The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose ...SparkBLAST, a parallelization of a sequence alignment application (BLAST) that employs cloud computing for the provisioning of computational resources and Apache Spark as the coordination framework. As a proof of concept, some radionuclide-resistant bacterial genomes were selected for similarity analysis.
Experiments in Google and Microsoft Azure clouds demonstrated that SparkBLAST outperforms an equivalent system implemented on Hadoop in terms of speedup and execution times.
The superior performance of SparkBLAST is mainly due to the in-memory operations available through the Spark framework, consequently reducing the number of local I/O operations required for distributed BLAST processing.
The cardiac growth process (hypertrophy) is a crucial phenomenon conserved across a wide array of species and is critically involved in the maintenance of cardiac homeostasis. This process enables an ...organism to adapt to changes in systemic demand and occurs due to a plethora of responses, depending on the type of signal or stimuli received. The growth of cardiac muscle cells in response to environmental conditions depends on the type, strength and duration of stimuli, and results in adaptive physiological responses or non-adaptive pathological responses. Thyroid hormones (TH) have a direct effect on the heart and induce a cardiac hypertrophy phenotype, which may evolve to heart failure. In this review, we summarize the literature on TH function in the heart by presenting results from experimental studies. We discuss the mechanistic aspects of TH associated with cardiac myocyte hypertrophy, increased cardiac myocyte contractility and electrical remodeling, as well as the associated signaling pathways. In addition to classical crosstalk with the sympathetic nervous system (SNS), emerging work pointing to the new endocrine interaction between TH and the renin-angiotensin system (RAS) is also explored. Given the inflammatory potential of the angiotensin II peptide, this new interaction may open the door for new therapeutic approaches which target the key mechanisms responsible for TH-induced cardiac hypertrophy.
Recent results obtained by Chindelevitch et al (2014) are challenged by Ebrahim et al, illustrating several issues in the reproducibility of computational biology methods.
Motivation: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with ...programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. Results: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application. Availability: The Taverna workflow system is available as open source and can be downloaded with example Scufl workflows from http://taverna.sourceforge.net
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of ...Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
The IBM Blue Gene/Q Interconnection Fabric Dong Chen; Eisley, N. A.; Heidelberger, P. ...
IEEE MICRO,
2012-Jan.-Feb., 2012-01-00, 20120101, Letnik:
32, Številka:
1
Journal Article
Recenzirano
This article describes the IBM Blue Gene/Q interconnection network and message unit. Blue Gene/Q is the third generation in the IBM Blue Gene line of massively parallel supercomputers and can be ...scaled to 20 petaflops and beyond. For better application scalability and performance, Blue Gene/Q has new routing algorithms and techniques to parallelize the injection and reception of packets in the network interface.
Nucleotides, e.g. ATP and ADP, are important signaling molecules, which elicit several biological responses. The degradation of nucleotides is catalyzed by a family of enzymes called NTPDases ...(nucleoside triphosphate diphosphohydrolases). The present study reports the enzymatic properties of a NTPDase (CD39, apyrase, ATP diphosphohydrolase) in brain membranes of zebrafish (
Danio rerio). This enzyme was cation-dependent, with a maximal rate for ATP and ADP hydrolysis in a pH range of 7.5–8.0 in the presence of Ca
2+ (5 mM). The enzyme displayed a maximal activity for ATP and ADP hydrolysis at 37 °C. It was able to hydrolyze purine and pyrimidine nucleosides 5′-di and triphosphates, being insensitive to classical ATPase inhibitors, such as ouabain (1 mM), N-ethylmaleimide (0.1 mM), orthovanadate (0.1 mM) and sodium azide (0.1 mM). A significant inhibition of ATP and ADP hydrolysis (68% and 34%, respectively) was observed in the presence of 20 mM sodium azide, used as a possible inhibitor of ATP diphosphohydrolase. Levamisole (1 mM) and tetramisole (1 mM), specific inhibitors of alkaline phosphatase and P1, P
5-di (adenosine 5′-) pentaphosphate, an inhibitor of adenylate kinase did not alter the enzyme activity. The presence of a NTPDase in brain membranes of zebrafish may be important for the modulation of nucleotide and nucleoside levels, controlling their actions on specific purinoceptors in central nervous system of this specie.
Intratumoral heterogeneity in glioblastoma multiforme (GBM) poses a significant barrier to therapy in certain subpopulation such as the tumor-initiating cell population, being shown to be refractory ...to conventional therapies. Oncolytic virotherapy has the potential to target multiple compartments within the tumor and thus circumvent some of the barriers facing conventional therapies. In this study, we investigate the oncolytic potential of myxoma virus (MYXV) alone and in combination with rapamycin in vitro and in vivo using human brain tumor-initiating cells (BTICs).
We cultured fresh GBM specimens as neurospheres and assayed their growth characteristics in vivo. We then tested the susceptibility of BTICs to MYXV infection with or without rapamycin in vitro and assessed viral biodistribution/survival in vivo in orthotopic xenografts.
The cultured neurospheres were found to retain stem cell markers in vivo, and they closely resembled human infiltrative GBM. In this study we determined that (i) all patient-derived BTICs tested, including those resistant to temozolomide, were susceptible to MYXV replication and killing in vitro; (ii) MYXV replicated within BTICs in vivo, and intratumoral administration of MYXV significantly prolonged survival of BTIC-bearing mice; (iii) combination therapy with MYXV and rapamycin improved antitumor activity, even in mice bearing "advanced" BTIC tumors; (iv) MYXV treatment decreased expression of stem cell markers in vitro and in vivo.
Our study suggests that MYXV in combination with rapamycin infects and kills both the BTICs and the differentiated compartments of GBM and may be an effective treatment even in TMZ-resistant patients.
Background
Prematurity is considered to be the leading cause of death in children under 5 years of age, with one child dying every 2 s. Smoking is known to be one of the factors associated with ...prematurity, with both immediate and late consequences. However, it is difficult to obtain concrete data on the relationship between smoking and spontaneous preterm birth.
Objective
The aim of this study was to evaluate the influence of active and passive smoking on spontaneous preterm birth.
Methods
This was a multicenter, cross‐sectional complementary study that included data on preterm births in 20 maternity hospitals in Brazil between 2011 and 2012. The relationship between smoking category (people who smoke PWS; people who smoke indirectly PWSI; and people who do not smoke PWDNS) and sociodemographic characteristics, birth, and neonatal data was assessed. Statistical analysis was performed using frequencies, percentages, the χ2 test, and stepwise comparisons, with a significance level of 5%.
Results
The original study included 5295 pregnant participants and their preterm infants. There were 1491 spontaneous preterm births (SPBs); 1191 preterm rupture of membranes; 1468 therapeutic preterm births; and 1146 term births. The proportion of women who were PWS during pregnancy was 13.5%, and 31.6% were PWSI. Pregnant individuals who smoked and who smoked indirectly had a higher incidence of SPBs (61.2%) compared with PWDNS (48.4%; P < 0.0001); however, multivariate analysis did not confirm causality.
Conclusions
This study did not confirm that smoking during pregnancy increases the risk of SPB. PWSI also did not have an increased incidence of spontaneous preterm birth or adverse neonatal outcomes.
Synopsis
Active and passive smoking during pregnancy are associated with, but do not directly cause, spontaneous preterm birth..
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