Competency Questions(CQs) play an important role in the ontology development lifecycle, as they represent the ontology requirements. Although the main methodologies describe and use CQs, the current practice of ontology engineering makes a superficial use of CQs. One of the main problems that hamper their proper use lies on the lack of tools that assist users to check if CQs are being fulfilled by the ontology being defined, particularly when these ontologies are defined in OWL (Ontology Web Language), under the Description Logic formalism. We propose a mechanism to support evaluating whether the ontology follows their correspondent CQs.

The reduction of hepatic microsomal transfer protein (MTP) activity results in fatty liver, worsening hepatic steatosis and fibrosis in chronic hepatitis C (CHC). The G allele of the MTP gene promoter, -493G/T, has been associated with lower transcriptional activity than the T allele. We investigated this association with metabolic and histological variables in patients with CHC. A total of 174 untreated patients with CHC were genotyped for MTP -493G/T by direct sequencing using PCR. All patients were negative for markers of Wilson's disease, hemochromatosis and autoimmune diseases and had current and past daily alcohol intake lower than 100 g/week. The sample distribution was in Hardy-Weinberg equilibrium. Among subjects with genotype 1, 56.8% of the patients with fibrosis grade 3+4 presented at least one G allele versus 34.3% of the patients with fibrosis grade 1+2 (OR = 1.8; 95%CI = 1.3-2.3). Logistic regression analysis with steatosis as the dependent variable identified genotypes GG+GT as independent protective factors against steatosis (OR = 0.4, 95%CI = 0.2-0.8; P = 0.01). The results suggest that the presence of the G allele of MTP -493G/T associated with lower hepatic MTP expression protects against steatosis in our CHC patients.

Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs). IND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements. Ambiguity of biological database content is addressed by a method that identifies implicit knowledge behind semantic annotations in biological databases and grounds it in an expressive upper-level ontology. The result is a seamless representation of database structure, content and annotations as OWL models.

Background/Aim: Hyperhomocysteinemia due to Methylenetetrahydrofolate Reductase (MTHFR) gene, in particular the C677T (Ala222Val) polymorphism were recently associated to steatosis and fibrosis. We analyzed the frequency of MTHFR gene in a cross-sectional study of patients affected by Chronic Hepatitis C (CHC) from Northeast of Brazil. Method: One hundred seven-four untreated patients with CHC were genotyped for the C677T MTHFR. Genomic DNA was extracted from peripheral blood cells and the C677T MTHFR polymorphism was identified by PCR-RFLP. The homocysteine (Hcy) levels were determined by chemiluminescence method. All patients were negative for markers of Wilson's disease, hemochromatosis and autoimmune diseases and have current and past daily alcohol intake less than 100 g/week. Results: Among subjects infected with CHC genotype non-1 the frequency of MTHFR genotypes TT was 9.8% versus 4.4% genotype 1 (p = 0.01). Nevertheless, association was found between the MTHFR genotype TT × CT/CC polymorphism and the degree of steatosis and fibrosis in both hepatitis C genotype (p < 0.05). A significant difference was found on plasma Hcy levels in patients with steatosis regardless of HCV genotype (p = 0.03). Conclusion: Our results indicate that plasma Hcy levels is highly prevalent in subjects with chronic hepatits C with steatosis regardless of HCV genotype and vitamin deficiency. The presence of genotype TT of MTHFR C677T polymorphism was more common in CHC genotype non-1 infected patient regardless of histopathological classification and genotype TT+CT frequencies were significant in the presence of fibrosis grade 1+2 and of steatosis in CHC infected patients from the northeast of Brazil regardless of HCV genotype. The genetic susceptibility of MTHFR C677T polymorphism should be confirmed in a large population.

Resumo A cooperação intergovernamental entre municípios de pequeno porte é operacionalizada por meio de consórcios de saúde, historicamente, no Sistema Único de Saúde (SUS). Tais iniciativas favoreceram a descentralização da saúde no contexto da municipalização. Entretanto, pouco se sabe sobre a sua implementação no processo de regionalização. Este estudo objetivou analisar as razões para a expansão dos consórcios intermunicipais de saúde conduzida pela autoridade sanitária estadual como um fenômeno político institucional novo na regionalização da saúde no SUS em Pernambuco. Trata-se de um estudo retrospectivo de caráter analítico com abordagem qualitativa. Realizaram-se quatro entrevistas semiestruturadas com gestores estaduais, as quais foram analisadas mediante técnica de método de condensação de significados proposta por Kvale. A Teoria das Representações Sociais guiou a análise dos dados. As razões para a indução do consorciamento intermunicipal foram: o fortalecimento da regionalização dos serviços de saúde; a ampliação de oferta e cogestão de serviços de saúde; a absorção de experiências exitosas e a necessidade da indução estadual das políticas regionais de saúde. Os consórcios se configuraram como uma possibilidade positiva na percepção dos gestores estaduais na regionalização de ações de saúde no estado; porém, estudos adicionais são necessários no que diz respeito ao impacto dos indicadores de saúde em escala regional.

Lymphatic filariasis (LF) is a neglected tropical disease associated with poverty and poor environmental conditions. With the inclusion of vector control activities in LF surveillance actions, there is a need to develop simple methods to identify areas with higher mosquito density and thus a higher consequent risk of W. bancrofti transmission. An ecological study was conducted in Igarassu, which is in the metropolitan region of Recife, Pernambuco, Brazil. The mosquitoes were captured in 2060 houses distributed across 117 census tracts. The vector density index (VDI), which measures the average number of lymphatic-filariasis-transmitting mosquitoes per number of houses collected in the risk stratum, was constructed. Moreover, the social deprivation indicator (SDI) was constructed and calculated through principal component factor analysis. An average of 242 female C. quinquefasciatus were found in the high-risk stratum, while the average in the low-risk stratum was 108. The overall VDI was 6.8 mosquitoes per household. The VDI for the high-risk stratum was 13.2 mosquitoes per household, while for the low/medium-risk stratum, it was 5.2. This study offers an SDI for the density of C. quinquefasciatus mosquitoes, which can help reduce the costs associated with data collection and allows for identifying priority areas for vector control actions.