Search

Background: Exposure to perfluoroalkyl substances may affect offspring immune development and thereby increase risk of childhood asthma, but the underlying mechanisms and asthma phenotype affected by such exposure is unknown. Methods: In the Danish COPSAC2010 cohort of 738 unselected pregnant women and their children plasma PFOS and PFOA concentrations were semi-quantified by untargeted metabolomics analyses and calibrated using a targeted pipeline in mothers (gestation week 24 and 1 week postpartum) and children (age ½, 1½ and 6 years). We examined associations between pregnancy and childhood PFOS and PFOA exposure and childhood infections, asthma, allergic sensitization, atopic dermatitis, and lung function measures, and studied potential mechanisms by integrating data on systemic low-grade inflammation (hs-CRP), functional immune responses, and epigenetics. Findings: Higher maternal PFOS and PFOA exposure during pregnancy showed association with a non-atopic asthma phenotype by age 6, a protection against sensitization, and no association with atopic asthma or lung function, or atopic dermatitis. The effect was primarily driven by prenatal exposure. There was no association with infection proneness, low-grade inflammation, altered immune responses or epigenetic changes. Interpretations: Prenatal exposure to PFOS and PFOA, but not childhood exposure, specifically increased the risk of low prevalent non-atopic asthma, whereas there was no effect on atopic asthma, lung function, or atopic dermatitis. Funding: All funding received by COPSAC are listed on www.copsac.com. The Lundbeck Foundation (Grant no R16-A1694); The Novo Nordic Foundation (Grant nos NNF20OC0061029, NNF170C0025014, NNF180C0031764); The Ministry of Health (Grant no 903516); Danish Council for Strategic Research (Grant no 0603-00280B); and The Capital Region Research Foundation have provided core support to the COPSAC research center. COPSAC acknowledges the National Facility for Exposomics (SciLifeLab, Sweden) for supporting calibration of the untargeted metabolomics PFAS data. BC and AS has received funding for this project from the European Union's Horizon 2020 research and innovation programme (BC: grant agreement No. 946228 DEFEND; AS: grant agreement No. 864764 HEDIMED).

We propose to leverage public vulnerability scanners to examine the servers where online digital projects are hosted and list their common vulnerabilities. Provided in an anonymized, aggregated fashion, this assessment will shed light on our hypothesis: cyber threats are a significant factor in the degradation of online projects.

The recently developed average latitudinal displacement (ALD) methodology is applied to assess the waviness of the austral winter subtropical and polar jets using three different reanalysis data sets. The analysis reveals both similarities and differences between the hemispheres with respect to aspects of the tendencies exhibited by both species of jets over the last 6 decades. As in the wintertime Northern Hemisphere, both jets in the Southern Hemisphere have become systematically wavier over the time series and the waviness of each jet evolves quite independently of the other during most cold seasons. Also, like its Northern Hemisphere equivalent, the Southern Hemisphere polar jet exhibits no trend in speed (though it is notably slower) while its poleward creep is statistically significant. In contrast to its Northern Hemisphere counterpart, the austral subtropical jet has undergone both a systematic increase in speed as well as a statistically significant poleward migration. Finally, composite differences between the waviest and least wavy seasons for each species suggest that the Southern Hemisphere’s lower stratospheric polar vortex is negatively impacted by unusually wavy tropopause-level jets of either species.

In forensic, medical and veterinary entomology, the ease and affordability of image data acquisition have resulted in whole-image analysis becoming an invaluable approach for species identification. Krawtchouk moment invariants are a classical mathematical transformation that can extract local features from an image, thus allowing subtle species-specific biological variations to be accentuated for subsequent analyses. We extracted Krawtchouk moment invariant features from binarised wing images of 759 male fly specimens from the Calliphoridae, Sarcophagidae, and Muscidae families (13 species and a species variant). Subsequently, we trained the Generalized, Unbiased, Interaction Detection and Estimation (GUIDE) random forests classifier using linear discriminants derived from these features and inferred the species identity of specimens from the test samples. Five-fold cross validation results show a 98.56 ± 0.38% (standard error) identification accuracy at the family level, and a 91.04 ± 1.33% identification accuracy at the species level. The mean F1-score of 0.89 ± 0.02 reflects good balance of precision and recall properties of the model. The present study consolidates findings from previous small pilot studies of the usefulness of wing venation patterns for inferring species identities. Thus, the stage is set for the development of a mature data analytic ecosystem for routine computer image-based identification of fly species that are of forensic, medical, and veterinary importance.

Additional file 2. REC Favourable Opinion.

Additional file 5. (The SPIRIT Checklist). Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT): a checklist for a set of scientific, ethical and administrative elements recommended to be listed in a protocol [21] .

Additional file 6. Full Protocol

Additional file 1. A copy of the Process Evaluation Participant Information Sheet (Medic, Manager, CNS) and Informed Consent Form.

Additional file 4. Patient Invitation Pack (including Patient Information Sheet and Informed Consent Form.

Background: The NORMAN Association (https:// www. norman-​netwo rk. com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https:// www. norman-​netwo rk. com/ nds/ SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https:// zenodo. org/ commu nities/ norman-​sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https:// pubch em. ncbi. nlm. nih. gov/) and the US EPA’s CompTox Chemicals Dashboard (https:// compt ox. epa. gov/ dashb oard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https:// pubch em. ncbi. nlm. nih. gov/ class ifica tion/# hid= 101). Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https:// www. norman-​netwo rk. com/ nds/ SLE/)., NORMAN Association, Luxembourg National Research Fund A18/BM/12341006, European Union's Horizon 2020 research and innovation programme 101036756, National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health (NIH), National Health and Medical Research Council (NHMRC) of Australia EL1 2009209, Australian Research Council DP190102476 Queensland Department of Health, Instituto de Salud Carlos III European Commission CP19/00060 European Union through Fondo Europeo de Desarrollo Regional (FEDER), Federal Ministry of Education & Research (BMBF) FKz: 02WRS1495 A/B/E, FWO 11G1821N, NIH via grant NIH NIGMS R01GM092218 NIH via grant NIH NCI 1R03CA222452-01, Vanderbilt Chemical Biology Interface training program 5T32GM065086-16, Netherlands Organization for Scientific Research (NWO) 15747, SOLUTIONS project (European Union's Seventh Framework Programme for research, technological development and demonstration) 603437, HBM4EU (European Union's Horizon 2020 research and innovation programme 733032, German Research Foundation (DFG) 441958208, NaToxAq (European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant 722493, German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU) (FKZ) 3716 67 416 0, German Federal Ministry for the Environment, Nature Conservation, Nuclear Safety and Consumer Protection (BMUV) Project (FKZ) 3719 65 408 0, EU Cohesion Funds within the project Monitoring and assessment of water body status 310011A366, Swiss Federal Office for the Environment (FOEN), Canadian Institutes of Health Research (CIHR) Genome Canada, MAVA foundation, Valery Foundation, National Science Foundation (NSF) RUI-1306074 National Natural Science Foundation of China (NSFC) 22193051 21906177, China Postdoctoral Science Foundation 2019M650863, Environmental Protection Administration, Executive Yuan, R.O.C. Taiwan (Taiwan EPA) 108C002871, Swiss Federal Office for the Environment, United States Environmental Protection Agency, Center for Forestry Research & Experimentation (CIEF), European Commission 2019/040, Marie Sklodowska-Curie grant 859891 European Commission European Commission Joint Research Centre 308610 289511, Joint Programming Initiative FOODBALL 2014-17 MCIN/AEI RYC2020-028901-I, ESF investing in your future, August T Larsson Guest Researcher Programme from the Swedish University of Agricultural Sciences, German Federal Ministry of Education and Research within the RiSKWa program 02WRS1273 02WRS1354, RECETOX research infrastructure (the Czech Ministry of Education, Youth and Sports) LM2018121, CETOCOEN PLUS project CZ.02.1.01/0.0/0.0/15_ 003/0000469 CETOCOEN EXCELLENCE Teaming 2 project - Czech ministry of Education, Youth and Sports CZ.02.1.01/0.0/0.0/1 7_043/0009632

DF-CONSORT: protocol for the rapid methodological review

Background: Prescribing clinicians have to negotiate ambiguities around information provision and consent for medications on a daily basis, despite the availability of professional guidance. Aim: This study aims to explore some of the many factors prescribing clinicians in the United Kingdom take into account when deciding what information to give to patients about medication choices, and when. Design: In depth face-to-face interviews, utilising both a hypothetical scenario and semi-structured prompts, were conducted in order to elicit extended reflections on how clinicians individually work through such dilemmas and make decisions. Setting/participants: Ten prescribing clinicians (doctors and nurses) from a large combined team of National Health Service (NHS) secondary and community palliative care providers in England. Results: Palliative care staff regularly face choices about information provision in prescribing discussions, in particular when considering whether information might increase distress. Participants presented three overlapping framings that helped them assess the range of factors that could potentially be taken into account; (1) assessing the individual patient, (2) tailoring the provision of information and (3) jointly forming a plan. Conclusions: Information provision about medication choices and effects is a demanding, ongoing process, requiring nuanced judgements that constitute an unacknowledged yet significant aspect of clinical workload. Although current medical guidelines allow clinical discretion about information provision, this can leave individual clinicians feeling vulnerable. Further evolution of guidelines needs to establish a more sophisticated way to acknowledge professional and legal requirements, whilst also promoting professional autonomy and judgement.

BackgroundIncomplete reporting of the design, conduct and analysis of early phase dose-finding trials can hinder interpretability and reproducibility, and lead to erroneous conclusions on tolerability and efficacy. This methodological review investigates the reporting quality of published trials using broadly the CONSORT 2010 checklist with added items unique to dose-finding trials.MethodsMEDLINE (PubMed) was searched for articles published in 2011-2020. Phase I or I/II trials, with planned interim dosing decisions (de/escalate, stay at the current level or an early stop), which aim to find a recommended dosing regimen(s) for further testing, were included. Data were extracted for 476 randomly selected trials, stratified by cancer/non-cancer settings.ResultsThe key items that are frequently not reported include: n (%) reported cancer(n=238) non-cancer (n=238)Methods Planned/maximum sample size 69 (29%) 105 (44%) with justification 35 (15%) 59 (25%) Recruitment method 19 (8%) 51 (21%) Oversight committees 39 (16%) 90 (38%) roles and structure 17 (7%) 40 (17%) Who makes dose decisions 10 (4%) 39 (16%) Definition of analysis population: dose-determination 108 (45%) 111 (47%) Safety 114 (48%) 129 (54%) key outcomes 100 (42%) 131 (56%) Rationale for starting dose 52 (22%) 42 (18%)Results Baseline demographic and clinical characteristics by each dose level 70 (29%) 148 (62%) Settings and locations where data were collected 86 (36%) 149 (63%) Participant flow diagram/table 85 (36%) 144 (61%) Losses/exclusions for each dose level 30 (13%) 85 (36%)Only 1 (0.4%) cancer trial was randomised compared to 180 (75.6%) non-cancer trials. Notably, very few trials (6.3%) provided accessible protocols. Improvement in the reporting over time is evident in some items, including participant flow and sample size justification.ConclusionImportant methodological features in design, conduct and analysis are frequently omitted. Overall, non-cancer trials appear to be better reported, as mainly randomised, they may have adopted CONSORT 2010 guidance. This review confirms the need for robust consensus-driven guidance for researchers and journals reporting dose-finding trials, to allow accurate assessment of their results to reduce research waste.

Additional file 1. Interview/focus group topic guide (minor adaptations made for each participant group as appropriate.

Additional file 2: Overview of the NORMAN-SLE website (DOCX format) as of 30 May 2022 [82].

La construcción del conocimiento puede verse como resultado del proceso activo del aprendizaje. Siguiendo este concepto en la actualidad podemos encontrar varias comunidades que se forman a partir de grupos de personas con intereses comunes para compartir y generar conocimiento. De estas comunidades, particularmente a las que brindan soporte computacional a las distintas etapas de la construcción de conocimiento las denominaremos Comunidades de Construcción de Conocimiento (CCC). La calidad del contenido en las CCC depende de la actividad y participación de sus miembros. Existen diferentes enfoques para alentar la participación de una CCC, por ejemplo, centrarse en atraer a los recién llegados o brindarles más atención u oportunidades de participación que a los miembros más antiguos de la comunidad. Un enfoque de tendencia es el uso de la ludificación. La ludificación es la aplicación de cualquier elemento de juegos o videojuegos en entornos no lúdicos. A través de estas estrategias, es factible mejorar la motivación para participar en diferentes escenarios de una CCC, así como guiar el tipo de participación que se ajuste mejor a los principios de la CCC. Una CCC podría enriquecerse mediante una ludificación que recompense la edición, la participación en discusiones con otros miembros, y diseminación de las producciones. Sin embargo, definir y probar un diseño ludificado en una CCC es un proceso largo que requiere iteraciones de configuración y evaluación que pueden resultar perjudiciales para la comunidad. Esto se debe a que el resultado de la aplicación de la ludificación no se puede predecir por completo. Una ludificación puede ser disruptiva para la comunidad si está mal configurada, por ejemplo, induciendo una competencia improductiva o desmotivando la participación. Esta tesis apoya la toma de decisión recomendando configuraciones, a fin de guiar al encargado de ludificar una comunidad. Tomando en consideración el contexto de incertidumbre inherente a la forma de trabajo colaborativo en las CCC. Para ello se desarrolla una metodología, que mediante el uso de aprendizaje por refuerzo (RL por sus siglas en ingles) y simulación basada en datos históricos configura ludificaciones para CCCs. Esta metodología a su vez, se presenta aplicada en el framework de RL desarrollado en este trabajo de tesis, llamado Historical Reinforcement Learning. Historical RL brinda soporte para la generación de entornos de aprendizaje por refuerzo que permitan entrenar agentes de RL en la tarea de configurar una ludificación para una determinada CCC. Dentro de sus características principales esta la compatibilidad con diversas librerías de agentes mediante el estándar de OpenAI Gym También facilita la integración de diversas comunidades y gestiona el flujo de datos históricos con los que se alimenta a la simulación. Finalmente introduce herramientas para el manejo de acciones por parte de los agentes y la entrega de recompensas a los mismos. En este trabajo se presentan también diversos casos de estudio donde se evalúa el alcance de la metodología, así como las capacidades del framework. Estos estudios demuestran una mejora respecto a la capacidad de configuración de la ludificación en un entorno no disruptivo para la comunidad., Facultad de Informática

Background: The NORMAN Association (https://www.norman-.network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-.network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https:// zenodo.org/communities/norman-.sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA's CompTox Chemicals Dashboard (https://comptox. epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101).Conclusions: The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the "one substance, one assessment" approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-.network.com/nds/SLE/).

Funder: Unitaid, BACKGROUND: There is an urgent unmet clinical need for the identification of novel therapeutics for the treatment of COVID-19. A number of COVID-19 late phase trial platforms have been developed to investigate (often repurposed) drugs both in the UK and globally (e.g. RECOVERY led by the University of Oxford and SOLIDARITY led by WHO). There is a pressing need to investigate novel candidates within early phase trial platforms, from which promising candidates can feed into established later phase platforms. AGILE grew from a UK-wide collaboration to undertake early stage clinical evaluation of candidates for SARS-CoV-2 infection to accelerate national and global healthcare interventions. METHODS/DESIGN: AGILE is a seamless phase I/IIa platform study to establish the optimum dose, determine the activity and safety of each candidate and recommend whether it should be evaluated further. Each candidate is evaluated in its own trial, either as an open label single arm healthy volunteer study or in patients, randomising between candidate and control usually in a 2:1 allocation in favour of the candidate. Each dose is assessed sequentially for safety usually in cohorts of 6 patients. Once a phase II dose has been identified, efficacy is assessed by seamlessly expanding into a larger cohort. AGILE is completely flexible in that the core design in the master protocol can be adapted for each candidate based on prior knowledge of the candidate (i.e. population, primary endpoint and sample size can be amended). This information is detailed in each candidate specific trial protocol of the master protocol. DISCUSSION: Few approved treatments for COVID-19 are available such as dexamethasone, remdesivir and tocilizumab in hospitalised patients. The AGILE platform aims to rapidly identify new efficacious and safe treatments to help end the current global COVID-19 pandemic. We currently have three candidate specific trials within this platform study that are open to recruitment. TRIAL REGISTRATION: EudraCT Number: 2020-001860-27 14 March 2020 ClinicalTrials.gov Identifier: NCT04746183 19 February 2021 ISRCTN reference: 27106947.

Accelerated melting of the Greenland Ice Sheet has increased freshwater delivery to the Arctic Ocean and amplified the need to understand the impact of Greenland Ice Sheet meltwater on Arctic greenhouse gas budgets. We evaluate subglacial discharge from the Greenland Ice Sheet for carbon dioxide (CO2) and methane (CH4) concentrations and δ13C values and use geochemical models to evaluate subglacial CH4 and CO2 sources and sinks. We compare discharge from southwest (a sub-catchment of the Isunnguata Glacier, sub-Isunnguata, and the Russell Glacier) and southern Greenland (Kiattut Sermiat). Meltwater CH4 concentrations vary by orders of magnitude between sites and are saturated with respect to atmospheric concentrations at Kiattut Sermiat. In contrast, meltwaters from southwest sites are supersaturated, even though oxidation reduces CH4 concentrations by up to 50 % during periods of low discharge. CO2 concentrations range from supersaturated at sub-Isunnguata to undersaturated at Kiattut Sermiat. CO2 is consumed by mineral weathering throughout the melt season at all sites; however, differences in the magnitude of subglacial CO2 sources result in meltwaters that are either sources or sinks of atmospheric CO2. At the sub-Isunnguata site, the predominant source of CO2 is organic matter (OM) remineralization. However, multiple or heterogeneous subglacial CO2 sources maintain atmospheric CO2 concentrations at Russell but not at Kiattut Sermiat, where CO2 is undersaturated. These results highlight a previously unrecognized degree of heterogeneity in greenhouse gas dynamics under the Greenland Ice Sheet. Future work should constrain the extent and controls of heterogeneity to improve our understanding of the impact of Greenland Ice Sheet melt on Arctic greenhouse gas budgets, as well as the role of continental ice sheets in greenhouse gas variations over glacial–interglacial timescales.

Despite being perhaps the foremost British meteorologist of the twentieth century, Reginald Sutcliffe has been understudied and underappreciated. His impact continues to this day every time you check the weather forecast. Reginald Sutcliffe and the Invention of Modern Weather Systems Science not only details Sutcliffe’s life and ideas, but it also illuminates the impact of social movements and the larger forces that propelled him on his consequential trajectory. Less than a century ago, a forecast of the weather tomorrow was considered a practical impossibility. This book makes the case that three important advances guided the development of modern dynamic meteorology, which led directly to the astounding progress in weather forecasting—and that Sutcliffe was the pioneer in all three of these foundational developments: the application of the quasi-geostrophic simplification to the equations governing atmospheric behavior, adoption of pressure as the vertical coordinate in analysis, and development of a diagnostic equation for vertical air motions. Shining a light on Sutcliffe’s life and work will, hopefully, inspire a renewed appreciation for the human dimension in scientific progress and the rich legacy bequeathed to societies wise enough to fully embrace investments in education and basic research. As climate change continues to grow more dire, modern extensions of Sutcliffe’s innovations increasingly offer some of the best tools we have for peering into the long-term future of our environment., https://docs.lib.purdue.edu/purduepress_previews/1069/thumbnail.jpg

Supplemental material, sj-pdf-1-jer-10.1177_14680874211018376 for Mapping the combustion modes of a dual-fuel compression ignition engine by Jonathan Martin and André Boehman in International Journal of Engine Research

Supplemental material, sj-pdf-1-jer-10.1177_14680874211018376 for Mapping the combustion modes of a dual-fuel compression ignition engine by Jonathan Martin and André Boehman in International Journal of Engine Research

The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU. The plan is to bring chemical risk assessors and managers together with scientists to accelerate method development and the production of necessary data and knowledge, and to facilitate the transition to next-generation evidence-based risk assessment, a non-toxic environment and the European Green Deal. The NORMAN Network is an independent, well-established and competent network of more than 80 organisations in the field of emerging substances and has enormous potential to contribute to the implementation of the PARC partnership. NORMAN stands ready to provide expert advice to PARC, drawing on its long experience in the development, harmonisation and testing of advanced tools in relation to chemicals of emerging concern and in support of a European Early Warning System to unravel the risks of contaminants of emerging concern (CECs) and close the gap between research and innovation and regulatory processes. In this commentary we highlight the tools developed by NORMAN that we consider most relevant to supporting the PARC initiative: (i) joint data space and cutting-edge research tools for risk assessment of contaminants of emerging concern; (ii) collaborative European framework to improve data quality and comparability; (iii) advanced data analysis tools for a European early warning system and (iv) support to national and European chemical risk assessment thanks to harnessing, combining and sharing evidence and expertise on CECs. By combining the extensive knowledge and experience of the NORMAN network with the financial and policy-related strengths of the PARC initiative, a large step towards the goal of a non-toxic environment can be taken.

The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

Accelerated melting of the Greenland Ice Sheet (GrIS) has increased freshwater delivery to the Arctic Ocean and amplified the need to understand the impact of GrIS meltwater on Arctic greenhouse gas (GHG) budgets. We measured carbon dioxide (CO2) and methane (CH4) concentrations and δ13C values and use geochemical models to evaluate subglacial CH4 and CO2 sources and sinks in water discharging from three subglacial outlets of the GrIS in southwest (Isunnguata and Russell Glaciers) and southern Greenland (Kiattut Sermiat). CH4 concentrations vary by orders of magnitude between sites and are saturated with respect to atmospheric concentrations at Kiattut Sermiat, but are supersaturated at southwest sites, even though oxidation reduces concentrations by up to 50 % during periods of low discharge. CO2 concentrations range from supersaturated at Isunnguata to undersaturated at Kiattut Sermiat. CO2 is consumed by mineral weathering throughout the melt season at all sites, however differences in the magnitude of subglacial CO2 sources result in meltwaters that are either sources or sinks of atmospheric CO2. The predominant source of CO2 at Isunnguata is organic matter (OM) remineralization, but Russell and Kiattut Sermiat sites have multiple or heterogeneous subglacial CO2 sources that maintain atmospheric CO2 concentrations at Russell but not at Kiattut Sermiat where CO2 is undersaturated. These results highlight the variability in GHG dynamics under the GrIS. Constraining this variability will improve our understanding of the impact of GrIS melt on Arctic GHG budgets, as well as the role of continental ice sheets in GHG variations over glacial-interglacial timescales.

International audience; Software testing, in particular acceptance testing, is a very important step in the development process of any application since it represents a way of matching the users’ expectations with the finished product ́s capabilities. Typically considered as a cumbersome activity, many efforts have been made to alleviate the burden of writing tests by, for instance, trying to generate them automatically. However, testing still remains a largely neglected step. In this paper we propose taking advantage of existing requirement artifacts to semi-automatically generate acceptance tests. This paper extends a previous paper in which we use Scenarios, a requirement artifact used to describe business processes and requirements, and Task/Method models, a modelling approach taken from the Artificial Intelligence field. The proposed approach derives a Task/Method model from Scenario (through rules) and from the Task/Method model specification, all alternatives in the flow of execution are provided. Using the proposed ideas, we show how the semi-automated generation of acceptance tests can be implemented by describing an ongoing development of a proof of concept web application designed to support the full process.

Additional file 3. Articles not used.

Additional file 8. Reported time trends or changes in concentrations.

Additional file 1. List of abbreviations.

Additional file 4. Critical appraisal checklist.

Additional file 7. Reanalysed time trends.

Additional file 2. Searches.

Tujuan dilakuka penelitian ini adalah memberitahukan Jumlah pengguna internet saat ini di Indonesia telah melampaui 50%

Additional file 2. Searches.

Additional file 1. List of abbreviations.

Additional file 3. Articles not used.

Additional file 7. Reanalysed time trends.

Additional file 4. Critical appraisal checklist.

Additional file 8. Reported time trends or changes in concentrations.

Rare earth element (REE) analyses were performed on 77 water samples and 5 sediment samples from the Indian River Lagoon system along the east coast of Florida. Groundwater samples were collected using nine multi-level piezometers installed along a shore-normal transect of the sandy subterranean estuary. Surface water samples were collected from Eau Gallie River and Crane Creek, the water column of the Indian River Lagoon above each piezometer, and the coastal Atlantic Ocean at Canova Beach. The REE concentrations of lagoon surface and subterranean estuary waters indicate that geochemical reactions within the subterranean estuary play a substantial role in the local REE cycle. The submarine groundwater discharge (SGD) flux of REEs calculated by using a modified form of the 1-dimensonal vertical-flow equation is comprised of a nearshore heavy REE (HREE) enriched advective source chiefly composed of terrestrial SGD, and a light REE (LREE) and middle REE (MREE) enriched source that originates from reductive dissolution of Fe(III) oxides/oxyhydroxides in the subterranean estuary and subsequent transport by bioirrigation to the overlying lagoon. The total SGD flux of REEs reveals that this sandy subterranean estuary is a source for light and middle REEs and a sink for the heavy REEs to coastal waters. The SGD Nd flux is estimated at 7.69 ± 1.02 mmol day-1, which is roughly equivalent to the effective local river flux to the Indian River Lagoon. Although our re-evaluated SGD flux of Nd to the Indian River Lagoon is lower than an earlier estimate, it represents a substantial input to the coastal ocean and thus provides additional insights into the global oceanic Nd budget and the “Nd Paradox”.

El objetivo principal de este trabajo es el desarrollo de un analizador de calidad basado en la tecnología FPGA para ayudar a la evaluación de la calidad de energía en sistemas trifásicos, ya que en los últimos años el crecimiento de las redes de distribución de energía, las cargas no lineales en el sistema y el uso de motores pueden provocar efectos a la red eléctrica, los cuales pueden tener un efecto muy significativo en el presupuesto a nivel industrial. Una deficiencia en la calidad de energía puede provocar costo de un mantenimiento frecuente, fallas en los equipos, paros de producción y multas por la compañía de suministro de energía. El desarrollo del presente trabajo muestra la metodología utilizada para el desarrollo del instrumento que incluye, el diseño de un circuito de acondicionamiento para las señales de alta corriente y voltaje que a su vez describe la etapa para aislar la parte de potencia con la electrónica. Así también se describe los protocolos de comunicación para los periféricos como el sistema de adquisición de datos, y el puerto para transmisión de datos. Una vez con los datos adquiridos por el sistema se procede a la implementación del diseño de hardware en el FPGA, el diseño describe el control principal para las diferentes tareas que realiza el analizador de calidad de energía, describe operaciones para el cálculo de índices de calidad de energía, con el resultado del diseño implementado observar las perturbaciones en la red examinando las variaciones en los índices de calidad de energía. El diseño de hardware es basado en las normas IEC 61000-4- 30 y IEC 61000-4-7, los cuales describen los métodos de medición de calidad de energía de forma técnica y métodos para el cálculo de armónicos e interarmónicos y la instrumentación. El dispositivo realiza el cálculo de voltaje pico, voltaje RMS, corriente pico, corriente RMS, factor de cresta, cálculo de interarmónicos y THD para cada uno de los canales de medición. También realiza el cálculo de potencia activa y potencia aparente para cada par de medición de corriente y voltaje. Los resultados de los cálculos fueron comparados con respecto a señales simuladas y se observó un error menor de 1% para cada índice de calidad con respecto al cálculo en el software Matlab, pero presentó mayor error cuando se implementó con el circuito de acondicionamiento, ya que los traductores no lineales presentan un error en la medición y ruidos producidos por los elementos del circuito de acondicionamiento, es por esto que un análisis profundo en este sistema es adecuado. De manera general el dispositivo sigue los requerimientos de las normas y es una forma viable para la evaluación de la calidad de energía. The main objective of this work is the development of a power quality analyzer based on FPGA technology to assist the evaluation of the quality of power in three-phase systems, since in recent years the growth of power distribution networks, the nonlinear loads in the system and the use of motors may cause electrical network effects, which can have a very significant effect on the industry-wide budget. A deficiency in power quality can cause frequent maintenance cost, equipment failures, production stoppages and fines for power supply company. The development of this work shows the methodology used for development of the instrument including the design of a circuit signal conditioning for high current and voltage which in turn describes the stage to isolate the power to the electronics. Well describes the communication protocols for peripherals such as the data acquisition system, and the port for data transmission. Once the data acquired by the system proceeds to the hardware implementation of the design in the FPGA, the design describes the primary control for the different tasks performed by the power quality analyzer, described operations to calculate quality indices energy , with the result of the design implemented disturbances observed in the network by examining the variations in power quality indices . The hardware design is based on IEC 61000-4-30 and IEC 61000-4-7, which describe the methods of measuring power quality technical manner and methods for the calculation of harmonics and interharmonics and instrumentation. The device performs the calculation of peak voltage, RMS voltage, peak current, RMS current, crest factor, and THD calculation interharmonics for each measurement channel. Also calculates active power and apparent power for each pair of current and voltage measurement. The results of the calculations were compared with respect to simulated signals and found an error less than 1 % for each quality index with respect to the calculation in Matlab software, but had higher error when implemented with conditioning circuit as nonlinear translators present a measurement error and noise produced by the conditioning circuit elements, which is why a thorough analysis in this system is adequate. Generally the device follows the requirements of the rules and is a viable way to assess the power quality.

The 2010-2011 New Zealand earthquakes induced significant liquefaction and associated lateral spreading displacements within the Canterbury Plains in and around the city of Christchurch. Massive amounts of soil ejecta and settlement of residential structures occurred in Christchurch and its eastern suburbs, with the most severe occurring along rivers and. Lateral spreading was particularly severe along the Avon River that flows through the affected area, with spreads extending 50 m to 100 m from the river and experiencing several meters of deformation. Remote sensing methods have advanced to a stage such that they can provide quantitative estimates of lateral spread deformations at a scale that is relevant for geotechnical earthquake engineering studies. This paper presents preliminary results from optical imagery correlation of the Christchurch that provides estimates of deformation patterns due to lateral spreading along the Avon River. These results show localized deformations associated with lateral spreading with magnitudes between 0.5 and 3.0 m. The deformation patterns show a change in direction at the river, confirming that the deformations are associated with the ground spreading towards the river.

The discovery of ubiquitin-like small archaeal modifier protein 2 (SAMP2) that forms covalent polymeric chains in Haloferax volcanii has generated tremendous interest in the function and regulation of this protein. At present, it remains unclear whether the Hfx. volcanii modifier protein SAMP1 has such polyubiquitinating-like activity. Although SAMP1 and SAMP2 use the same conjugation machinery to modify their target proteins, each can impart distinct functional consequences. To better understand the mechanism of SAMP2 conjugation, we have sought to characterize the biophysical and structural properties of the protein from Hfx. volcanii. SAMP2 is only partially structured under mesohalic solution conditions and adopts a well-folded compact conformation in the presence of 2.5M of NaCl. Its 2.3-Å-resolution crystal structure reveals a characteristic α/β central core domain and a unique β-hinge motif. This motif anchors an unusual C-terminal extension comprising the diglycine tail as well as two lysine residues that can potentially serve to interlink SAMP2 moieties. Mutational alternation of the structural malleability of this β-hinge motif essentially abolishes the conjugation activity of SAMP2 in vivo. In addition, NMR structural studies of the putative ubiquitin-like protein HVO_2177 from Hfx. volcanii show that like SAMP1, HVO_2177 forms a classic β-grasp fold in a salt-independent manner. These results provide insights into the structure-function relationship of sampylating proteins of fundamental importance in post-translational protein modification and environmental cues in Archaea.

At Transport Canada’s request, the National Research Council of Canada (NRC) examined potential safety issues related to leaks from natural gas Class 2 trucks in Canada. This work involved performing a literature review in order to establish the required parameters to perform computational fluid dynamics (CFD) simulations of different leak scenarios of Class 2 compressed natural gas (CNG) vehicles inside parking garages., Prepared for: ecoTECHNOLOGY for Vehicles Stewardship and Sustainable Transportation Programs, Transport Canada