genome editing
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Rescooped by Fesquet didier from Enseignement Supérieur et Recherche en France
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L'état de l'emploi scientifique en France

L'état de l'emploi scientifique en France | genome editing | Scoop.it

L'état de l'emploi scientifique 2016 correspond à une publication statistique biennale. Elle rassemble des études et statistiques permettant d'éclairer les différents domaines d'activité des personnels qui relèvent de l'emploi scientifique en France. Il couvre à la fois la recherche menée dans les organismes et les établissements d'enseignement supérieur et celle réalisée en entreprise. (...) - La Documentation française, septembre 2016


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European Commissioner Moedas: "Journal papers based on EU-funded science should be free to access"

European Commissioner Moedas: "Journal papers based on EU-funded science should be free to access" | genome editing | Scoop.it
The days of open science have arrived and it is time to move from pay-to-read to free-to-read, says the R&D Commissioner.
Via Bernard Rentier
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Bernard Rentier's curator insight, April 6, 3:26 AM
"Publishers want to keep their subscriptions and applied research labs are concerned about IP".- Indeed, publishers have to worry about their subscriptions because of the change of paradigm. Every time a paradigm has changed in history, business models have had to adapt or disappear (this is why they want us to pay for publishing). And again, cost will be proportional to publisher's prestige...- On the other hand, applied research labs and industry don't have to worry about IP (intellectual property). OA has nothing to do with IP. IP rights preservation is only concerned about whether to publish or not and not at all about how to publish (traditional or OA).
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Statement on Genome Editing Technologies

Statement on Genome Editing Technologies | genome editing | Scoop.it

Council of Europe supports new genome editing technologies, but within certain limits
Strasbourg ...

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Arguments about CRISPR technology: A Revolution of Science | CD Genomics Blog

Arguments about CRISPR technology: A Revolution of Science | CD Genomics Blog | genome editing | Scoop.it

Via Sherry
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Sherry's curator insight, September 1, 2015 9:39 PM

Yes, CRISPR technology is  a revolution for biology.

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CRISPR-Cpf1 May Outsnip CRISPR-Cas9 | GEN News Highlights | GEN

CRISPR-Cpf1 May Outsnip CRISPR-Cas9 | GEN News Highlights | GEN | genome editing | Scoop.it

Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.

Fesquet didier's insight:

les techniques de genome editing evoluent vite...impressionnant travail du labo f zhang

 

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Nobel laureate Randy Schekman on how journals like Nature, Cell and Science are damaging science

Nobel laureate Randy Schekman on how journals like Nature, Cell and Science are damaging science | genome editing | Scoop.it

Randy Schekman: "The incentives offered by top journals distort science, just as big bonuses distort banking"


Via Bernard Rentier
Fesquet didier's insight:

pas d'issue tant que les comites d'evaluation ne jureront que par "NCS".

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Bernard Rentier's curator insight, September 3, 2015 5:18 AM
The only honest way to evaluate researchers and research teams is on the quality of their work, not through the distorting prism of who publishes it. Harder but more fair and more responsible.
Gilbert C FAURE's curator insight, September 3, 2015 5:25 AM

it was 2013

any change since?

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WATCH: Here's an easy way to subtract by adding

WATCH: Here's an easy way to subtract by adding | genome editing | Scoop.it
Okay, so let's just get this one out of the way first - there are calculators, and they're actually pretty amazing at doing maths. But it's time to dust that tired, old brain off so we can learn a great little arithmetic trick, courtesy of the...

Via Olgy Gary
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cela me semble en fait..compliqué!

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Olgy Gary's curator insight, May 5, 2015 11:03 PM

Fascinating... and sort of fun to see it worked out. According to the Minute Physics 3.13 min. video, it's how computers carry out subtractions... they do it by adding! 

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The war against humanities at Britain's universities

The war against humanities at Britain's universities | genome editing | Scoop.it

Our universities are squeezing every ounce of efficiency out of lecturers and focusing on the ‘profitable’ areas of science, tech and maths. Could the humanities be wiped out? (...) - The Guardian, by Alex Preston, 29 March 2015


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un phénomène général...encore un coup de l'excellence :-)

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Physical scientists offer outside-the-box idea for funding U.S. basic research

Physical scientists offer outside-the-box idea for funding U.S. basic research | genome editing | Scoop.it

Researchers float idea of National Research Bank, a $100 billion endowment.

 

SAN ANTONIO, TEXAS—Researchers across the United States are well aware that times are tight. Despite a recent budget proposal from the Obama administration to increase spending on federal R&D by 7% next year, dollars flowing to research have largely been flat in recent years, and declining when inflation is taken into account. The long-term outlook is even worse. Growing federal commitments to Medicare, Medicaid, social security, and interest on the federal debt continue to chew up a greater proportion of the federal budget. The money for “discretionary” items that’s left over—including R&D—is expected to drop to 23% of the federal budget by 2040, down from 67% in 1970 and 36% in 2012. So it’s perhaps no surprise that basic researchers are beginning to look for new sources of support. (...) - Science, by Robert F. Service, 4 March 2015


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Mapping the precision of genome editing - Nature Biotech.

Mapping the precision of genome editing - Nature Biotech. | genome editing | Scoop.it

Gabriel et al, 2015

Precise genome engineering in live cells at any locus promises to facilitate basic research and to enable personalized medicine. In particular, the recent development of the CRISPR-Cas9 system into a versatile and easy-to-use editing tool1 has been celebrated as a scientific breakthrough in the field. As genome engineering is adapted to clinical applications, a high level of precision—especially the avoidance of editing at sites other than the intended target—will be indispensable. In this issue, three very timely studies2, 3, 4 report methods for identifying off-target double-strand breaks produced by CRISPR-associated (Cas)9 nucleases and another class of programmable nucleases known as transcription activator–like effector nucleases (TALENs). Wang et al.2 and Tsai et al.3 rely on integration of a foreign DNA bait sequence into off-target double-strand breaks, whereas Frock et al.4 detect translocations of endogenous genomic sequences to the intended cleavage site (Fig. 1). All three methods attain an unprecedented level of comprehensiveness and sensitivity in off-target detection. The papers also highlight that the specificity of nucleases varies widely and must be evaluated case by case.


Via dromius
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encore le debat du OT...!

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Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology - Plant Biotech. J.

Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology - Plant Biotech. J. | genome editing | Scoop.it

(via T. Lahaye, thx)

Shan et al, 2015

Fragrant rice is favoured worldwide because of its agreeable scent. The presence of a defective badh2 allele encoding betaine aldehyde dehydrogenase (BADH2) results in the synthesis of 2-acetyl-1-pyrroline (2AP), which is a major fragrance compound. Here, transcription activator-like effector nucleases (TALENs) were engineered to target and disrupt the OsBADH2 gene. Six heterozygous mutants (30%) were recovered from 20 transgenic hygromycin-resistant lines. Sanger sequencing confirmed that these lines had various indel mutations at the TALEN target site. All six transmitted the BADH2 mutations to the T1 generation; and four T1 mutant lines tested also efficiently transmitted the mutations to the T2 generation. Mutant plants carrying only the desired DNA sequence change but not the TALEN transgene were obtained by segregation in the T1 and T2 generations. The 2AP content of rice grains of the T1 lines with homozygous mutations increased from 0 to 0.35–0.75 mg/kg, which was similar to the content of a positive control variety harbouring the badh2-E7 mutation. We also simultaneously introduced three different pairs of TALENs targeting three separate rice genes into rice cells by bombardment and obtained lines with mutations in one, two and all three genes. These results indicate that targeted mutagenesis using TALENs is a useful approach to creating important agronomic traits.


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Quel est le poids du hasard dans l'apparition des cancers ?

Quel est le poids du hasard dans l'apparition des cancers ? | genome editing | Scoop.it

Le Monde.fr version mobile - Selon une étude, deux tiers des tumeurs relèveraient de mutations aléatoires plutôt que de facteurs cancérigènes ou génétiques. Mais deux des cancers les plus répandus n'ont pas été pris en compte.


Via catherine cerisey
Fesquet didier's insight:

Papier de science qui  suscite pas mal de reaction sur  le web,.pas lu mais il me semble assez intuitif qu'un tissu qui  se renouvelle  (prolifere) soit plus sujet à des anomalies survenant dans le comportement cellules souches...mais racontél par un big name..c'est plus sérieux. N'empêche que dans les faits..pas mal de cancer sont induits par nos comportements.. à risque.

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Les nucléases, de fabuleux outils pour la chirurgie du génome : les ... - bulletins-electroniques.com

Les nucléases, de fabuleux outils pour la chirurgie du génome : les ... - bulletins-electroniques.com | genome editing | Scoop.it
Les Bulletins Electroniques des Ambassades de France - un service ADIT
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Which Journals Ask for Cell Line Authentication?

Lots of people ask me this question.  So I like to keep a list online to share with everyone.  If you spot any mistakes or can think of any journals I have missed, please leave a comment to let me know.

 

The journals or publishers that I have found with some kind of authentication requirement are listed below.  Requirements vary with each journal - for example, Nature has a checklist that sets out reporting requirements for cell lines, including authentication testing status.  The International Journal of Cancer has a mandatory requirement for authentication, and authors are asked about this specifically during manuscript submission.

 

Including a requirement for cell line authentication means more effort from everyone involved - editors, reviewers and authors.  But the end result is more reliable research.  Kudos to all involved here.

 

Eight AACR journals, including Cancer Research
http://www.aacrjournals.org/site/InstrAuthors/ifora.xhtml#celllineuse

 

200+ BioMed Central journals, including BMC Cancer

http://www.biomedcentral.com/about/editorialpolicies#StandardsofReporting

 

Five Endocrine Society journals, including the Journal of Clinical Endocrinology and Metabolism
http://press.endocrine.org/page/authors#mozTocId949960

 

All Nature journals, including Nature and Nature Methods
http://www.nature.com/authors/policies/availability.html#further

 

Three Society for Endocrinology journals, including Journal of Endocrinology
http://joe.endocrinology-journals.org/site/misc/For-Authors.xhtml

 

Biotechniques

http://www.biotechniques.com/authors/

 

Carcinogenesis
http://www.oxfordjournals.org/our_journals/carcin/for_authors/general.html

 

Cell Biochemistry and Biophysics
http://www.springer.com/life+sciences/biochemistry+%26+biophysics/journal/12013

 

Cell Biology International
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1095-8355/homepage/ForAuthors.html

 

International Journal of Cancer
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0215/homepage/ForAuthors.html

 

Investigative Ophthalmology & Visual Science

http://iovs.arvojournals.org/ss/forauthors.aspx

 

In Vitro Cellular & Developmental Biology - Animal
http://www.sivb.org/info_IVA.pdf

 

Journal of Molecular Biology
http://www.elsevier.com/wps/find/journaldescription.cws_home/622890/authorinstructions#N10E75

 

Journal of the National Cancer Institute
http://www.oxfordjournals.org/our_journals/jnci/for_authors/ms_prep.html

 

Molecular Vision
http://www.molvis.org/molvis/instructions.html

 

Neuro-Oncology
http://www.oxfordjournals.org/our_journals/neuonc/for_authors/

 

PLOS One

http://www.plosone.org/static/guidelines#cell


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a growing problem!
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A proposed regulatory framework for genome-edited crops - Nature Genetics

A proposed regulatory framework for genome-edited crops - Nature Genetics | genome editing | Scoop.it

Huang et al, 2016

Crop breeding is being revolutionized by rapid progress in DNA sequencing and targeted alteration of DNA sequences by genome editing. Here we propose a regulatory framework for precision breeding with 'genome-edited crops' (GECs) so that society can fully benefit from the latest advances in plant genetics and genomics.


Via dromius
Fesquet didier's insight:

l'OGM propre...genome editing of the gliadin loci in wheat is wellcome

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Analysis of protein-coding genetic variation in 60,706 humans

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Via Genomeducator
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nice database that illustrates genome variations

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Genomeducator's curator insight, November 2, 2015 1:54 PM
Highlights from this paper: The location of genes intolerant of LOF mutations (79% of which have no established disease phenotype)Efficient filtering for disease causing variants - they recommend the highest allele frequency in any one population (“popmax”) rather than the average (“global”) allele frequency The dubious nature of many "pathogenic" variants reported in databases. "The average ExAC participant harbors ~53 variants reported as disease-causing in two widely-used databases of disease-causing variants..." -- most of which had  implausibly high (>1%) AF in at least one population. The average ExAC exome contains 0.89 reportedly Mendelian variants in well-characterized dominant disease genes at <1% popmax AF and 0.20 at <0.1% popmax AF. Incomplete penetrance a major supposed source.
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Researchers Led by George Church Simplify Powerful CRISP/Cas9 Gene Editing Tool by Developing Interactive Software to Find Guide RNAs Predicted to be Highly Specific and Highly Active for Their Gen...

Researchers Led by George Church Simplify Powerful CRISP/Cas9 Gene Editing Tool by Developing Interactive Software to Find Guide RNAs Predicted to be Highly Specific and Highly Active for Their Gen... | genome editing | Scoop.it
Researchers Led by George Church Simplify Powerful CRISP/Cas9 Gene Editing Tool by Developing Interactive Softwar… http://t.co/50A8cP6qSn
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Cancer du sein : la piste des cellules souches à l'origine des métastases est avérée (dépêche APM )

LONDRES, 23 septembre 2015 (APM) - Les métastases des cancers seraient dues à la dissémination d'une catégorie particulière de cellules ayant des propriétés de cellules souches, selon une étude dans un modèle de cancer du sein qui pourrait orienter la recherche sur la prévention des métastases, publiée mercredi dans Nature.Ce travail de l'université de San Francisco confirme l'hypothèse en vogue, mais qui n'était jusqu'à présent pas démontrée, que les métastases seraient dérivées d'une minorité de cellules tumorales ayant des caractéristiques différentes des autres.Les chercheurs ont étudié des souris auxquelles une tumeur mammaire humaine était greffée, en s'intéressant aux métastases de cette tumeur, en étudiant le profil d'expression génétique des cellules métastatiques.Ils ont constaté que lorsque la métastase est encore petite, elle est composée de cellules différentes de la majorité des cellules de la tumeur primaire, et qui ont des caractéristiques de cellules souches.Puis, dans les métastases plus grosses, les cellules de nouveau ressemblent à celles de la tumeur primaire.De plus, les chercheurs ont découvert que des cellules ayant des caractéristiques de cellules souches existent, en minorité, dans la tumeur primaire. Ces cellules représentent en moyenne 1,4% de la tumeur primaire, mais avec des variations selon les tumeurs, et ils ont constaté que plus la tumeur primaire contient de ces cellules particulières, plus le risque de métastase est élevé."Ces résultats sont en faveur d'un modèle hiérarchique dans lequel les métastases sont initiées par des cellules de type cellule souche, qui prolifèrent puis se différencient pour produire une maladie métastatique avancée", commentent les auteurs.Ils proposent également une piste de traitement. Comme ces cellules souches expriment peu l'oncogène MYC lorsqu'elles sont à l'état dormant mais surexpriment MYC quand elles se mettent à proliférer, ils ont testé un agent actif sur les tumeurs exprimant MYC, le dinaciclib.Chez des souris portant une tumeur primaire, après quatre semaines, alors que des cellules métastatiques étaient détectées chez 44% des contrôles, cela n'a été le cas que chez 4% des animaux traités par dinaciclib (Merck & Co).Ainsi, indépendamment du traitement visant à réduire la tumeur primaire dans son ensemble, il pourrait être intéressant de cibler aussi spécifiquement les cellules ayant un potentiel métastatique.(Nature, publication en ligne du 23 septembre)


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Sequential cancer mutations in cultured human intestinal stem cells : Nature : Nature Publishing Group

Sequential cancer mutations in cultured human intestinal stem cells : Nature : Nature Publishing Group | genome editing | Scoop.it
Crypt stem cells represent the cells of origin for intestinal neoplasia. Both mouse and human intestinal stem cells can be cultured in medium containing the stem-cell-niche factors WNT, R-spondin, epidermal growth factor (EGF) and noggin over long time periods as epithelial organoids that remain genetically and phenotypically stable. Here we utilize CRISPR/Cas9 technology for targeted gene modification of four of the most commonly mutated colorectal cancer genes (APC, P53 (also known as TP53), KRAS and SMAD4) in cultured human intestinal stem cells. Mutant organoids can be selected by removing individual growth factors from the culture medium. Quadruple mutants grow independently of all stem-cell-niche factors and tolerate the presence of the P53 stabilizer nutlin-3. Upon xenotransplantation into mice, quadruple mutants grow as tumours with features of invasive carcinoma. Finally, combined loss of APC and P53 is sufficient for the appearance of extensive aneuploidy, a hallmark of tumour progression.

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Fast and sensitive detection of indels induced by precise gene targeting - Nucl. Acids Res.

Yang et al, 2015

The nuclease-based gene editing tools are rapidly transforming capabilities for altering the genome of cells and organisms with great precision and in high throughput studies. A major limitation in application of precise gene editing lies in lack of sensitive and fast methods to detect and characterize the induced DNA changes. Precise gene editing induces double-stranded DNA breaks that are repaired by error-prone non-homologous end joining leading to introduction of insertions and deletions (indels) at the target site. These indels are often small and difficult and laborious to detect by traditional methods. Here we present a method for fast, sensitive and simple indel detection that accurately defines indel sizes down to ±1 bp. The method coined IDAA for Indel Detection by Amplicon Analysis is based on tri-primer amplicon labelling and DNA capillary electrophoresis detection, and IDAA is amenable for high throughput analysis.

 


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Editor quits journal over pay-for-expedited peer-review offer

Authors can pay open-access journal extra to get reviewed in less than 3 weeks


Via Bernard Rentier
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Une nouvelle évolution du business  qu'est devenu la publication scientifique. Chapeau à cet éditeur qui a préfère démissionner.

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Bernard Rentier's curator insight, March 28, 2015 3:50 PM
Not unexpected. "Pay-to-publish" has an inherent loophole in itself and it reflects a serious ethical problem...
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Therapeutic genome editing: prospects and challenges : Nature Medicine : Nature Publishing Group

Therapeutic genome editing: prospects and challenges : Nature Medicine : Nature Publishing Group | genome editing | Scoop.it
“Turitz Cox et al, 2015Recent advances in the development of genome editing technologies based on programmable nucleases have substantially improved our ability to make precise changes in the genomes of eukaryotic cells. Genome editing is already broadening our ability to elucidate the contribution of genetics to disease by facilitating the creation of more accurate cellular and animal models of pathological processes. A particularly tantalizing application of programmable nucleases is the potential to directly correct genetic mutations in affected tissues and cells to treat diseases that are refractory to traditional therapies. Here we discuss current progress toward developing programmable nuclease–based therapies as well as future prospects and challenges.”
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A one-grant limit: NIH institute puts squeeze on flush investigators

Those with generous no-strings funding will be limited to one grant.

In the latest example of budget stretching at the National Institutes of Health (NIH), the agency’s basic science institute is imposing a strict one-grant limit on scientists who already have plentiful no-strings support. The move could free up at least $6 million, or 25 grants for other scientists. (...) - ScienceInsider, by Jocelyn Kaiser, 14 January 2015


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contre le cumul des mandats des politiques...mais aussi contre le cumul des gros  financements...simple bon sens de nos jours.

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L’avenir difficile du financement de la recherche

L’avenir difficile du financement de la recherche | genome editing | Scoop.it

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Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases - Nature Biotech.

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases - Nature Biotech. | genome editing | Scoop.it

Frock et al, 2014

Although great progress has been made in the characterization of the off-target effects of engineered nucleases, sensitive and unbiased genome-wide methods for the detection of off-target cleavage events and potential collateral damage are still lacking. Here we describe a linear amplification–mediated modification of a previously published high-throughput, genome-wide, translocation sequencing (HTGTS) method that robustly detects DNA double-stranded breaks (DSBs) generated by engineered nucleases across the human genome based on their translocation to other endogenous or ectopic DSBs. HTGTS with different Cas9:sgRNA or TALEN nucleases revealed off-target hotspot numbers for given nucleases that ranged from a few or none to dozens or more, and extended the number of known off-targets for certain previously characterized nucleases more than tenfold. We also identified translocations between bona fide nuclease targets on homologous chromosomes, an undesired collateral effect that has not been described previously. Finally, HTGTS confirmed that the Cas9D10A paired nickase approach suppresses off-target cleavage genome-wide.


Via dromius
Fesquet didier's insight:

off target ou pas off targets...the debate is still on going...hope the wt has reported does not induce that much OT...can't believe

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