The Need to Upgrade All OA Mandates to Add Immediate-Institutional-Deposit Requirement

Rick Anderson [RA] wrote:

“[A] policy that actually makes deposit mandatory is a mandate? But it appears that many of the institutional policies listed on the ROARMAP site… as “mandates”? actually require no deposit at all. A few examples would be those of MIT (“The Provost or Provost’s designate will waive application of the policy for a particular article upon written notification by the author”), the University of Oregon library (“The Dean of the Libraries will waive application of the policy for a particular article upon written notification by the author”), and the University of Glasgow (“Staff are asked to deposit a copy of peer-reviewed, published journal articles and conference proceedings into Enlighten, where copyright allows, as soon as possible after publication.”)? [T]hey are policies that require no deposit? [W]hy the insistence on calling such policies “mandates”? If they make no action mandatory, then why not simply call them policies? 

I agree that some of the “mandates” in ROARMAP are not really mandatory, although Merriam-Webster does give two senses of “mandate”:

1  : an authoritative command…
2 :  an authorization to act…

Academics do need both: an official requirement (similar to publish or perish) (1) and official backing from their institutions and funders (2), to empower them to deal with their publishers.

But many of the first wave of mandates are indeed weak, and some are not even mandates at all. 

They are, however, increasingly being upgraded to ID/OA (immediate-deposit/optional-access):

In the UK, HEFCE/REF’s new policy will effectively make all funded research in the UK ID/OA, and the institutions will have to be the ones to ensure that researchers comply. 

The EC’s new Horizon2020 is likewise an immediate-deposit mandate. 

Many (including me) are working hard to try to ensure that the US OSTP mandate and the Canadian Tri-Agency mandate will be ID/OA too. 

Both Minho and QUT have recently upgraded their institutional mandates to ID/OA. And several institutional mandate adoptions have lately been ID/OA.

The hope had originally been that the Harvard/MIT-style OA mandates, because they were (i) self-imposed faculty consensus policies, would be even more effective than administrative mandates, and that because they (ii) formally pre-assigned certain rights by default to their institutions in advance of submission for publication, they would strengthen authors’ negotiating position with publishers. 

Each Faculty member grants to (university name) permission to make available his or her scholarly articles and to exercise the copyright in those articles? Each Faculty member will provide an electronic copy of the author?s final version of each article no later than the date of its publication [e.g., by depositing it in the institutional repository]?

But in practice the Harvard/MIT-model OA mandates (often just called OA “policies”) seem to have turned out to be less effective than had been hoped: 

First, the Harvard model had (a) had to allow author waivers, which in and of itself rendered the policy non-mandatory; but this in itself is not the problem, because only about 5% of authors formally request a waiver. 

The problem is that (b) most authors neither waive nor deposit

The exact proportion of compliance is not known, because the policy is not binding on all faculty (because at Harvard not all Faculties have adopted it, and because at MIT a lot of collaborative project research is not bound by it) and (c) universities in general currently have no way of knowing what their total published research output is. (Enabling institutions to keep track of their  own research output was in fact one of the secondary purposes of OA mandates and institutional repositories.)

So, as with other OA policies, implementation at Harvard and MIT has been reduced to librarians trying to chase after authors to provide their papers, or trying to retrieve their authors’ published papers from the web (where they have sometimes been made OA on institution-external sites). I believe librarians even try to retrieve their institutional authors’  papers from publishers’ websites, when the library has licensed access — but then they languish while the library or repository staff try to figure out whether or when they have the right to deposit them. (This, despite the fact that there are only 5% waivers of the default rights-retention clause!)

It is quite problematic that because of its distinguished source the Harvard OA policy model is being widely emulated in the US even though it is now 5 years since it was first adopted in 2008 and yet there are no data available on how well it works compared to other mandate models (or no mandate at all).

In principle, if Harvard takes it seriously that 95% of Harvard faculty have not waived a default rights-assignment policy, then they can make 95% of Harvard papers OA in Harvard’s institutional repository immediately. The question is: which version? If authors have not provided their final refereed drafts, it is unclear what can be done with the publisher’s PDF.

The Glasgow policy — I agree it’s not really a mandate, and I have just downgraded it to a non-mandate in ROARMAP — is the weakest kind of OA policy of all: “Deposit if and when your publisher says you can!”

This is why it’s so important that institutional and funder mandates should be (I) upgraded to all require immediate deposit and (II) harmonized to all require institutional deposit, with (III) deposit designated as the sole official mechanism for submitting refereed journal articles for individual performance review, institutional research assessment, research funding applications and fulfillment, and official academic CVs. 

(If institutional rights assignment is waived, the publisher has an OA embargo, and the author wishes to comply with the embargo, access to the deposit can be set as Closed Access instead of OA, and the repository’s automated request-a-copy Button can provide “Almost-OA” during the embargo with one click each from each requestor and the author. But the deposit must be immediate in any case.)

The UK’s HEFCE REF2020 and the EU’s EC Horizon2020 mandates should soon both be harmonizing institutional mandates in this direction. Let’s hope the US, Canada, Latin America, Australia and the rest of the research world will soon follow suit. OA is already fully within reach and absurdly overdue. Let’s this time have the good sense to grasp it.

Stevan Harnad

Responses to Canada’s Tri-Agency Draft Open Access Policy

From the Canadian Association of Research Libraries
Noteworthy: 8 university libraries across will welcome articles from researchers at other universities to facilitate adoption of this policy!

ACOA / APLAC Response (submitted December 12)
Noteworthy: ACOA / APLAC’s final recommendation is to eliminate the open access publishing option as part of the policy. Researchers should deposit in a Canadian-based open access archive whether they publish with an open access or toll access journal.

My response (submitted October 16):

IFLA supports copyright exceptions for Text and Data Mining

Yesterday International Federation of Library Associations and Institutions (IFLA) issued a welcome statement on TDM: Snippets:

IFLA maintains that legal certainty for text and data mining (TDM) can only be achieved by (statutory) exceptions. As an organization committed to the principle of freedom of access to information, and the belief that information should be utilised without restriction in ways vital to the educational and cultural well-being of communities, IFLA believes TDM to be an essential tool to the advancement of learning, and new forms of creation.

We live in an era of “Big Data”. OECD figures show that more digital information was created between 2008 – 2011 than in all previous recorded history (World Economic Forum (2012) ‘Global Information Technology Report: living in a hyper-connected world’ p.59, No human can read such vast volumes of information, which is why “computer based reading”, using tools such as text and data mining, is so important.

Research organisations see TDM as an engine to improve the performance of science by speeding up new potential discoveries based upon existing literature without the need for further laboratory based research.  TDM is a tool also increasingly being used by researchers and creators in the arts and humanities fields, to offer new interpretations of history, literature and art. Libraries are also increasingly undertaking TDM themselves, to improve information services and offer new insights into their collections. Government data sets are also increasingly being made available to researchers, archives and libraries undertaking TDM, as they offer much potential economic value in an era of Big Data. Commercial innovators are also utilising TDM.

The technical act of copying involved in the process of TDM falls by accident, not intention, within the complexity of copyright laws – in fact analysis of facts and data has been the basis of learning for millennia. As TDM simply employs computers to “read” material and extract facts one already has the right as a human to read and extract facts from, it is difficult to see how the technical copying by a computer can be used to justify copyright and database laws regulating this activity.

“That these new uses happen to fall within the scope of copyright regulation is essentially a side effect of how copyright has been defined, rather than being directly relevant to what copyright is supposed to protect.” (Hargreaves Review of Intellectual Property and Growth (2011), UK Intellectual Property Office,  

TDM is one of several new tools in the digital environment to which copyright norms devised 300 years ago do not readily apply.


Researchers must be able to share the results of text and data mining, as long as these results are not substitutable for the original copyright work – irrespective of copyright law, database law or contractual terms to the contrary. Without this right, legal uncertainty may prevent important research and data driven innovation putting researchers, institutions and innovators at risk.

IFLA does not support licensing as an appropriate solution for TDM. If a researcher or research institution, or another user accessing information through their library, has lawfully acquired digital content, including databases, the right to read this content should encompass the right to mine. Further, the sheer volume and diversity of information that can be utilised for text and data mining, which extends far beyond already licensed research data bases, and which are not viewed in silos, makes a licence-driven solution close to impossible.

The Mechanics Behind the Magic

I like Scott Pluchak’s posting. We share a vision…

If you’re interested in some of the objective evidence on the adoption rate (still too slow) and the effectiveness (quite remarkable, though depending on mandate-type) of OA self-archiving mandates, have a look at ROARMAP and the references below.

(You might also have heard of the US OSTP, EU Horizon2020 and UK HEFCE/REF2020 mandates, soon to come.)

Scott is certainly right that my thinking has been magical:

1. In 1994: I thought it would be enough to just just say “self-archive” and next day all researchers on the planet would do it. (Next day came, and nothing happened.)

2. It was magical thinking also to create CogPrints in 1997, in case researchers in my field weren’t self-archiving because they didn’t have a central place to self-archive (no success).

3. Magical thought too, that creating EPrints in 2000 (from which DSpace too emerged) — so that all institutions could create their own OA repositories — would do the trick (no dice).

4. A series of studies inspired by Lawrence 2001 — demonstrating that OA increases citations — made no significant difference either.

5. But then in 2003, things began to pick up, with the adoption of the very first Green OA mandate (Southampton ECS), followed by several more (notably QUT in Australia and U Minho in Portugal). ROARMAP launched, but adoptions were still just a trickle: decidedly unmagical.

6. Then in 2004 the UK Select Committee recommended that all UK institutions and funders mandate Green OA. And the trickle became a trend — but still a very sluggish one. And most of the mandates were weak, ineffective ones. It would have taken magic to make them work.

7. So in 2006, Peter Suber and I independently proposed the immediate-deposit/optional-access mandate (ID/OA) (Peter called it the “dual-deposit-release” mandate), Southampton designed the automated request-a-copy Button for EPrints and Eloy Rodrigues designed its counterpart for DSpace. (Perhaps it was still magical thinking to imagine they would work — or would even be adopted.)

8. But then in 2007, Bernard Rentier, rector of the University of Liège, became the first to adopt the ID/OA mandate and the Button.

9. We then waited a few years to see whether it would work.

10. And by 2010 it became evident that ID/OA + Button was working, and generating over 80% OA compared to about 30% for the weaker mandates and even less without mandates. And no magic was needed.

Meanwhile, Gold OA had been making some headway too, but even more slowly than Green, because it required authors to switch journals and because it cost them extra money; and in 2013 the economist John Houghton (in collaboration with publishing consultant Alma Swan) described exactly why Green needed to come first.

Is it magical to think the adoption of ID/OA + Button will become universal in the next few years? Perhaps. But let’s be empirical, and wait for the evidence.

Meanwhile, I — and many others — will keep “tirelessly trotting out the facts” rather than just waiting passively? And does 110 really sound all that hedgehoggy to you? Seems more foxy to me (and a fox who is more of a pragmatist than just a preacher, polemicist or prestidigitator). — But then I love both of those little creatures (the foxes and the hedgehogs), and would never either wear their hides or eat their flesh, any more than I would those of any other feeling creature (including pragmatists, preachers, polemicists and prestidigitators). And that’s a lot bigger and more important thing than OA…

Gargouri, Y., Larivière, V., & Harnad, S. (2013) Ten-year Analysis of University of Minho Green OA Self-Archiving Mandate (in E Rodrigues, Ed. title to come)

Gargouri, Y, Lariviere, V, Gingras, Y, Brody, T, Carr, L and Harnad, S (2012b) Testing the Finch Hypothesis on Green OA Mandate Ineffectiveness. In Open Access Week 2012

Hitchcock, S. (2013) The effect of open access and downloads (‘hits’) on citation impact: a bibliography of studies.

Houghton, J. & Swan, A. (2013) Planting the Green Seeds for a Golden Harvest: Comments and Clarifications on “Going for Gold”. D-Lib Magazine 19 (1/2).

Rentier, B., & Thirion, P. (2011). The Liège ORBi model: Mandatory policy without rights retention but linked to assessment processes.

Sale, A., Couture, M., Rodrigues, E., Carr, L. & Harnad, S. (2012) Open Access Mandates and the “Fair Dealing” Button. In: Dynamic Fair Dealing: Creating Canadian Culture Online (Rosemary J. Coombe & Darren Wershler, Eds.)

Content Mining: Recent progress

A lot has happened in the last month and it’s kept me so busy that I haven’t blogged as much as I would have liked.

The simple message is that we are starting to mine the scholarly literature on global scale, starting with the easiest (sociopolitical) areas . We’ve started to build the community, build the tools and deploy the results. I am not frightened by scale, as there are in-place solutions.

The most important thing is community. If there’s a perceived need then CM will happen and fast. And on Tuesday we made massive community progress.

We met PLoS in the Haymakers pub (Cambridge) and talked about how they could help us crawl a daily PLoS. Then PLoS held an OpenDrinks in KingsCross London. Everyone was excited about the way scholarly communication could – and in some cases will – open up. BioMedCentral (AmyeK), CrossRef (GeoffB) and lots of OKFers. I came away with the strong feeling that we agree on the Why, Whether of CM and have now moved to How?

We’re doing a “soft launch” of the Content Mine. Something new every day. Advocacy and news from all sectors of the community. Debugging as we go. So we’ve started, not with a bang, but a snowflake. The avalanche will come.

One of the most important things is that we have set up an OKFN mailing list for CM. . Mailing lists are one of the best ways of collecting ideas, resources, community. If you have questions, offers of help, insights – please post. It’s a friendly community.

Some community milestones


2013-11-14 I was invited to present at UK Serials Group (core of librarians, publishers, university admin) and that gave me the chance to put slides together It was well received and the delegates were interested in CM. UKSG recorded a video “Scientific Data costs billions but most is thrown away – what should be done?”. It’s at (ca 25 mins). Many thanks.

2013-11-27 Open-science Oxford. . Wonderful event run by Jenny Molloy. It meant I had to get a portable demo ready (more below)



2013-11-25 CKAN/the Datahub. I decided we should use CKAN (OKFN) for the extracted content. CKAN is an open system for managing metadata and URL-based data storage. I think it will do very well for us. It’s got a vibrant developer and user community. Mark Wainwright gave us an excellent intro . We’ve learned how to use it – having people online really helps – and we are doing our bit by contributing back a revised CKANClient-J. You are welcome to browse, e.g. but please realise that this is Open Science – we are building it as we go. For example “In vivo” isn’t a species – it’s a false positive and we are refining the filters daily.

We’ve been joined by Mark Williamson and Andy Howlett in the Unilever Centre. They are doing a great job in helping refactor the existing code and framework. Andy’s working on a plugin mechanism so that if YOU want to – say – search for galaxies we can make it easy to insert an Astro plugin. Mark has done a huge job on making the system robust and distributable – the commandline-interface and deployment we used in Oxford. We are aiming at a system which is very easy to deploy so that when we run workshops it will be easy for all participants.

The latest tools are all on Bitbucket:

    Visitor (plugin) architecture for adding discipline-specific analyses.
  • A crawler architecture. (currently PLoSOne and soon BMC). I hope to make this very general so it’s easy-er to create crawlers. Crawlers are never fun. They reflect the horrible effects of creating information for sighted humans only. But they are an excellent place for crowd contributions – one crawler per publishers/journal. And a CKAN Datahub repo client.
  • . Computer vision for scientific diagrams. All the basic technology exists, with Java solutions for almost all. I’ve been pleasantly surprised how well it performs. It’s experimental. I did a lot on Hough, but it looks like Thinning and Segmentation is actually better. OCR is a problem – Tesseract is C++ and very messy, JavaOCR ought to be the answer but is impenetrable, Lookup (Cross-correlation) is not quite what I want. I think I’m going to have to write a scientific OCR. Anyone interested in joining is very welcome. It won’t be as hairy as it sounds – I have some ideas.



I am a strong believer in – create a standard simple way of doing things so the number of options you HAVE to specify is small. So, for example, if no –output is given the system puts them in a known place. That also helps community – you can Skype: ” can you find plos/2013-12-13/daily.log in your /extracted folder?”

And documentation

We like the Bitbucket Wiki and its markdown. It’s relatively easy to record what we have done and what we want people to do.

So – watch out for content appearing flake by flake.


And join in…


Content-mining: how can I help?

I got a request today offering help for CM. Great! CM isn’t a single activity –ideally it’s a community of collaborating people and organizations combining resources. The first thing you can do is join, and post to, Here’s what I replied:

I’m delighted to have had an enquiry of help for content-mining. The good news is:

*Everyone has a role to play in content-mining*

Here are some important areas – please submit others. There are lots of micro-tasks that everyone can become involved in.


* identifying a need

* coordinating a community effort

* summarising current practice (e.g. rights, barriers, resources)

* creating resources (e.g.corpora)

* running a project


* identifying sites to mine

* collecting bibliographic metadata (e.g. tables of content)

* agreeing web-friendly protocols (e.g. delay times)

* writing or finding crawlers

* creating or deploying crawl scripts

* managing workflow manually or or automatically

* recording crawl log

* saving crawled materials


* formalising structure of document (e.g. sections)

* creating or finding vocabularies for annotation

==generic tools==

* crawlers

* PDF readers

* flat text readers

* graphics analyzers

* image analyzers


* customization

==natural language==


* collection of NLP tools

* vocabularies

* corpora for training

* training

* testing

* domain tools

== graphics==

* reconstruction of diagrams from primitives

* SVG tools


* selection

* croppings

* binarisation

* edge detection/segemnts

* optical character recognition


* fonts


* reconstruction

* interpretation




* annotation

* links


* maths

* chemistry

* geo

* dates

* units of measurement


* document structure

* sentiment analysis




* mailing lists

* crowdcrafting

Remember Aaron Swartz in January and join the New Hampshire walk

Larry Lessig has mailed today to remember Aaron Swartz and to join a many-day walk through New Hampshire. Is anything planned in UK/Europe?

Seven years ago this January, Aaron Swartz visited me in Berlin to convince me to give up my work on intellectual property and take up the fight against corruption. Nothing sane would get done within IP — or anywhere else — he believed, until we released our political system from the stranglehold of moneyed interests and corporate influence. He convinced me. 

On January 11, the anniversary of Aaron’s death, we will begin a 185-mile walk along the length of New Hampshire, to continue the fight that Aaron began. Along the way, we will recruit as many New Hampshirites as we can to the battle against corruption. We want every presidential candidate at every New Hampshire primary event to be asked just one question: “How will you fix the corruption in Washington?” 

Click here to show your support for this historic march — and help fight back against political corruption.

Aaron brought a contagious idealism to everything he did. That idealism inspired thousands to join the battle against SOPA and PIPA. But as he believed, it was the thousands — and not him — that won that fight. As he said in the last speech he gave, “We won this fight because everyone made themselves the hero of their own story. Everyone took it as their job to save this crucial freedom and threw themselves into it.”  

His idealism continues in the work that the incredible Demand Progress community has done over the last few years. Now we need that idealism, and this community, to spread to the fight against corruption. 

We’re marching from Dixville Notch (the place the New Hampshire primary begins) to Nashua to save our democracy. Click here to join — or support us however you can.

If you can walk, join us. Even for just a day, join us. If you can’t walk with us, then help us by spreading the word. Tell your New England friends about this insane idea. And if you don’t have any friends in the northeast, then you can pay the NE-Friendless Tax by chipping in whatever you can — from $10 to whatever.

Please do as Aaron convinced me to do 7 years ago: join this fight too. Two years ago, in the SOPA fight, you took on DC’s most powerful lobby, and beat it. If we can can recruit 10 times the support, we can take on the power of all DC lobbyists, and restore a democracy to this Republic. 

Whether you lend your feet, your voice or your dollars, we need you in this fight. This January, and every January, until we win.

See you on the road. 

– Lessig

Demand Progress and Rootstrikers

PS — If you’d like to sponsor me on the walk, you can do that here.

Paid for by Demand Progress ( and not authorized by any candidate or candidate’s committee. Contributions are not deductible as charitable contributions for federal income tax purposes.

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Merry Christmas and a Happy New Year

It is that time of year again, when we all aim to take a well-earned day or two off work. As a result, SHERPA Services (RoMEO, JULIET, FACT and OpenDOAR) will be on reduced staffing from the 13th December 2013 until the 6th January 2014. All enquiries will be answered in due course.

In additional news, due to scheduled maintenance, there may be some disruption to SHERPA Services (RoMEO, JULIET, FACT and OpenDOAR) on the evening of Tuesday 17th December 2013. We apologise for any inconvenience that this causes.

We wish you all a Merry Christmas and Happy New Year.

Content Mining starts today!

There is now an unstoppable interest and desire for content-mining. People want to know how, when where – what the problems are … all sorts of things. So Jenny Molloy and Katelyn Rogers (OKFN) have set up a mailing list. join in the normal way:

Here’s my second post:

Many thanks to Jenny Molloy and Katelyn Rogers for setting up this list.


Last night we had a get-together in London catalysed by PLoS with

representation from OKFN, BioMedCentral, CrossRef, eLife, … all the usual

suspects … and there was lots of discussion about content mining and I

encouraged people to post their ideas to this list.


Here are some potential topics:


* what’s a responsible way to run a crawler over content?

* what are current practises obtaining content

* what are the legal and contractual aspects of CM?

* what types of content can be mined? What are the technical, social,

contractual bases?

* what software exists?

* how do I do Natural language processing

* what can I get from images?

* where can we put the mined content?

* where can we find dictionaries for annotating content?

* where’s the next meeting on content-mining?




We are also developing the technology very rapidly. We have two trial datasets in the CKAN where we’ve extracted species and we’ll be discussing these over the next 2-3 days. The intention is to extract facts from about 150 PLoSONE articles every day and put them in the Datahub. We’re talking with Amye Kennall from BioMedCentral about the best way to crawl all of BMC daily and we’ll be revisiting BMC after Ross’s viva. We’ve asked Geoff Builder from CrossRef to post some exciting ideas which we discussed last night …


(Must rush to the OKF/BL hack/love-in today…)




Evolutionary Applications Publishes issue 6.8

EVA-issue-6-8The December issue of Evolutionary Applications has been published online. The issue features an image of Whitefish (Coregonus macrophthalmus) on its cover pertaining to a study by Hirsch and colleagues on potential for future divergence in restored aquatic habitats.  The Editor-in-Chief: Louis Bernatchez has also highlighted the following articles as of particularly interest:

purple_lock_open Dynamics of growth factor production in monolayers of cancer cells and evolution of resistance to anticancer therapies
by Marco Archetti
Summary: In this article the authors use evolutionary game theory to study the dynamics of the production of growth factors by monolayers of cancer cells and to understand the effect of therapies that target growth factors.

purple_lock_open Herbicide-resistant weeds: from research and knowledge to future needs by Roberto Busi, Martin M. Vila-Aiub, Hugh J. Beckie, Todd A. Gaines, Danica E. Goggin, Shiv S. Kaundun, Myrtille Lacoste, Paul Neve, Scott J. Nissen, Jason K. Norsworthy, Michael Renton, Dale L. Shaner, Patrick J. Tranel, Terry Wright, Qin Yu and Stephen B. Powles

Summary: In this Perspective article the authors explore the areas and highlight future challenges of synthetic herbicide resistance research towards integrated and (evolutionary) sustainable weed management in major field crops.

purple_lock_open The effects of synthetic estrogen exposure on premating and postmating episodes of selection in sex-role-reversed Gulf pipefish by Emily Rose, Kimberly A. Paczolt and Adam G. Jones

Summary: In this study the authors aimed to understand the effects of a synthetic estrogen (EE2) exposure on the sex-role-reversed mating system in pipefish and the resulting strength of selection in Gulf pipefish.

As always, 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, and also strongly encourage submissions of papers making use of modern genomics or other molecular 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 >

Sign up to receive email content alerts here >

MicrobiologyOpen Publishes Issue 2:6

MicrobiologyOpenThe December issue of MicrobiologyOpen can be viewed online now!

MicrobiologyOpen is a broad scope, peer reviewed journal delivering rapid decisions and fast publication of microbial science.  The journal gives priority to reports of quality research, pure or applied, that further our understanding of microbial interactions and microbial processes.

Editor-in-Chief, Pierre Cornelis has highlighted the papers below from the latest issue:

purple_lock_openDeveloping an international Pseudomonas aeruginosa reference panel
Anthony De Soyza, Amanda J. Hall, Eshwar Mahenthiralingam, Pavel Drevinek, Wieslaw Kaca, Zuzanna Drulis-Kawa, Stoyanka R. Stoitsova, Veronika Toth, Tom Coenye, James E. A. Zlosnik, Jane L. Burns, Isabel Sá-Correia, Daniel De Vos, Jean-Paul Pirnay, Timothy J. Kidd, David Reid, Jim Manos, Jens Klockgether, Lutz Wiehlmann, Burkhard Tümmler, Siobhán McClean, Craig Winstanley

Summary: Pseudomonas aeruginosa is a major opportunistic pathogen, especially in relation to cystic fibrosis. In this study a panel of 43 P.aeruginosa strains designed to reflect the diversity of this pathogen were collated.


Canonical and non-canonical EcfG sigma factors control the general stress response in Rhizobium etli
Ann Jans, Maarten Vercruysse, Shanjun Gao, Kristof Engelen, Ivo Lambrichts, Maarten Fauvart, Jan Michiels

Summary: This work explores the hierarchical relation between Rhizobium etli extracytoplasmic function sigma factors ?EcfG1 and ?EcfG2, core components of the general stress response. The authors propose a modified model for general stress response regulation in R. etli as they find that, contrary to reports in other species, ?EcfG1 and ?EcfG2 act in parallel, as nodes of a complex regulatory network, rather than in series, as elements of a linear regulatory cascade. Based on a phylogenetic analysis and considering the prevalence of ?-proteobacterial genomes with multiple ?EcfG copies, this model may also be applicable to numerous other species. 

purple_lock_openMolecular analysis of the UV-inducible pili operon from Sulfolobus acidocaldarius
Marleen van Wolferen, Ma?gorzata Ajon, Arnold J. M. Driessen, Sonja-Verena Albers

Summary: This study is an in depth analysis of the UV inducible pili system of S. acidocaldarius which is used as a community based DNA repair system. Except for UpsX, all other components of the ups pili are essential for pili formation and DNA exchange.

Submit you paper here>   Sign up for eToC Alerts here>

Would you share your genome sequence? Come to the Panton Arms on Monday!

On Monday, December 16, 2013 from 6:30 PM to 8:30 PM (GMT) Cambridge, United Kingdom

we are running our second Open Science meeting, in the Panton Arms. It’s led by Fiona Nielsen, founder of DNADigest, a non-profit startup :

The genomic era is at our doorstep together with a lot of promises to personalized medicine – But what exactly is a genome? Do I have to share it? Do I have to share it all? With whom should I share it? What ethical issues might arise? What are my rights concerning my genome? – ”

Fiona came round for dinner on Monday and we had a discussion of what’s involved – people want their genome to be private, but they also wish it to be used by others for science. These are difficult to reconcile (I have been rightly taken to task on this blog for not recognising the difficulty). It’s said that data can be either anonymous or useful but not both. See for a recent blog post.

So DNADigest ( is looking for solutions. It’s a hard problem, but if it’s crackable Fiona and colleagues will crack it… From her site…


The genomics revolution is already here

The techniques for researching and characterising genomics diseases are available to both researchers (next generation DNA sequencing) and the general public (in the form of personal testing), so we should soon be able to diagnose any genetic disease by sequencing a patient’s DNA.
This is the ultimate goal of research into all genetic diseases, including into hereditary diseases and cancer.

But the sharing of the data isn’t

However, while data output is flooding research centres around the world and genomics results are published in highly prestigious journals, the sharing of the data that enables this research is embarrassingly limited.

The data ownership, the legal consent of the patients involved, the privacy of the patients involved and the mere volume and complexity of these datasets are a major hindrance to sharing of personal genetics data.

So genetic discoveries remain hidden

As a result, many research units are currently maintaining their own ‘silos’ of potentially valuable sequence and patient data. Needless to say, there may be several big genetic discoveries “out there” already sequenced, but not discovered, because no-one has had the means to bring together the matching pieces of the puzzle.

Solution: Secure the data, share the knowledge

DNAdigest is a non-profit organisation, founded for the purpose of solving the problem of accessing genomics data for research purposes, while addressing all of the above concerns.

DNAdigest presents a secure mechanism for querying genome data, which would otherwise not be shared with the broader research community.



Reptilian Sibling Rivalry

Do you ever fight with your siblings? Unless you’re regularly biting, head-butting, and threatening each other all night long, things could probably be worse. The authors of a new PLOS ONE study investigate how well crocodilians get along with each other as youngsters.

Researchers observed seven species of hatchling and juvenile captive-raised crocodilians in Darwin, Australia and Chennai, India. The animals were divided into small groups and then introduced into new mixed water and land enclosures. The scientists counted, classified, and analyzed instances of aggressive interactions, postures and behavior among the animals. Because crocodilians are at their most active in the evenings and during the night (and at their most amiable during the day), the authors analyzed footage from 4pm until 8am the next morning.

Siblings aren’t always so bad: juvenile Siamese crocodiles socializing

Siblings aren’t always so bad: juvenile Siamese crocodiles socializing

Some but not all of the awesome aggressive behaviors the authors observed during the study included:

  • Biting: “Jaws closed shut on an opponent.” Bites range from light mouthing to prolonged bites.
  • Head pushing: “Head is pushed into an opponent.”
  • Inflated posture: The crocodilian extends upward on its legs and arches its back downward to appear large and dominant. Other species also modify their posture in a similar fashion when challenged—two classic examples are cats and puffer fish.

  • Tail wagging: Crocodilians (like cats and many other animals) wag their tails as a way to signal and respond to aggression. They also sometimes tail wag as a windup to increase the force of a bite or a side head strike.
  • Side head strikes: One individual thrusts his or her head sideways into another’s.

Based on the observed behaviors, the authors classified the seven species according to levels of aggression. The authors suggest that the significant overall differences in relative temperament likely arise from each species’ unique ecological environment and adaptations. Some species, like the American alligator, the gharial (native to India), and the freshwater crocodile, were highly tolerant of one another and had relatively few aggressive interactions. When these species did display aggressive behavior, the vast majority of aggressive incidents appeared to be accidental and low-intensity. Other more aggressive species, like the saltwater crocodile and the New Guinea crocodile, displayed pronounced dominance patterns and had a higher incidence of deliberate, intense aggression.  These species used direct challenges like biting to establish dominance, and submissive behaviors such as raising the head into the air to yield.  Bites and head pushes were the most common forms of aggressive contact across all the species, although many behaviors were species-specific. For example, slender-snouted crocodilians tended to avoid aggressive interactions and the most potentially damaging behaviors, perhaps due to a relatively higher risk of injury.

The researchers suggest that aggressive behavior in young crocodilians could be a survival strategy to help them learn social queues and minimize their chances of being injured in social settings. The extent of the hatchling’s aggression may affect how long it takes them to abandon their initial family groups. Babies will spend anywhere from a few weeks to a few years with siblings and a small number of adults, until (like so many humans) they leave their families and strike out on their own “due to a growing intolerance of each other.”

The authors indicate that this research may have implications for effectively rearing multiple species in captivity and may also inform the planning, management, and success of effective reintroduction and conservation programs worldwide.

Related Content:

Determinants of Habitat Selection by Hatchling Australian Freshwater Crocodiles

Why the Long Face? The Mechanics of Mandibular Symphysis Proportions in Crocodiles

Citation: Brien ML, Lang JW, Webb GJ, Stevenson C, Christian KA (2013) The Good, the Bad, and the Ugly: Agonistic Behaviour in Juvenile Crocodilians. PLoS ONE 8(12): e80872. doi:10.1371/journal.pone.0080872

Images: Siamese crocodiles picture by chem7, other pictures taken from Figure 1 of the published paper.

The unstoppable growth of high quality open access resources (December 2013 early year-end edition of the Dramatic Growth of Open Access)

As shown in this chart (thanks to César Villamizar), the number of articles indexed in PubMed for which free fulltext is available within 3 years of publication is now over 800,000, or 28% of the articles indexed.  This growth is an important indication of the dramatic growth of high quality open access resources. The U.S. National Institutes of Health, responsible for the PubMed index, does not index junk!

Recently Peter Gruss, President of the Max Planck Society wrote about the unstoppable rise of open access. The 2013 early year-end edition of the Dramatic Growth of Open Access confirms this unstoppable rise, featuring a number of notable areas of growth and important milestones, with a focus on numbers that are indicators of growth of high quality open access resources.

Congratulations are due to the Public Library of Science as recently PLoS celebrated a milestone of its 100,000th article. The number of journals actively participating in PubMedCentral continues to rise. In the past year, the number of journals actively participating in PMC increased by 215 – about one title per working day. There are now more than 1,000 journals in PMC with all articles open access.

The number of research funding agencies and institutions with open access mandates continues to rise. 12 more institutional open access mandates have been added to ROARMAP since September 30th! Mandates by funding agencies and prestigious research institutions and universities ensure that the growth of open access features high quality articles, due to the vetting processes involved in assessing funding grant requests and institutional hiring, tenure and promotion practices. 

Congratulations to the Directory of Open Access Journals for passing another very recent milestone of 10 thousand titles!  Due to continuous improvement DOAJ was deleting as many titles as it was adding earlier this year – for this reason, the growth in DOAJ reflects not only quantity but quality as poorer journals have been weeded. Dramatic as the growth of open access has been to date, it looks like we can count on a ramping up of growth in 2014, when the first discipline-wide transition to open access, in particle physics, is implemented as SCOAP3 is set to begin January 1, 2014. 

Internet Archive continues to amaze, having added 1.8 million texts this past year for a total of more than 5 million texts!

A special thank you to César Villamizar, a student in our School of Information Studies and research assistant, for help with this issue’s data and charts – and a well-deserved Happy Holidays and New Year to everyone in the open access movement!

The full data and chart are available to download from uO recherche. This post is part of the Dramatic Growth of Open Access series.

Call for participation: resource requirements for small scholar-led not-for-profit open access scholarly publishing

Are you are a scholar involved in small not-for-profit open access publishing (from one to three journals, occasional conference proceedings, or small-scale monograph publishing)? Or, would your small not-for-profit publishing operation  like to switch to open access if the economic logistics can be worked out? If so, you are invited to participate in an interview (half hour to an hour) designed to further flesh out the resource requirements needed to sustain this kind of open access publishing.
Results of these interviews will form the basis for further research, including case studies and focus groups, in preparation for a larger project on the economics of global transition to open access. It is anticipated that results of this study will be useful in the development of business practices for open access publishing, and inform open access policy. Participants can choose whether their contributions will be anonymous and confidential or open and acknowledged.
To volunteer or for further information, please contact Heather Morrison re: study title: resource requirements for small scholar-led not-for-profit open access
Dr. Heather Morrison
Assistant Professor
École des sciences de l'information / School of Information Studies
University of Ottawa
Heather dot Morrison at uottawa dot ca