Detecting Network Communities: An Application to Phylogenetic Analysis

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis

Efeitos genotóxicos e alterações de enzimas hepáticas em trabalhadores do refino de petróleo Genotoxic effects and hepatic enzymes alterations among petroleum refinery workers

Um estudo de casos e controles, aninhado num estudo de coorte, investigou a associação entre efeitos genotóxicos e alteração de enzimas hepáticas em trabalhadores de uma refinaria de petróleo do Nordeste. Foram examinados todos os dez novos casos de alterações de enzimas hepáticas - gama-glutamil transferase (GGT) e alanina aminotransferase (ALT) - ocorridos em 2002. Dez trabalhadores sem alterações de GGT ou ALT foram selecionados como controles. Os efeitos do fumo, sexo, idade e consumo de café foram controlados. O efeito genotóxico foi avaliado pela técnica de trocas entre cromátides irmãs (TCI) e alterações cromossômicas (AC) estruturais. As médias de TCI por célula (3,92 ± 1,04 versus 4,25 ± 1,47) e de ACE (8,85 ± 3,4 versus 9,1 ± 3,7) não diferiram de forma significante entre casos e controles respectivamente.<br>A case-control study, nested in a cohort study, investigated the association between genotoxic effects and hepatic enzymes alterations among workers in a petroleum refinery, Northeast Brazil. Ten cases of hepatic enzymes alterations - gamma-glutamyltransferase (GGT) and Alanine aminotransferase (ALT) - representing all incident cases occurring in the refinery during 2002, were examined. Ten workers without GGT and ALT alterations were selected as controls. The effects of smoking, sex, age and coffee consumption were controlled. The genotoxic effects were evaluated by the sister chromatid exchange (SCE) and by the chromosomal aberrations (CA) techniques. Mean SCE per cell (3.92 ± 1.04 versus 4.25 ± 1.47) and CA per cell (8.85 ± 3.4 versus 9.1 ± 3.7) did not differ significantly between cases and controls respectively

Alterações hepáticas em trabalhadores de uma refinaria de petróleo e em uma população de referência no Estado da Bahia, Brasil Liver changes in workers at an oil refinery and in a reference population in the state of Bahia, Brazil

OBJETIVO: Determinar a prevalência de alterações nas enzimas hepáticas de trabalhadores de uma refinaria de petróleo localizada no Estado da Bahia em comparação a uma população de referência não ocupacionalmente exposta a produtos químicos, e descrever os fatores associados à variação nessa prevalência. MÉTODO: Foram avaliados os trabalhadores da refinaria e os funcionários do escritório da gerência administrativa da empresa, situada em Salvador, capital do Estado da Bahia. Estudaram-se amostras de sangue de 692 trabalhadores da refinaria e de 377 trabalhadores da população de referência. Classificaram-se como casos de alterações hepáticas indivíduos que apresentaram valores acima dos padrões de referência simultaneamente para gama-glutamiltransferase (GGT) (>50 U/L para o sexo masculino e >32 U/L para o sexo feminino) e alanina aminotrans- ferase (ALT) (>50 U/L). Foram coletadas informações sobre idade, sexo, peso, altura, tempo de serviço, uso de álcool, hábito de fumar, exercício físico, exposição ocupacional a produtos químicos, uso de equipamento de proteção individual e antecedentes médicos de hepatite, icterícia e obesidade. RESULTADOS: A prevalência de alterações hepáticas na refinaria foi de 15,3% (IC95%: 12,5 a 18,1), contra 3,8% (IC95%: 1,8 a 5,8) na população de referência. A análise de regressão logística múltipla estimou que os trabalhadores da refinaria apresentavam uma prevalência de alterações hepáticas 3,56 vezes maior (IC95%: 1,99 a 6,38) do que a prevalência observada na população de referência, independentemente de outras covariáveis relevantes, como obesidade, prática de exercícios físicos, fumo e bebida alcoólica. CONCLUSÕES: Os resultados sugerem que a exposição ocupacional desempenha um papel importante na determinação das alterações hepáticas nos trabalhadores dessa refinaria de petróleo.<br>OBJECTIVE: To determine the prevalence of liver changes in workers at an oil refinery located in the state of Bahia, Brazil, as compared to a reference population with no occupational exposure to chemical products, and to describe the factors associated with the observed differences in prevalence. METHODS: We studied workers at the refinery and at the company's central management office located in the city of Salvador, which is the state capital. Blood samples of 692 refinery workers and 377 workers from the reference population were analyzed. Cases were defined as individuals presenting high serum levels of both gamma-glutamyltransferase (GGT) and alanine aminotransferase (ALT) (GGT > 50 U/L for males and > 32 U/L for females; ALT > 50 U/L). Data were collected on age, sex, weight, height, years working for the company, use of alcohol, smoking habits, physical exercise, occupational exposure to chemical products, use of personal safety equipment, and medical history of hepatitis, jaundice, and obesity. RESULTS: The prevalence of liver changes among refinery workers was 15.3% (95% CI: 12.5 to 18.1), vs. 3.8% (95% CI: 1,8 to 5,8) in the reference population. According to multiple logistic regression analysis, the prevalence of liver changes among refinery workers was 3.56 times greater (95% CI: 1,99 to 6,38) than in the reference population, regardless of the presence of other relevant co-variables, such as obesity, exercise, smoking, and alcohol consumption. CONCLUSIONS: These results suggest that occupational exposure may play a major role in the development of liver changes among workers at the oil refinery where the study was carried out

Institutions, Informality, and Wage Flexibility: Evidence from Brazil IMF Working Paper Western Hemisphere Department Institutions, Informality, and Wage Flexibility: Evidence from Brazil Prepared by Marcello Estevão and Irineu de Carvalho Filho* Authoriz

Abstract Even though institutions are created to protect workers, they may interfere with labor market functioning, raise unemployment, and end up being circumvented by informal contracts. This paper uses Brazilian microeconomic data to show that the institutional changes introduced by the 1988 Constitution lowered the sensitivity of real wages to changes in labor market slack and could have contributed to the ensuing higher rates of unemployment in the country. Moreover, the paper shows that states that faced higher increases in informality (i.e., illegal work contracts) following the introduction of the new Constitution tended to have smaller drops in wage responsiveness to macroeconomic conditions, thus suggesting that informality serves as a escape valve to an overregulated environment. JEL Classification Numbers:E26, J30, J5

The development of an enzyme-linked immunosorbent assay for Trypanosoma vivax antibodies and its use in epidemiological surveys

There are data indicating that the distribution of Trypanosoma vivax in the Brazilian territory is expanding with potential to reach other areas, where the vectors are present. The detection of anti-trypanosomal antibodies in serum provides important information of the trypanosomal status in cattle herds. For this reason, an enzyme-linked immunosorbent assay (Tv-ELISA-Ab) with crude antigen from one Brazilian isolate of T. vivax was developed and evaluated. The sensitivity and specificity were respectively 97.6 and 96.9%. In the evaluation of cross-reactions, three calves inoculated with T. evansi trypimastigotes blood forms showed optical densities (OD) under the cut-off during the whole experimental period, except one at 45 days post-inoculation. With relation to Babesia bovis, B. bigemina, and Anaplasma marginale, which are endemic hemoparasites in the studied area, the cross-reactions were shown to be 5.7, 5.3, and 1.1%, respectively. The first serological survey of Pantanal and state of Pará showed that T. vivax is widespread, although regions within both areas had significantly different prevalences. Therefore, this Tv-ELISA-Ab may be a more appropriate test for epidemiological studies in developing countries because the diagnostic laboratories in most countries may be able to perform an ELISA, which is not true for polymerase chain reaction

Terapia de reposição enzimática para as mucopolissacaridoses I, II e VI: recomendações de um grupo de especialistas brasileiros Enzyme replacement therapy for mucopolysaccharidoses I, II and VI: recommendations from a group of Brazilian F experts

As mucopolissacaridoses (MPS) são doenças genéticas raras causadas pela deficiência de enzimas lisossômicas específicas que afetam o catabolismo de glicosaminoglicanos (GAG). O acúmulo de GAG em vários órgãos e tecidos nos pacientes afetados pelas MPS resulta em uma série de sinais e sintomas, integrantes de um quadro clínico multissistêmico que compromete ossos e articulações, vias respiratórias, sistema cardiovascular e muitos outros órgãos e tecidos, incluindo, em alguns casos, as funções cognitivas. Já foram identificados 11 defeitos enzimáticos que causam sete tipos diferentes de MPS. Antes do advento de terapias dirigidas para a restauração da atividade da enzima deficiente, o tratamento das MPS tinha como principal foco a prevenção e o cuidado das complicações, aspecto ainda bastante importante no manejo desses pacientes. Na década de 80 foi proposto o tratamento das MPS com transplante de medula óssea/transplante de células tronco hematopoiéticas (TMO/TCTH) e na década de 90 começou o desenvolvimento da Terapia de Reposição Enzimática (TRE), que se tornou uma realidade aprovada para uso clínico nas MPS I, II e VI na primeira década do século 21. Os autores deste trabalho têm a convicção de que um melhor futuro para os pacientes afetados pelas MPS depende da identificação, compreensão e manejo adequado das manifestações multissistêmicas dessas doenças, incluindo medidas de suporte (que devem fazer parte da assistência multidisciplinar regular destes pacientes) e terapias específicas. Embora a inibição da síntese de GAG e o resgate da atividade enzimática com moléculas pequenas também possam vir a ter um papel no manejo das MPS, o grande avanço disponível no momento é a TRE intravenosa. A TRE permitiu modificar radicalmente o panorama do tratamento das mucopolissacaridoses I, II e VI na última década, sendo que ainda pode estender seus benefícios em breve para a MPS IV A (cuja TRE já está em desenvolvimento clínico), com perspectivas para o tratamento da MPS III A e do déficit cognitivo na MPS II através de administração da enzima diretamente no sistema nervoso central (SNC). Um grande número de centros brasileiros, incluindo serviços de todas as regiões do país, já têm experiência com TRE para MPS I, II e VI. Essa experiência foi adquirida não só com o tratamento de pacientes como também com a participação de alguns grupos em ensaios clínicos envolvendo TRE para essas condições. Somados os três tipos de MPS, mais de 250 pacientes já foram tratados com TRE em nosso país. A experiência dos profissionais brasileiros, somada aos dados disponíveis na literatura internacional, permitiu elaborar este documento, produzido com o objetivo de reunir e harmonizar as informações disponíveis sobre o tratamento destas doenças graves e progressivas, mas que, felizmente, são hoje tratáveis, uma realidade que traz novas perspectivas para os pacientes brasileiros afetados por essas condições.<br>Mucopolysaccharidoses (MPS) are rare genetic diseases caused by deficiency of specific lysosomal enzymes that affect catabolism of glycosaminoglycans (GAG). Accumulation of GAG in various organs and tissues in MPS patients results in a series of signs and symptoms, producing a multisystemic condition affecting bones and joints, the respiratory and cardiovascular systems and many other organs and tissues, including in some cases, cognitive performance. So far, eleven enzyme defects that cause seven different types of MPS have been identified. Before introduction of therapies to restore deficient enzyme activity, treatment of MPS focused primnarily on prevention and care of complications, still a very important aspect in the management of these patients. In the 80's treatment of MPS with bone marrow transplantation/hematopoietic stem cells transplantation (BMT/HSCT) was proposed and in the 90's, enzyme replacement therapy (ERT),began to be developed and was approved for clinical use in MPS I, II and VI in the first decade of the 21st century. The authors of this paper are convinced that a better future for patients affected by mucopolysaccharidoses depends upon identifying, understanding and appropriately managing the multisystemic manifestations of these diseases. This includes the provision of support measures (which should be part of regular multidisciplinary care of these patients) and of specific therapies. Although inhibition of synthesis of GAG and the recovery of enzyme activity with small molecules also may play a role in the management of MPS, the breakthrough is the currently available intravenous ERT. ERT radically changed the setting for treatment of mucopolysaccharidosis I, II and VI in the last decade., Benefits can even be extended soon to MPS IV A (ERT for this condition is already in clinical development), with prediction for treatment of MPS III A and the cognitive deficit in MPS II by administration of the enzyme directly into the central nervous system (CNS). A large number of Brazilian services, from all regions of the country, already have experience with ERT for MPS I, II and VI. This experience was gained not only by treating patients but also with the participation of some groups in clinical trials involving ERT for these conditions. Summing up the three types of MPS, more than 250 patients have already been treated with ERT in Brazil. The experience of professionals coupled to the data available in international literature, allowed us to elaborate this document, produced with the goal of bringing together and harmonize the information available for the treatment of these severe and progressive diseases, which, fortunately, are now treatable, a situation which bring new perspectives for Brazilian patients, affected by these conditions