A Workflows Roadmap for the Geosciences

The EarthCube Workflows Community Group was formed in March 2012 as part of the NSF EarthCube initiative in response to initial discussions in EarthCube that occurred during 2011. Workflows are used to manage complex computations that have many steps or use large data. Workflow systems assist scientists to select models appropriate for their data, configure them with appropriate parameters, and execute them efficiently. The EarthCube community saw great value in workflow technologies for the future of geosciences. The goal of the EarthCube Workflows Community Group was to begin to elicit requirements for workflows in geosciences, ascertain the state of the art and current practices, identify current gaps in both the use of and capabilities of current workflow systems in the earth sciences through use case studies, and identify grand challenges for the next decade along with the possible paths to addressing those challenges. The group was asked to produce a roadmap for workflows in geosciences. Three other Community Groups were formed (Data, Semantics and Ontologies, and Governance), and each was asked to create a roadmap in their area. The group held a series of virtual and face-to-face workshops to solicit participation from the geosciences community and other relevant researchers. The EarthCube Workflows Community Group set up a public web site where all their activities were made open for participation from the community and all documents were posted for public access and editing (https://sites.google.com/site/earthcubeworkflow/). Presentations and discussions were recorded and posted on the site. A key result of the work of the EarthCube Workflows Community Group activities in Spring and Summer 2012 was the creation of a workflows roadmap for the geosciences. An initial roadmap document for the EarthCube community that was first released in June 2012 and presented to the EarthCube community. A revised roadmap was delivered to the community in August 2012. The roadmap serves as a living document created as a group effort with provisions and a process to update and extend it over time.This document represents the final roadmap of the NSF EarthCube Community Group for workflows in the geosciences. Community feedback is always welcome, as the roadmap will be revised and extended while EarthCube activities continue.This work was supported through National Science Foundation under grant # EAR-1238216 as part of the NSF EarthCube initiative. EarthCube is an innovative and longterm cross-directorate initiative of the US National Science Foundation

ANKOS publisher application system and its impact on the e-resource evaluation process

The Publisher Application System (PAS) is a Web-based archiving and online evaluation system developed by the Database Evaluation Group (DEG), one of the working groups formed within the Anatolian University Libraries Consortium (ANKOS). The DEG was formed in 2008 to inquire and evaluate e-resources suited to the needs of the consortium; to follow up similar consortial activities worldwide as well as developments in connection with the scientific publishing industry; and to determine, implement, and improve pricing models in accordance with the prevailing economic, legal, and academic system. Development of the PAS was essential to ensure standardization and sustainability towards a more detailed and effective analysis of e-resources qualifying for evaluation by ANKOS. The PAS played an important part not only in establishing and defining the workflow of the DEG, but also in creating an archive of both the e-resources submitted to the consortium and the applicant publishers/agents submitting these resources. This article outlines the process that started with the foundation of the DEG through the formation of the PAS as well as the present setup of the system. It is also hoped that this case study will have a positive contribution to the processes being followed by the persons and the groups engaged in similar activities.pre-prin

Reproducibility of scientific workflows execution using cloud-aware provenance (ReCAP)

© 2018, Springer-Verlag GmbH Austria, part of Springer Nature. Provenance of scientific workflows has been considered a mean to provide workflow reproducibility. However, the provenance approaches adopted so far are not applicable in the context of Cloud because the provenance trace lacks the Cloud information. This paper presents a novel approach that collects the Cloud-aware provenance and represents it as a graph. The workflow execution reproducibility on the Cloud is determined by comparing the workflow provenance at three levels i.e., workflow structure, execution infrastructure and workflow outputs. The experimental evaluation shows that the implemented approach can detect changes in the provenance traces and the outputs produced by the workflow

ANKOS publisher application system and its impact on the e-resource evaluation process

The Publisher Application System (PAS) is a Web-based archiving and online evaluation system developed by the Database Evaluation Group (DEG), one of the working groups formed within the Anatolian University Libraries Consortium (ANKOS). The DEG was formed in 2008 to inquire and evaluate e-resources suited to the needs of the consortium; to follow up similar consortial activities worldwide as well as developments in connection with the scientific publishing industry; and to determine, implement, and improve pricing models in accordance with the prevailing economic, legal, and academic system. Development of the PAS was essential to ensure standardization and sustainability towards a more detailed and effective analysis of e-resources qualifying for evaluation by ANKOS. The PAS played an important part not only in establishing and defining the workflow of the DEG, but also in creating an archive of both the e-resources submitted to the consortium and the applicant publishers/agents submitting these resources. This article outlines the process that started with the foundation of the DEG through the formation of the PAS as well as the present setup of the system. It is also hoped that this case study will have a positive contribution to the processes being followed by the persons and the groups engaged in similar activities.pre-prin

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Integrating plant physiology into simulation of fire behavior and effects

Wildfires are a global crisis, but current fire models fail to capture vegetation response to changing climate. With drought and elevated temperature increasing the importance of vegetation dynamics to fire behavior, and the advent of next generation models capable of capturing increasingly complex physical processes, we provide a renewed focus on representation of woody vegetation in fire models. Currently, the most advanced representations of fire behavior and biophysical fire effects are found in distinct classes of fine-scale models and do not capture variation in live fuel (i.e. living plant) properties. We demonstrate that plant water and carbon dynamics, which influence combustion and heat transfer into the plant and often dictate plant survival, provide the mechanistic linkage between fire behavior and effects. Our conceptual framework linking remotely sensed estimates of plant water and carbon to fine-scale models of fire behavior and effects could be a critical first step toward improving the fidelity of the coarse scale models that are now relied upon for global fire forecasting. This process-based approach will be essential to capturing the influence of physiological responses to drought and warming on live fuel conditions, strengthening the science needed to guide fire managers in an uncertain future

Infection prevention and control practice for Crimean-Congo hemorrhagic fever - A multicenter cross-sectional survey in Eurasia

<div><p>Background</p><p>Crimean Congo Hemorrhagic Fever (CCHF) is a life threatening acute viral infection that presents significant risk of nosocomial transmission to healthcare workers.</p><p>Aim</p><p>Evaluation of CCHF infection prevention and control (IP&C) practices in healthcare facilities that routinely manage CCHF cases in Eurasia.</p><p>Methods</p><p>A cross-sectional CCHF IP&C survey was designed and distributed to CCHF centers in 10 endemic Eurasian countries in 2016.</p><p>Results</p><p>Twenty-three responses were received from centers in Turkey, Pakistan, Russia, Georgia, Kosovo, Bulgaria, Oman, Iran, India and Kazakhstan. All units had dedicated isolation rooms for CCHF, with cohorting of confirmed cases in 15/23 centers and cohorting of suspect and confirmed cases in 9/23 centers. There was adequate personal protective equipment (PPE) in 22/23 facilities, with 21/23 facilities reporting routine use of PPE for CCHF patients. Adequate staffing levels to provide care reported in 14/23 locations. All centers reported having a high risk CCHFV nosocomial exposure in last five years, with 5 centers reporting more than 5 exposures. Education was provided annually in most centers (13/23), with additional training requested in PPE use (11/23), PPE donning/doffing (12/23), environmental disinfection (12/23) and waste management (14/23).</p><p>Conclusions</p><p>Staff and patient safety must be improved and healthcare associated CCHF exposure and transmission eliminated. Improvements are recommended in isolation capacity in healthcare facilities, use of PPE and maintenance of adequate staffing levels. We recommend further audit of IP&C practice at individual units in endemic areas, as part of national quality assurance programs.</p></div

Impact of neuraminidase inhibitors on influenza A(H1N1)pdm09‐related pneumonia: an individual participant data meta‐analysis

BACKGROUND: The impact of neuraminidase inhibitors (NAIs) on influenza‐related pneumonia (IRP) is not established. Our objective was to investigate the association between NAI treatment and IRP incidence and outcomes in patients hospitalised with A(H1N1)pdm09 virus infection. METHODS: A worldwide meta‐analysis of individual participant data from 20 634 hospitalised patients with laboratory‐confirmed A(H1N1)pdm09 (n = 20 021) or clinically diagnosed (n = 613) ‘pandemic influenza’. The primary outcome was radiologically confirmed IRP. Odds ratios (OR) were estimated using generalised linear mixed modelling, adjusting for NAI treatment propensity, antibiotics and corticosteroids. RESULTS: Of 20 634 included participants, 5978 (29·0%) had IRP; conversely, 3349 (16·2%) had confirmed the absence of radiographic pneumonia (the comparator). Early NAI treatment (within 2 days of symptom onset) versus no NAI was not significantly associated with IRP [adj. OR 0·83 (95% CI 0·64–1·06; P = 0·136)]. Among the 5978 patients with IRP, early NAI treatment versus none did not impact on mortality [adj. OR = 0·72 (0·44–1·17; P = 0·180)] or likelihood of requiring ventilatory support [adj. OR = 1·17 (0·71–1·92; P = 0·537)], but early treatment versus later significantly reduced mortality [adj. OR = 0·70 (0·55–0·88; P = 0·003)] and likelihood of requiring ventilatory support [adj. OR = 0·68 (0·54–0·85; P = 0·001)]. CONCLUSIONS: Early NAI treatment of patients hospitalised with A(H1N1)pdm09 virus infection versus no treatment did not reduce the likelihood of IRP. However, in patients who developed IRP, early NAI treatment versus later reduced the likelihood of mortality and needing ventilatory support