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

Echocardiographic Predictors of Worse Outcome After Cardiac Resynchronization Therapy

AbstractBackground:Cardiac resynchronization therapy (CRT) is the recommended treatment by leading global guidelines. However, 30%-40% of selected patients are non-responders.Objective:To develop an echocardiographic model to predict cardiac death or transplantation (Tx) 1 year after CRT.Method:Observational, prospective study, with the inclusion of 116 patients, aged 64.89 ± 11.18 years, 69.8% male, 68,1% in NYHA FC III and 31,9% in FC IV, 71.55% with left bundle-branch block, and median ejection fraction (EF) of 29%. Evaluations were made in the pre‑implantation period and 6-12 months after that, and correlated with cardiac mortality/Tx at the end of follow-up. Cox and logistic regression analyses were performed with ROC and Kaplan-Meier curves. The model was internally validated by bootstrapping.Results:There were 29 (25%) deaths/Tx during follow-up of 34.09 ± 17.9 months. Cardiac mortality/Tx was 16.3%. In the multivariate Cox model, EF < 30%, grade III/IV diastolic dysfunction and grade III mitral regurgitation at 6‑12 months were independently related to increased cardiac mortality or Tx, with hazard ratios of 3.1, 4.63 and 7.11, respectively. The area under the ROC curve was 0.78.Conclusion:EF lower than 30%, severe diastolic dysfunction and severe mitral regurgitation indicate poor prognosis 1 year after CRT. The combination of two of those variables indicate the need for other treatment options

Myxomycetes do Parque Zoobotânico de Teresina, Piauí, Brasil Myxomycetes of the Parque Zoobotânico - Teresina, Piauí, Brazil

Visando ampliar o conhecimento sobre a mixobiota do Piauí, foram realizadas coletas no Parque Zoobotânico de Teresina (05º 05' 12'' S, 42º 48' 48'' WG). A vegetação do Parque caracteriza-se como um cerradão com representantes da mata de cocais, que oferecem substratos potencialmente favoráveis ao desenvolvimento de Myxomycetes. Esporocarpos foram coletados no período chuvoso e início da estiagem (março a junho de 1999), identificados e depositados no herbário UFP (Universidade Federal de Pernambuco). Foram obtidas 101 amostras, correspondentes a 19 espécies, distribuídas nas famílias Ceratiomyxaceae (Ceratiomyxa fruticulosa (Mull.) Macbr., Clastodermataceae (Clastoderma debaryanum Blytt), Cribrariaceae (Cribraria microcarpa (Schrad.) Pers., C. violacea Rex, Dictydium canceilatum* (Batsch.) Macbr.), Enteridiaceae (Lycogala exiguum* Morgan.), Physaraceae (Craterium aureum* (Schum.) Rost., Physarum bogoriense* Racib., P. melleum (Berk. & Br.) Massee, P. nucleatum Rex, P. pusilium* (Berk. & Curt.) G. Lister), Trichiaceae (Arcyria denudata (L.) Wett., A. cinerea (Bull.) Pers., Hemitrichia calyculata (Speg.) Farr, H. serpula (Scop.) Rost., Metatrichia vesparium (Batsch) Nann.-Brem., Perichaena depressa Lib.) e Stemonitaceae (Comatricha typhoides (Bull.) Rost., Stemonitis smithii Macbr.). Exceto H. calyculata e H. serpula, todos os táxons são referidos pela primeira vez para o município de Teresina; as espécies assinaladas com um asterisco constituem novos registros para o Piauí.<br>Aiming to increase the knowledge about the myxobiota of Piauí State, Brazil, collections were done in the undertaken Zoobotanical Park of Teresina (05° 05' 12'' S, 42° 48' 48'' WG). The vegetation of the Park is a savanna ("cerradão") with "cocais" forest representative, offering substrates potentially favorable to the development of Myxomycetes. Sporocarps were collected in the rainy season (March to June 1999), identified and deposited at the UFP herbarium (Federal University of Pernambuco). One hundred and one samples were collected, corresponding to 19 species, distributed in the families: Ceratiomyxaceae (Ceratiomyxa fruticulosa (Mull.) Macbr., Clastodermataceae (Clastoderma debaryanum Blytt), Cribrariaceae (Cribraria microcarpa (Schrad.) Pers., C. violacea Rex, Dictydium cancellatum* (Batsch.) Macbr.), Emeridiaceae (Lycogala exiguum* Morgan), Physaraceae (Craterium aureum* (Schum.) Rost., Physarum bogoriense* Racib., P. melleum (Berk. & Br.) Massee, P. nucleatum Rex, P. pusilium* (Berk. & Curt.) G. Lister), Trichiaceae (Arcyria denudata (L.) Wett., A. cinerea (Bull.) Pers., Hemitrichia calyculata (Speg.) Farr, H. serpula (Scop.) Rost., Metatrichia vesparium (Batsch) Nann.-Brem., Perichaena depressa Lib.) and Stemonitaceae (Comatricha typhoides (Bull.) Rost., Stemonitis smithii Macbr.). With the exception of H. calyculata and H. serpula, all taxa are referred for the first time for the Municipality of Teresina, and the species with an asterisk constitute new record for the State of Piauí

Preliminary investigation of Culicidae species in South Pantanal, Brazil and their potential importance in arbovirus transmission Investigação preliminar das espécies de culicídeos do Pantanal Sul brasileiro e sua potencial importância na transmissão de arbovírus

In view of the high circulation of migratory birds and the environmental and climatic conditions which favor the proliferation of arthropods, the Brazilian Pantanal is susceptible to circulation of arboviruses. However, the amount of data concerning arbovirus vectors in this area is scarce; therefore the aim of this study was to conduct a preliminary investigation of Culicidae species in the Nhecolândia Sub-region of South Pantanal, Brazil and their potential importance in the arbovirus transmission. A total of 3684 specimens of mosquitoes were captured, 1689 of which caught in the rainy season of 2007, were divided into 78 pools and submitted to viral isolation, Semi-Nested RT-PCR and Nested RT-PCR, with a view to identifying the most important arboviruses in Brazil. Simultaneously, 70 specimens of ticks found blood-feeding on horses were also submitted to the same virological assays. No virus was isolated and viral nucleic-acid detection by RT-PCR was also negative. Nevertheless, a total of 22 Culicidae species were identified, ten of which had previously been reported as vectors of important arboviruses. The diversity of species found blood-feeding on human and horse hosts together with the arboviruses circulation previously reported suggest that the Nhecolândia Sub-region of South Pantanal is an important area for arbovirus surveillance in Brazil.<br>Regiões como o Pantanal brasileiro, que apresentam fatores como riqueza de fauna silvestre incluindo circulação de aves migratórias e condições ambientais e climáticas favoráveis à proliferação de artrópodes estão potencialmente sujeitas à circulação de arbovírus. Entretanto, poucos trabalhos foram realizados acerca da presença de arbovírus em potenciais vetores no Pantanal. Neste sentido o principal objetivo deste trabalho foi conduzir uma investigação preliminar para presença de arbovírus em amostragens de culicídeos capturados na Sub-região da Nhecolândia no Pantanal Sul. Um total de 3684 mosquitos foi capturado, dos quais 78 grupos compondo uma amostragem de 1789 espécimes foram submetidos às técnicas de isolamento viral e RT-PCR para os mais importantes arbovírus no Brasil. Simultaneamente, 70 espécimes de carrapatos capturados durante hematofagia em cavalos também foram submetidos à pesquisa viral. Não houve isolamento viral em nenhuma amostra analisada e os resultados de detecção de ácido nucléico viral foram também negativos. Entretanto, foram identificadas 22 espécies de culicídeos, dez das quais previamente reportadas como vetores de importantes arbovírus. A competência vetorial de espécies capturadas durante hematofagia em humanos e cavalos aliada ao relato prévio de circulação de arbovírus sugerem a Sub-região da Nhecolândia como uma importante área de vigilância para arbovírus no Centro-Oeste do Brasil

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data