Parallel computation of the reachability graph of petri net models with semantic information

Formal verification plays a crucial role when dealing with correctness of systems. In a previous work, the authors proposed a class of models, the Unary Resource Description Framework Petri Nets (U-RDF-PN), which integrated Petri nets and (RDF-based) semantic information. The work also proposed a model checking approach for the analysis of system behavioural properties that made use of the net reachability graph. Computing such a graph, specially when dealing with high-level structures as RDF graphs, is a very expensive task that must be considered. This paper describes the development of a parallel solution for the computation of the reachability graph of U-RDF-PN models. Besides that, the paper presents some experimental results when the tool was deployed in cluster and cloud frameworks. The results not only show the improvement in the total time required for computing the graph, but also the high scalability of the solution, which make it very useful thanks to the current (and future) availability of cloud infrastructures

SDRS: a new lossless dimensionality reduction for text corpora

In recent years, most content-based spam filters have been implemented using Machine Learning (ML) approaches by means of token-based representations of textual contents. After introducing multiple performance enhancements, the impact has been virtually irrelevant. Recent studies have introduced synset-based content representations as a reliable way to improve classification, as well as different forms to take advantage of semantic information to address problems, such as dimensionality reduction. These preliminary solutions present some limitations and enforce simplifications that must be gradually redefined in order to obtain significant improvements in spam content filtering. This study addresses the problem of feature reduction by introducing a new semantic-based proposal (SDRS) that avoids losing knowledge (lossless). Synset-features can be semantically grouped by taking advantage of taxonomic relations (mainly hypernyms) provided by BabelNet ontological dictionary (e.g. “Viagra” and “Cialis” can be summarized into the single features “anti-impotence drug”, “drug” or “chemical substance” depending on the generalization of 1, 2 or 3 levels). In order to decide how many levels should be used to generalize each synset of a dataset, our proposal takes advantage of Multi-Objective Evolutionary Algorithms (MOEA) and particularly, of the Non-dominated Sorting Genetic Algorithm (NSGA-II). We have compared the performance achieved by a Naïve Bayes classifier, using both token-based and synset-based dataset representations, with and without executing dimensional reductions. As a result, our lossless semantic reduction strategy was able to find optimal semantic-based feature grouping strategies for the input texts, leading to a better performance of Naïve Bayes classifiers.info:eu-repo/semantics/acceptedVersio

Multi-objective evolutionary optimization for dimensionality reduction of texts represented by synsets

Despite new developments in machine learning classification techniques, improving the accuracy of spam filtering is a difficult task due to linguistic phenomena that limit its effectiveness. In particular, we highlight polysemy, synonymy, the usage of hypernyms/hyponyms, and the presence of irrelevant/confusing words. These problems should be solved at the pre-processing stage to avoid using inconsistent information in the building of classification models. Previous studies have suggested that the use of synset-based representation strategies could be successfully used to solve synonymy and polysemy problems. Complementarily, it is possible to take advantage of hyponymy/hypernymy-based to implement dimensionality reduction strategies. These strategies could unify textual terms to model the intentions of the document without losing any information (e.g., bringing together the synsets “viagra”, “ciallis”, “levitra” and other representing similar drugs by using “virility drug” which is a hyponym for all of them). These feature reduction schemes are known as lossless strategies as the information is not removed but only generalised. However, in some types of text classification problems (such as spam filtering) it may not be worthwhile to keep all the information and let dimensionality reduction algorithms discard information that may be irrelevant or confusing. In this work, we are introducing the feature reduction as a multi-objective optimisation problem to be solved using a Multi-Objective Evolutionary Algorithm (MOEA). Our algorithm allows, with minor modifications, to implement lossless (using only semantic-based synset grouping), low-loss (discarding irrelevant information and using semantic-based synset grouping) or lossy (discarding only irrelevant information) strategies. The contribution of this study is two-fold: (i) to introduce different dimensionality reduction methods (lossless, low-loss and lossy) as an optimization problem that can be solved using MOEA and (ii) to provide an experimental comparison of lossless and low-loss schemes for text representation. The results obtained support the usefulness of the low-loss method to improve the efficiency of classifiers.info:eu-repo/semantics/publishedVersio

Development of a screening tool enabling identification of infants and toddlers at risk for family abuse and neglect : A feasibility study from three South European countries

Background: Child abuse is a health and social problem, and few screening instruments are available for the detection of risk in primary health care. The aim was to develop a screening instrument to be used by professionals in the public health care sector, thus enabling the detection of infants and toddlers at risk of emotional and physical abuse and neglect, and to provide evidence for the feasibility of the instrument in Cyprus, Greece and Spain. Method: A total of 50 health professionals from paediatric public health-care centres in the three countries were involved in a three-step process for guiding the development of the screening tool and its application. Results: A nine-item screening tool, consisting of items assessing relational emotional abuse, physical abuse and other risk factors, was developed. The screening tool was applied on a total of 219 families with 0 to 3-year-old children attending public health centres in the three countries. Clinicians reported that they agreed on the inclusion of the questions (86.4-100%) and that they found the questions to be useful for the clinical evaluation of the family (63.2-100%). Conclusion: The screening tool shows considerable face validity and was reported feasible by an international set of clinician

Monoamine oxidase A (MAOA) interaction with parenting practices on callous-unemotional traits in preschoolers

Background and Objectives: From a gene-by-environment perspective, parenting in interaction with the polymorphism in the Monoamine oxidase A (MAOA) gene (MAOA-uVNTR) might also be associated with increased callous-unemotional traits (CU) in preschoolers. MAOA-uVNTR results in differential enzyme activity, so that high-activity alleles (MAOA-H) are linked to reduced dopamine, serotonin, and norepinephrine availability in comparison to low-activity allele (MAOA-L). As MAOA-uVNTR has been previously described to moderate the relationship between childhood parental maltreatment and aggressive and antisocial behavior, it may also play a role in CU traits etiology

Maternal psychological distress in primary care and association with child behavioural outcomes at age three

Observational studies indicate children whose mothers have poor mental health are at increased risk of socio-emotional behavioural difficulties, but it is unknown whether these outcomes vary by the mothers’ mental health recognition and treatment status. To examine this question, we analysed linked longitudinal primary care and research data from 1078 women enrolled in the Born in Bradford cohort. A latent class analysis of treatment status and self-reported distress broadly categorised women as (a) not having a common mental disorder (CMD) that persisted through pregnancy and the first 2 years after delivery (N = 756, 70.1 %), (b) treated for CMD (N = 67, 6.2 %), or (c) untreated (N = 255, 23.7 %). Compared to children of mothers without CMD, 3-year-old children with mothers classified as having untreated CMD had higher standardised factor scores on the Strengths and Difficulties Questionnaire (d = 0.32), as did children with mothers classified as having treated CMD (d = 0.27). Results were only slightly attenuated in adjusted analyses. Children of mothers with CMD may be at risk for socio-emotional and behavioural difficulties. The development of effective treatments for CMD needs to be balanced by greater attempts to identify and treat women. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00787-015-0777-2) contains supplementary material, which is available to authorized users

Viruses Previously Identified in Brazil as Belonging to HIV-1 CRF72_BF1 Represent Two Closely Related Circulating Recombinant Forms, One of Which, Designated CRF122_BF1, Is Also Circulating in Spain

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Those derived from recombination between subtype B and subsubtype F1, with 18 reported, most of them of South American origin, are among the most diverse. In this study, we identified a HIV-1 BF1 recombinant cluster that is expanding in Spain, transmitted mainly via heterosexual contact, which, analyzed in near full-length genomes in four viruses, exhibited a coincident BF1 mosaic structure, with 12 breakpoints, that fully coincided with that of two viruses (10BR_MG003 and 10BR_MG005) from Brazil, previously classified as CRF72_BF1. The three remaining Brazilian viruses (10BR_MG002, 10BR_MG004, and 10BR_MG008) previously identified as CRF72_BF1 exhibited mosaic structures highly similar, but not identical, to that of the Spanish viruses and to 10BR_MG003 and 10BR_MG005, with discrepant subtypes in two short genome segments, located in pol and gp120env. Based on these results, we propose that the five viruses from Brazil previously identified as CRF72_BF1 actually belong to two closely related CRFs, one comprising 10BR_MG002, 10BR_MG004, and 10BR_MG008, which keep their CRF72_BF1 designation, and the other, designated CRF122_BF1, comprising 10BR_MG003, 10BR_MG005, and the viruses of the identified Spanish cluster. Three other BF1 recombinant genomes, two from Brazil and one from Italy, previously identified as unique recombinant forms, were classified as CRF72_BF1. CRF122_BF1, but not CRF72_BF1, was associated with protease L89M substitution, which was reported to contribute to antiretroviral drug resistance. Phylodynamic analyses estimate the emergence of CRF122_BF1 in Brazil around 1987. Given their close phylogenetic relationship and similar structures, the grouping of CRF72_BF1 and CRF122_BF1 in a CRF family is proposed.This work was funded through Acción Estratégica en Salud Intramural (AESI), Instituto de Salud Carlos III, projects “Estudios Sobre Vigilancia Epidemiológica Molecular del VIH-1 en España”, PI16CIII/00033, and “Epidemiología Molecular del VIH-1 en España y su Utilidad Para Investigaciones Biológicas y en Vacunas“, PI19CIII/00042, and through scientific agreement with Consellería de Sanidade, Government of Galicia (MVI 1004/16).S

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A+T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyses have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales+mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyses on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A+T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyses raise doubts about the monophyly of the newly proposed Pelagibacteraceae family

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits