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Archives for : marzo2014

orthAgogue: an agile tool for the rapid prediction of orthology relations

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Motivation: The comparison of genes and gene products across species depends on high-quality tools to determine the relationships between gene or protein sequences from various species. Although some excellent applications are available and widely used, their performance leaves room for improvement.

Results: We developed orthAgogue: a multithreaded C application for high-speed estimation of homology relations in massive datasets, operated via a flexible and easy command-line interface.

 


See on bioinformatics.oxfordjournals.org

iCall: A genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array

See on Scoop.itCuriosopernatura

Motivation: Next-generation genotyping microarrays have been designed with insights from 1000 Genomes Project and whole exome-sequencing studies. These arrays additionally include variants that are typically present at lower frequencies. Determining the genotypes of these variants from hybridization intensities is challenging as there is less support to locate the presence of the minor alleles when the allele counts are low. Existing algorithms are mainly designed for calling common variants and are notorious for failing to generate accurate calls for low-frequency and rare variants. Here we introduce a new calling algorithm, iCall, to call genotypes for variants across the whole spectrum of allele frequencies.

Results: We benchmarked iCall against four of the most commonly used algorithms, GenCall, optiCall, illuminus and GenoSNP, as well as a post-processing caller zCall that adopted a two-stage calling design. Normalized hybridization intensities for 12,370 individuals genotyped on the Illumina HumanExome BeadChip were considered, of which 81 individuals were also whole-genome sequenced. The sequence calls were used to benchmark the accuracy of the genotype calling and our comparisons indicated that iCall outperforms all four single-stage calling algorithms in terms of call rates and concordance, particularly in the calling accuracy of minor alleles which is the principal concern for rare and low-frequency variants. The application of zCall to post-process the output from iCall also produced marginally improved performance to the combination of zCall and GenCall.

Availability: iCall is implemented in C++ for use on Linux operating systems and is available for download athttp://www.statgen.nus.edu.sg/~software/icall.html.

Contact: zhoujin@nus.edu.sg, statyy@nus.edu.sg


See on bioinformatics.oxfordjournals.org

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 www.microbiologybytes.com

Flu viruses derive from a global selective sweep in the 1870s

See on Scoop.itCuriosopernatura


A single event seems to have set the stage for all pandemics since.


See on arstechnica.com

Scientists Use 3-D Printer To Help Create Prototype Next-Gen Pacemaker

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Researchers at the University of Illinois at Urbana-Champaign and Washington University in St. Louis have developed a new device that may one day help prevent heart attacks.

 

Unlike existing pacemakers and implantable defibrillators that are one-size-fits-all, the new device is a thin, elastic membrane designed to stretch over the heart like a custom-made glove.

 

The new cardiac device — a thin, stretchable membrane imprinted with a spider-web-like network of sensors and electrodes — is custom-designed to fit over the heart and contract and expand with it as it beats. 

University of Illinois materials scientist John Rogers co-led the team that invented the new device. He says they used high-resolution imaging, computer modeling, and a 3-D printer to create a plastic model of a heart. Then, they used that as a mold to make a thin, elastic membrane designed to fit snugly over the real heart’s surface.

Rogers compares the silicon version to the heart’s natural membrane, the pericardium. “But this artificial pericardium is instrumented with high quality, man-made devices that can sense and interact with the heart in different ways that are relevant to clinical cardiology,” Rogers said.

Washington University biomedical engineer Igor Efimov helped design and test the new device. He says the membrane’s spider-web-like network of specialized electrodes can continuously monitor the heart’s electrical activity and keep it beating at a healthy rate.

“When it senses such a catastrophic event as a heart attack or arrhythmia, it can also apply a high definition therapy,” Efimov said.

 

“So it can apply stimuli, electrical stimuli, from different locations on the device in an optimal fashion to stop this arrhythmia and prevent sudden cardiac death.”

 

Efimov calls the new device a huge advance and hopes it will be approved for use in patients in 10 to 15 years.


See on news.stlpublicradio.org

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

See on Scoop.itCuriosopernatura

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

Top Physician Information Sources by Mobile Device

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The infographic above illustrates the top physician information sources by frequency of mobile device usage on smartphones/tablets. 

 

source: http://hitconsultant.net/2014/02/20/infographic-top-physician-information-sources-mobile-device/

 


See on hitconsultant.net

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