Squid – a simple bioinformatics grid

BACKGROUND: BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. RESULTS: Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. CONCLUSION: Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example

DrosoPhyla: genomic resources for drosophilid phylogeny and systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4000 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the groups and genera in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred well-supported group and species trees for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics

First report of partial albinism in genus Thrichomys (Rodentia: Echimyidae)

Reports about albinism in rodents are common. In the family Echimyidae, however, albinism is very rare. This is the second case of coat color variation reported within Echimyidae and the first for the genus Thrichomys. The pelages of Thrichomys pachyurus individuals with normal and variant coat color were observed under a fluorescent artificial light and were examined with a stereoscopic microscope. The descriptions of pelage color were based on the book "Color Standards and Color Nomenclature". The predominantly white pattern of coat color in individuals of T. pachyurus suggests a partial albinism caused by delay in migration time of melanoblasts from neural crest to epidermis. The habitat of T. pachyurus has a heavy vegetative cover, which offers natural protection against predators and high-quality nutrition.Registros de albinismo em roedores são comuns. Na família Echimyidae, no entanto, albinismo é muito raro. Este é o segundo caso de variação da cor da pelagem registrado para Echimyidae e o primeiro para o gênero Thrichomys. A pelagem de indivíduos de Thrichomys pachyurus com a cor normal e a variante foram observados sob luz fluorescente artificial e foram examinados com um microscópio estereoscópico. As descrições da cor da pelagem foram baseados no livro "Color Standards and Color Nomenclature". O padrão predominantemente branco da cor da pelagem no indivíduo de T. pachyurus sugere um abinismo parcial causado pelo atraso no tempo de migração dos melanoblastos da crista neural para a epiderme. O habitat de T. pachyurus tem uma densa cobertura vegetal, que oferece proteção natural contra predadores e nutrição de alta qualidade

IT governance frameworks: A literature review of Brazilian publications

IT (Information Technology) governance has been a widely studied subject. This has generated different definitions and conceptual models to explain it. We conduct a concept-centric literature review based on a literature reference model. We used three literature frameworks to identify key-variables to evaluate and classify Brazilian IT governance publications. These variables were used to classify 90 Brazilian publications from 2004 to 2012. The authors chose Brazil due to its economic growth and companies’ internationalization on the last years. The organizations are fonder to regulatory and compliance marks due to market visibility, driving them towards IT governance practices due to growing dependence on IT. The frameworks used in the country are usually developed abroad - then verification on how they fit with Brazilian organizations is relevant to business management. The study shows that; the most used methodology is the case study; 90% of the papers were written in Portuguese; the IT alignment is cited, but not evaluated; few cases are related to small and medium business; and decision structures are not discussed. The authors conclude presenting a conceptual model summarizing all the models and Brazilian companies’ particularities

Treatment Outcome of Acute Promyelocytic Leukemia with Modified Aida Protocol

We analyzed the outcome of a series of 19 newly diagnosed patients with acute promyelocytic leukemia treated with AIDA modified protocol, using mitoxantrone in place of idarubicin. Eleven patients achieved morphologic CR (58%). The remaining 8 patients had induction failure due to death during induction. Ten of eleven patients in CR achieved molecular remission after induction therapy and all the 8 patients had molecular remission after consolidation. Eight patients completed the three consolidation courses as scheduled and then proceeded to maintenance therapy. After a median follow up of 52 months, no molecular or hematological relapse has occurred. The 4-year disease-free survival is 82%. The study showed the antileukemic efficacy of mitoxantrone and that it could be used as a reasonable option in anthracycline-based strategies in APL

Preoperative left ventricular ejection fraction and left atrium reverse remodeling after mitral regurgitation surgery

Background: Left atrium enlargement has been associated with cardiac events in patients with mitral regurgitation (MR). Left atrium reverse remodeling (LARR) occur after surgical correction of MR, but the preoperative predictors of this phenomenon are not well known. It is therefore important to identify preoperative predictors for postoperative LARR.Methods: We enrolled 62 patients with chronic severe MR (prolapse or flail leaflet) who underwent successful mitral valve surgery (repair or replacement); all with pre-and postoperative echocardiography. LARR was defined as a reduction in left atrium volume index (LAVI) of >= 25%. Stepwise multiple regression analysis was used to identify independent predictors of LARR.Results: LARR occurred in 46 patients (74.2%), with the mean LAVI decreasing from 85.5 mL/m(2) to 49.7 mL/m(2) (p = 25% with a sensitivity of 71.7% and a specificity of 56.3%.Conclusions: LARR occurs frequently after mitral valve surgery and is associated with preoperative LVEF higher than 63.5%.Inst Dante Pazzanese Cardiol, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, São Paulo, BrazilDisciplina Cardiol, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, São Paulo, BrazilWeb of Scienc

Cell Therapy in Chagas Disease

Chagas disease which is caused by the parasite Trypanosoma cruzi is an important cause of cardiomyopathy in Latin America. In later stages chagasic cardiomyopathy is associated with congestive heart failure which is often refractory to medical therapy. In these individuals heart transplantation has been attempted. However, this procedure is fraught with many problems attributable to the surgery and the postsurgical administration of immunosuppressive drugs. Studies in mice suggest that the transplantation of bone-marrow-derived cells ameliorates the inflammation and fibrosis in the heart associated with this infection. Cardiac magnetic resonance imaging reveals that bone marrow transplantation ameliorates the infection induced right ventricular enlargement. On the basis of these animal studies the safety of autologous bone marrow transplantation has been assessed in patients with chagasic end-stage heart disease. The initial results are encouraging and more studies need to be performed