The Bag Semantics of Ontology-Based Data Access

Ontology-based data access (OBDA) is a popular approach for integrating and querying multiple data sources by means of a shared ontology. The ontology is linked to the sources using mappings, which assign views over the data to ontology predicates. Motivated by the need for OBDA systems supporting database-style aggregate queries, we propose a bag semantics for OBDA, where duplicate tuples in the views defined by the mappings are retained, as is the case in standard databases. We show that bag semantics makes conjunctive query answering in OBDA coNP-hard in data complexity. To regain tractability, we consider a rather general class of queries and show its rewritability to a generalisation of the relational calculus to bags

Statistical Analysis of Human Parasitic Infections

In longitudinal studies, measurements are taken over time or space on the same individual. A wide variety of well-established procedures exist for modelling these data such as t-tests, the use of summary measures, analysis of variance and the method of maximum likelihood. The latter seems to be the most appropriate approach since its estimates are consistent and efficient for large samples and it deals directly with problems of missing data. Here, much emphasis is given to the model proposed by A. Azzalini (1994), which is not only based on the method of maximum likelihood but it also incorporates an appropriate correlation structure for the measurements on a single individual across time. This model is applied in a real data example. It concerns a cohort study of about 1,100 individuals from China and Nigeria, where an infectious disease is widely spread. Treatment is given to control the prevalence and intensity of the disease. Our aim was to assess the way in which factors such as age and sex are related with the above outcomes, estimate the size of the effect of the treatment, as well as the time needed for prevalence and intensity to reach the pre-treatment level as a result of reinfection and make comparisons between two different types of treatment. However, a major problem arises due to the high frequency of missing data. In this case, a generalized linear model is fitted, which although it does not take into account the correlation over time, its methods of inference are based on well-founded theory under the assumption of independent errors. In addition, the use of smoothing techniques to explore trends in the data in a non parametric manner is described. This provides a means of modelling the data without making parametric assumptions. Finally, the methodology of generalized additive models is used to explore non-linear effects in a model comparison setting. Such models provide a means of checking more formally on linearity assumptions and also provide a way of modelling the data even when these effects are non-linear but can be assumed to be smooth. However, they have to be treated with care since their methods of inference are approximate

Prevention of fish photobacteriosis. Comparison of the efficacy of intraperitoneally administered commercial and experimental vaccines

Two commercial multivalent vaccines against vibriosis, caused by Vibrio anguillarum serotype(s) and photobacteriosis, caused by Photobacterium damsela subsp. piscicida, one with oil adjuvant (AJ) and the other,being an aqueous solution (AV), and an experimental monovalent (Ph. damselae subsp. piscicida) vaccine inactivated with formalin or heat, namely EVF and EVH, were tested in laboratory trials on sea bass (Dicentrarchus labrax) in respect to their efficacy against experimentally induced photobacteriosis. The first trial aiming at high bacterial pressure was carried out 34 days post-vaccination and resulted in 90% mortalities in the control. The relative per cent survival (RPS) of vaccinated fish was calculated at 24, 3.7, 0 and 0 for the AJ, AV, EVF and EVH formulations, respectively. The second trial aiming at medium bacterial pressure was carried out 49 days post-vaccination and resulted in 45% mortalities in the control. The relative per cent survival (RPS) of vaccinated fish was calculated at 100, 92.7, 77.8 and 66.7 for the AJ, EVF, EVH and AV, formulations, respectively. Apparently, under both these high and medium bacterial pressure conditions, the commercial vaccine AJ performed better than the commercial vaccine AV, while under medium pressure there was no statistical difference between the performance of EVF and AJ. The measurement of specific antibody titers in sera collected from all fish groups 49 days post-vaccination, showed high levels in the fish vaccinated with the AJ vaccine, almost three times lower levels for the AV and EVF vaccines and even lower levels for the EVH vaccine. Results are discussed in respect to the choices mariculture companies have in selecting a commercial vaccine against photobacteriosis and possible alternatives, which, if commercially developed, may reduce vaccine cost

Mini-Cog for the diagnosis of Alzheimer's disease dementia and other dementias within a secondary care setting

© 2014 The Cochrane Collaboration. This is the protocol for a review and there is no abstract. The objectives are as follows: To determine the diagnostic accuracy of the Mini-Cog for detecting Alzheimer's disease dementia and related dementias in a secondary care setting. To investigate the heterogeneity of test accuracy in the included studies and potential sources of heterogeneity. These potential sources of heterogeneity will include the baseline prevalence of dementia in study samples, thresholds used to determine positive test results, the type of dementia (Alzheimer's disease dementia or all causes of dementia), and aspects of study design related to study quality. We will also identify gaps in the evidence where further research is required

Tumour necrosis factor-α inhibitor therapy in chronic physical illness: A systematic review and meta-analysis of the effect on depression and anxiety

Objective: Depression is more common among individuals with chronic physical illness than in the general population New treatments for severe and chronic inflammatory conditions which inhibit tumour necrosis factor alpha (TNF-α), a pro-inflammatory cytokine, may be able to shed some light on the role of inflammatory mediators in depression This systematic review and meta-analysis of randomised controlled trials determined the effects of TNF-α inhibitor therapy on depression and anxiety in people with chronic physical illness. Methods: Seven databases were searched from inception to January 2014: AMED, Central, Cochrane Database of Systematic Reviews, CINAHL, Embase, MEDLINE, and PsycINFO. Articles were screened for inclusion independently by two reviewers. Data extraction and appraisal were conducted by one reviewer and checked by a second. Random-effects meta-analyses were performed. Results: Six randomised controlled trials (reported in seven articles) met eligibility criteria and were included in the final review. In total 2540 participants were enrolled across the trials, with participants presenting with rheumatoid arthritis (n = 3 trials), psoriasis (n = 2) or ankylosing spondylitis (n = 1). Meta-analyses, using standardised mean differences, showed evidence of small reductions in depression (- 0.24; 95% CI - 0.33 to - 0.14; p < 0.001), and anxiety (- 0.17; 95% CI - 0.31 to - 0.02; p = 0.02). Conclusion: TNF-α inhibitor therapy reduces depression in people with chronic disease though the effects are small. Whilst this is consistent with inflammation contributing to the development of depression, further studies investigating a more detailed timeline of changes in depression, inflammatory biomarkers and disease activity status are required.National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care SouthWest Peninsul

Diagnostic accuracy of single baseline measurement of Elecsys Troponin T high-sensitive assay for diagnosis of acute myocardial infarction in emergency department: systematic review and meta-analysis

Published onlineJournal ArticleMeta-AnalysisResearch Support, Non-U.S. Gov'tReviewOBJECTIVE: To obtain summary estimates of the accuracy of a single baseline measurement of the Elecsys Troponin T high-sensitive assay (Roche Diagnostics) for the diagnosis of acute myocardial infarction in patients presenting to the emergency department. DESIGN: Systematic review and meta-analysis of diagnostic test accuracy studies. DATA SOURCES: Medline, Embase, and other relevant electronic databases were searched for papers published between January 2006 and December 2013. STUDY SELECTION: Studies were included if they evaluated the diagnostic accuracy of a single baseline measurement of Elecsys Troponin T high-sensitive assay for the diagnosis of acute myocardial infarction in patients presenting to the emergency department with suspected acute coronary syndrome. STUDY APPRAISAL AND DATA SYNTHESIS: The first author screened all titles and abstracts identified through the searches and selected all potentially relevant papers. The screening of the full texts, the data extraction, and the methodological quality assessment, using the adapted QUADAS-2 tool, were conducted independently by two reviewers with disagreements being resolved through discussion or arbitration. If appropriate, meta-analysis was conducted using the hierarchical bivariate model. RESULTS: Twenty three studies reported the performance of the evaluated assay at presentation. The results for 14 ng/L and 3-5 ng/L cut-off values were pooled separately. At 14 ng/L (20 papers), the summary sensitivity was 89.5% (95% confidence interval 86.3% to 92.1%) and the summary specificity was 77.1% (68.7% to 83.7%). At 3-5 ng/L (six papers), the summary sensitivity was 97.4% (94.9% to 98.7%) and the summary specificity was 42.4% (31.2% to 54.5%). This means that if 21 of 100 consecutive patients have the target condition (21%, the median prevalence across the studies), 2 (95% confidence interval 2 to 3) of 21 patients with acute myocardial infarction will be missed (false negatives) if 14 ng/L is used as a cut-off value and 18 (13 to 25) of 79 patients without acute myocardial infarction will test positive (false positives). If the 3-5 ng/L cut-off value is used, <1 (0 to 1) patient with acute myocardial infarction will be missed and 46 (36 to 54) patients without acute myocardial infarction will test positive. CONCLUSIONS: The results indicate that a single baseline measurement of the Elecsys Troponin T high-sensitive assay could be used to rule out acute myocardial infarction if lower cut-off values such as 3 ng/L or 5 ng/L are used. However, this method should be part of a comprehensive triage strategy and may not be appropriate for patients who present less than three hours after symptom onset. Care must also be exercised because of the higher imprecision of the evaluated assay and the greater effect of lot-to-lot reagent variation at low troponin concentrations. SYSTEMATIC REVIEW REGISTRATION: PROSPERO registration number CRD42013003926.This research was funded by the South West Academic Health Science Network (AHSN) and the National Institute for Health Research (NIHR) Collaboration for Leadership for Applied Health Research and Care for the South West Peninsula

Regulation of the CoA Biosynthetic Complex Assembly in Mammalian Cells

Coenzyme A (CoA) is an essential cofactor present in all living cells. Under physiological conditions, CoA mainly functions to generate metabolically active CoA thioesters, which are indispensable for cellular metabolism, the regulation of gene expression, and the biosynthesis of neurotransmitters. When cells are exposed to oxidative or metabolic stress, CoA acts as an important cellular antioxidant that protects protein thiols from overoxidation, and this function is mediated by protein CoAlation. CoA and its derivatives are strictly maintained at levels controlled by nutrients, hormones, metabolites, and cellular stresses. Dysregulation of their biosynthesis and homeostasis has deleterious consequences and has been noted in a range of pathological conditions, including cancer, diabetes, Reye’s syndrome, cardiac hypertrophy, and neurodegeneration. The biochemistry of CoA biosynthesis, which involves five enzymatic steps, has been extensively studied. However, the existence of a CoA biosynthetic complex and the mode of its regulation in mammalian cells are unknown. In this study, we report the assembly of all five enzymes that drive CoA biosynthesis, in HEK293/Pank1β and A549 cells, using the in situ proximity ligation assay. Furthermore, we show that the association of CoA biosynthetic enzymes is strongly upregulated in response to serum starvation and oxidative stress, whereas insulin and growth factor signaling downregulate their assembly