domenica, maggio 25, 2014
The Importance of Shaking Things Up
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That recent study on active learning continues to generate some press, including a new interview with Carl Wieman about why traditional lectures are problematic. Wieman is pretty blunt about his opinions on the subject, which will come as no surprise to people in the AMO physics community… Anyway, while most of the rest of the…
See on scienceblogs.com
How To Install Ubuntu Server 14.04 LTS Trusty Tahr | Ubuntu Server Guide
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This guide will describes the basic how to installing Ubuntu Server 14.04 from beginning to end. As already we know, Ubuntu Server 14.04 LTS with codenamed
See on ubuntuserverguide.com
Now researchers can explore genomic data across space and time
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The figure above is part of a four-step procedure for the multiscale segmentation of genomic signals.
See on isbmolecularme.com
A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences
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PLOS Computational Biology is an open-access (Guide to #Genomics and #Bioinformatics Training for Clinical and Public Audiences http://bit.ly/1mnSSsf http://bit.ly/1mnSQAr)…
See on www.ploscompbiol.org
Possible Dark Matter Detected at Milky Way’s Core Could Hint at New Force of Nature — NOVA Next | PBS
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Excess gamma-ray light coming from the center of our galaxy could be scientists’ first-ever indirect evidence of dark matter.
See on www.pbs.org
Scientists Generate 3D Structure for the Malaria Parasite Genome
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Abstract – “A research team led by a cell biologist at the University of California, Riverside has generated a 3D model of the human malaria parasite genome at three different stages in the parasite’s life cycle — the first time such 3D architecture has been generated during the progression of the life cycle of a parasite .”
See on ucrtoday.ucr.edu
domenica, aprile 06, 2014
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
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PLOS Computational Biology is an open-access
See on www.ploscompbiol.org
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
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Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR.Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors.Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
See on peerj.com
sabato, marzo 08, 2014
From Scourge to Cure: Viruses Versus Cancer
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Viruses versus cancer. Who’s your money on?
With [oncolytic viruses] OV cancer therapeutics entering advanced-stage trials and showing clinical efficacy, strategies that further broaden OV targeting and replication capacity to address the heterogeneous nature of tumours and their associated vascular and stromal architecture will be extremely useful. Since such heterogeneity not only exists between patients but also within a given tumour/patient, where the metabolism, signal transduction, and antiviral states of cancer cells can be variably abnormal and, therefore, variably support OV replication, combinatorial strategies will be essential to promoting reliable tumour control and regression. Finally, continued efforts to identify components innate to the complex tumour microenvironment that promote OV replication will be critical to further improving OVs and developing new engineering strategies.
See on http://bit.ly/PcJVpW
Flu viruses derive from a global selective sweep in the 1870s
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A single event seems to have set the stage for all pandemics since.
See on arstechnica.com
Giant virus resurrected from 30,000-year-old ice
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Largest virus yet discovered hints at viral diversity trapped in permafrost.
See on www.nature.com
Comparing Genome Editing Technologies
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ZFN, TALEN, and CRISPR/Cas systems help scientists dissect
the vast amount of information accumulated through
the Genomic Revolution.
See on www.genengnews.com
Nanotechnology needle arrays for drug delivery
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The ultimate goal of nanotechnology-enabled drug delivery, especially with regard to cancer therapy, is to ferry most of the administered drug to the target, while eliminating the accumulation of the drug at any non-target tissues.
Nanomedicine applications with targeted nanoparticles are expected to revolutionize cancer therapy. The use of such nanoparticles to deliver therapeutic agents is currently being studied as a promising method by which drugs can be effectively targeted to specific cells in the body, such as tumor cells.
See on www.nanowerk.com
Scientists Create Genetically Modified Cells That Protect Against HIV
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The treatment is considered radical, and the results were drawn from a small scale human trial, but for the first time in medical history, researchers have boosted their patients’ ability to fight HIV by replacing some of their natural immune cells with genetically modified versions.
See on io9.com
lunedì, febbraio 24, 2014
SunPower Continues to Drive Down the Cost Curve
I thought you’d be interested in the following article. Click the link to read it in full:
SunPower Continues to Drive Down the Cost Curve
http://bit.ly/1k3hVhV
Inviato da iPhone
mercoledì, febbraio 19, 2014
A synchronized global sweep of the internal genes of modern avian influenza virus : Nature : Nature Publishing Group
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Zoonotic infectious diseases such as influenza continue to pose a grave threat to human health. However, the factors that mediate the emergence of RNA viruses such as influenza[thinsp]A virus (IAV) are still incompletely understood. Phylogenetic inference is crucial to reconstructing the origins and tracing the flow of IAV within and between hosts. Here we show that explicitly allowing IAV host lineages to have independent rates of molecular evolution is necessary for reliable phylogenetic inference of IAV and that methods that do not do so, including /`relaxed/’ molecular clock models, can be positively misleading. A phylogenomic analysis using a host-specific local clock model recovers extremely consistent evolutionary histories across all genomic segments and demonstrates that the equine H7N7 lineage is a sister clade to strains from birds[mdash]as well as those from humans, swine and the equine H3N8 lineage[mdash]sharing an ancestor with them in the mid to late 1800s. Moreover, major western and eastern hemisphere avian influenza lineages inferred for each gene coalesce in the late 1800s. On the basis of these phylogenies and the synchrony of these key nodes, we infer that the internal genes of avian influenza virus (AIV) underwent a global selective sweep beginning in the late 1800s, a process that continued throughout the twentieth century and up to the present. The resulting western hemispheric AIV lineage subsequently contributed most of the genomic segments to the 1918 pandemic virus and, independently, the 1963 equine H3N8 panzootic lineage. This approach provides a clear resolution of evolutionary patterns and processes in IAV, including the flow of viral genes and genomes within and between host lineages.
See on www.nature.com
