Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

A process for mining science & technology documents databases, illustrated for the case of "knowledge discovery and data mining"

This paper presents a process of mining research & development abstract databases to profile current status and to project potential developments for target technologies, The process is called "technology opportunities analysis." This article steps through the process using a sample data set of abstracts from the INSPEC database on the topic o "knowledge discovery and data mining." The paper offers a set of specific indicators suitable for mining such databases to understand innovation prospects. In illustrating the uses of such indicators, it offers some insights into the status of knowledge discovery research*.

Infant mortality rates according to socioeconomic status in a Brazilian city

OBJECTIVE: Data from municipal databases can be used to plan interventions aimed at reducing inequities in health care. The objective of the study was to determine the distribution of infant mortality according to an urban geoeconomic classification using routinely collected municipal data. METHODS: All live births (total of 42,381) and infant deaths (total of 731) that occurred between 1994 and 1998 in Ribeirão Preto, Brazil, were considered. Four different geoeconomic areas were defined according to the family head's income in each administrative urban zone. RESULTS: The trends for infant mortality rate and its different components, neonatal mortality rate and post-neonatal mortality rate, decreased in Ribeirão Preto from 1994 to 1998 (chi-square for trend, p<0.05). These rates were inversely correlated with the distribution of lower salaries in the geoeconomic areas (less than 5 minimum wages per family head), in particular the post-neonatal mortality rate (chi-square for trend, p<0.05). Finally, the poor area showed a steady increase in excess infant mortality. CONCLUSIONS: The results indicate that infant mortality rates are associated with social inequality and can be monitored using municipal databases. The findings also suggest an increase in the impact of social inequality on infant health in Ribeirão Preto, especially in the poor area. The monitoring of health inequalities using municipal databases may be an increasingly more useful tool given the continuous decentralization of health management at the municipal level in Brazil.

Probabilistic linkage in household survey on hospital care usage

OBJECTIVE: To evaluate the potential advantages and limitations of the use of the Brazilian hospital admission authorization forms database and the probabilistic record linkage methodology for the validation of reported utilization of hospital care services in household surveys. METHODS: A total of 2,288 households interviews were conducted in the county of Duque de Caxias, Brazil. Information on the occurrence of at least one hospital admission in the year preceding the interview was obtained from a total of 10,733 household members. The 130 records of household members who reported at least one hospital admission in a public hospital were linked to a hospital database with 801,587 records, using an automatic probabilistic approach combined with an extensive clerical review. RESULTS: Seventy-four (57%) of the 130 household members were identified in the hospital database. Yet only 60 subjects (46%) showed a record of hospitalization in the hospital database in the study period. Hospital admissions due to a surgery procedure were significantly more likely to have been identified in the hospital database. The low level of concordance seen in the study can be explained by the following factors: errors in the linkage process; a telescoping effect; and an incomplete record in the hospital database. CONCLUSIONS: The use of hospital administrative databases and probabilistic linkage methodology may represent a methodological alternative for the validation of reported utilization of health care services, but some strategies should be employed in order to minimize the problems related to the use of this methodology in non-ideal conditions. Ideally, a single identifier, such as a personal health insurance number, and the universal coverage of the database would be desirable.

Estimativa de validade de um novo método de isolamento de vírus rábico

OBJETIVOS: Nenhum estudo de base populacional foi realizado para mostrar o uso potencial de diagnóstico virológico do vírus rábico. O estudo realizado teve por objetivo estimar parâmetros de acurácia para o isolamento de vírus rábico em célula McCoy, como um método alternativo, e comparar com o uso da célula N2A, considerada método de referência. MÉTODOS: Foi realizado um inquérito em 120 morcegos coletados aleatoriamente, na Mata Atlântica, no Estado de São Paulo. Utilizou-se a reação de imunofluorescência para a detecção do vírus rábico isolado no cérebro desses morcegos, avaliado nos dois sistemas de cultivos celulares. Dois bancos de dados foram formados com os resultados. A análise foi feita com o programa Computer Methods for Diagnosis Tests (CMDT), utilizando a técnica de two-graph-receiver operating characteristic (TG-ROC) para obter os parâmetros de sensibilidade e especificidade, além de outros indicadores, tais como eficácia, valor preditivo positivo, valor preditivo negativo e razão de verossimilhança. RESULTADOS: A célula N2A apresentou 90% de sensibilidade e especificidade, enquanto que a célula McCoy obteve 95% para os mesmos parâmetros. Os valores foram baseados em pontos de cortes otimizados para cada uma das células. CONCLUSÕES: Observou-se que a célula McCoy permite obter estimativas de acurácia superiores aos resultados observados com a célula de N2A, representando um método alternativo eficaz no isolamento do vírus rábico.

Mental health and psychiatry research in Brazil: scientific production from 1999 to 2003

OBJECTIVE: To assess the extent of mental health scientific production in Brazil from 1999 to 2003, and to identify the nature of the publications generated, their sources of finance and the ways of publicly disseminating the research findings. METHODS: Searches for publications were conducted in the Medline and PsychInfo databases for the period 1999-2003. A semi-structured questionnaire developed by an international team was applied to 626 mental health researchers, covering each interviewee's educational background, research experience, access to funding sources, public impact and research priorities. The sample was composed by 626 mental health researchers identified from 792 publications indexed on Medline and PsychInfo databases for the period above, and from a list of reviewers of Revista Brasileira de Psiquiatria. RESULTS: In Brazil, 792 publications were produced by 525 authors between 1999 and 2003 (441 indexed in Medline and 398 in the ISI database). The main topics were: depression (29.1%), substance misuse (14.6%), psychoses (10%), childhood disorders (7%) and dementia (6.7%). Among the 626 Brazilian mental health researchers, 329 answered the questionnaire. CONCLUSIONS: There were steadily increasing numbers of Brazilian articles on mental health published in foreign journals from 1999 to 2003: the number of articles in Medline tripled and it doubled in the ISI database. The content of these articles corresponded to the priorities within mental health, but there is a need for better interlinking between researchers and mental health policymakers.

Comorbidity adjustment index for the international classification of diseases, 10

OBJECTIVE: To develop a Charlson-like comorbidity index based on clinical conditions and weights of the original Charlson comorbidity index. METHODS: Clinical conditions and weights were adapted from the International Classification of Diseases, 10th revision and applied to a single hospital admission diagnosis. The study included 3,733 patients over 18 years of age who were admitted to a public general hospital in the city of Rio de Janeiro, southeast Brazil, between Jan 2001 and Jan 2003. The index distribution was analyzed by gender, type of admission, blood transfusion, intensive care unit admission, age and length of hospital stay. Two logistic regression models were developed to predict in-hospital mortality including: a) the aforementioned variables and the risk-adjustment index (full model); and b) the risk-adjustment index and patient's age (reduced model). RESULTS: Of all patients analyzed, 22.3% had risk scores >1, and their mortality rate was 4.5% (66.0% of them had scores >1). Except for gender and type of admission, all variables were retained in the logistic regression. The models including the developed risk index had an area under the receiver operating characteristic curve of 0.86 (full model), and 0.76 (reduced model). Each unit increase in the risk score was associated with nearly 50% increase in the odds of in-hospital death. CONCLUSIONS: The risk index developed was able to effectively discriminate the odds of in-hospital death which can be useful when limited information is available from hospital databases.

Surveillance of mother-to-child HIV transmission: socioeconomic and health care coverage indicators

OBJECTIVE: To identify clustering areas of infants exposed to HIV during pregnancy and their association with indicators of primary care coverage and socioeconomic condition. METHODS: Ecological study where the unit of analysis was primary care coverage areas in the city of Porto Alegre, Southern Brazil, in 2003. Geographical Information System and spatial analysis tools were used to describe indicators of primary care coverage areas and socioeconomic condition, and estimate the prevalence of liveborn infants exposed to HIV during pregnancy and delivery. Data was obtained from Brazilian national databases. The association between different indicators was assessed using Spearman's nonparametric test. RESULTS: There was found an association between HIV infection and high birth rates (r=0.22, p<0.01) and lack of prenatal care (r=0.15, p<0.05). The highest HIV infection rates were seen in areas with poor socioeconomic conditions and difficult access to health services (r=0.28, p<0.01). The association found between higher rate of prenatal care among HIV-infected women and adequate immunization coverage (r=0.35, p<0.01) indicates that early detection of HIV infection is effective in those areas with better primary care services. CONCLUSIONS: Urban poverty is a strong determinant of mother-to-child HIV transmission but this trend can be fought with health surveillance at the primary care level.

Análise TG-ROC de testes de imunofluorescência no diagnóstico de leishmaniose visceral canina

OBJETIVO: Analisar a acurácia do diagnóstico de dois protocolos de imunofluorescência indireta para leishmaniose visceral canina. MÉTODOS: Cães provenientes de inquérito soroepidemiológico realizado em área endêmica nos municípios de Araçatuba e de Andradina, na região noroeste do estado de São Paulo, em 2003, e área não endêmica da região metropolitana de São Paulo, foram utilizados para avaliar comparativamente dois protocolos da reação de imunofluorescência indireta (RIFI) para leishmaniose: um utilizando antígeno heterólogo Leishmania major (RIFI-BM) e outro utilizando antígeno homólogo Leishmania chagasi (RIFI-CH). Para estimar acurácia utilizou-se a análise two-graph receiver operating characteristic (TG-ROC). A análise TG-ROC comparou as leituras da diluição 1:20 do antígeno homólogo (RIFI-CH), consideradas como teste referência, com as diluições da RIFI-BM (antígeno heterólogo). RESULTADOS: A diluição 1:20 do teste RIFI-CH apresentou o melhor coeficiente de contingência (0,755) e a maior força de associação entre as duas variáveis estudadas (qui-quadrado=124,3), sendo considerada a diluição-referência do teste nas comparações com as diferentes diluições do teste RIFI-BM. Os melhores resultados do RIFI-BM foram obtidos na diluição 1:40, com melhor coeficiente de contingência (0,680) e maior força de associação (qui-quadrado=80,8). Com a mudança do ponto de corte sugerido nesta análise para a diluição 1:40 da RIFI-BM, o valor do parâmetro especificidade aumentou de 57,5% para 97,7%, embora a diluição 1:80 tivesse apresentado a melhor estimativa para sensibilidade (80,2%) com o novo ponto de corte. CONCLUSÕES: A análise TG-ROC pode fornecer importantes informações sobre os testes de diagnósticos, além de apresentar sugestões sobre pontos de cortes que podem melhorar as estimativas de sensibilidade e especificidade do teste, e avaliá-los a luz do melhor custo-benefício.

How many low birthweight babies in low- and middle-income countries are preterm?

OBJECTIVE: To assess the prevalence of preterm birth among low birthweight babies in low and middle-income countries. METHODS: Major databases (PubMed, LILACS, Google Scholar) were searched for studies on the prevalence of term and preterm LBW babies with field work carried out after 1990 in low- and middle-income countries. Regression methods were used to model this proportion according to LBW prevalence levels. RESULTS: According to 47 studies from 27 low- and middle-income countries, approximately half of all LBW babies are preterm rather than one in three as assumed in studies previous to the 1990s. CONCLUSIONS: The estimate of a substantially higher number of LBW preterm babies has important policy implications in view of special health care needs of these infants. As for earlier projections, our findings are limited by the relative lack of population-based studies.

Use of accelerometry to measure physical activity in adults and the elderly

OBJECTIVE: To review the use of accelerometry as an objective measure of physical activity in adults and elderly people. METHODS: A systematic review of studies on the use of accelerometty as an objective measure to assess physical activity in adults were examined in PubMed Central, Web of Knowledge, EBSCO and Medline databases from March 29 to April 15, 2010. The following keywords were used: "accelerometry," "accelerometer," "physical activity," "PA," "patterns," "levels," "adults," "older adults," and "elderly," either alone or in combination using "AND" or "OR." The reference lists of the articles retrieved were examined to capture any other potentially relevant article. Of 899 studies initially identified, only 18 were fully reviewed, and their outcome measures abstracted and analyzed. RESULTS: Eleven studies were conducted in North America (United States), five in Europe, one in Africa (Cameroon) and one in Australia. Very few enrolled older people, and only one study reported the season or time of year when data was collected. The articles selected had different methods, analyses, and results, which prevented comparison between studies. CONCLUSIONS: There is a need to standardize study methods for data reporting to allow comparisons of results across studies and monitor changes in populations. These data can help design more adequate strategies for monitoring and promotion of physical activity.

Prevalence of alcohol and tobacco use among Brazilian adolescents: a systematic review

OBJECTIVE: To analyze alcohol and tobacco use among Brazilian adolescents and identify higher-risk subgroups. METHODS: A systematic review of the literature was conducted. Searches were performed using four databases (LILACS, MEDLINE /PubMed, Web of Science, and Google Scholar), specialized websites and the references cited in retrieved articles. The search was done in English and Portuguese and there was no limit on the year of publication (up to June 2011). From the search, 59 studies met all the inclusion criteria: to involve Brazilian adolescents aged 10-19 years; to assess the prevalence of alcohol and/or tobacco use; to use questionnaires or structured interviews to measure the variables of interest; and to be a school or population-based study that used methodological procedures to ensure representativeness of the target population (i.e. random sampling). RESULTS: The prevalence of current alcohol use (at the time of the investigation or in the previous month) ranged from 23.0% to 67.7%. The mean prevalence was 34.9% (reflecting the central trend of the estimates found in the studies). The prevalence of current tobacco use ranged from 2.4% to 22.0%, and the mean prevalence was 9.3%. A large proportion of the studies estimated prevalences of frequent alcohol use (66.7%) and heavy alcohol use (36.8%) of more than 10%. However, most studies found prevalences of frequent and heavy tobacco use of less than 10%. The Brazilian literature has highlighted that environmental factors (religiosity, working conditions, and substance use among family and friends) and psychosocial factors (such as conflicts with parents and feelings of negativeness and loneliness) are associated with the tobacco and alcohol use among adolescents. CONCLUSIONS: The results suggest that consumption of alcohol and tobacco among adolescents has reached alarming prevalences in various localities in Brazil. Since unhealthy behavior tends to continue from adolescence into adulthood, public policies aimed towards reducing alcohol and tobacco use among Brazilians over the medium and long terms may direct young people and the subgroups at higher risk towards such behavior.

Association between Schistosomiasis mansoni and hepatitis C: systematic review

OBJECTIVE: To perform a systematic review of the prevalence of the HCV/ S. mansoni co-infection and associated factors in Schistosoma mansoni -infected populations. METHODS: The bibliographic search was carried out using the Medline, Lilacs, SciELO, Cochrane Library and Ibecs databases. The criteria for the studies' selection and the extraction data were based on systematic review methods. Forty five studies were found, with nine being excluded in a first screening. Thirteen articles were used for data extraction. RESULTS: The HCV infection rates in schistosomiasis populations range from 1% in Ethiopia to 50% in Egypt. Several studies had poorly defined methodologies, even in areas characterized by an association between hepatitis C and schistosomiasis, such as Brazil and Egypt, which meant conclusions were inconsistent. HCV infection rates in schistosomotic populations were heterogeneous and risk factors for acquiring the virus varied widely. CONCLUSIONS: Despite the limitations, this review may help to identify regions with higher rates of hepatitis C and schistosomiasis association. However, more studies are necessary for the development of public health policies on prevention and control of both diseases.

Obesity and dental caries: systematic review

OBJECTIVE Identifying, through a systematic literature review, evidence of a possible association between obesity and dental caries. METHODS A search of articles published between 2005 and January 2012 was performed in the Medline/PubMed, LILACS and Web of Science databases. The quality of scientific evidence of the selected articles was assessed by the items proposed for observational studies in the Downs & Black instrument. RESULTS Initially, 537 references were found; after checking the titles and abstracts by two independent researchers, twenty-eight articles were selected for complete reading. Ten of them that assessed the primary and/or permanent dentition observed a positive association between obesity and dental caries and one study found an inverse association. According to the Downs & Black classification, thirteen articles with good scientific evidence were found. CONCLUSIONS The present review did not find sufficient evidence regarding the association between obesity and dental caries, and it did not clarify the possible role of diet and other possible effect modifiers on this association.