Elsevier charge for re-use of author-paid Open Access article in teaching

The legacy publishers are not shy of promoting “their” latest articles under the #openaccess twitter tag. Here’s todays from Elsevier. You might think that when an author had paid APCs to publish an article as “Open Access” you’d be allowed to use it for teaching 50 students. But no. I asked for permission – as an academic – to re-use 3 pictures from this article for teaching. And I am to be charged 82 dollars for

Let’s review …

  • Bowen and colleagues do some research.
  • They draw the diagrams to support the research
  • They PAY Elsevier so the whole world can read this

And Elsevier still refuse to allow this to be used for teaching without additional payment.

So what happens?

Either the lecturers break the law and show the pictures to the students. Or they refuse to show the pictures, which is bad education and bad science and immoral.

And no-one except me and a few others get angry. Because after all it’s only taxpayers’ money we are spending anyway.


Does the Royal Society of Chemistry “deliver on its commitments” on Open Access?

Nearly a year ago I blogged that the Royal Society of Chemistry was charging ca 100 USD per student for re-use of a 2-page “Open Access” article (http://blogs.ch.cam.ac.uk/pmr/2012/11/06/royal-society-of-chemistry-will-charge-students-for-re-using-gold-open-access-articles ). The RSC has responded (very slowly) and in June replied to this blog: http://blogs.ch.cam.ac.uk/pmr/2012/11/06/royal-society-of-chemistry-will-charge-students-for-re-using-gold-open-access-articles/#comment-138142 :

An update, to show we deliver on our commitments:

We’ve fixed the Rights Permissions problem on OA articles. Now also clear licence information on the article, including CC-BY as an option.

e.g. http://doi.org/mt4

So I went back to the article:

Clicked on “Request permissions” and got:

So just the same 100 USD per student. This has been “fixed”? “Delivering on commitments”? Doesn’t look as if the RSC even tried it (it takes 2 minutes to check).

Now I don’t suspect that RSC are deliberately continuing to try to charge people for Open Access articles. But it raises the question of their competence – and probably many other publishers – in assuming that Open Access articles are managed properly. And any errors seem to be in the publishers’ favour.




NEW – Customized PLOS ONE Email Alerts by Subject Area

PLOS ONE publishes hundreds of articles each week, and keeping up with it all is a challenge. Now you can tailor Journal Alerts to suit your specific research interests, saving valuable time. These new custom weekly emails will deliver the research you are interested in straight to your inbox. Here’s how to set it up:

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Here, you can choose to receive a custom email alert with up to 12 subject areas.   Search for a specific subject, or navigate through the drop-down taxonomy categories to find subject areas you are interested in. You will also see an option to receive all new articles via e-mail.

We hope this helps customize alerts about new PLOS ONE research to your interests, and discover research in new fields as well.  We welcome your thoughts and suggestions on anything we can do to improve this experience further.

Physiological Reports Publishes issue 1.2

Physiological ReportsPhysiological Reports has now closed its latest issue. Below are the articles which have been highlighted by Editor-in-Chief Susan Wray from this issue:

purple_lock_open The distribution of the preferred directions of the ON–OFF direction selective ganglion cells in the rabbit retina requires refinement after eye opening
Ya-Chien Chan and Chuan-Chin Chiao
Summary: The present study shows that the preferred directions of selective ganglion cells (DSGCs) at around the time of eye opening are not distinctly segregated but rather are diffusely distributed along four canonical axes. We also demonstrate that the diffuse pattern of preferred direction distribution does not correlate with the directional tuning strength of DSGCs, indicating that the maturations of direction selectivity and preferred direction are independent processes. Our finding indicates that four subtypes of DSGCs undergo significant refinement after eye opening to reach their adult form.

purple_lock_open Decreased stability of erythroblastic islands in integrin ?3-deficient mice
Zhenghui Wang, Olga Vogel, Gisela Kuhn, Max Gassmann and Johannes Vogel
Summary: Erythropoiesis, a quite unique biological process, creates the only a-nucleated cell of our body, the red blood cell (RBC). It crucially requires a specialized microstructure called erythroblastic island (EI) for timing of erythroblast differentiation including extrusion of the nucleus and release of the young RBCs into the circulation. Here we provide new and unexpected data as to a role of integrin ?3 for timing the final detachment of young RBCs from EI. For example membranes of peripheral RBCs of integrin ?3 deficient mice contained calnexin, a chaperone that is normally completely lost during terminal differentiation of reticulocytes prior to their release into the circulation.

purple_lock_open Subcutaneous adipose tissue transplantation in diet-induced obese mice attenuates metabolic dysregulation while removal exacerbates it
Michelle T. Foster, Samir Softic, Jody Caldwell, Rohit Kohli, Annette D. deKloet and Randy J. Seeley
Summary: Leptin (A) and insulin (B) concentrations were significantly increased in all HFD groups, but those with heterotransplantations. Heterotransplantation restored insulin and leptin levels to chow control levels, whereas removal of subcutaneous adipose tissue induced increases greater than HFD control mice. Although hepatic insulin sensitivity was decreased by HFD, heterotransplantation in HFD mice restored hepatic insulin sensitivity to chow controls levels (C). Subcutaneous fat removal in HFD fed mice did not changes hepatic insulin sensitivity. Different letters indicate significance P ? 0.05.

purple_lock_open Portable acoustic myography – a realistic noninvasive method for assessment of muscle activity and coordination in human subjects in most home and sports settings
Adrian P. Harrison, Bente Danneskiold-Samsøe and Else M. Bartels
Summary: Muscle sound gives a local picture of muscles involved in a particular movement and is independent of electrical signals between nerves and muscle fibres. Our aim was to develop a setup for muscle-sound assessment, which could be reliably applied in any local setting. Sound recording was shown to be an easy non-invasive method for assessment of muscle function during movement with the possibility of being applied in most clinical, sports and home settings.

The first 100 articles accepted for publication in the journal are free of charge. There is still time to submit a paper to the journal and have the publication fee waived.
Submit your article here >

American Neurological Association and Wiley launch New Open Access Journal

LSJ-13-55252-WOAI-NW-ACTN-CoverWiley and the American Neurological Association (ANA) announced today a partnership to launch Annals of Clinical and Translational Neurology, a new online-only, open access journal. Annals of Clinical and Translational Neurology  will publish original research and scholarly reviews focused on the mechanisms and treatments of diseases of the nervous system, high-impact topics in neurologic education and other topics of interest to the clinical neuroscience community.

The journal is supported by Annals of Neurology, which is owned by the ANA, co-sponsored by the Child Neurology Society and published by Wiley. With a 2013 Impact Factor of 11.193, Annals of Neurology is among the most prestigious peer-reviewed clinical neurology journals worldwide. The high selectivity of Annals of Neurology will support the development of Annals of Clinical and Translational Neurology and provide global community of researchers and clinicians with a dynamic outlet for scientific and clinical content.

“We are extremely excited to offer a journal that taps into the extraordinary clinical and translational science that is being conducted in our neurology departments across the world,” said ANA President Eva L. Feldman, MD, PhD, the Russell N. DeJong Professor of Neurology at the University of Michigan. “By offering an open access journal, the ANA can provide another publishing platform for investigators committed to understanding and treating disorders of the nervous system. Ultimately that benefits both the fields of neuroscience and neurology and will lead to the development of new and much needed therapies.”

John “Jack” Kessler, MD, has been appointed Editor-in-Chief of Annals of Clinical and Translational Neurology. Dr. Kessler is the Ken and Ruth Davee Professor of Stem Cell Biology at Northwestern University.

“I am honored and excited to have been chosen to be the editor of this new journal,” Kessler said. “Open access publication of clinical and scientific advances is becoming more common for biomedical research. The creation of Annals of Clinical and Translational Neurology as a partner journal to the Annals of Neurology is a timely and exciting new venture that should greatly enhance the rapid dissemination of high quality research.”

“Wiley has published Annals of Neurology since 2001 and we greatly value our long-standing and highly successful partnership with the ANA,” said Shawn Morton, Journal Publishing Director for Medicine at Wiley. “We are highly optimistic that Annals of Clinical and Translational Neurology will provide a timely means to further extend and develop this much-valued relationship.”

The journal will publish articles under a Creative Commons License enabling authors to be fully compliant with open access requirements of funding organizations where they apply. All articles will be published open access on Wiley Online Library and deposited in PubMed Central immediately upon publication.

A publication fee will be payable by authors on acceptance of their articles. Authors affiliated with, or funded by, an organization that has a Wiley Open Access Account can publish without directly paying any publication charges.

Annals of Clinical and Translational Neurology is available at www.annalsctn.org.

#rfringe13 Consuming Linked Open Data Workshop

Today is the first (half) day of Repository Fringe in Edinburgh and we are having Workshops. Chris Gutteridge from Southampton is running one on Consuming Linked Open Data:

RDF & Linked Open Data are terms becoming more common in the repository community, but what are they and why should you care?

Open data is only useful if people are using it! This workshop will give a hyperbole-free introduction to using the technologies. Attendees will learn how to use PHP to consume RDF data and do useful things with it, including doing some stuff with bibliographic data.

This workshop will be run by Christopher Gutteridge, developer of the award winning University of Southampton Open Data Service and more recently founder of data.ac.uk, and Patrick McSweeney, notorious University of Southampton developer.

Requirements: ideally you will bring your own laptop with PHP installed (Apple & many Linux machines will have it installed by default), and a text editor. Don’t panic if you don’t have any PHP programming experience, you are welcome to buddy up with somebody who does.

Well, I like workshops and want to help make them successful so I signed up and the numbers have since trebled.

I must admit that I have no use or linking for PHP. It’s a broken language for Unicode – and I do a lot with Unicode. And it’s possible to write very bad code. But hey ho… So I went to find an installation for Windows and got into one of those chains…

“Cannot find MSCV01.dll”. Search on the web. “You must install Visual Studio C++”. What??? I thought I had seen the last of Visual Studio when Chem4Word finished. So try more search. “You need an Apache server”. You can’t install that without FTP, Fake Email Server, Tomcat, Perl and goodness knows what. So I have installed about 8 things I didn’t want to get something I didn’t want running…

But I am approaching the workshop in a very positive spirit and can now help other attendees install the same stuff…

Ok – what and why is Linked Open Data? It’s described by a mug:

The most important thing is that


The problem is that most academics don’t put their data on the web. Most academics just let their data decay. Governments are telling them that they must have data management plans. Academics ignore them. This isn’t true in bioscience or crystallography or astronomy. But:



Not quite true. Wikipedia is doing a great job of systematising data. But they can only do what people make available.



OK, let’s move to biodiversity. After all the future of our planet – in some part – depends on knowing about species and ecosystems. 10,000+ phylogenetic trees are published each year. How much of that data is on the web? Guess.

Wrong! It’s not zero. It’s 4%!

Linked Open Data is a great idea. I support it.

But you can’t link data when there isn’t any.

Well, like the first telephone, one site by itself is not much use. It’s not Linked Open Data, it’s LINKABLE. To be linkable the data provider has to:

  • Understand the data on the site and have a formal description of each bit (“semantics”). It’s no good labelling it “tree” if you don’t know whether it’s a tree preservation order or a phylogenetic tree. You need some formal of vocabulary. (Posh word is “ontology”).
  • Give each bit of data a unique identifier. The posh name is “URI”. If you make it unique on your site and combine it with the domain name that’s roughly what a URI is.
  • If the chunks of your data have relevance to other chunks of your data you can add links. Then the site is an example of internally linked open data.

But the real value of LINKED comes when others to link to it. And for that you have to:

  • Create data that other people want
  • Make it easy for them to find it and use it

And that’s very difficult. Because the academic system implicitly tells people not to do this. No reward points. So no-one does it.

Well I and my group did it. We made 200000 computational chemistry calculations available in DSpace. It was too difficult to use. It’s months of wasted work.

We’ve tried again, this time on our own server, with RDF!

No-one want to use it.

We’ve done the same for crystal structures. And now Ross and I are going to do the same for phylogenetic trees.

We are mad. We are hoping that the huge interest in Open Data (data.gov.uk, data.gov, etc) will lead people to start linking data sources. We are hoping that people want phylogenetic trees. We never learn.

The time is coming. At some stage scholars/universities will realise the value of domain repositories. Will they help support them? In the way they have poured money into Institutional Repositories? I doubt it. So the value has to come from funding bodies governments and – I think – foundations like Wikimedia who are years ahead of academia in their thinking.

Anyway today Chris is pointing us to bibliographic data. JISC supported us to create #openbib some years ago and we helped national libraries to Open their metadata and to create a protocol (BibJSON).

See you there at 1400

In the deep, bioluminescent bacteria bloom bright


Imagine swimming to the bottom of the sea, the water growing impossibly deep and dark the farther you travel. At these depths, beyond the reach of the sun, live strange new sources of light. Fish, jellyfish, and even bacteria light up these midnight waters.

According to new research in PLOS ONE, the light of this deep-sea bioluminescence waxes and wanes with seasonal changes on earth’s surface. In the Mediterranean winter, cold winds cause surface water to cool. As the surface cools, it becomes denser than the water beneath it, and begins to sink. Convection can also cause this layer to expand, potentially extending it to the Mediterranean Sea’s basin floor. When these phenomena occur side by side, as they can in the northwestern part of the Mediterranean Sea, carbon matter from the surface circulates into deeper waters. Think of it as Nature’s way of stirring the pot.

This wintry stir spreads a wave of changing temperatures, water composition and organic matter into the depths of the ocean, which correlates with a burst of bioluminescence activity. Over the course of two and a half years, the researchers recorded two water stirring incidents, followed by periods of bioluminescent activity. In each instance, winter stirring resulted in bioluminescent blooms lasting several weeks in the following spring or summer.

That being said, this phenomenon is likely to change in the coming years. According to the researchers, as climate change continues to affect the sea, convection activity which helps stir the waters and introduce much-needed carbon to the deep sea may decrease by the end of the 21st century. In the meantime, it is important to document deep-sea activity to better understand any actual or forecasted changes.


Citation: Tamburini C, Canals M, Durrieu de Madron X, Houpert L, Lefèvre D, et al. (2013) Deep-Sea Bioluminescence Blooms after Dense Water Formation at the Ocean Surface. PLoS ONE 8(7): e67523. doi:10.1371/journal.pone.0067523

Image: Biolumplate, from Wikimedia Commons.

Evolutionary Applications Publishes issue 6.5

Evolutionary ApplicationsEvolutionary Applications has published a new issue exploring the ways in which evolutionary biology addresses biological questions of health, social and economic relevance.  The issue features an image of a young wood frog on its cover.  Editor-in-Chief: Louis Bernatchez has highlighted the articles below as particularly noteworthy:

purple_lock_open Molecular genetics and genomics generate new insights into invertebrate pest invasions by Heather Kirk, Silvia Dorn and Dominique Mazzi
Summary: This article reviews current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and highlights shortcomings from the current body of research. It also discusses recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis and highlights how these advances will enhance our understanding of these areas.

purple_lock_open Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii) by Jonathan Q. Richmond, Kelly R. Barr, Adam R. Backlin, Amy G. Vandergast and Robert N. Fisher
Summary: This study reviews the extensive decline in populations of the California red-legged frog (Rana draytonii) since the 1960s due to contemporary disturbance. The authors conclude that while the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.

purple_lock_open Genetic and life-history changes associated with fisheries-induced population collapse by Lilian Pukk, Anna Kuparinen, Leili Järv, Riho Gross and Anti Vasemägi
Summary: This article investigates the evolutinary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. This study demonstrates the value of combining genetic and phenotypic analyses in the context of long-term genetic monitoring and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.

In 2013 we have expanded the scope of Evolutionary Applications. As before, we are keen to encourage papers applying concepts from evolutionary biology to address biological questions of health, social and economic relevance across a vast array of applied disciplines. We now also strongly encourage submissions of papers making use of modern molecular and genetic methods to address important questions in an applied evolutionary framework. For more information please visit the aims and scopes page.

Submit your article to Evolutionary Applications here >

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World at Sea

How multitudes of people
can gather to gawk daily
at these magnificent, miserable creatures
being forced through round after round
of revolting Skinnerian circus tricks,
having been brutally wrenched
from their devastated families
to be pitilessly imprisoned
for the rest of their wretched, reduced lives
in holding containers,
tormented day and night
by echoes from their own hopeless sonar cries
while food-deprived and “trained”
to do whatever it takes
to draw delighted cheers
from grinning crowds of humans of all ages…

Did it really require this revealing new movie, Blackfish, to open our eyes to the ugly, shameful fact that this, and all things like this, are wrong, horribly, unforgiveably wrong?

That we provide the mindless market for such heartless abuse, in order to make our children laugh, is as much a condemnation of the sociopathic spectatorship as of the merciless, mercenary management of sadistic sea circuses — and all their land counterparts.

Perhaps the most chilling anomaly is how the “trainers” — of whom some, clearly, “turned,” eventually, after years of having been willing accomplices to the abuse of these helpless animals — were themselves “trained” (by the management along with self-deception) to overlook the obvious in exchange for the fees and the celebrity (“just following orders”? “being professional”?). It seems to have been various blends of venality and sensation-seeking, though some got into it and then got attached to their prisoners and stayed so as to use what little leverage they had to make their fate less worse, rather than abandon them altogether. — Or maybe that was just what they said for the camera? (I hope not.)

But most macabre of all was that some professed to have become Seaworld trainers to fulfill a dream that Seaworld itself had instilled in them as a child.

Tilikum’s punishment for having been kidnapped and abused for decades:

Solitary confinement
to provide sperm
for breeding more orcas
to be wrenched from their mothers
and put into entertainment servitude
for the rest of their miserable lives
to inspire more children
about the wonders of the sea

“Holes in the Tree of Life”: Why and how phylogenetic data must be published

Ross Mounce @rmounce and Joseph W Brown have been tweeting about the lack of data to support published phylogenetic studies. (Readers of this blog will know that Ross and I start work in October to extract trees from published PDFs – an awful statement of how bad the situation is.)

Very simply, phylogenetic data is key to our understanding of the history, ecology and biodiversity of the planet. If we don’t understand species then we shall lose them, and if we don’t understand how species interact we shall lose ecosystems. Look into the details of pollination and often the loss of one species affects others directly. (Though Darwin was wrong about cats->->-> clover http://triscience.com/Species/Field/the-cats-to-clover-chain/doculite_view ).

Most peer-reviewed phylogenetics is in closed journals (40 USD for a 1 day read). It’s appallingly arrogant to assume that anyone who needs it (academics) can get the info. But worse, almost none of the data are published. Phylogenetic trees are mainly computed using molecular information (DNA of key genes) and are costly. Yet the data are relatively simple. They are well understood (30+ years of sequence / gene repositories) and they are compact (accession numbers are often fine). An uncompressed tree costs perhaps a few Kb and with indexing/compression a complete study could be published in ca 1 Mb. That’s less than the size of many single images!

Here’s what sparked the discussion. http://www.botanyconference.org/engine/search/index.php?func=detail&aid=167 I’ll give it in full, and argue that any reasonably literate person could understand it. I have highlighted some parts

Missing data lead to holes in the tree of life.

The fundamental importance of archiving scientific datasets has received increasing attention over the past several years, and failure to properly archive data can adversely affect study reproducibility. However, in plant systematics (or evolutionary biology) there has been no comprehensive review that examines the deposition practices of the underlying phylogenetic datasets and trees that are the foundation of the discipline. Furthermore, there is little understanding of how the deposition rate of DNA sequence alignments and phylogenetic trees has changed over time. In the process of gathering data to build the first tree of life for all ~1.9 million named species (the Open Tree of Life Project), we sifted through over 7200 peer-reviewed phylogenetic studies published between the years 2000 and 2012. Our survey covered over 100 journals and included publications focusing on green plants, animals, fungi, microbial eukaryotes, bacteria, and archaea. This broad survey included 1243 seed plant publications. Overall, we found that only 17% of examined studies made nucleotide alignment data and/or trees available in an accessible repository such as TreeBASE or Dryad. Within seed plants, only 24% of studies from the past 12 years have been archived. Furthermore, most corresponding authors (54% for seed plants) that we contacted for un-deposited datasets and trees did not respond to our repeated (2) requests for data. Thus, most of the trees and alignments produced during the past several decades is essentially lost forever. The plant systematics community needs to significantly improve data deposition practices to ensure that crucial data (trees, alignments) are archived and thus freely available to other interested scientists. Our results illustrate that voluntary data submission policies have not worked, and dictate the urgent need to adopt new policies requiring public archiving of DNA sequence alignments and trees in a routine manner as is done routinely with raw sequence data. These stark findings should encourage the systematic community as well as journal editorials to adopt data sharing policies that require deposition of alignments and resulting phylogenetic trees in established databases prior to publication.

Very simply (this applies to many subjects):

Many/most authors don’t care about making their science available to the world. The final result of their work is a “scholarly article”, not useful, reusable, verifiable science that can be built on, re-used by policy makers and citizens. The authors do not feel that being publicly funded gives them any obligations to the public. The ivory tower only rewards their work in the torrid market of scholarship, not the wider value to the world.

It has worked in some subjects – sequences/genes, crystal structures, galaxies. Here the disciplines have developed cultures where scientists are expected and then mandated to deposit data. The commonest ways are (a) on publishers’s websites (e.g. crystallography) and (b) in domain repositories (e.g. sequences).

Making phylogenetic data available for each study is technically straightforward. The bytecount is insignificant in today’s world. The standards and protocols (e.g. nexml) exist. The problem is 99% a people problem.

The problem is community. In some cases the learned societies are more concerned to generate income than to service science (Where are the publishers that actually make subscription material available to the world within – say – 6 months of publication?) Many are actually making it more difficult. The last 12 months have confirmed that most legacy publishers are part of the problem, not the solution.

So how, if publishers are antagonistic or indifferent to requiring publication data do we manage it? The Universities are totally vapid today – they have shown no leadership. So the only clear path is funders mandates.

And that will work. I’ve seen the pressure in the US that the NSF mandate on data management has applied and I think it’s starting to work. That’s got to happen everywhere. So my message to funders is:

Mandate the deposition of data at time of publication. And if not, chop 10% off the grant.

That works. It’s a lot of work, but it’s a trivial amount compared with the current loss of data (which I estimate as >> 100 Billion USD per year).




#rfringe13 Repositories for scientific data with #animalgarden

We are going to the Repository Fringe this week and are going to present a PechaKucha. What’s that? It’s 20 slides of 20 seconds each that change automatically. So 400 seconds in all. And the first one has to introduce you and that last says thanks. You can see some past ones at http://www.youtube.com/playlist?list=PL692EDA7EE606D73C.PMR has a slot called “Capturing and Publishing Scientific Data”. He’s asked us [#animalgarden] to create the slides


We’re #animalgarden – we make photocomics about openness. Here’s one we made about #openbibliography. http://blogs.ch.cam.ac.uk/pmr/2012/09/14/animalgarden-at-digital-research-2012-openbiblio-and-bibsoup-and-okfest/. It won second prize. (We don’t do it for the prizes, we do it because we like making photocomics).

PMR doesn’t think Institutional repositories work for scientific data (or publications). He thinks we need domain repositories (e.g. proteins, galaxies, phylogenetic trees, molecules, crystal structures, materials, etc. So we’re going to present the issues as a photocomic.

We all take different roles

Here’s Chuff (the OKFN Okapi) advocating open data, clean penguin being a hacker, and OWL (geddit?) representing the Semantic Web. We’re thinking about props and roles (PMR hasn’t worked out the story yet).

Back to work … See you at #rfringe13

MicrobiologyOpen Publishes its 100th Article!

MicrobiologyOpenMicrobiologyOpen has now published its 100th article! The journal published its first papers in January 2012 and since that time has accepted excellent papers across the broad scope of the journal, covering all aspects of Microbial Science. We are delighted by the success of this new open access journal. It was accepted for indexing in MEDLINE within its first year of publication.

The 100th article published in the journal is:

purple_lock_open TusA(YhhP) and IscS are required for molybdenum-cofactor-dependent base-analog detoxification
by Stanislav G. Kozmin, Elena I. Stepchenkova and Roel M. Schaaper
Summary: We show that Escherichia coli mutants deficient in the sulfurtransferase TusA or the cysteine desulfurase IscS are hypersensitive to the toxic effects of the adenine analog 6-N-hydroxylaminopurine (HAP). This sensitivity is similar to and epistatic with the HAP sensitivity of moa mutants, which defective in biosynthesis of the molybdenum cofactor (Moco). Our results suggest that TusA and IscS are critical for the insertion of the dithiolene sulfurs in Moco that coordinate the molybdenum atom.

Visit the journal homepage to see our new landing page celebrating the MicrobiologyOpen 100! This highlights the top downloaded and top cited articles from within the first 100 papers, and also shows the geographical spread of our author base and the subject areas covered by the journal.

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#pantonfellow update; making videos is fun

We are currently processing the applications for our Panton Fellowships (sponsored by CCIA – http://en.wikipedia.org/wiki/Computer_%26_Communications_Industry_Association to whom many thanks). On Thursday Michelle Brook and I worked on this in C4CC – the OKFN’s London hangout:

Firstly many thanks to everyone who applied (and those who spread the word). Obviously we won’t give any personal details at this stage. This year we expanded the eligibility to “Europe” and we’ve had applications from north east south west which is very gratifying.

It’s a pleasure and privilege to read the applications (and I’ve read them thoroughly). People are doing exciting things and having exciting ideas. We appreciate the time you’ve put in.

The Panton Advisory Board (which does the analysis and selection) includes Tim Hubbard, Cameron Neylon, Rufus Pollock, John Wilbanks and myself and is serviced by Michelle. The remit of the Fellowships is broad – it should be based on the ideas of Panton (Open Science Data) and should further those aims, but we looking for applicants to come up with new ideas – and we aren’t afraid of risk. It’s important that the Fellows engage with a community and aim to make an impact but we don’t constrain how. Although it’s absolutely not required it’s gratifying to see applicants who have already come up with ideas and tried them.

It’s very difficult to judge people from a CV and a paper proposal so after an initial selection we ask a short list of applicants to prepare a short video or similar as a complementary way of showing themselves and their ideas. This isn’t judged on technical quality but how the person and idea come over (i.e. you don’t have to hire a specialist! – phones and PCs have reasonable cameras. ) If you can’t read the detail, then it shouldn’t be there!

And I wouldn’t ask anyone to do something I wouldn’t. Two years ago I applied for a Shuttleworth Foundation fellowship which required a 4.5 minute video. The timing caught me in the wilds of Washington State (PNNL) without a video camera. I re-used some existing footage and got enormous help from Jenny Molloy. She used the services in Oxford Computing Services – each night she would edit the latest version and send it to me (9 hours out of phase). So there was only one turnround a day – I would make some written comments and we might have a short Skype. I think it actually turned out quite well.

When I got back I found I had been selected for the next stage and had to make a different video. I couldn’t impose on Jenny, so I found out how to do it on a PC. And it was nowhere near as difficult as I thought. I used “Windows Live Movie Maker” as an editor (which came bundled with the machine). I’m not promoting this product but it worked for me in a rush. I could shoot and edit and release as WMV files (these cannot be read everywhere and I have since moved to using the FLOSS Handbrake for converting to better more compact more universal formats such as MP4).

I didn’t get a Fellowship, but the experience was really valuable. It sharpened by ideas and my technology hugely. Most competitive grant applications are unsuccessful – this is due to competition and not necessarily because they are flawed. So if you are a current Panton applicant and aren’t selected don’t regard your application as necessarily bad. And perhaps look for somewhere different to apply to with a (possibly modified) proposal.

With tools such as Doodle, Googledocs and Skype it’s easy to get synchronous and asynchronous communication over a few days. At least 2 and possibly more Board members are out of the country so we have to aim for restricted hours for Skype – but we’ve done this before and it’s universal in OKFN activities.

Thanks again to all applicants.


Our fair deal for a fair digital future

Our Fair Deal http://ourfairdeal.org/ is crowdsourcing ideas for what we the people want to see in trade agreements like the Trans Pacific Partnership (TPP) currently being negotiated. Go to the Our Fair Deal to learn more or to participate, or to this OpenMedia site which has a convenient form to fill out.

Here is my vision for A Fair Deal:

Trade treaty negotiations involve broad-based, open consultation with the public and all groups with an interest in participating. We should be hearing about what is happening from our elected representatives, not through leaks! This is completely in the spirit of what governments say that they want to do – it would fulfill the commitments made by many of our governments through the Open Government Partnership.

Copyright should be fair, balanced, and reflect not only the desires of “copyright holders”, but also the important and not entirely understood role that copying has always played in the development of human civilization. Human language, manners, and basic life skills are learned by copying. Storytelling, music, and arts aren’t just about a few people making a living; they are about all of us building communities, expressing and fulfilling our potential. Artists have always copied from each other – the latest techniques, approaches, philosophies. New movements in art and music involve a lot of copying, and this is not inconsistent with artists making a living. Balance is also needed to provide an environment that can facilitate ongoing creativity and innovation, as excessively strong intellectual property rules favour a few owners of “intellectual property”. This is a system that appears likely to lead to concentration of ownership in the hands of a few, as has been the trend with scholarly publishing in the last few decades.

In order to achieve a more fair and balanced copyright, here is what I see as needing to happen: 

  •  there already is an international body dedicated to intellectual property, the World Intellectual Property Organization (WIPO) – discussions of intellectual property and copyright should be limited to this forum and removed from other international negotiations. If governments are negotiating with countries that are not signatory to WIPO, then signing WIPO could be part of the negotiations 
  • formally recognize at something like an international constitution that culture, community, and the public interest are important goals, not just economic benefits of intellectual property. For example, strong intellectual property laws designed to protect the profits of pharmaceutical companies at the expense of the health of those who cannot afford the medicines, are not good public policy. This does not mean that the interests of the industry are irrelevant, rather that we need to recognize that this not the only thing that is relevant – ultimately, the purpose of a pharmaceutical industry should be the health of the public, with economic sustainability of the industry a key but secondary sub-goal.
  • make open access – free online access to everywhere, everywhere with an internet connection with few or no copyright restrictions – the default for all information and resources paid for by the public (government data and publications, government-funded scholarly research)
  • eliminate automatic copyright; require a creator to take at least some simple step (e.g. the inverse of creative commons) in order to assert copyright 
  • limit the term of copyright to 10 years with one extension on request 
  • expand fair dealing – support strong net neutrality 
  • support strong personal privacy protection measures everywhere 
  • added July 27: the penalties for copyright infractions should be proportionate to the infraction, and to other types of societal penalties. Downloading movies for personal viewing should at most be at about the level of hopping on a bus without paying.

That’s my vision. What’s yours? Please participate!

Thank you very much to the organizers of Our Fair Deal for providing a venue for this crowdsourcing.

Putting the brakes on blood clots

blood clots Helena de PuigWhether you get a paper cut or have a bad accident, our bodies respond  with a near-universal command: when bleeding, clot. Within seconds of skin being broken, a cascade of cells and proteins align at precise positions to hold the breach. They form a fine mesh to stop blood flow, identify offensive invaders (splinter or microbe?) and recruit cells to clean up the mess. The operation is swift, precise, and for minor injuries, leaves no trace.

For major wounds and during surgeries though, doctors must use anti-coagulant drugs to stop the clotting process and ensure a free flow of blood. However, once an anti-coagulant is used, the only way to reinitiate the process of clotting is to wait for the drug to run out.

Now, a laser-controlled gold switch could change that wait, as researchers have developed a way to switch blood clotting on and off with the flick of a nanoparticle switch. The switch relies on the ability of paired particles to release two different DNA molecules from their surface depending on the wavelength of laser light used to turn the switch on. When released, one piece of DNA binds to thrombin, a key protein in the clotting cascade, and blocks its activity, preventing coagulation. When the complementary DNA piece is released from the nanoparticle, it acts as an antidote, releasing thrombin to restore clotting.

Prior to this advance, there was no way to restore clotting after an anticoagulant was administered. As Kimberly Hamad-Schifferli, senior author on the study, explained in an MIT news release, “It’s like you have a light bulb, and you can turn it on with the switch just fine, but you can’t turn it off. You have to wait for it to burn out.”

The new method developed in this study could provide doctors and researchers with a more precise way to control where and when blood coagulates during surgery and healing. In the MIT news release, Luke Lee, a professor of bioengineering at the University of California at Berkeley (not an author on the study), elaborates, “It’s really a fascinating idea that you can control blood clotting not just one way but by having two different optical antennae to create two-way control. It’s an innovative and creative way to interface with biological systems.”

Citation: de Puig H, Cifuentes Rius A, Flemister D, Baxamusa SH, Hamad-Schifferli K (2013) Selective Light-Triggered Release of DNA from Gold Nanorods Switches Blood Clotting On and Off. PLoS ONE 8(7): e68511. doi:10.1371/journal.pone.0068511

Image: Red blood cells with gold nanorods (yellow dots) on their surfaces. The blue represents a fixing polymer. credit: Helena de Puig