A Port Graph Rewriting Approach to Relational Database Modelling

International audienceWe present new algorithms to compute the Syntactic Closure and the Minimal Cover of a set of functional dependencies, using strategic port graph rewriting. We specify a Visual Domain Specific Language to model relational database schemata as port graphs, and provide an extension to port graph rewriting rules. Using these rules we implement strategies to compute a syntactic closure, analyse it and find minimal covers, essential for schema normalisation. The graph program provides a visual description of the computation steps coupled with analysis features not available in other approaches. We prove soundness and completeness of the computed closure. This methodology is implemented in PORGY

Towards certain fixes with editing rules and master data

A variety of integrity constraints have been studied for data cleaning. While these constraints can detect the presence of errors, they fall short of guiding us to correct the errors. Indeed, data repairing based on these constraints may notfind certain fixes that are absolutely correct, and worse, may introduce new errors when repairing the data. We propose a method for finding certain fixes, based on master data, a notion of certain regions, and a class of editing rules. A certain region is a set of attributes that are assured correct by the users. Given a certain region and master data, editing rules tell us what attributes to fix and how to update them. We show how the method can be used in data monitoring and enrichment. We develop techniques for reasoning about editing rules, to decide whether they lead to a unique fix and whether they are able to fix all the attributes in a tuple, relative to master data and a certain region. We also provide an algorithm to identify minimal certain regions, such that a certain fix is warranted by editing rules and master data as long as one of the regions is correct. We experimentally verify the effectiveness and scalability of the algorithm

Recent acquisition of Helicobacter pylori by Baka Pygmies

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors

Multi-Ancestry Genome-Wide Association Analyses Improve Resolution of Genes and Pathways Influencing Lung Function and Chronic Obstructive Pulmonary Disease Risk

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies

Epilepsy Caused by an Abnormal Alternative Splicing with Dosage Effect of the SV2A Gene in a Chicken Model

Photosensitive reflex epilepsy is caused by the combination of an individual's enhanced sensitivity with relevant light stimuli, such as stroboscopic lights or video games. This is the most common reflex epilepsy in humans; it is characterized by the photoparoxysmal response, which is an abnormal electroencephalographic reaction, and seizures triggered by intermittent light stimulation. Here, by using genetic mapping, sequencing and functional analyses, we report that a mutation in the acceptor site of the second intron of SV2A (the gene encoding synaptic vesicle glycoprotein 2A) is causing photosensitive reflex epilepsy in a unique vertebrate model, the Fepi chicken strain, a spontaneous model where the neurological disorder is inherited as an autosomal recessive mutation. This mutation causes an aberrant splicing event and significantly reduces the level of SV2A mRNA in homozygous carriers. Levetiracetam, a second generation antiepileptic drug, is known to bind SV2A, and SV2A knock-out mice develop seizures soon after birth and usually die within three weeks. The Fepi chicken survives to adulthood and responds to levetiracetam, suggesting that the low-level expression of SV2A in these animals is sufficient to allow survival, but does not protect against seizures. Thus, the Fepi chicken model shows that the role of the SV2A pathway in the brain is conserved between birds and mammals, in spite of a large phylogenetic distance. The Fepi model appears particularly useful for further studies of physiopathology of reflex epilepsy, in comparison with induced models of epilepsy in rodents. Consequently, SV2A is a very attractive candidate gene for analysis in the context of both mono- and polygenic generalized epilepsies in humans

COBRA framework to evaluate e-government services: A citizen-centric perspective

E-government services involve many stakeholders who have different objectives that can have an impact on success. Among these stakeholders, citizens are the primary stakeholders of government activities. Accordingly, their satisfaction plays an important role in e-government success. Although several models have been proposed to assess the success of e-government services through measuring users' satisfaction levels, they fail to provide a comprehensive evaluation model. This study provides an insight and critical analysis of the extant literature to identify the most critical factors and their manifested variables for user satisfaction in the provision of e-government services. The various manifested variables are then grouped into a new quantitative analysis framework consisting of four main constructs: cost; benefit; risk and opportunity (COBRA) by analogy to the well-known SWOT qualitative analysis framework. The COBRA measurement scale is developed, tested, refined and validated on a sample group of e-government service users in Turkey. A structured equation model is used to establish relationships among the identified constructs, associated variables and users' satisfaction. The results confirm that COBRA framework is a useful approach for evaluating the success of e-government services from citizens' perspective and it can be generalised to other perspectives and measurement contexts. Crown Copyright © 2014.PIAP-GA-2008-230658) from the European Union Framework Program and another grant (NPRP 09-1023-5-158) from the Qatar National Research Fund (amember of Qatar Foundation

Semantics of Database Transformations

Database transformations arise in many different settings including database integration, evolution of database systems, and implementing user views and data entry tools. This paper surveys approaches that have been taken to problems in these settings, assesses their strengths and weaknesses, and develops require ments on a formal model for specifying and implementing database transformations. We also consider the problem of insuring the correctness of database transformations. In particular, we demonstrate that the usefulness of correctness conditions such as information preservation is hindered by the interactions of transformations and database constraints, and the limited expressive power of established database constraint languages. We conclude that more general notions of correctness are required, and that there is a need for a uniform formalism for expressing both database transformations and constraints, and reasoning about their interactions, Finally we introduce WOL, a declarative language for specifying and implementing database transformations and constraints. We briefly describe the WOL language and its semantics, and argue that it addresses many of the requirements on a formalism for dealing with general database transformations

Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain

The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; starlike features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia

Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK

Smoking is a leading risk factor for many of the top ten causes of death worldwide. Of the 1.3 billion smokers globally, 80% live in low- and middle-income countries, where the number of deaths due to tobacco use is expected to double in the next decade according to the World Health Organization. Genetic studies have helped to identify biological pathways for smoking behaviours, but have mostly focussed on individuals of European ancestry or living in either North America or Europe. We performed a genome-wide association study of two smoking behaviour traits in 10,558 men of African ancestry living in five African countries and the UK. Eight independent variants were associated with either smoking initiation or cessation at P-value < 5 × 10-6, four being monomorphic or rare in European populations. Gene prioritisation strategy highlighted five genes, including SEMA6D, previously described as associated with several smoking behaviour traits. These results confirm the importance of analysing underrepresented populations in genetic epidemiology, and the urgent need for larger genomic studies to boost discovery power to better understand smoking behaviours, as well as many other traits