Semantic relations extraction from unstructured information for domain ontologies enrichment

Based in internet growth, through semantic web, together with communication speed improvement and fast development of storage device sizes, data and information volume rises considerably every day. Because of this, in the last few years there has been a growing interest in structures for formal representation with suitable characteristics, such as the possibility to organize data and information, as well as the reuse of its contents aimed for the generation of new knowledge. Controlled Vocabulary, specifically Ontologies, present themselves in the lead as one of such structures of representation with high potential. Not only allow for data representation, as well as the reuse of such data for knowledge extraction, coupled with its subsequent storage through not so complex formalisms. However, for the purpose of assuring that ontology knowledge is always up to date, they need maintenance. Ontology Learning is an area which studies the details of update and maintenance of ontologies. It is worth noting that relevant literature already presents first results on automatic maintenance of ontologies, but still in a very early stage. Human-based processes are still the current way to update and maintain an ontology, which turns this into a cumbersome task. The generation of new knowledge aimed for ontology growth can be done based in Data Mining techniques, which is an area that studies techniques for data processing, pattern discovery and knowledge extraction in IT systems. This work aims at proposing a novel semi-automatic method for knowledge extraction from unstructured data sources, using Data Mining techniques, namely through pattern discovery, focused in improving the precision of concept and its semantic relations present in an ontology. In order to verify the applicability of the proposed method, a proof of concept was developed, presenting its results, which were applied in building and construction sector.

Produção de resíduos hospitalares na prestação de cuidados domiciliários

RESUMO - Os resíduos hospitalares (RH) perigosos — Grupos III e IV — produzidos na prestação de cuidados domiciliários (CD), dada a sua composição, infecciosidade, toxicidade, mobilidade e persistência, constituem um perigo relevante. A exposição a estes resíduos traduz-se num risco importante para os profissionais de saúde, doentes e seus familiares. Dado que em muitas situações estes resíduos ficam no domicílio dos doentes, sendo posteriormente depositados nos contentores camarários, o risco é alargado ao público em geral, aos catadores e aos profissionais de recolha de resíduos sólidos urbanos dos municípios. Através de um estudo observacional, transversal, com componente analítica, da produção de RH pretende-se determinar e caracterizar os quantitativos dos Grupos III e IV produzidos na prestação de CD em 2003 no concelho da Amadora, identificando também o seu destino final. Utiliza- se uma amostra aleatória do universo de doentes submetidos a tratamento domiciliário em 2003 e efectua-se a análise da associação estatística das variáveis peso do Grupo III e peso do Grupo IV com as variáveis relativas às características do doente (sexo, idade e doença), do tratamento (duração e periodicidade) e sazonais (época do ano). A média do peso produzido dos RH por acto prestado é de 213,1 g para o Grupo III e de 3,8 g para o Grupo IV. Estima--se uma produção de RH do Grupo III na prestação de CD, em 2003, no concelho da Amadora entre 8,8 e 11,4 t e para os RH do Grupo IV um valor de 10,2 kg. Verifica-se que, por acto prestado, a produção média de resíduos do Grupo III é maior nos doentes mais idosos, nas úlceras varicosas, no pé diabético, na escara de pressão, nas situações de maior duração do tratamento e nos doentes submetidos a três tratamentos por semana. Também por acto prestado, a produção média de RH do Grupo IV é maior nos doentes mais novos, na patologia osteo-articular, na infecção, no acidente, no pós-operatório, nas situações de menor duração do tratamento e nos doentes submetidos a seis tratamentos por semana (o que está relacionado com as patologias em causa). As produções médias, por acto prestado, de ambos os grupos não apresentam relação com as variáveis idade e época do ano. Todos os RH produzidos nos actos prestados em CD, em 2003, no concelho da Amadora foram depositados nos contentores municipais. Recomendam-se acções de formação e de informação dirigidas aos profissionais de saúde e ao público em geral, a criação de condições para que os RH produzidos nos CD sejam transportados, em condições adequadas, para os centros de saúde e uma articulação entre os órgãos de gestão dos centros de saúde, a autarquia, os operadores de gestão de RH e os serviços de saúde pública no sentido de serem encontradas soluções apropriadas e inovadoras relativamente à gestão dos RH produzidos na prestação de CD.

Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity?

We assessed aquatic hyphomycete diversity in autumn and spring on oak leaves decomposing in five streams along a gradient of eutrophication in the Northwest of Portugal. Diversity was assessed through microscopy-based (identification by spore morphology) and DNA-based techniques (Denaturing Gradient Gel Electrophoresis and 454 pyrosequencing). Pyrosequencing revealed five times greater diversity than DGGE. About 21% of all aquatic hyphomycete species were exclusively detected by pyrosequencing and 26% exclusively by spore identification. In some streams, more than half of the recorded species would have remained undetected if we had relied only on spore identification. Nevertheless, in spring aquatic hyphomycete diversity was higher based on spore identification, probably because many species occurring in this season are not yet connected to ITS barcodes in genetic databases. Pyrosequencing was a powerful tool for revealing aquatic hyphomycete diversity on decomposing plant litter in streams and we strongly encourage researchers to continue the effort in barcoding fungal species.

Exploring silk based biomaterials functionalized with antimicrobial peptides to prevent surgical site infections

Surgical site infections (SSI) often occur after invasive surgery, which is as a serious health problem, making it important to develop new biomaterials to prevent infections. Spider silk is a natural biomaterial with excellent biocompatibility, low immunogenicity and controllable biodegradability. Through recombinant DNA technology, spider silk-based materials can be bioengineered and functionalized with antimicrobial (AM) peptides 1. The aim of this study is to develop new materials by combining spider silk chimeric proteins with AM properties and silk fibroin extracted from Bombyx mori cocoons to prevent microbial infection. Here, spider silk domains derived from the dragline sequence of the spider Nephila clavipes (6 mer and 15 mer) were fused with the AM peptides Hepcidin and Human Neutrophil peptide 1 (HNP1). The spider silk domain maintained its self-assembly features allowing the formation of beta-sheets to lock in structures without any chemical cross-linking. The AM properties of the developed chimeric proteins showed that 6 mer + HNP1 protein had a broad microbicidal activity against pathogens. The 6 mer + HNP-1 protein was then assembled with different percentages of silk fibroin into multifunctional films. In vitro cell studies with a human fibroblasts cell line (MRC5) showed nontoxic and cytocompatible behavior of the films. The positive cellular response, together with structural properties, suggests that this new fusion protein plus silk fibroin may be good candidates as multifunctional materials to prevent SSI.

Comportamiento tribomecánico de sistemas de sustrato: recubrimiento duros

En aplicaciones como la conformación en frío, donde los metales duros recubiertos con películas de naturaleza cerámica son ampliamente empleados, la existencia de un contacto mecánico repetitivo induce tensiones Hertzianas y origina el fallo por fatiga. En este trabajo, se investigan diversos recubrimientos cerámicos depositados por deposición física desde fase vapor sobre calidades diferentes de metal duro y un acero rápido pulvimetalúrgico para evaluar sus respectivas respuesta al contacto y comportamiento a fatiga. El trabajo experimental incluye la caracterización de los sistemas mediante ensayos de rayado y nanoindentación y la evaluación de las curvas tensión-deformación de indentación esférica de los sustratos, tanto desnudos como recubiertos, poniendo especial atención en determinar las tensiones de contacto críticas asociadas a la deformación plástica y a la aparición de grietas circulares en la superficie recubierta. A este estudio, le siguen numerosos ensayos a fatiga a cargas inferiores a aquéllas identificadas como críticas bajo carga monotónica y para un número de ciclos comprendido entre 1.000 y 1.000.000 de ciclos. Los resultados experimentales indican que las películas cerámicas no parecen desempeñar un papel relevante en la aparición de la cedencia plástica, siendo la deformación plástica global controlada por la deformación del sustrato. No obstante, para tensiones elevadas de indentación durante el régimen plástico, existe la aparición de grietas circulares en los recubrimientos cerámicos. Además, la aparición de las mismas es sensible a la fatiga por contacto. Este análisis mecánico se complementa con una inspección detallada del daño generado en profundidad y superficie.

Activity of ancestral restriction factors against ancient retroviruses

Analysis of TRIM5α and APOBEC3G genes suggests that these two restriction factors underwent strong positive selection throughout primate evolution. This pressure was possibly imposed by ancient exogenous retroviruses, of which endogenous retroviruses are remnants. Our study aims to assess in vitro the activity of these factors against ancient retroviruses by reconstructing their ancestral gag sequences, as well as the ancestral TRIM5α and APOBEC3G for primates. Based on evolutionary genomics approach, we reconstructed ancestors of the two largest families of human endogenous retroviruses (HERV), namely HERV-K and HERV-H, as well as primate ancestral TRIM5α and APOBEC3G variants. The oldest TRIM5α sequence was the catarhinne TRIM5α, common ancestor of Old World monkeys and hominoids, dated from 25 million years ago (mya). From the oldest, to the youngest, ancestral TRIM5α variants showed less restriction of HIV-1 in vitro [1]. Likewise three ancestral APOBEC3Gs sequences common to hominoids (18 mya), Old World monkeys, and catarhinnes (25 mya) were reconstructed. All ancestral APOBEC3G variants inhibited efficiently HIV-1Δvif in vitro, compared to modern APOBEC3Gs. The ability of Vif proteins (HIV-1, HIV-2, SIVmac and SIVagm) to counteract their activity tallied with the residue 128 on ancestral APOBEC3Gs. Moreover we are attempting to reconstruct older ancestral sequences of both restriction factors by using prosimian orthologue sequences. An infectious onemillion- years-old HERV-KCON previously reconstituted was shown to be resistant to modern TRIM5α and APOBEC3G [2]. Our ancestral TRIM5α and APOBEC3G variants were inactive against HERV-KCON. Besides we reconstructed chimeric HERV-K bearing ancestral capsids (up to 7 mya) that resulted in infectious viruses resistant to modern and ancestral TRIM5α. Likewise HERV-K viruses bearing ancestral nucleocapsids will be tested for ancestral and modern APOBEC3G restriction. In silico reconstruction and structural modeling of ancestral HERV-H capsids resulted in structures homologous to that of the gammaretrovirus MLV. Thus we are attempting to construct chimeric MLV virus bearing HERV-H ancestral capsids. These chimeric ancestral HERVs will be tested for infectivity and restriction by ancestral TRIM5α. Similarly chimeric MLV viruses bearing ancestral HERV-H nucleocapsids will be reconstructed and tested for APOBEC3G restriction.

Group A rotavirus genotypes and the ongoing Brazilian experience: a review

Brazil was the first Latin American country to introduce universal group A rotavirus (RV-A) vaccination in March 2006, resulting in a unique epidemiological scenario. Since RV-A first identification in Brazil, 2,691 RV-A-positive stool samples, collected between 1982- 2007, were typed by independent research groups throughout the country. In the pre-vaccination era, 2,492 RV-A-positive samples collected from 1982-2005 were successfully typed, while 199 samples were analyzed from 2006-2007. According to the reviewed studies, there were two important times in the pre-vaccination era: (i) the period from 1982-1995, during which the detection of G5P[8] RV-A, in addition to the classical genotypes G1-4, challenged vaccine development programs; and (ii) the period from 1996-2005, during which genotype G9P[8] emerged, following a global trend. The rate of G2P[4] RV-A detection decreased from 26% (173/653) during 1982-1995 to 2% (43/1,839) during 1996-2005. The overall detection rate of RV-A genotypes from 1982-2005 was as follows: 43% (n = 1,079) G1P[8]/G1P[not typed (NT)]; 20% (n = 488) G9P[8]/G9P[NT]; 9% (n = 216) G2P[4]/G2P[NT]; 6% (n = 151) G3P[8]/G3P[NT]; 4% (n = 103) G4P[8]/G4P[NT]; and 4% (n = 94) G5P[8]/G5P[NT]. Mixed infections accounted for 189 (7%) of the positive samples, while atypical G/P combinations or other genotypes, including G6, G8, G10 and G12, were identified in 172 (7%) samples. The initial surveillance studies carried out in several Brazilian states with RV-A-positive samples collected in 2006 and 2007 show a predominance of G2P[4] strains (148/199 or 74%). Herein, we review RV-A typing studies carried out since the 1980s in Brazil, highlighting the dynamics of RV-A strain circulation profiles before and early after universal use of RV-A vaccine in Brazil.

Experimental benznidazole treatment of Trypanosoma cruzi II strains isolated from children of the Jequitinhonha Valley, Minas Gerais, Brazil, with Chagas disease

Trypanosoma cruzi strains from distinct geographic areas show differences in drug resistance and association between parasites genetic and treatment response has been observed. Considering that benznidazole (BZ) can reduce the parasite burden and tissues damage, even in not cured animals and individuals, the goal is to assess the drug response to BZ of T. cruzi II strains isolated from children of the Jequitinhonha Valley, state of Minas Gerais, Brazil, before treatment. Mice infected and treated with BZ in both phases of infection were compared with the untreated and evaluated by fresh blood examination, haemoculture, polymerase chain reaction, conventional (ELISA) and non-conventional (FC-ALTA) serologies. In mice treated in the acute phase, a significant decrease in parasitaemia was observed for all strains. Positive parasitological and/or serological tests in animals treated during the acute and chronic (95.1-100%) phases showed that most of the strains were BZ resistant. However, beneficial effect was demonstrated because significant reduction (p < 0.05%) and/or suppression of parasitaemia was observed in mice infected with all strains (acute phase), associated to reduction/elimination of inflammation and fibrosis for two/eight strains. BZ offered some benefit, even in not cured animals, what suggest that BZ use may be recommended at least for recent chronic infection of the studied region.

Sexual dimorphism of the human mandible: demonstration by elliptical Fourier analysis.

A new quantitative approach of the mandibular sexual dimorphism, based on computer-aided image analysis and elliptical Fourier analysis of the mandibular outline in lateral view is presented. This method was applied to a series of 117 dentulous mandibles from 69 male and 48 female individuals native of Rhenish countries. Statistical discriminant analysis of the elliptical Fourier harmonics allowed the demonstration of a significant sexual dimorphism in 97.1% of males and 91.7% of females, i.e. in a higher proportion than in previous studies using classical metrical approaches. This original method opens interesting perspectives for increasing the accuracy of sex identification in current anthropological practice and in forensic procedures.

Hypertension and microvascular remodelling

In the present review, microvascular remodelling refers to alterations in the structure of resistance vessels contributing to elevated systemic vascular resistance in hypertension. We start with some historical aspects, underscoring the importance of Folkow's contribution made half a century ago. We then move to some basic concepts on the biomechanics of blood vessels, and explicit the definitions proposed by Mulvany for specific forms of remodelling, especially inward eutrophic and inward hypertrophic. The available evidence for the existence of remodelled resistance vessels in hypertension comes next, with relatively more weight given to human, in comparison with animal data. Mechanisms are discussed. The impact of antihypertensive drug treatment on remodelling is described, again with emphasis on human data. Some details are given on the three studies to date which point to remodelling of subcutaneous resistance arteries as an independent predictor of cardiovascular risk in hypertensive patients. We terminate by considering the potential role of remodelling in the pathogenesis of end-organ damage and in the perpetuation of hypertension.

Nuevo disipador para edificación sismorresistente. 1ª parte: caracterización y modelos de predicción

A new energy dissipator, based on yielding of steel under shear response, has been developed and recently tested. It is H shaped and web stiffened. Yielding moin part is mechanized from one piece of rectangular shoped steel bar. Its conception let obtain thin and well-stiffened web cross sections without welded parts. Main experimentally obtained charecteristics are a yielding point near 0.5 mm of displacement, yielding loads between 14 kN and 20 kN and a dissipated energy, before damage appears in the web, from 10 kJ to 21 kJ. All tested specimens have developed large deformations without web buckling. Whe web degradation appers, flanges and stiffeners keep dissipating an important amount of energy. Proposed numerical models and simple mathematical expressions offer well correlated results when compared to the experimental ones

El fet migratori a Catalunya i els processos d'identificació nacional en la població nouvinguda

En el marc de la recerca sobre identitats i nova ciutadania, l’objecte d’aquest treball és reconèixer elements clau dels processos d’identificació nacional a Catalunya en la població nouvinguda, i identificar els factors que n'afavoreixen la seva vinculació comunitària. La recerca s'ha desenvolupat en un primer bloc analitzant la perspectiva sociològica entorn a la idea d’identitat, així com l’evolució del discurs identitari a Catalunya, a fi de continuar desenvolupant amb profunditat el debat sobre identitat i nació en relació al fet migratori i la diversitat social existent. En un segon bloc d’anàlisi, la recerca fixa la mirada a una dotzena de casos treballats a través d’històries de vida de diverses realitats migratòries del nostre país corresponents a les diverses onades del segle XX, tant d’immigració espanyola com d'immigració de fora de l'Estat espanyol. La voluntat d’aquest segon bloc és extreure experiències socials d’interpretacions individuals que assenyalin quins elements permeten o dificulten la mobilitat social, quines experiències tenen valor identitari i de quin tipus, i quins fenòmens esdevenen rellevants en la configuració d’espais de referència i identificació nacional a nivell individual. Finalment s’incorpora un apartat d’entrevistes en profunditat a diversos actors socials i polítics rellevants a fi de reconèixer aquells elements que centren el discurs de la “nova cultura pública comuna”. L’objectiu és interrelacionar el discurs polític i filosòfic actual amb l’experiència biogràfica de les persones, assenyalant aquells elements que han estat significatius per a la seva identitat com a catalans i catalanes o, ans al contrari, que no han afavorit una situació en aquests termes. En aquest sentit la pregunta que vincula aquest espai de reflexió és: Quins elements afavoreixen la identificació nacional englobant la diversitat social existent i quins mecanismes d'adhesió hi podrien funcionar?

Human synthetic lethal inference as potential anti-cancer target gene detection

Background: Two genes are called synthetic lethal (SL) if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these mutated genes' SL partners may provide specific anti-cancer drug candidates, with minor perturbations to the healthy cells. Since existent SL data is mainly restricted to yeast screenings, the road towards human SL candidates is limited to inference methods. Results: In the present work, we use phylogenetic analysis and database manipulation (BioGRID for interactions, Ensembl and NCBI for homology, Gene Ontology for GO attributes) in order to reconstruct the phylogenetically-inferred SL gene network for human. In addition, available data on cancer mutated genes (COSMIC and Cancer Gene Census databases) as well as on existent approved drugs (DrugBank database) supports our selection of cancer-therapy candidates.Conclusions: Our work provides a complementary alternative to the current methods for drug discovering and gene target identification in anti-cancer research. Novel SL screening analysis and the use of highly curated databases would contribute to improve the results of this methodology.

An observational study of the 7 September 2005 Barcelona tornado outbreak

This paper presents an observational study of the tornado outbreak that took place on the 7 September 2005 in the Llobregat delta river, affecting a densely populated and urbanised area and the Barcelona International airport (NE Spain). The site survey confirmed at least five short-lived tornadoes. Four of them were weak (F0, F1) and the other one was significant (F2 on the Fujita scale). They started mostly as waterspouts and moved later inland causing extensive damage estimated in 9 million Euros, three injured people but fortunately no fatalities. Large scale forcing was provided by upper level diffluence and low level warm air advection. Satellite and weather radar images revealed the development of the cells that spawned the waterspouts along a mesoscale convergence line in a highly sheared and relatively low buoyant environment. Further analysis indicated characteristics that could be attributed indistinctively to non-supercell or to mini-supercell thunderstorms.

Flood Plain Management & Hazard Mitigation Task Force Report, August 2008

The Flood Plain Management and Hazard Mitigation Task Force emphasizes the long-term benefits of mitigation and management to the entire state in preventing or reducing damages from floods and other hazards faced in Iowa. Investments in efforts to manage watershed areas and to mitigate any damages from floods or other disaster events benefit individuals, families, communities, agriculture, business and industry, and certainly public entities and infrastructure. The Task Force encourages the Rebuild Iowa Advisory Commission to balance the immediate needs for rebuilding to include the beginning of the investments required to effectively mitigate future damage and maintain effective policy in Iowa’s watersheds. The significance of the damage seen in Iowa from the tornadoes, storms, and floods of 2008 include the loss of eighteen Iowans in disaster-related events. This alone should inspire investment in mitigation efforts for all hazards. Much of the damage resulting from the disasters can be tied to floodplain management and hazard mitigation, pointing the way toward enhanced efforts and new initiatives to safeguard lives, property, and communities’ economic health. Even so, it must be recognized that the weather events throughout last winter and spring added impetus to the rains and storms that ultimately resulted in record flooding. Some perspective must be maintained as planning progresses and significant investments in mitigation are considered to meet a specific level of safety and protection from future threats. The Task Force identified a number of issues, and four were agreed-upon as those with the highest priority to be addressed by the Task Force through a set of recommendations.