ASU, IBM move ultrafast, low-cost DNA sequencing technology a step closer to reality

Biology News - 2 hours 18 min ago

A team of scientists from Arizona State University's Biodesign Institute and IBM's T.J. Watson Research Center have developed a prototype DNA reader that could make whole genome profiling an everyday practice in medicine.

Categories: Biology News, General

Lionfish analysis reveals most vulnerable prey as invasion continues

Biology News - 2 hours 18 min ago

Stephanie Green studies lionfish in The Bahamas. If you live in lionfish territory in the Atlantic Ocean, the last thing you want to be is a small fish with a long, skinny body, resting by yourself at night, near the bottom of the seafloor.

Categories: Biology News, General

Gates Foundation announces world’s strongest policy on open access research

Nature Newsblog - Fri, 2014-11-21 13:39

The Bill & Melinda Gates Foundation has announced the world’s strongest policy in support of open research and open data. If strictly enforced, it would prevent Gates-funded researchers from publishing in well-known journals such as Nature and Science.

On 20 November, the medical charity, of Seattle, Washington, announced that from January 2015, researchers it funds must make open their resulting papers and underlying data-sets immediately upon publication — and must make that research available for commercial re-use. “We believe that published research resulting from our funding should be promptly and broadly disseminated,” the foundation states. It says it will pay the necessary publication fees (which often amount to thousands of dollars per article).

The Foundation is allowing two years’ grace: until 2017, researchers may apply a 12-month delay before their articles and data are made free. At first glance, this suggests that authors may still — for now — publish in journals that do not offer immediate open-access (OA) publishing, such as Science and Nature. These journals permit researchers to archive their peer-reviewed manuscripts elsewhere online, usually after a delay of 6-12 months following publication.

Allowing a year’s delay makes the charity’s open-access policy similar to those of other medical funders, such as the Wellcome Trust or the US National Institutes of Health (NIH). But the charity’s intention to close off this option by 2017 might put pressure on paywalled journals to create an open-access publishing route.

However, the Gates Foundation’s policy has a second, more onerous twist which appears to put it directly in conflict with many non-OA journals now, rather than in 2017. Once made open, papers must be published under a license that legally allows unrestricted re-use — including for commercial purposes. This might include ‘mining’ the text with computer software to draw conclusions and mix it with other work, distributing translations of the text, or selling republished versions.  In the parlance of Creative Commons, a non-profit organization based in Mountain View, California, this is the CC-BY licence (where BY indicates that credit must be given to the author of the original work).

This demand goes further than any other funding agency has dared. The UK’s Wellcome Trust, for example, demands a CC-BY license when it is paying for a paper’s publication — but does not require it for the archived version of a manuscript published in a paywalled journal. Indeed, many researchers actively dislike the thought of allowing such liberal re-use of their work, surveys have suggested. But Gates Foundation spokeswoman Amy Enright says that “author-archived articles (even those made available after a 12-month delay) will need to be available after the 12 month period on terms and conditions equivalent to those in a CC-BY license.”

Most non-OA publishers do not permit authors to apply a CC-BY license to their archived, open, manuscripts. Nature, for example, states that openly archived manuscripts may not be re-used for commercial purposes. So do the American Association for the Advancement of ScienceElsevier and Wiley and many other publishers (in relation to their non-OA journals).

“It’s a major change. It would be major if publishers that didn’t previously use CC-BY start to use it, even for the subset of authors funded by the Gates Foundation. It would be major if publishers that didn’t previously allow immediate or unembargoed OA start to allow it, again even for that subset of authors. And of course it would be major if some publishers refused to publish Gates-funded authors,” says Peter Suber, director of the Office for Scholarly Communication at Harvard University in Cambridge, Massachusetts.

“You could say that Gates-funded authors can’t publish in journals that refuse to use CC-BY. Or you could say that those journals can’t publish Gates-funded authors. It may look like a stand-off but I think it’s the start of a negotiation,” Suber adds — noting that when the NIH’s policy was announced in 2008, many publishers did not want to accommodate all its terms, but now all do.

That said, the Gates Foundation does not leave as large a footprint in the research literature as the NIH. It only funded 2,802 research articles in 2012 and 2013, Enright notes; 30% of these were published in open access journals. (Much of the charity’s funding goes to development projects, rather than to research which will be published in journals).

The Gates Foundation also is not clear on how it will enforce its mandate; many researchers are still resistant to the idea of open data, for instance. (And most open access mandates are not in fact strictly enforced; only recently have the NIH and the Wellcome Trust begun to crack down). But Enright says the charity will be tracking what happens and will write to non-compliant researchers if needs be. “We believe that the foundation’s Open Access Policy is in alignment with current practice and trends in research funded in the public interest.  Hence, we expect that the policy will be readily understood, adopted and complied with by the researchers we fund,” she says.

Categories: General, News

Indirect costs: Keeping the lights on

Nature - Wed, 2014-11-19 13:45

Indirect costs: Keeping the lights on

Nature 515, 7527 (2014).

Author: Heidi Ledford

Every year, the US government gives research institutions billions of dollars towards infrastructure and administrative support. A Nature investigation reveals who is benefiting most.

Categories: General, Nature

New book list, November 5, 2014

Ernst Mayr Library Blog - Thu, 2014-11-06 13:46

Aus der Urzeit aufgetaucht: Bilddokumentation über sensationelle Wal- und Haifunde aus Schleswig-Holstein.

[By] Gerhard Höpfner. Lübeck: Museum für Natur und Umwelt der Hansestadt Lübeck, die Lübecker Museen Kulturstiftung: Naturwissenschaftlicher Verein zu Lübeck, 2014. HOLLIS# 014219000

QE882.C5 H67 2014


Catalogue of invertebrate collection deposited in the Department of Zoology, the University Museum, the University of Tokyo. Pt. 1-3.

Edited by Rei Ueshima. Tōkyō: Tōkyō Daigaku Sōgō Kenkyū Hakubutsukan, 2006-<2011>. HOLLIS# 010583640

QL362.7.T65 2006


Catalogue of the Kojiro Shiraishi insect collection, the University Museum, the University of Tokyo. Odonata.

[By] Shin-ichi Suda, Yuki Sugiura, Katsuhiro Awano, Yulina Kato, Hayato Ito, Yasuhiro Ito & Masaya Yago. Tōkyō: Tōkyō Daigaku Sōgō Kenkyū Hakubutsukan, 2013. HOLLIS# 014218917

QL520.25.J3 T64 2013


Catalogue of the Shigeru Eda insect collection, the University Museum, the University of Tokyo. Part I, Lepidoptera, Rhopalocera.

[By] Katsuhiro Awano, Hideyuki Ozawa, Masaya Yago & Yoshiaki Nishino. Tōkyō: Tōkyō Daigaku Sōgō Kenkyū Hakubutsukan, 2012. HOLLIS# 014218958

QL545.2.T64 2012


Catalogue of the Suguru Igarashi insect collection, the University Museum, the University of Tokyo.

[By] Motohiro Harada, Motomu Teshirogi, Hideyuki Ozawa & Masaya Yago. Tōkyō: Tōkyō Daigaku Sōgō Kenkyū Hakubutsukan, 2012. HOLLIS# 014218886

QL561.P2 T64 2012


Freshwater mussels of Florida.

By James D. Williams, Robert S. Butler, Gary L. Warren, and Nathan A. Johnson; with special thanks to Sherry L. Bostick, Richard T. Bryant. Tuscaloosa: The University of Alabama Press, [2014]. HOLLIS# 014215323

QL430.6.W553 2014


The gamekeepers: Wisconsin wildlife conservation from WCD to CWD.

By David L. Gjestson. Madison, WI: Wisconsin Department of Natural Resources, 2013. HOLLIS# 014212930

SK355.G47 2013


Guide to the butterflies of the Palearctic Region. Vol. 5, pt. 2: Pieridae, pt. II. Subfamily Coliadinae, tribe Coliadini.

Editor: G. C. Bozano. Milano: Onmes Artes; 1999. HOLLIS# 009115949

QL546.G84 1999 v. 5, pt. 2


Kai no seitai.

Henshū Iwanami Shoten Henshūbu; kanshū Taki Isao, Horikoshi Masuoki; shashin Iwanami Eiga Seisakujo. Tōkyō: Iwanami Shoten, Shōwa 29 [1954]. HOLLIS# 014214504

QL430.4.K24 1954


Malacofauna pliocenica Toscana. Vol. 9: Gastropoda fine Scaphopoda.

[By] C. Chirli; [fotografia, Enrico Ulivi]. Firenze: C. Chirli, [1997]-HOLLIS# 007803888

QE801.C44 1997 v. 9


Marine Benthic Dinoflagellates: Unveiling their Worldwide Biodiversity.

By Mona Hoppenrath, Shauna A. Murray, Nicolas Chomérat, Takeo Horiguchi. Stuttgart: Schweizerbart’sche Verlagsbuchhandlung, [2014]. HOLLIS# 014218768

QK569.D56 H66 2014


The meaning of human existence.

By Edward O. Wilson. First edition. New York: Liveright Publishing Corporation, a division of W.W. Norton & Company, [2014]. HOLLIS# 014172978

BD450.W5225 2014


The monkey’s voyage: how improbable journeys shaped the history of life.

By Alan de Queiroz. New York: Basic Books, 2013. HOLLIS# 013986969



Moths of Glamorgan.

By David Gilmore, David Slade & Barry Stewart. Helston, Cornwall: Atropos Publishing, 2014. HOLLIS# 014203695

QL555.G7 G45 2014


The nature of classification: relationships and kinds in the natural sciences.

By John S. Wilkins, University of Melbourne, Australia; and Malte C. Ebach, University of New South Wales, Australia. Houndmills, Basingstoke, Hampshire; New York: Palgrave Macmillan, 2014. HOLLIS# 013904444



Nihon no kaigara = Shells of Japan.

Compiled by Iwanami Shoten Henshūbu. Tokyo: Iwanami Shoten, Shōwa 30 [1955]. HOLLIS# 014214495

QL430.4.N44 1955


Paradoxical platypus: hobnobbing with duckbills.

By David Fleay. [Burleigh Town, Qld.]: Friends of Fleays Association Inc., 2009. HOLLIS# 014174677

QL737.M72 F54 2009


The retina: an approachable part of the brain.

By John E. Dowling. Rev. ed. Cambridge, Mass.: Belknap Press of Harvard University Press, 2012. HOLLIS# 012800957

QP479.D65 2012


Shen qi de hai bei.

Cai Yingya; Xie Shaohe bian zhu. Shantou: Shantou da xue chu ban she, 2001. HOLLIS# 014214521

QL430.4.C24 2001


Shen qi de hai bei. (Vol. 1-5).

Cai Yingya ; Xie Shaohe bian zhu. Shantou: Shantou da xue chu ban she, 2001. HOLLIS# 014214525

QL430.4.C243 2001 v. 1-5


A systematic catalogue of the scale insect family Margarodidae (Hemiptera: Coccoidea) of the world.

By Yair Ben-Dov; in collaboration with Douglass R. Miller and Gary A.P. Gibson. Wimborne, UK: Intercept Limited, c2005. HOLLIS# 009795723

QL527.M37 B45 2005

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