Timing techniques with picosecond-order accuracy for novel gaseous detectors

A simulation model is developed to train Artificial Neural Networks (ANN), for precise timing of PICOSEC Micromegas detector signals. The aim is to develop fast, online timing algorithms as well as minimising the information to be saved during data acquisition. PICOSEC waveforms were collected and digitised by a fast oscilloscope during a femptosecond-laser test beam run. A data set comprising waveforms collected with attenuated laser beam intensity, eradicating the emission of more than one photoelectron per light pulse from the PICOSEC photocathode, was utilised by a simulation algorithm to generate waveforms to train an ANN. A second data set of multi-photoelectron waveforms was used to evaluate the ANN performance in determining the PICOSEC Signal Arrival Time, relative to a fast photodiode time-reference. The ANN timing performance is the same as the results of a full offline signal processing, achieving a timing precision of 18.3$\pm$0.6 ps.Comment: 4 pages, 6 figure

European primary datasets of alien bacteria and viruses

Bacteria and viruses are a natural component of Earth biodiversity and play an essential role in biochemical and geological cycles. They may also pose problems outside their native range, where they can negatively impact on natural resources, wildlife, and human health. To address these challenges and develop sustainable conservation strategies, a thorough understanding of their invasion related- factors is needed: origin, country and year of introduction, and pathways dynamics. Yet, alien bacteria and viruses are underrepresented in invasion ecology studies, which limits our ability to quantify their impacts and address future introductions. This study provides primary datasets of alien bacteria and viruses of plants and animals present in the European environment. The datasets contain expert-revised data on 446 taxa and their invasion related- factors across terrestrial and aquatic environments. Taxa information are complemented with spatial occurrences. The datasets provide a basis for collaborative initiatives to improve the collection of alien bacteria and viruses' data, and a starting point for data-driven conservation practices

Citizen Science and Open Data: a model for Invasive Alien Species in Europe

Invasive Alien Species (IAS) are a growing threat to Europe's biodiversity. The implementation of European Union Regulation on IAS can benefit from the involvement of the public in IAS recording and management through Citizen Science (CS) initiatives. Aiming to tackle issues related with the use of CS projects on IAS topics, a dedicated workshop titled “Citizen Science and Open Data: a model for Invasive Alien Species in Europe” was organized by the Joint Research Centre (JRC) and the European Cooperation in Science and Technology (COST Association). Fifty key stakeholders from all Europe, including two Members of the European Parliament, attended the workshop. With a clear focus on IAS, the workshop aimed at addressing the following issues: a) CS and policy, b) citizen engagement, and c) CS data management. Nine short presentations provided input on CS and IAS issues. Participants discussed specific topics in several round tables (“world café” style) and reported back their conclusions to the audience and full assembly moderated discussions. Overall, the workshop enabled the sharing of ideas, approaches and best practices regarding CS and IAS. Specific opportunities and pitfalls of using CS data in the whole policy cycle for IAS were recognized. Concerning the implementation of the IAS Regulation, CS data could complement official surveillance systems, and contribute to the early warning of the IAS of Union concern after appropriate validation by the Member States’ competent authorities. CS projects can additionally increase awareness and empower citizens. Attendees pointed out the importance for further public engagement in CS projects on IAS that demonstrate specific initiatives and approaches and analyze lessons learned from past experiences. In addition, the workshop noted that the data gathered from different CS projects on IAS are fragmented. It highlighted the need for using an open and accessible platform to upload data originating from CS sources or to mirror validated data into a single, easy-to-use web service, in line with the EU Open Science Strategic Priority. The workshop provided ten key recommendations of best practices for CS projects on IAS, addressed to researchers, policy makers and implementing authorities, indicating future research and policy directions and opportunities

Assessment of the environmental status in Hellenic coastal waters (Eastern Mediterranean): from the Water Framework Directive to the Marine Strategy Water Framework Directive.

A  methodology is presented to assess the environmental status sensu the Marine Strategy Water Framework Directive (MSFD) based on data obtained from the monitoring of water quality in the Hellenic coastal waters within the Water Framework Directive (WFD).   An adapted decision tree used for integrating the results of the WFD in the Basque country was applied. Modifications lie to the evaluation of the physicochemical status based on a eutrophication index developed for Eastern Mediterranean waters. Results on hydromorphological, physicochemical and biological elements are presented. The chemical status was evaluated based on measurements of heavy metals in water. The evaluation of the biological quality was based on the use of metrics developed for phytoplankton biomass, benthic macroinvertebrates and macroalgae updated to accommodate MSFD needs. Results on the integrative status of the water bodies were validated by correlating classification results with a pressure index and environmental indicators in water column and sediment. Following this decision tree the majority of stations expected to be at risk of achieving the good status were found in moderate status. Benthos was found to be the element with the closest agreement with the integrated final status having an increased weighting in the decision tree. The quality of benthos and in some  limited cases  the eutrophication index determined largely the final status. The highest disagreement with the integrative classification was produced by macroalgae. All indicators used correlated with water and sediment parameters but benthos correlated better with sediment factors while phytoplankton and eutrophication index with water column parameters

In vivo validation of a miniaturized electrochemical oxygen sensor for measuring intestinal oxygen tension

Recent advances in the fields of electronics and microfabrication techniques have led to the development of implantable medical devices for use within the field of precision medicine. Monitoring visceral surface tissue O2 tension (ptO2) by means of an implantable sensor is potentially useful in many clinical situations including the peri-operative management of patients undergoing intestinal resection and anastomosis. This concept could provide a means by which treatment could be tailored to individual patients. This study describes the in vivo validation of a novel miniaturised electrochemical O2 sensor to provide real-time data on intestinal ptO2. A single O2 sensor was placed onto the serosal surface of the small intestine of anaesthetised rats that were exposed to ischaemic (superior mesenteric artery occlusion) and hypoxaemic (alterations in inspired fractional O2 concentrations) insults. Control experiments demonstrated that the sensors function and remain stable in an in vivo environment. Intestinal ptO2 decreased following superior mesenteric artery occlusion and with reductions in inspired O2 concentrations. These results were reversible after reinstating blood flow or increasing inspired O2 concentrations. We have successfully developed an anaesthetised rat intestinal ischaemic and hypoxic model for validation of a miniaturised O2 sensor to provide real-time measurement of intestinal ptO2. Our results support further validation of the sensors in physiological conditions using a large animal model to provide evidence of their use in clinical applications where monitoring visceral surface tissue O2 tension is important

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

Background: The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly’s biology and proposing alternative control methods to pesticide use. Results: Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR. Conclusions: The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome’s organization, function and evolution and is poised to provide avenues for sterile insect technique approaches

Applying the convention on biological diversity pathway classification to alien species in Europe

The number of alien species arriving within new regions has increased at unprecedented rates. Managing the pathways through which alien species arrive and spread is important to reduce the threat of biological invasions. Harmonising information on pathways across individual sectors and user groups is therefore critical to underpin policy and action. The European Alien Species Information Network (EASIN) has been developed to easily facilitate open access to data of alien species in Europe. The Convention on Biological Diversity (CBD) Pathway Classification framework has become a global standard for the classification of pathways. We followed a structured approach to assign pathway information within EASIN for a subset of alien species in Europe, which covered 4169 species, spanning taxonomic groups and environments. We document constraints and challenges associated with implementing the CBD Pathway Classification framework and propose potential amendments to increase clarity. This study is unique in the scope of taxonomic coverage and also in the inclusion of primary (independent introductions to Europe) and secondary (means of dispersal for species expansion within Europe, after their initial introduction) modes of introduction. In addition, we summarise the patterns of introduction pathways within this subset of alien species within the context of Europe. Based on the analyses, we confirm that the CBD Pathway Classification framework offers a robust, hierarchical system suitable for the classification of alien species introduction and spread across a wide range of taxonomic groups and environments. However, simple modifications could improve interpretation of the pathway categories ensuring consistent application across databases and information systems at local, national, regional, continental and global scales. Improving consistency would also help in the development of pathway action plans, as required by EU legislation

Test structures for optimizing polymer electrolyte performance in a microfabricated electrochemical oxygen sensor

Test structures were produced for optimizing the design and fabrication of a patterned solid polymer electrolyte in an electrochemical oxygen sensor. Measurements showed that choice of photoresist developer and the underlying insulator material affected durability of the polymer structures. Test electrodes covered by the polymer were effective at supporting electrochemical oxygen detection