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Ars Technica -
1 hours and 56 minutes ago
pThe promise of personalized medicine is that we can tailor therapies to individuals based on a
knowledge of their genetics. A new study suggests the same applies to placeboes./ppa
href="http://arstechnica.com/news.ars/post/20081203-study-shows-promise-for-placebos-as-personalized-medicine.html"Read
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Ars Technica -
1 hours and 56 minutes ago
pThe promise of personalized medicine is that we can tailor therapies to individuals based on a
knowledge of their genetics. A new study suggests the same applies to placeboes./ppa
href="http://arstechnica.com/news.ars/post/20081203-study-shows-promise-for-placebos-as-personalized-medicine.html"Read
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Blu-ray.com - Blu-ray Disc news -
16 hours and 51 minutes ago
Lionsgate Home Entertainment has announced the special features for three of their upcoming films,
including 'Saw V', 'Repo! The Genetic Opera', and 'W.'. The first two films are due to hit store
shelves on January 20th, while 'W.' will come out a few weeks later on February 10th. Technical
specs have still yet to be announced, but you can expect to see a combination of AVC video and a
DTS-HD Master Audio soundtrack....brbra href="http://www.blu-ray.com/news/?id=2130"Read full
article at Blu-ray.com/a
|
CiteULike: Borelli's watchlist -
18 hours and 40 minutes ago
iBreast Cancer Research, Vol. 9 (05 December 2007), 114./ibr /br /With the characterization of the
human genome, as well as advances in technology to determine genetic variability across the genomes
of populations, there has been focused effort on the identification of cancer susceptibility
alleles through the use of genome-wide association studies. These efforts have recently resulted in
identification of a susceptibility locus for breast cancer by several groups, although the
increases in risk are modest. While genome-wide association studies will probably lead to
discoveries of potentially important previously unstudied pathways in cancer etiology, the role of
the environment, particularly gene-environment interactions, in breast cancer etiology should not
be overlooked.br /iChristine Ambrosone/i
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CiteULike: Borelli's watchlist -
18 hours and 50 minutes ago
iInternational journal of cancer. Journal international du cancer (19 September 2008)/ibr /br
/MicroRNA (miRNA) plays an important role in tumorigenesis, but whether miRNA is a cancer
predisposition factor or not is still unknown. Considering the fact that miRNA regulates a number
of tumor suppressor genes (TSGs) and oncogenes, genetic variations in miRNA genes could affect the
levels of expression of TSGs or oncogenes and, thereby, cancer risk. To test this hypothesis, we
screened genetic variants in 17 selected miRNA genes, which are predicted to regulate key breast
cancer genes, in 42 patients with familial breast cancer. Seven novel genetic variants were
observed in 7 primary or precursor miRNA genes. Among them, 1 rare variant in the precursor of
miR-30c-1 and 1 rare variant in the primary precursor of miR-17 were only observed in noncarriers
of BRCA1/2 mutations. In functional assays, these 2 variants resulted in conformational changes in
the predicted secondary structures, and consequently altered the expression of mature miR-30c-1 and
miR-17. In the target in vitro assay, we observed that miR-17 could bind to the 3'UTR of BRCA1
mRNAs, which is predicted to be a target for miR-17. Our findings suggest that functional genetic
variants in miRNA genes can potentially alter the regulation of key breast cancer genes. Whether
they confer genetic susceptibility to breast cancer remains to be determined. (c) 2008 Wiley-Liss,
Inc.br /iJie Shen, Christine B Ambrosone, Hua Zhao/i

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CiteULike: Borelli's watchlist -
19 hours and 12 minutes ago
iNucl. Acids Res. (10 November 2008), gkn873./ibr /br /Plant hormones are small organic molecules
that influence almost every aspect of plant growth and development. Genetic and molecular studies
have revealed a large number of genes that are involved in responses to numerous plant hormones,
including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid,
and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a
systematic and comprehensive view of genes participating in plant hormonal regulation, as well as
morphological phenotypes controlled by plant hormones. Based on data from mutant studies,
transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in
the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology
is developed to precisely describe myriad hormone-regulated morphological processes with
standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly
get access to information about these hormone-related genes, including sequences, functional
category, mutant information, phenotypic description, microarray data and linked publications.
Several applications of this database in studying plant hormonal regulation and hormone cross-talk
will be presented and discussed. 10.1093/nar/gkn873br /iZhi-Yu Peng, Xin Zhou, Linchuan Li,
Xiangchun Yu, Hongjiang Li, Zhiqiang Jiang, Guangyu Cao, Mingyi Bai, Xingchun Wang, Caifu Jiang,
Haibin Lu, Xianhui Hou, Lijia Qu, Zhiyong Wang, Jianru Zuo, Xiangdong Fu, Zhen Su, Songgang Li,
Hongwei Guo/i

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TechCrunch -
22 hours and 19 minutes ago
This guest post is written by Matt
Rutherford, Web Strategist and technology producer for Charlie
Rose. Matt focuses on the macro themes affecting the internet and the wider world. You can
read Matt’s previous guest post, Larry Lessig Defends Copyright, Loves Charlie Rose
Remixes,
here.
Who protects the internet? In part, it’s this man
– General Kevin
Chilton, US STRATCOM commander and the head of all military cyber warfare. We’re
broadcasting an interview tonight with General Chilton, in which he discusses the threat of cyber
warfare, along with his other remits of space warfare and the US nuclear deterrent. Chilton is
fascinating, and amongst other things has been a NASA space shuttle pilot, logging over 700 hours
in space. You can watch the full interview here (and it is
embedded below).
The discussion with General Chilton brings to light a crucial question, however. Is the internet
actually protected? The military remit is to defend the .mil networks, prevent online espionage,
and develop offensive strike capabilities. But who’s protecting the rest? Given its
integration with every aspect of our lives and economy, it’s surprising just how little we
know about who defends our electronic nervous system.
The Threat
There’s copious discussion about exactly how vulnerable the US is to online attack. The
alleged Russian DoS attacks on Estonia in 2007, and on Georgia this summer, highlighted the
potential damage of state sponsored attacks. China has also been developing cyber warfare
capabilities for some time, mounting online intelligence operations against Taiwan, and almost certainly against
the US. The Chinese military has openly stated that it plans to be able to win an
“informationized war” by the middle of this century. Russia, Israel and Romania are
also alleged to have high-level cyber warfare capabilities.
This developing threat from state actors led Sami Saydjari, CEO of Cyber Defense LLC, to testify
(pdf) to the US
House Committee of Homeland Security in 2007, saying: “The US is vulnerable to a
strategically crippling cyber attack from nation-state-class adversaries.” Such an attack
has the potential to turn the US “from being a superpower to a third-world nation
practically overnight.”
I should point out that many have disputed the apocalyptic nature of Saydjari’s statement.
Kevin Mitnick, the reformed hacker, noted in a recent phone call:
“Could we face a mass DOS attack, as in Georgia and Estonia? I don’t think so. I
think it would be more of a surveillance operation to get intelligence. Technically you could
have a mass attack against the thirteen root nameservers around the world. But as for cyber war,
I don’t think we’re at that point yet, I think it’s over-stated.”
Regardless of the impact of an offensive cyber attack, everyone appears to agree on the insidious
danger from online intelligence gathering. Former counter-terrorism chief Richard Clarke
eloquently summarized this in Foreign Policy recently:
“People tend to think about attacks that change things—turn off
power grids, or whatever. And while that’s possible, what is happening every day is quite
devastating, even though it doesn’t have a kinetic impact and there are no body bags.
What’s happening every day is that all of our information is being stolen. So, we pay
billions of dollars for research and development, both in the government and the private sector,
for engineering, for pharmaceuticals, for bioengineering, genetic stuff... and all that
information gets stolen for one one-thousandth of the cost that it took to develop
it.”
Who protects us?
The problem is that it isn’t clear who has the remit for comprehensive defense of the
internet. The US military and intelligence agencies defend government networks and track targets
online, both domestically and abroad. A new Bush-ordained funding boost in January this year will
help them become more coordinated. However, as Richard Clarke goes on to note, “the problem
is that much of what we need to protect is not in the U.S. government; it’s in our private
companies and our private networks”.
The Department of Homeland Security’s National Cyber Security Division operates various
public-private initiatives, such as the rather prosaic National Cyber Security
Awareness Month. But beyond this, the general response appears highly fragmented with little
grand oversight or public-private coordination. I emailed Jonathan Zittrain to ask his opinion on
‘who protects the internet’. He replied:
“Basically no one. At most, a number of loose confederations of computer scientists and
engineers who seek to devise better protocols and practices — unincorporated groups like
the Internet Engineering Task Force and the North American Network Operators Group. But the fact
remains that no one really owns security online, which leads to gated communities with firewalls
— a highly unreliable and wasteful way to try to assure security.”
Hackers to the rescue?
When Obama appoints a white house CTO, there will at least be an official figurehead in charge of
this matter. Proposed candidates for the role currently include Eric Schmidt, Steve Ballmer, Jeff
Bezos and Julius Genachowski from IAC.
However, perhaps the future of internet security really lies in the hands of the community.
Indeed, Jonathan Zittrain talked about ‘good
hackers’ on our show in May, and he argues the importance of community policing in
The Future of the
Internet. The last few years of the internet have been about empowering the masses, and
removing intermediary apparatus – so why not leverage the community to defend
its cyber territory? Indeed, this is already happening, to a certain extent. Just look at
Dan Kaminsky, a computer
consultant who discovered a fundamental flaw in DNS, allowing him control over any website
online. This flaw was astounding in what it gave access to – yet Dan Kaminsky
didn’t turn to a government agency or organization, or abuse the hack himself. Instead he
made a phone call to Paul Vixie, one of the creators of the BIND9 DNS routing software, and they
assembled a team of civilians and private companies to resolve this apocalyptic vulnerability.
It will be interesting to see what happens from here. And whilst it’s certainly
entertaining to envision vigilante hackers and rag-tag groups of high school kids overcoming
nation states, I think there’s more serious matters at stake. The way that the internet
community reacts and operates with state apparatus in defending against cyber threats will be a
crucial indicator of our future society. How reliant are we on the nation-state to protect us?
Will it ever be possible for internet communities to erode the relevance of the nation state? Or
will the internet turn out to be just as Hobbesian as the real world has been?
Charlie Rose’s discussions with General Kevin Chilton and Jonathan Zittrain are available
at our website, charlierose.com.
Matt Rutherford can be reached at matt@charlierose.com.
Crunch Network: MobileCrunch
Mobile Gadgets and Applications, Delivered Daily.


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Wired Top Stories -
1 days and 2 hours ago
!-- pageType= magazinewide slug= pl_print section= culture subsection= education headline= How
Comics Can Save Us From Scientific Ignorance authorName= Barry Harbaugh -- pWhat's the solution to
America's crisis in science education? More comic books. In December comes citea
href="http://us.macmillan.com/thestuffoflife"The Stuff of Life/a: A Graphic Guide to Genetics and
DNA/cite, a remarkably thorough explanation of the science of genetics, from Mendel to Venter, with
a strand of social urgency spliced in. "If there was ever a time that we needed a push to make
science a priority, it's now," says Howard Zimmerman, the book's editor and, not coincidentally, a
former elementary-school science teacher. "Advances in treatments for disease cannot take place in
a society that shuns science." Zimmerman works with the New York literary publishing house Hill and
Wang, which discovered Elie Weisel and has been creating a new niche for itself as one of the
premiere producers of major graphic "nonfiction novels" like the war on terror primer citeAfter
9/11/cite and the bio-comic citeRonald Reagan/cite./p pciteStuff of Life/cite is the first in a
series dedicated to the hard sciences. The author is Mark Schultz, a DC Comics veteran and creator
of the postapocalyptic classic citea
href="http://www.darkhorse.com/Books/11-653/Xenozoic-Tales-Volume-1-TPB"Xenozoic Tales/a/cite. The
160-page work, illustrated by Kevin Cannon and Zander Cannon (improbably, no genetic relation),
covers the regenerative processes of DNA, human migratory patterns, cloned apples, and stem cells.
In a rapidly changing field, it's as up-to-date and accurate as possible./p pSchultz, like
Zimmerman, was attracted by the possibilities of using comics as an educational medium. "It's not
prose, and it's not documentary film," Schultz says. "It's kind of its own animal." And the graphic
novel market is drawing in different readers than he's accustomed to at DC. "The manga phenomenon,"
he notes as one example, "is attracting new demographics, like younger women, who weren't picking
up on traditional comics."/p pNot that this is the first time comics have been enlisted for
educational purposes. The field goes back to the 1940s, when Will Eisner turned Army instruction
manuals into a href="http://www.nytimes.com/2005/01/05/books/05eisner.html"graphic guides for
soldiers/a. Also, there's Larry Gonick's citeCartoon Guides/cite of the '80s, with his citeCartoon
Guide to Genetics/cite being the most obvious precursor here. citeStuff of Life/cite builds on
Gonick, updating his science and employing a silly yet more effective narrativemdash;alien
scientist Bloort 183 presents a PowerPoint on human genetics to his slow-learning leader./p pUp
next? Possibly evolution. After all, Zimmerman says, "more than half of adult Americans think Earth
is about 6,000 years old."/pbr style="clear: both;"/ a style='font-size: 10px; color: maroon;'
href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:c697aae688cafb8ebff3f3dfc81ef4b1:kWNqo0CWaxUCPlQ862WjV%2Balw1dDPHHbxsG5R6RLNumBA6dqmaUzJ0rIFAtYHrLeXcoxw9t1S6%2FvCQ%3D%3D'img
border='0' title='Add to Facebook' alt='Add to Facebook'
src='http://www.pheedo.com/images/mm/facebook.gif'//a a style='font-size: 10px; color: maroon;'
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src='http://www.pheedo.com/images/mm/reddit.png'//a a style='font-size: 10px; color: maroon;'
href='http://www.pheedo.com/hostedMorselClick.php?hfmm=v3:ff53e8831b23a3ca1b664762b4ec2d64:qdsrAbd53IpU3uv9X3yTGy9dDBJt3P8FLT42bezjy2bBgstcBO4kp8FLCSXp9eAosvHFSzqJUCEA'img
border='0' title='Add to digg' alt='Add to digg' src='http://www.pheedo.com/images/mm/digg.gif'//a
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border='0' title='Add to Google' alt='Add to Google'
src='http://www.pheedo.com/images/mm/google.png'//a br style="clear: both;"/ a
href="http://www.pheedo.com/click.phdo?s=ca0551678d4065f628e3993770cdbd2fp=1"img alt=""
style="border: 0;" border="0"
src="http://www.pheedo.com/img.phdo?s=ca0551678d4065f628e3993770cdbd2fp=1"//a img
src="http://www.pheedo.com/feeds/tracker.php?i=ca0551678d4065f628e3993770cdbd2f" style="display:
none;" border="0" height="1" width="1" alt=""/ pa
href="http://feeds.wired.com/~a/wired/index?a=ZuR1VA"img
src="http://feeds.wired.com/~a/wired/index?i=ZuR1VA" border="0"/img/a/pimg
src="http://feeds.wired.com/~r/wired/index/~4/473261696" height="1" width="1"/

|
CiteULike: Borelli's watchlist -
1 days and 3 hours ago
iGenomics (24 July 2008)/ibr /br /We are studying variable selection in multiple regression models
in which molecular markers and/or gene-expression measurements as well as intensity measurements
from protein spectra serve as predictors for the outcome variable (i.e., trait or disease state).
Finding genetic biomarkers and searching genetic-epidemiological factors can be formulated as a
statistical problem of variable selection, in which, from a large set of candidates, a small number
of trait-associated predictors are identified. We illustrate our approach by analyzing the data
available for chronic fatigue syndrome (CFS). CFS is a complex disease from several aspects, e.g.,
it is difficult to diagnose and difficult to quantify. To identify biomarkers we used microarray
data and SELDI-TOF-based proteomics data. We also analyzed genetic marker information for a large
number of SNPs for an overlapping set of individuals. The objectives of the analyses were to
identify markers specific to fatigue that are also possibly exclusive to CFS. The use of such
models can be motivated, for example, by the search for new biomarkers for the diagnosis and
prognosis of cancer and measures of response to therapy. Generally, for this we use Bayesian
hierarchical modeling and Markov Chain Monte Carlo computation.br /iM Bhattacharjee, C H Botting, M
J Sillanpää/i

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Guardian Unlimited -
1 days and 5 hours ago
divimg alt=""
src="http://hits.guardian.co.uk/b/ss/guardiangu-feeds/1/H.15.1/80822?ns=guardianpageName=Environment%3A+%27Super+ants%27+threaten+UK+gardens%2C+scientists+warnch=Environmentc3=guardian.co.ukc4=Wildlife+%28Environment%29%2CEnvironment%2CUK+news%2CGardens+%28Life+and+style%29%2CScience%2CZoologyc5=Environment+Conservation%2CHomes+and+Gardens%2CNot+commercially+useful%2CEthical+Livingc6=James+Randersonc7=2008_12_03c8=1127551c9=articlec10=GUc11=Environmentc12=Wildlifec13=c14=h2=GU%2FEnvironment%2FWildlife"
width="1" height="1" //divpAn ant species that forms huge supercolonies and infests gardens and
parks is marching rapidly across Europe and will soon invade the UK, according to entomologists who
are monitoring its spread./ppThe colonies can swell to 10 or 100 times the size of those of common
garden ants and scientists warn that they can cause significant damage to plants. /pp"When I saw
this ant for the first time, I simply could not believe there could be so many garden ants in the
same lawn," says Prof Jacobus Boomsma at the University of Copenhagen, one of its co-discoverers
almost 20 years ago./pp"We reckon it's only a matter of time before [it invades the UK]."/ppThe
invasive garden ant or ema
href="http://www.antweb.org/description.do?name=neglectusgenus=lasiusrank=speciesproject=macaronesiaants"Lasius
neglectus/a/em was first identified in 1990 when it was found infesting an entire neighbourhood in
Budapest, Hungary./pp"This ant basically looks like the garden ant that everybody knows, so you
don't really become suspicious if you see a few of those crawling around because they are
everywhere," he said. It has since become a major pest in central Europe and has spread as far as
Jena in Germany, Ghent in Belgium and Warsaw in Poland./ppBoomsma and his team think it is moved
around by the horticultural trade because it hides inside plant pots. "That is the most reasonable
hypothesis for how these ants get transported because the ants themselves have lost the ability to
fly so they are very poor disbursers," he said./ppIn research published today in the journal PLoS
One, the team used genetic techniques to work out where the ants originated and what makes them so
successful at taking over new regions. One reason is that they are able to form super-colonies.
/ppThe ants occupy many interconnected nests with many queens. Because they are related, the ants
in these nests do not show territorial aggression. When they reach new locations the parasites that
usually keep the ants in check are no longer there, so they are able to expand their colonies
rapidly./pp"We found that invasive garden ants developed from species in the Black Sea region that
have natural populations with small networks of interconnected nests with many queens that mate
underground and don't fly. /pp"It is now becoming clear that rather many ant species share this
lifestyle, so it is no surprise that a number of them have become invasive pests with giant
super-colonies based on the same principles," said Dr Sylvia Cremer, at the University of
Regensburg./ppDr Jes Pedersen, a co-author at the University of Copenhagen, said: "The future will
therefore see many more ants become invasive, so it is about time we understand their biology. This
study is a major step in that direction."/ppMuch of the damage that the invasive garden ant causes
is connected with the herds of aphids that it tends. The ants have a symbiotic relationship with
the aphids in which the aphids provide sugary food while the ants provide protection from
predators. /ppWith the ants around, aphid populations expand to large numbers causing damage to
plants and releasing sticky secretions that create a mess on parked cars. Because the ant colonies
are so large they can cause a nuisance by invading homes and spoiling food./ppInvasive ants have
caused much more significant damage in other countries. The imported red fire ant, which has a
nasty sting, causes $750m (£500m) of damage in the US each year to crops and livestock. The
Argentine ant has spread along 6,000km of coastline in southern Europe, exterminating many local
insects./pdiv style="float: left; margin-right: 10px; margin-bottom: 10px;"ullia
href="http://www.guardian.co.uk/environment/wildlife"Wildlife/a/lilia
href="http://www.guardian.co.uk/lifeandstyle/gardens"Gardens/a/lilia
href="http://www.guardian.co.uk/science/zoology"Zoology/a/li/ul/diva
href="http://www.guardian.co.uk"guardian.co.uk/a copy; Guardian News Media Limited 2008 | Use of
this content is subject to our a
href="http://users.guardian.co.uk/help/article/0,,933909,00.html"Terms Conditions/a | a
href="http://www.guardian.co.uk/webfeeds/1,,1309488,00.html"More Feeds/a pa
href="http://feedads.googleadservices.com/~at/o3WUv1Oe4LJ5LdDrZqSllcEf89k/a"img
src="http://feedads.googleadservices.com/~at/o3WUv1Oe4LJ5LdDrZqSllcEf89k/i" border="0"
ismap="true"/img/a/p

|
CiteULike: Borelli's watchlist -
1 days and 6 hours ago
iGenome Biology, Vol. 9 (24 November 2008), R165./ibr /br /Whole genome tiling arrays are a key
tool for profiling global genetic and expression variation. In this study we present our methods
for detecting transcript level variation, splicing variation and allele specific expression in
Arabidopsis thaliana. We also developed a generalized Hidden Markov Model for profiling transcribed
fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful
platform for dissecting natural transcriptome variation at multi-dimension and high resolution.br
/iXu, Justin Borevitz/i
|
PNAS - RSS feed of Early Edition articles -
1 days and 7 hours ago
The Tuberous Sclerosis Complex component, TSC1, functions as a tumor suppressor via its
regulation of diverse cellular processes, particularly cell...
|
Nature -
1 days and 7 hours ago
Publication Date: 2008 Nov 30 PMID: 19043401br/Authors: O'Gorman, C. M. - Fuller, H. T. - Dyer, P.
S.br/Journal: Naturebr/br/Aspergillus fumigatus is a saprotrophic fungus whose spores are
ubiquitous in the atmosphere. It is also an opportunistic human pathogen in immunocompromised
individuals, causing potentially lethal invasive infections, and is associated with severe asthma
and sinusitis. The species is only known to reproduce by asexual means, but there has been
accumulating evidence for recombination and gene flow from population genetic studies, genome
analysis, the presence of mating-type genes and expression of sex-related genes in the fungus. Here
we show that A. fumigatus possesses a fully functional sexual reproductive cycle that leads to the
production of cleistothecia and ascospores, and the teleomorph Neosartorya fumigata is described.
The species has a heterothallic breeding system; isolates of complementary mating types are
required for sex to occur. We demonstrate increased genotypic variation resulting from
recombination between mating type and DNA fingerprint markers in ascospore progeny from an Irish
environmental subpopulation. The ability of A. fumigatus to engage in sexual reproduction is highly
significant in understanding the biology and evolution of the species. The presence of a sexual
cycle provides an invaluable tool for classical genetic analyses and will facilitate research into
the genetic basis of pathogenicity and fungicide resistance in A. fumigatus, with the aim of
improving methods for the control of aspergillosis. These results also yield insights into the
potential for sexual reproduction in other supposedly 'asexual' fungi.br/br/post to: a href =
http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19043401title=Entrez+PubmedCiteULike/a

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High-Def Digest: All High-Def Disc News -
1 days and 9 hours ago
In an early announcement to retailers, Lionsgate has set a late-January Blu-ray debut for the
rock-horror opus 'Repo! The Genetic Opera.' Starring Sarah Brightman and Paris Hilton and directed
by 'Saw'...img src="http://feeds.feedburner.com/~r/highdefdigestallnews/~4/472721609" height="1"
width="1"/
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DVDRAMA : Les News -
1 days and 17 hours ago
Cela faisait longtemps que nous ne vous avions pas parlé de Repo! The Genetic Opera, une
curiosité rock et gentiment gore qui pourrait sonner comme la rédemption de Darren
Lynn Bousma[...]
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