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

Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

Article purchased; Published online: 3 August 2017Cassava (Manihot esculenta (L.) Crantz) is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and micronutrient density, particularly of provitamin A, traits that are negatively correlated, are among the primary selection objectives in cassava breeding. This study aimed at identifying genetic markers associated with these traits and uncovering the potential underlying cause of their negative correlation - whether linkage and/or pleiotropy. A genome-wide association mapping using 672 clones genotyped at 72,279 SNP loci was carried out. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness was identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that co-located with the 24.1 Mbp peak for carotenoid content was identified. Haplotypes at these loci explained a large proportion of the phenotypic variability. Evidence of mega-base-scale linkage disequilibrium around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid (phytoene synthase) and starch biosynthesis (UDP-glucose pyrophosphorylase and sucrose synthase) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate on the genetic architecture of carotenoids and dry matter in cassava and provides an opportunity to accelerate genetic improvement of these traits

The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models

Background:It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities-home to two-thirds of the African population-is driven by intra-community sexual networks versus viral introductions from outside of communities.Methods and Findings:We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7-3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%-42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%-70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai.Conclusions:Our findings suggest that HIV introductions into communities are common and account for a significant proportion of new HIV infections acquired outside of households in rural Uganda, though the extent to which this is true elsewhere in Africa remains unknown. Our results also suggest that HIV prevention efforts should be implemented at spatial scales broader than the community and should target key populations likely responsible for introductions into communities.Please see later in the article for the Editors' Summary

Quality of life perception of type 1 diabetic patients treated with insulin analogs and receiving medication review with follow-up in a public health care service from Ponta Grossa-PR, Brazil

ABSTRACT Glycemic control in patients with diabetes mellitus type 1 (DM1) reduces the risk of complications but requires a rigorous health care routine. Thus, diabetes education is central to increasing treatment compliance and self-care practices. This study aimed to evaluate the quality of life (QoL) and glycemic control of DM1 patients being treated with insulin analogs and receiving medication review with follow-up. This was a transversal study that included 110 patients registered at the 3rd Health Regional of Ponta Grossa-PR, aged &#8805; 18 years, and receiving pharmaceutical care for at least 1 year. The Diabetes Quality of Life Measure (DQOL)-Brazil was used to evaluate QoL. The data were statistically analyzed using SPSS version 17.0 with 95% confidence levels. Of the 110 patients, 58.2% were women. The average age was 33.7 years (±10.5), and the average glycated hemoglobin (HbA1c) value was 8% (±1.4). The mean total DQOL-Brazil score was 2.11 (95% confidence interval, 2.02 - 2.21). All DQOL-Brazil scores were lower in patients with HbA1c &#8804; 8%, indicating a better QoL. Good glycemic control, thus, appears to have a positive influence on the QoL, and pharmaceutical interventions are able to contribute to the achievement of therapeutic targets

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes