A flexible framework for assessing the quality of crowdsourced data

Ponencias, comunicaciones y pósters presentados en el 17th AGILE Conference on Geographic Information Science "Connecting a Digital Europe through Location and Place", celebrado en la Universitat Jaume I del 3 al 6 de junio de 2014.Crowdsourcing as a means of data collection has produced previously unavailable data assets and enriched existing ones, but its quality can be highly variable. This presents several challenges to potential end users that are concerned with the validation and quality assurance of the data collected. Being able to quantify the uncertainty, define and measure the different quality elements associated with crowdsourced data, and introduce means for dynamically assessing and improving it is the focus of this paper. We argue that the required quality assurance and quality control is dependent on the studied domain, the style of crowdsourcing and the goals of the study. We describe a framework for qualifying geolocated data collected from non-authoritative sources that enables assessment for specific case studies by creating a workflow supported by an ontological description of a range of choices. The top levels of this ontology describe seven pillars of quality checks and assessments that present a range of techniques to qualify, improve or reject data. Our generic operational framework allows for extension of this ontology to specific applied domains. This will facilitate quality assurance in real-time or for post-processing to validate data and produce quality metadata. It enables a system that dynamically optimises the usability value of the data captured. A case study illustrates this framework

The role of macrophages and polymorphs in the levan-induced inhibition of Lewis lung carcinoma in C57BL mice.

High-mol.-wt levan injected locally inhibits the growth of Lewis lung carcinoma in C57BL mice. The inhibition is dependent on the number of tumour cells injected and on the dose of levan. The inhibition decreases tumour incidence and size as well as prolonging survival. The polysaccharide is most effective when injected daily beginning on the day of tumour-cell inoculation. Treatment begun on later dates is less effective. Treatment begun one day before tumour-cell inoculation enhances tumour growth. Histological studies showed that levan induces an intense polymorphonuclear (PMN) reaction followed by accumulation of vacuolated, levan-laden macrophages. Both PMN and activated macrophages seemed to have an inhibitory effect upon the growth of the tumour. The effector role of PMN was not explained by the histological study. Tumour cells in close contact with levan-laden macrophages appeared mostly necrotic. Administration of levan begun one day before tumour-cell inoculation produced a similar reaction, but the infiltrating cells did not appear to approach and damage the tumour cells

Full meta objects for flexible geoprocessing workflows: profiling WPS or BPMN?

The design and execution of scientific workflows is an important and necessary function within many disciplines. In the geospatial community, workflows are used to generate and quality assure new spatial datasets based on sequences of processing steps or complex modelling. Using BPMN for representing these workflows allows stakeholders to discuss the scientific conceptual approach behind this modelling whilst also being able to execute its encoding in XML. Previous research has focused on developing frameworks, including a BPMN workflow engine, capable of orchestrating OGC Web Processing Services and thus enabling construction of interoperable workflows comprised of distributed resources. These could populate, for example, the GEOSS repository. However, to date, such work has focused on executing workflows with direct access to the pre-defined data inputs and outputs, with a lack of flexibility and efficiency in semantic interoperability or data management during composition and execution. This article suggests a meta-approach based on two possible configurations that enable workflow orchestration at a meta level using a direct coupling with a metadata catalogue. The designs of a Web Processing Service profile and of a BPMN profile are presented as potential approaches to abstract the data interchange between the processing steps of a workflow. The paper concludes with a discussion of how these approaches may be extended and how complete workflows might be registered and managed using catalogues services

Message to complementary and alternative medicine: evidence is a better friend than power

BACKGROUND: Evidence-based medicine (EBM) is being embraced by an increasing number of practitioners and advocates of complementary and alternative medicine (CAM). A significant constituency within CAM, however, appears to have substantive doubts about EBM and some are expressly hostile. DISCUSSION: Many of the arguments raised against EBM within the CAM community are based on a caricature radically at odds with established, accepted and published principles of EBM practice. Contrary to what has sometimes been argued, EBM is not cookbook medicine that ignores individual needs. Neither does EBM mandate that only proven therapies should be used. Before EBM, decisions on health care tended to be based on tradition, power and influence. Such modes usually act to the disadvantage of marginal groups. CONCLUSION: By placing CAM on an equal footing with conventional medicine - what matters for both is evidence of effectiveness - EBM provides an opportunity for CAM to find an appropriate and just place in health care

Retrospective observational study to assess the clinical management and outcomes of hospitalised patients with complicated urinary tract infection in countries with high prevalence of multidrug resistant Gram-negative bacteria (RESCUING)

INTRODUCTION: The emergence of multidrug resistant (MDR) Gram-negative bacteria (GNB), including carbapenemase-producing strains, has become a major therapeutic challenge. These MDR isolates are often involved in complicated urinary tract infection (cUTI), and are associated with poor clinical outcomes. The study has been designed to gain insight into the epidemiology, clinical management, outcome and healthcare cost of patients with cUTI, especially in countries with high prevalence of MDR GNB. METHODS AND ANALYSIS: This multinational and multicentre observational, retrospective study will identify cases from 1 January 2013 to 31 December 2014 in order to collect data on patients with cUTI as a cause of hospital admission, and patients who develop cUTI during their hospital stay. The primary end point will be treatment failure defined as the presence of any of the following criteria: (1) signs or symptoms of cUTI present at diagnosis that have not improved by days 5–7 with appropriate antibiotic therapy, (2) new cUTI-related symptoms that have developed within 30 days of diagnosis, (3) urine culture taken within 30 days of diagnosis, either during or after completion of therapy, that grows ≥104 colony-forming unit/mL of the original pathogen and (4) death irrespective of cause within 30 days of the cUTI diagnosis. SAMPLE SIZE: 1000 patients afford a power of 0.83 (α=0.05) to detect an absolute difference of 10% in the treatment failure rate between MDR bacteria and other pathogens. This should allow for the introduction of about 20 independent risk factors (or their interaction) in a logistic regression model looking at risk factors for failure. ETHICS AND DISSEMINATION: Approval will be sought from all relevant Research Ethics Committees. Publication of this study will be considered as a joint publication by the participating investigator leads, and will follow the recommendations of the International Committee of Medical Journal Editors (ICMJE)

Mutations in protocadherin 15 and cadherin 23 affect tip links and mechanotransduction in mammalian sensory hair cells

Immunocytochemical studies have shown that protocadherin-15 (PCDH15) and cadherin-23 (CDH23) are associated with tip links, structures thought to gate the mechanotransducer channels of hair cells in the sensory epithelia of the inner ear. The present report describes functional and structural analyses of hair cells from Pcdh15av3J (av3J), Pcdh15av6J (av6J) and Cdh23v2J (v2J) mice. The av3J and v2J mice carry point mutations that are predicted to introduce premature stop codons in the transcripts for Pcdh15 and Cdh23, respectively, and av6J mice have an in-frame deletion predicted to remove most of the 9th cadherin ectodomain from PCDH15. Severe disruption of hair-bundle morphology is observed throughout the early-postnatal cochlea in av3J/av3J and v2J/v2J mice. In contrast, only mild-to-moderate bundle disruption is evident in the av6J/av6J mice. Hair cells from av3J/av3J mice are unaffected by aminoglycosides and fail to load with [3H]-gentamicin or FM1-43, compounds that permeate the hair cell's mechanotransducer channels. In contrast, hair cells from av6J/av6J mice load with both FM1-43 and [3H]-gentamicin, and are aminoglycoside sensitive. Transducer currents can be recorded from hair cells of all three mutants but are reduced in amplitude in all mutants and have abnormal directional sensitivity in the av3J/av3J and v2J/v2J mutants. Scanning electron microscopy of early postnatal cochlear hair cells reveals tip-link like links in av6J/av6J mice, substantially reduced numbers of links in the av3J/av3J mice and virtually none in the v2J/v2J mice. Analysis of mature vestibular hair bundles reveals an absence of tip links in the av3J/av3J and v2J/v2J mice and a reduction in av6J/av6J mice. These results therefore provide genetic evidence consistent with PCDH15 and CDH23 being part of the tip-link complex and necessary for normal mechanotransduction

Clinical impact of a commercially available multiplex PCR system for rapid detection of pathogens in patients with presumed sepsis

<p>Abstract</p> <p>Background</p> <p>Timely identification of pathogens is crucial to minimize mortality in patients with severe infections. Detection of bacterial and fungal pathogens in blood by nucleic acid amplification promises to yield results faster than blood cultures (BC). We analyzed the clinical impact of a commercially available multiplex PCR system in patients with suspected sepsis.</p> <p>Methods</p> <p>Blood samples from patients with presumed sepsis were cultured with the Bactec 9240™ system (Becton Dickinson, Heidelberg, Germany) and aliquots subjected to analysis with the LightCycler^®SeptiFast^®(SF) Test (Roche Diagnostics, Mannheim, Germany) at a tertiary care centre. For samples with PCR-detected pathogens, the actual impact on clinical management was determined by chart review. Furthermore a comparison between the time to a positive blood culture result and the SF result, based on a fictive assumption that it was done either on a once or twice daily basis, was made.</p> <p>Results</p> <p>Of 101 blood samples from 77 patients, 63 (62%) yielded concordant negative results, 14 (13%) concordant positive and 9 (9%) were BC positive only. In 14 (13%) samples pathogens were detected by SF only, resulting in adjustment of antibiotic therapy in 5 patients (7,7% of patients). In 3 samples a treatment adjustment would have been made earlier resulting in a total of 8 adjustments in all 101 samples (8%).</p> <p>Conclusion</p> <p>The addition of multiplex PCR to conventional blood cultures had a relevant impact on clinical management for a subset of patients with presumed sepsis.</p

Earth observation for citizen science validation, or citizen science for earth observation validation? The role of quality assurance of volunteered observations

Environmental policy involving citizen science (CS) is of growing interest. In support of this open data stream of information, validation or quality assessment of the CS geo-located data to their appropriate usage for evidence-based policy making needs a flexible and easily adaptable data curation process ensuring transparency. Addressing these needs, this paper describes an approach for automatic quality assurance as proposed by the Citizen OBservatory WEB (COBWEB) FP7 project. This approach is based upon a workflow composition that combines different quality controls, each belonging to seven categories or “pillars”. Each pillar focuses on a specific dimension in the types of reasoning algorithms for CS data qualification. These pillars attribute values to a range of quality elements belonging to three complementary quality models. Additional data from various sources, such as Earth Observation (EO) data, are often included as part of the inputs of quality controls within the pillars. However, qualified CS data can also contribute to the validation of EO data. Therefore, the question of validation can be considered as “two sides of the same coin”. Based on an invasive species CS study, concerning Fallopia japonica (Japanese knotweed), the paper discusses the flexibility and usefulness of qualifying CS data, either when using an EO data product for the validation within the quality assurance process, or validating an EO data product that describes the risk of occurrence of the plant. Both validation paths are found to be improved by quality assurance of the CS data. Addressing the reliability of CS open data, issues and limitations of the role of quality assurance for validation, due to the quality of secondary data used within the automatic workflow, are described, e.g., error propagation, paving the route to improvements in the approach

Citizen OBservatory WEB (COBWEB): A Generic Infrastructure Platform to Facilitate the Collection of Citizen Science Data for Environmental Monitoring

COBWEB has used the UNESCO World Network of Biosphere Reserves as a testbed for researching and developing a generic crowdsourcing infrastructure platform for environmental monitoring. A major challenge is dealing with what is necessarily a complex problem requiring sophisticated solutions balanced with the need to present sometimes unsophisticated users with comprehensible and useable software. The components of the COBWEB platform are at different Technology Readiness Levels. This short paper outlines the overall solution and points to quality assurance, standardisation and semantic interoperability as key areas requiring further attention