History of chemically and radiatively important atmospheric gases from the Advanced Global Atmospheric Gases Experiment (AGAGE)

We present the organization, instrumentation, datasets, data interpretation, modeling, and accomplishments of the multinational global atmospheric measurement program AGAGE (Advanced Global Atmospheric Gases Experiment). AGAGE is distinguished by its capability to measure globally, at high frequency, and at multiple sites all the important species in the Montreal Protocol and all the important non-carbon-dioxide (non-CO₂) gases assessed by the Intergovernmental Panel on Climate Change (CO₂ is also measured at several sites). The scientific objectives of AGAGE are important in furthering our understanding of global chemical and climatic phenomena. They are the following: (1) to accurately measure the temporal and spatial distributions of anthropogenic gases that contribute the majority of reactive halogen to the stratosphere and/or are strong infrared absorbers (chlorocarbons, chlorofluorocarbons – CFCs, bromocarbons, hydrochlorofluorocarbons – HCFCs, hydrofluorocarbons – HFCs and polyfluorinated compounds (perfluorocarbons – PFCs), nitrogen trifluoride – NF₃, sulfuryl fluoride – SO₂F₂, and sulfur hexafluoride – SF₆) and use these measurements to determine the global rates of their emission and/or destruction (i.e., lifetimes); (2) to accurately measure the global distributions and temporal behaviors and determine the sources and sinks of non-CO₂ biogenic–anthropogenic gases important to climate change and/or ozone depletion (methane – CH₄, nitrous oxide – N₂O, carbon monoxide – CO, molecular hydrogen – H₂, methyl chloride – CH₃Cl, and methyl bromide – CH₃Br); (3) to identify new long-lived greenhouse and ozone-depleting gases (e.g., SO₂F₂, NF₃, heavy PFCs (C₄F₁₀, C₅F₁₂, C₆F₁₄, C₇F₁₆, and C₈F₁₈) and hydrofluoroolefins (HFOs; e.g., CH₂  =  CFCF₃) have been identified in AGAGE), initiate the real-time monitoring of these new gases, and reconstruct their past histories from AGAGE, air archive, and firn air measurements; (4) to determine the average concentrations and trends of tropospheric hydroxyl radicals (OH) from the rates of destruction of atmospheric trichloroethane (CH₃CCl₃), HFCs, and HCFCs and estimates of their emissions; (5) to determine from atmospheric observations and estimates of their destruction rates the magnitudes and distributions by region of surface sources and sinks of all measured gases; (6) to provide accurate data on the global accumulation of many of these trace gases that are used to test the synoptic-, regional-, and global-scale circulations predicted by three-dimensional models; and (7) to provide global and regional measurements of methane, carbon monoxide, and molecular hydrogen and estimates of hydroxyl levels to test primary atmospheric oxidation pathways at midlatitudes and the tropics. Network Information and Data Repository: <a href="http://agage.mit.edu/data" target="_blank">http://agage.mit.edu/data</a> or <a href="http://cdiac.ess-dive.lbl.gov/ndps/alegage.html" target="_blank">http://cdiac.ess-dive.lbl.gov/ndps/alegage.html</a> (<a href="https://doi.org/10.3334/CDIAC/atg.db1001" target="_blank">https://doi.org/10.3334/CDIAC/atg.db1001</a>)

A Conceptual Modelling Approach to Visualising Linked Data

Increasing numbers of Linked Open Datasets are being published, and many possible data visualisations may be appropriate for a user's given exploration or analysis task over a dataset. Users may therefore find it difficult to identify visualisations that meet their data exploration or analyses needs. We propose an approach that creates conceptual models of groups of commonly used data visualisations, which can be used to analyse the data and users' queries so as to automatically generate recommendations of possible visualisations. To our knowledge, this is the first work to propose a conceptual modelling approach to recommending visualisations for Linked Data

Duty, desire or indifference? A qualitative study of patient decisions about recruitment to an epilepsy treatment trial

BACKGROUND: Epilepsy is a common neurological condition, in which drugs are the mainstay of treatment and drugs trials are commonplace. Understanding why patients might or might not opt to participate in epilepsy drug trials is therefore of some importance, particularly at a time of rapid drug development and testing; and the findings may also have wider applicability. This study examined the role of patient perceptions in the decision-making process about recruitment to an RCT (the SANAD Trial) that compared different antiepileptic drug treatments for the management of new-onset seizures and epilepsy. METHODS: In-depth interviews with 23 patients recruited from four study centres. All interviews were tape-recorded and transcribed; the transcripts were analysed thematically using a qualitative data analysis package. RESULTS: Of the nineteen informants who agreed to participate in SANAD, none agreed for purely altruistic reasons. The four informants who declined all did so for very specific reasons of self-interest. Informants' perceptions of the nature of the trial, of the drugs subject to trial, and of their own involvement were all highly influential in their decision-making. Informants either perceived the trial as potentially beneficial or unlikely to be harmful, and so agreed to participate; or as potentially harmful or unlikely to be beneficial and so declined to participate. CONCLUSION: Most patients applied 'weak altruism', while maintaining self-interest. An emphasis on the safety and equivalence of treatments allowed some patients to be indifferent to the question of involvement. There was evidence that some participants were subject to 'therapeutic misconceptions'. The findings highlight the individual nature of trials but nonetheless raise some generic issues in relation to their design and conduct

Cigarette smoking, genetic polymorphisms and colorectal cancer risk: the Fukuoka Colorectal Cancer Study

Background: It is uncertain whether smoking is related to colorectal cancer risk. Cytochrome P-450 CYP1A1, glutathione-S-transferase (GST) and NAD(P)H:quinone oxidoreductase 1 (NQO1) are important enzymes in the metabolism of tobacco carcinogens, and functional genetic polymorphisms are known for these enzymes. We investigated the relation of cigarette smoking and related genetic polymorphisms to colorectal cancer risk, with special reference to the interaction between smoking and genetic polymorphism. Methods: We used data from the Fukuoka Colorectal Cancer Study, a population-based case-control study, including 685 cases and 778 controls who gave informed consent to genetic analysis. Interview was conducted to assess lifestyle factors, and DNA was extracted from buffy coat. Results: In comparison with lifelong nonsmokers, the odds ratios (OR) of colorectal cancer for &lt;400, 400-799 and ≥800 cigarette-years were 0.65 (95 % confidence interval [CI], 0.45-0.89), 1.16 (0.83-1.62) and 1.14 (0.73-1.77), respectively. A decreased risk associated with light smoking was observed only for colon cancer, and rectal cancer showed an increased risk among those with ≥400 cigarette-years (OR 1.60, 95 % CI 1.04-2.45). None of the polymorphisms under study was singly associated with colorectal cancer risk. Of the gene-gene interactions studied, the composite genotype of CYP1A1*2A or CYP1A1*2C and GSTT1 polymorphisms was associated with a decreased risk of colorecta

Repeated Assessments of Informed Consent Comprehension among HIV-Infected Participants of a Three-Year Clinical Trial in Botswana

Informed consent (IC) has been an international standard for decades for the ethical conduct of clinical trials. Yet frequently study participants have incomplete understanding of key issues, a problem exacerbated by language barriers or lack of familiarity with research concepts. Few investigators measure participant comprehension of IC, while even fewer conduct interim assessments once a trial is underway.We assessed comprehension of IC using a 20-question true/false quiz administered in 6-month intervals in the context of a placebo-controlled, randomized trial for the prevention of tuberculosis among HIV-infected adults in Botswana (2004-2009). Quizzes were offered in both Setswana and English. To enroll in the TB trial, participants were required to have ≥ 16/20 correct responses. We examined concepts understood and the degree to which understanding changed over three-years. We analyzed 5,555 quizzes from 1,835 participants. The participants' highest education levels were: 28% primary, 59% secondary, 9% tertiary and 7% no formal education. Eighty percent of participants passed the enrollment quiz (Quiz1) on their first attempt and the remainder passed on their second attempt. Those having higher than primary education and those who took the quiz in English were more likely to receive a passing score on their first attempt (adjusted odds ratios and 95% confidence intervals, 3.1 (2.4-4.0) and 1.5 (1.2, 1.9), respectively). The trial's purpose or procedures were understood by 90-100% of participants, while 44-77% understood randomization, placebos, or risks. Participants who failed Quiz1 on their initial attempt were more likely to fail quizzes later in the trial. Pass rates improved with quiz re-administration in subsequent years.Administration of a comprehension quiz at enrollment and during follow-up was feasible in a large, international collaboration and efficiently determined IC comprehension by trial participants. Strategies to improve understanding of concepts like placebos and randomization are needed. Comprehension assessments throughout a study may reinforce key concepts

Ontology-based end-user visual query formulation: Why, what, who, how, and which?

Value creation in an organisation is a time-sensitive and data-intensive process, yet it is often delayed and bounded by the reliance on IT experts extracting data for domain experts. Hence, there is a need for providing people who are not professional developers with the flexibility to pose relatively complex and ad hoc queries in an easy and intuitive way. In this respect, visual methods for query formulation undertake the challenge of making querying independent of users’ technical skills and the knowledge of the underlying textual query language and the structure of data. An ontology is more promising than the logical schema of the underlying data for guiding users in formulating queries, since it provides a richer vocabulary closer to the users’ understanding. However, on the one hand, today the most of world’s enterprise data reside in relational databases rather than triple stores, and on the other, visual query formulation has become more compelling due to ever-increasing data size and complexity—known as Big Data. This article presents and argues for ontology-based visual query formulation for end-users; discusses its feasibility in terms of ontology-based data access, which virtualises legacy relational databases as RDF, and the dimensions of Big Data; presents key conceptual aspects and dimensions, challenges, and requirements; and reviews, categorises, and discusses notable approaches and systems

Global and regional emissions estimates of 1,1-difluoroethane (HFC-152a, CH3CHF2) from in situ and air archive observations

High frequency, in situ observations from 11 globally distributed sites for the period 1994–2014 and archived air measurements dating from 1978 onward have been used to determine the global growth rate of 1,1-difluoroethane (HFC-152a, CH3CHF2). These observations have been combined with a range of atmospheric transport models to derive global emission estimates in a top-down approach. HFC-152a is a greenhouse gas with a short atmospheric lifetime of about 1.5 years. Since it does not contain chlorine or bromine, HFC-152a makes no direct contribution to the destruction of stratospheric ozone and is therefore used as a substitute for the ozone depleting chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs). The concentration of HFC-152a has grown substantially since the first direct measurements in 1994, reaching a maximum annual global growth rate of 0.84 ± 0.05 ppt yr−1 in 2006, implying a substantial increase in emissions up to 2006. However, since 2007, the annual rate of growth has slowed to 0.38 ± 0.04 ppt yr−1 in 2010 with a further decline to an annual average rate of growth in 2013–2014 of −0.06 ± 0.05 ppt yr−1. The annual average Northern Hemisphere (NH) mole fraction in 1994 was 1.2 ppt rising to an annual average mole fraction of 10.1 ppt in 2014. Average annual mole fractions in the Southern Hemisphere (SH) in 1998 and 2014 were 0.84 and 4.5 ppt, respectively. We estimate global emissions of HFC-152a have risen from 7.3 ± 5.6 Gg yr−1 in 1994 to a maximum of 54.4 ± 17.1 Gg yr−1 in 2011, declining to 52.5 ± 20.1 Gg yr−1 in 2014 or 7.2 ± 2.8 Tg-CO2 eq yr−1. Analysis of mole fraction enhancements above regional background atmospheric levels suggests substantial emissions from North America, Asia, and Europe. Global HFC emissions (so called “bottom up” emissions) reported by the United Nations Framework Convention on Climate Change (UNFCCC) are based on cumulative national emission data reported to the UNFCCC, which in turn are based on national consumption data. There appears to be a significant underestimate ( >  20 Gg) of “bottom-up” reported emissions of HFC-152a, possibly arising from largely underestimated USA emissions and undeclared Asian emissions