 5) were equipped with the following facilities to reduce drift: •Single and double row tunnel with re-circulation of not deposited plant protection products (recycling) •Reflector system with integrated recycling system, which redirects the spray jet coming out of the treated row •Fan with different air conduction, sensor controlled nozzle regulation and airflow adjustment Testing in practice has demonstrated that single row sprayers and also double row sprayers are suited for use in regions with plenty of water. Regarding the deposition of spray liquid in orchards it became clear that only tunnel sprayers, which are distinguished by a shielded application zone, achieve extremely even and continuously high spray deposits of approximately 20% in relation to the application rate. Single row sprayers with fan unit and electrically adjustable shields on the fan outlet generated an average of 16 to 18% of spray liquid deposits. The drift results showed that all sprayers could achieve a drift reduction of more than 95%. Precondition would be the use of coarse, drift-reducing nozzles and the reduction of the airflow rate in the initial 5 rows close to water bodies. Sprayers equipped with a recycling system or sensor technology bring about an additional economical benefit due to their rate of saved product. The single row tunnel sprayer was able to achieve an average reduction of approx. 50% by flexibly adjusting to row widths. The double row tunnel sprayers achieved approx. a 19% reduction on average. Sensor technology accomplished reductions of 12 to 19%. Biological efficiency of all sprayers was sufficient. However, a certain unsteadiness cannot be entirely excluded for reflector and sensor controlled sprayers. From an economic point of view, the single row tunnel sprayer pays already from an orchard size of 8–10 ha and is thus comparable with single row sprayers. The double row technologies are only worth the effort on coherent areas from 20 ha upwards. Their utilization was very demanding compared to single row sprayers but lead to a clout increase of approx. 80%. Coarse nozzles created more spraying spots. This aspect is presently only relevant regarding direct marketing of products and sorting without unloading in water. The results of water body monitoring confirmed mainly the high drift reduction of the tested recycling sprayer and of the sprayer equipped with cross flow fan and sensor technology. According to water body monitoring, the three other tested sprayers achieved a lower drift reduction rate. Water protection was not adhered to in all cases with drift reduction rates below 99%, calculated from water body monitoring.   &nbsp

Quantum Statistics of Surface Plasmon Polaritons in Metallic Stripe Waveguides

Single surface plasmon polaritons are excited using photons generated via spontaneous parametric down-conversion. The mean excitation rates, intensity correlations and Fock state populations are studied. The observed dependence of the second order coherence in our experiment is consistent with a linear uncorrelated Markovian environment in the quantum regime. Our results provide important information about the effect of loss for assessing the potential of plasmonic waveguides for future nanophotonic circuitry in the quantum regime.Comment: 21 pages, 6 figures, published in Nano Letters, publication date (web): March 27 (2012

Functional electrical stimulation driven by a brain–computer interface in acute and subacute stroke patients impacts beta power and long-range temporal correlation

Functional electrical stimulation (FES) is a standard rehabilitation approach applied by therapists to aid motor recovery in a paretic limb post-stroke. Information pertaining to the timing of a movement attempt can be obtained from changes in the power of oscillatory electrophysiological activity in motor cortical regions, derived from scalp electroencephalographic (EEG) recordings. The use of a brain–computer interface (BCI), to enable delivery of FES within a tight temporal window with a movement attempt detected in scalp EEG, is associated with greater motor recovery than conventional FES application in patients in the chronic phase post-stroke. We hypothesized that the heightened neural plasticity early post-stroke could further enhance motor recovery and that motor improvements would be accompanied by changes in the motor cortical sensorimotor rhythm after compared with before treatment. Here we assessed clinical outcome and changes in the sensorimotor rhythm in patients following subcortical stroke affecting the non-dominant hemisphere from a study comparing timing of FES delivery using a BCI, with a Sham group, receiving FES with no such temporal relationship. The BCI group showed greater clinical improvement following the treatment, particularly early post-stroke, and a greater decrease in beta oscillatory power and long-range temporal correlation over contralateral (ipsilesional) motor cortex. The electrophysiological changes are consistent with a reduction in compensatory processes and a transition towards a subcritical state when movement is triggered at the time of movement detection based on motor cortical oscillations

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world\u27s major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications