Interacting with Statistical Linked Data via OLAP Operations

Abstract. Online Analytical Processing (OLAP) promises an interface to analyse Linked Data containing statistics going beyond other interaction paradigms such as follow-your-nose browsers, faceted-search interfaces and query builders. Transforming statistical Linked Data into a star schema to populate a relational database and applying a common OLAP engine do not allow to optimise OLAP queries on RDF or to directly propagate changes of Linked Data sources to clients. Therefore, as a new way to interact with statistics published as Linked Data, we investigate the problem of executing OLAP queries via SPARQL on an RDF store. For that, we first define projection, slice, dice and roll-up operations on single data cubes published as Linked Data reusing the RDF Data Cube vocabulary and show how a nested set of operations lead to an OLAP query. Second, we show how to transform an OLAP query to a SPARQL query which generates all required tuples from the data cube. In a small experiment, we show the applicability of our OLAPto-SPARQL mapping in answering a business question in the financial domain

Two-component system vicrk regulates functions associated with establishment of streptococcus sanguinis in biofilms

Streptococcus sanguinis is a commensal pioneer colonizer of teeth and an opportunistic pathogen of infectious endocarditis. The establishment of S. sanguinis in host sites likely requires dynamic fitting of the cell wall in response to local stimuli. In this study, we investigated the two-component system (TCS) VicRK in S. sanguinis (VicRKSs), which regulates genes of cell wall biogenesis, biofilm formation, and virulence in opportunistic pathogens. A vicK knockout mutant obtained from strain SK36 (SKvic) showed slight reductions in aerobic growth and resistance to oxidative stress but an impaired ability to form biofilms, a phenotype restored in the complemented mutant. The biofilm-defective phenotype was associated with reduced amounts of extracellular DNA during aerobic growth, with reduced production of H2O2, a metabolic product associated with DNA release, and with inhibitory capacity of S. sanguinis competitor species. No changes in autolysis or cell surface hydrophobicity were detected in SKvic. Reverse transcription-quantitative PCR (RT-qPCR), electrophoretic mobility shift assays (EMSA), and promoter sequence analyses revealed that VicR directly regulates genes encoding murein hydrolases (SSA_0094, cwdP, and gbpB) and spxB, which encodes pyruvate oxidase for H2O2 production. Genes previously associated with spxB expression (spxR, ccpA, ackA, and tpK) were not transcriptionally affected in SKvic. RT-qPCR analyses of S. sanguinis biofilm cells further showed upregulation of VicRK targets (spxB, gbpB, and SSA_0094) and other genes for biofilm formation (gtfP and comE) compared to expression in planktonic cells. This study provides evidence that VicRKSs regulates functions crucial for S. sanguinis establishment in biofilms and identifies novel VicRK targets potentially involved in hydrolytic activities of the cell wall required for these functions.Streptococcus sanguinis is a commensal pioneer colonizer of teeth and an opportunistic pathogen of infectious endocarditis. The establishment of S. sanguinis in host sites likely requires dynamic fitting of the cell wall in response to local stimuli. In t821249414951FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL E NÍVEL SUPERIOR2009/54182-7; 2008/58333-7; 2009/50547-0sem informaçã

An international study of the prevalence of substance use in patients with delusional infestation

To the Editor: Delusional infestation (DI) is a disorder characterised by the belief of being infested with living organisms or objects.1 Insects and worms are the most common concerns. Objects, such as fibers or threads, are increasingly reported by patients. DI can be primary or secondary to mental illness, physical illness, prescribed medication, and misuse of substances such as amphetamines, cannabis, codeine, cocaine, or opiates. Dermatologists are usually the specialists to whom a patient with DI is referred because patients believe that they have primarily a skin diseas

‘No Time to be Lost!’: Ethical Considerations on Consent for Inclusion in Emergency Pharmacological Research in Severe Traumatic Brain Injury in the European Union

Severe Traumatic Brain Injury (TBI) remains a major cause of death and disability afflicting mostly young adult males and elderly people, resulting in high economic costs to society. Therapeutic approaches focus on reducing the risk on secondary brain injury. Specific ethical issues pertaining in clinical testing of pharmacological neuroprotective agents in TBI include the emergency nature of the research, the incapacity of the patients to informed consent before inclusion, short therapeutic time windows, and a risk-benefit ratio based on concept that in relation to the severity of the trauma, significant adverse side effects may be acceptable for possible beneficial treatments. Randomized controlled phase III trials investigating the safety and efficacy of agents in TBI with promising benefit, conducted in acute emergency situations with short therapeutic time windows, should allow randomization under deferred consent or waiver of consent. Making progress in knowledge of treatment in acute neurological and other intensive care conditions is only possible if national regulations and legislations allow waiver of consent or deferred consent for clinical trials

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>)

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

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

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