A complete radio study of SNR G15.4+0.1 from new GMRT observations

Aims. The supernova remnant (SNR) G15.4+0.1 is considered to be the possible counterpart of the γ-ray source HESS J1818−154. With the goal of getting a complete view of this remnant and understanding the nature of the gamma-ray flux, we conducted a detailed radio study that includes the search for pulsations and a model of the broadband emission for the SNR G15.4+0.1/HESS J1818−154 system. Methods. Low-frequency imaging at 624 MHz and pulsar observations at 624 and 1404 MHz towards G15.4+0.1 were carried out with the Giant Metrewave Radio Telescope (GMRT). We correlated the new radio data with observations of the source at X-ray and infrared wavelengths from XMM-Newton and Herschel observatories, respectively. To characterize the neutral hydrogen (HI) medium towards G15.4+0.1, we used data from the Southern Galactic Plane Survey. We modelled the spectral energy distribution (SED) using both hadronic and leptonic scenarios. Results. From the combination of the new GMRT observations with existing data, we derived a continuum spectral index alpha = -0.62 +- 0.03 for the whole remnant. The local synchrotron spectra of G15.4+0.1, calculated from the combination of the GMRT data with 330 MHz observations from the Very Large Array, tends to be flatter in the central part of the remnant, accompanying the region where the blast wave is impinging molecular gas. No spectral index trace was found indicating the radio counterpart to the pulsar wind nebula proposed from X-ray observations. In addition, the search for radio pulsations yielded negative results. Emission at far-infrared wavelengths is observed in the region where the SNR shock is interacting with dense molecular clumps. We also identified HI features forming a shell that wraps most of the outer border of G15.4+0.1. Characteristic parameters were estimated for the shocked HI gas. We found that either a purely hadronic or leptonic model is compatible with the broadband emission known so far.Fil: Supán, Jorge Leonardo. Consejo Nacional de Investigaciónes Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; ArgentinaFil: Castelletti, Gabriela Marta. Consejo Nacional de Investigaciónes Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; ArgentinaFil: Joshi, B. C.. National Centre for Radio Astrophysics; IndiaFil: Surnis, M. P.. National Centre for Radio Astrophysics; IndiaFil: Supanitsky, Alberto Daniel. Consejo Nacional de Investigaciónes Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Astronomía y Física del Espacio. - Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Astronomía y Física del Espacio; Argentin

Towards optimal concolic testing

ACM Distinguished Paper Award</p

Inflammatory molecules produced by meniscus and synovium in early and end-stage osteoarthritis: a coculture study

The aim of this study was to identify the molecules and pathways involved in the cross-talk between meniscus and synovium that may play a critical role in osteoarthritis (OA) pathophysiology. Samples of synovium and meniscus were collected from patients with early and end-stage OA and cultured alone or cocultured. Cytokines, chemokines, metalloproteases, and their inhibitors were evaluated at the gene and protein levels. The extracellular matrix (ECM) changes were also investigated. In early OA cultures, higher levels of interleukin-6 (IL-6) and IL-8 messenger RNA were expressed by synovium and meniscus in coculture compared with meniscus cultured alone. RANTES release was significantly increased when the two tissues were cocultured compared with meniscus cultured alone. Increased levels of matrix metalloproteinase-3\ua0(MMP-3) and MMP-10 proteins, as well as increased release of glycosaminoglycans and aggrecan CS846 epitope, were observed when synovium was cocultured with meniscus. In end-stage OA cultures, increased levels of IL-8 and monocyte chemoattractant\ua0protein-1\ua0(MCP-1) proteins were released in cocultures compared with cultures of meniscus alone. Chemokine (C-C motif) ligand 21 (CCL21) protein release was higher in meniscus cultured alone and in coculture compared with synovium cultured alone. Increased levels of MMP-3 and 10 proteins were observed when tissues were cocultured compared with meniscus cultured alone. Aggrecan CS846 epitope release was increased in cocultures compared with cultures of either tissue cultured alone. Our study showed the production of inflammatory molecules by synovium and meniscus which could trigger inflammatory signals in early OA patients, and induce ECM loss in the progressive and final stages of OA pathology

Epidemiological Profile of Precocious Neonatal Mortality in the Period 2008 to 2015 in Porto Velho, Rondonia, Brazil

The objective of this study was to describe the epidemiological profile of precocious neonatal infant mortality in the city of Porto Velho, Rondonia. A quantitative, descriptive study with an ecological approach was carried out. The data source used was secondary, originating from the linkage between SINASC and SIM databases, from the Health Surveillance Agency of the Rondonia Health Department. For treatment, absolute frequency analyzes were performed. The neonatal infant mortality rate was 9.7 deaths per thousand live births, with a predominance of the preterm neonatal patient: 7.2 deaths per thousand live births. Of the deaths, 482 (72.8%) occurred in the precocious neonatal period (0 to 6 days) and 164 (24.7%) in the late neonatal 7 to 27 days of life. The findings indicate the need to improve the quality of health care services available in the city, both prenatal and obstetric care in the neonatal period

The use of artificial neural network in identifying swine vocalization

Animal welfare has been an important research topic in animal production mainly in its ways of assessment. Vocalization is found to be an interesting tool for evaluating welfare as it provides data in a non-invasive way as well as it allows easy automation of process. The present research had as objective the implementation of an algorithm based on artificial neural network that had the potential of identifying vocalization related to welfare pattern indicatives. The research was done in two parts, the first was the development of the algorithm, and the second its validation with data from the field. Previous records allowed the development of the algorithm from behaviors observed in sows housed in farrowing cages. Matlab® software was used for implementing the network. It was selected a retropropagation gradient algorithm for training the network with the following stop criteria: maximum of 5,000 interactions or error quadratic addition smaller than 0.1. Validation was done with sows and piglets housed in commercial farm. Among the usual behaviors the ones that deserved enhancement were: the feed dispute at farrowing and the eventual risk of involuntary aggression between the piglets or between those and the sow. The algorithm was able to identify through the noise intensity the inherent risk situation of piglets welfare reduction.O bem-estar dos animais tem sido importante tópico de pesquisa na produção animal, principalmente no tocante às formas de sua avaliação. Na avaliação do bem-estar animal, a vocalização mostra-se como ferramenta interessante, por fornecer dados de forma não-invasiva, podendo também ser facilmente automatizada. O presente trabalho teve o objetivo de implementar algoritmo baseado em redes neurais artificiais, capaz de reconhecer vocalizações relacionadas com padrões indicativos de bem-estar. A pesquisa teve duas partes, sendo a primeira o desenvolvimento do algoritmo, e a segunda, sua validação com dados de campo. Registros prévios permitiram o desenvolvimento do algoritmo, a partir de comportamentos observados em porcas alojadas em gaiolas de maternidade. O software Matlab® foi utilizado na implementação da rede. Foi selecionado um algoritmo de gradiente de retropropagação para treinar a rede com os seguintes critérios de parada: máximo de 5.000 iterações ou soma quadrática do erro menor que 0,1. A validação deu-se com porcas e leitões alojados em granja comercial. Dentre os comportamentos usuais, os que mereceram destaque foram: a disputa por alimento no momento das mamadas e o eventual risco de agressão involuntária entre os leitões ou entre esses e a porca. O algoritmo foi capaz de reconhecer, por meio da intensidade do ruído, a situação inerente ao risco de redução do bem-estar dos leitões.20421

Germline Mutations in FAN1 Cause Hereditary Colorectal Cancer by Impairing DNA Repair

Identification of genes associated with hereditary cancers facilitates management of patients with family histories of cancer. We performed exome sequencing of DNA from 3 individuals from a family with colorectal cancer who met the Amsterdam criteria for risk of hereditary nonpolyposis colorectal cancer. These individuals had mismatch repair-proficient tumors and each carried nonsense variant in the FANCD2/FANCI-associated nuclease 1 gene (FAN1), which encodes a nuclease involved in DNA inter-strand cross-link repair. We sequenced FAN1 in 176 additional families with histories of colorectal cancer and performed in vitro functional analyses of the mutant forms of FAN1 identified. We detected FAN1 mutations in approximately 3% of families who met the Amsterdam criteria and had mismatch repair-proficient cancers with no previously associated mutations. These findings link colorectal cancer predisposition to the Fanconi anemia DNA repair pathway, supporting the connection between genome integrity and cancer risk

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

BACKGROUND: Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional metrics. The BioCreative III Protein-Protein Interaction (PPI) tasks were motivated by such considerations, trying to address aspects including how the end user would oversee the generated output, for instance by providing ranked results, textual evidence for human interpretation or measuring time savings by using automated systems. Detecting articles describing complex biological events like PPIs was addressed in the Article Classification Task (ACT), where participants were asked to implement tools for detecting PPI-describing abstracts. Therefore the BCIII-ACT corpus was provided, which includes a training, development and test set of over 12,000 PPI relevant and non-relevant PubMed abstracts labeled manually by domain experts and recording also the human classification times. The Interaction Method Task (IMT) went beyond abstracts and required mining for associations between more than 3,500 full text articles and interaction detection method ontology concepts that had been applied to detect the PPIs reported in them.RESULTS:A total of 11 teams participated in at least one of the two PPI tasks (10 in ACT and 8 in the IMT) and a total of 62 persons were involved either as participants or in preparing data sets/evaluating these tasks. Per task, each team was allowed to submit five runs offline and another five online via the BioCreative Meta-Server. From the 52 runs submitted for the ACT, the highest Matthew's Correlation Coefficient (MCC) score measured was 0.55 at an accuracy of 89 and the best AUC iP/R was 68. Most ACT teams explored machine learning methods, some of them also used lexical resources like MeSH terms, PSI-MI concepts or particular lists of verbs and nouns, some integrated NER approaches. For the IMT, a total of 42 runs were evaluated by comparing systems against manually generated annotations done by curators from the BioGRID and MINT databases. The highest AUC iP/R achieved by any run was 53, the best MCC score 0.55. In case of competitive systems with an acceptable recall (above 35) the macro-averaged precision ranged between 50 and 80, with a maximum F-Score of 55. CONCLUSIONS: The results of the ACT task of BioCreative III indicate that classification of large unbalanced article collections reflecting the real class imbalance is still challenging. Nevertheless, text-mining tools that report ranked lists of relevant articles for manual selection can potentially reduce the time needed to identify half of the relevant articles to less than 1/4 of the time when compared to unranked results. Detecting associations between full text articles and interaction detection method PSI-MI terms (IMT) is more difficult than might be anticipated. This is due to the variability of method term mentions, errors resulting from pre-processing of articles provided as PDF files, and the heterogeneity and different granularity of method term concepts encountered in the ontology. However, combining the sophisticated techniques developed by the participants with supporting evidence strings derived from the articles for human interpretation could result in practical modules for biological annotation workflows

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards

Validation of the Short Version (TLS-15) of the Triangular Love Scale (TLS-45) Across 37 Languages

Love is a phenomenon that occurs across the world and affects many aspects of human life, including the choice of, and process of bonding with, a romantic partner. Thus, developing a reliable and valid measure of love experiences is crucial. One of the most popular tools to quantify love is Sternberg’s 45-item Triangular Love Scale (TLS-45), which measures three love components: intimacy, passion, and commitment. However, our literature review reveals that most studies (64%) use a broad variety of shortened versions of the TLS-45. Here, aiming to achieve scientific consensus and improve the reliability, comparability, and generalizability of results across studies, we developed a short version of the scale—the TLS-15—comprised of 15 items with 5-point, rather than 9-point, response scales. In Study 1 (N = 7,332), we re-analyzed secondary data from a large-scale multinational study that validated the original TLS-45 to establish whether the scale could be truncated. In Study 2 (N = 307), we provided evidence for the three-factor structure of the TLS-15 and its reliability. Study 3 (N = 413) confirmed convergent validity and test–retest stability of the TLS-15. Study 4 (N = 60,311) presented a large-scale validation across 37 linguistic versions of the TLS-15 on a cross-cultural sample spanning every continent of the globe. The overall results provide support for the reliability, validity, and cross-cultural invariance of the TLS-15, which can be used as a measure of love components—either separately or jointly as a three-factor measure