Monthly Archives: September 2012

Open Access discussion at Imperial Colledge London, 27th September

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“On 27th September 2012 the Imperial College SciCommForum held a follow up discussion on open access to publicly funded research in response to the Finch Report and RCUK Policy.  

We were joined by Mark Thorley (NERC, RCUK) and Professor Stephen Curry (Imperial College) and Richard Van Noorden (Nature News) chaired the discussion. We had representatives from HEFCE, Wellcome Trust, RLUK, MRC, NIMR, Imperial College Library – and more – in the audience, and the discussion continued on Twitter under the hashtag #icoa. 

With thanks to Professor Stephen Webster (Imperial College) for funding. 

Twitter: @SciCommForum”

The audio of the discussion was uploaded yesterday and can be found here on figshare:- http://figshare.com/articles/Open_Access:_Going_for_Gold_/96158

Peter Suber: "The UK can do better…"

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Mark Thorley wrote: “Stevan, …As an advocate of Open Access I would like to think that you appreciate the fact that the UK is leading the world here…”

Mark, no, the UK is no longer leading the world with its new Finch/RCUK/BIS OA policy.

It’s time to heed OA advocates that have been at this far longer than you, and fix the RCUK Policy:

Peter Suber: “The UK can do better. In fact, the RCUK can do better. Its 2006 policy was better than the new policy. It only needed to be enforced.”

The RCUK Policy is fixable. Indeed it can be made much better than the old RCUK policy. And the UK can once again take the worldwide lead in OA Policy:

I. Drop the 9 words that make the RCUK Policy say the opposite of what it means.

II. Adopt an effective compliance-verification mechanism for Green OA self-archiving:

(IIa) Deposit must be in the fundee’s institutional repository.
      (This makes each UK institution responsible for monitoring and verifying timely compliance.)
(IIb) All articles must be deposited immediately upon acceptance for publication.
      (Publisher embargoes apply only to the date on which the deposit is made OA.)
(IIc) Repository deposit must be designated the sole mechanism for submitting publications for UK research assessment (REF).
      (Articles’ deposit URL required in all requests for RCUK funding or renewal.)

It is still widely hoped that RCUK will act in a flexible, constructive way rather than a rigid, dogmatic one, in the face of the growing expression of the concerns of the research community and its OA advocates, in the UK and worldwide, about the ambiguity and the potential for perverse effects of the new RCUK OA Policy.

Stevan Harnad

BOAI-10 RECOMMENDATIONS

— 1.1. Every institution of higher education should have a policy assuring that peer-reviewed versions of all future scholarly articles by faculty members are deposited in the institution?s designated repository…

— Deposits should be made as early as possible, ideally at the time of acceptance, and no later than the date of formal publication.

— University policies should respect faculty freedom to submit new work to the journals of their choice. [emphasis added]

— University policies should encourage but not require publication in OA journals [emphasis added] …

— 1.3. Every research funding agency, public or private, should have a policy assuring that peer-reviewed versions of all future scholarly articles reporting funded research are deposited in a suitable repository and made OA as soon as practicable.

— Deposits should be made as early as possible, ideally at the time of acceptance, and no later than the date of formal publication…

Four More Questions For Mark Thorley About RCUK Open Access Policy

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Mark Thorley has posted “RCUK Open Access Policy ? When to go Green and When to go Gold” on the RCUK site.

Here are four further questions about the policy:

1. Policy Wording. As repeatedly pointed out and acknowledged at the Imperial College Forum, the wording of the present RCUK policy is confusing and leads to the widespread misunderstanding that fundees may not choose (free) Green (6-12) unless the journal does not offer (paid) Gold (CC-BY). If the intended meaning is that funded may freely choose Green or Gold, isn’t the right place to say that — and to prevent this confusion and misunderstanding — in the wording of the policy itself? rather than just in accompanying guidance to the interpretation of the wording of the policy?

2. Perverse Effects. Is RCUK not concerned that only allowing fundees to publish in journals that offer either (paid) CC-BY Gold or (free) 6-12 Green (or both) will simply induce subscription journals (60% of which currently allow immediate, unembargoed Green) to now offer hybrid (paid) CC-BY Gold while increasing their Green option to 13+ to make sure that UK authors must pay for Gold?

3. Benefits of 6% CC-BY. The UK produces 6% of worldwide research output. What benefit is it to UK industry, or to UK wealth creation, or to UK research, for the UK to pay (hybrid) subscription publishers worldwide 6% extra, over and above what they are already being paid for subscriptions, in order to make (only) the UK’s own 6% of worldwide research output CC-BY Gold? Is it worth the extra UK research money, diverted from research? or the loss (to both the UK and the rest of the world) of Green OA from the rest of the world (94%), because RCUK gives subscription publishers worldwide the irresistible incentive to offer a hybrid Gold option and increase their Green embargo lengths (while the rest of the world, unlike the UK, cannot afford — or does not wish — to subsidize hybrid publishers over and above what they are already paying them in subscriptions)?

4. Green Compliance Mechanisms. There seem to be plans in the making for verifying compliance with RCUK’s paid Gold option. What are RCUK’s plans for verifying compliance with the Green OA option? A requirement to deposit is not even mentioned in the current RCUK Policy’s wording: just a requirement to choose an RCUK-compliant journal.

A selection of influential PLOS ONE papers on tropical medicine and malaria

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For the XVIII International Congress for Tropical Medicine and Malaria Conference in Rio de Janeiro, PLOS ONE is highlighting eight recent articles.  Since January 2011, PLOS ONE has published almost 700 articles in the areas of tropical neglected diseases, tropical medicine, and malaria.  We’re sharing with you some of the papers that have received the most attention.  The authors on these papers come from across the globe, representing Brazil, Colombia, Ethiopia, France, the Netherlands, Papua New Guinea, Spain, Sri Lanka, Switzerland, the United Kingdom, and the United States.

One paper in particular has stood out.  Researchers found a novel therapy that could revolutionize the treatment of viral infections from the common cold to Ebola.  The therapy eliminates cells that contain viral RNA while leaving uninfected cells unharmed.  In the study, the therapy was effective against 15 different viruses, including dengue flavivirus, rhinoviruses, and H1N1 influenza virus.

An article published last month reported that malaria incidence in Sri Lanka has declined by 99.9% since 1999, despite ongoing conflict in the country.  The success of the malaria program could be explained in part by effective prevention measures, early detection, and maintaining the program in conflict zones.  In less than a month, the paper has received over 1,000 views.

Bacteria on people’s skin can affect how attractive they seem to malaria-transmitting mosquitoes.  Research published last December found that malaria mosquitoes preferred people whose skin had an increased number of bacteria but fewer overall types.  The article received significant press coverage and has been viewed almost 10,000 times.

Although a vaccine that blocks malaria transmission is theoretically possible, several obstacles have prevented its development, including producing Plasmodium parasite antigens in a cost-effective manner.  A paper published in May 2012 showed algae can make Plasmodium proteins that can elicit an antibody response.  This approach could bring down overall costs of a vaccine.  Since publication this paper has been viewed over 3,500 times.

A different approach to combatting malaria is to increase the mosquito’s defenses against the parasite.  A paper published in January 2011 showed that it is possible to insert an anti-malarial gene into a specific location in the Anopheles gambiae genome.  This technique decreased infections of Plasmodium yoelii nigeriensis and could be effective against other Plasmodium parasites.  Since publication this paper has received over 2,000 views.

The results from a World Health Organization-led effort to estimate the global incidence of leishmaniasis, a parasitic disease spread by sandflies, published in May 2012.  To obtain an accurate estimate of the disease burden, the authors collected data from 98 countries and 3 territories.  The authors stressed the importance of this in-depth assessment in helping policy makers and aid organizations determine funding priorities for this underreported disease.  The paper has been viewed over 5,000 times.

One strategy parasites use to evade the host’s immune system, initiate infection, and even manipulate host behavior is to imitate the host’s proteins.  A study published in March 2011 presented a method for scanning entire parasite genomes to identify proteins that are mimicking host proteins.  The paper received over 4,000 views and was featured on the This Week in Parasitism podcast.

Finally, a new method for diagnosing infection by Schistosoma mansoni, the parasite that causes schistosomiasis, was published in June 2012.  This method, which is based on detecting the parasite’s DNA, provides greater sensitivity than the most routinely used diagnostic approach, requires only a urine sample, and has a relatively low cost.

If you are at the ICTMM, we hope that you have had a chance to stop by the PLOS booth, pick up one of the PLOS ONE postcards, and meet staff from PLOS Pathogens and PLOS Neglected Tropical Diseases.

Acknowledgment:  Thank you to Martin Fenner for helping us use the PLOS Article Level Metrics to identify influential PLOS ONE papers in the areas of tropical neglected diseases, tropical medicine, and malaria.

Rick Rylance (CEO, AHRC) on RCUK on Green (and Embargoes)

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Rick Rylance (CEO, AHRC) in Independent onRCUK policy:

“because we recognise that? the? pay-to-publish “gold” model of Open Access.. is not always available, we’ve retained a mixed model for the time being. This means that if there is not a to pay-to-publish option, researchers can opt for the “green” model of open access where the paper would be available via a repository after an embargo period? [emphasis added]

Why “for the time being”?

Why (cost-free) Green only if (paid) Gold unavailable?

Why is Green described as embargoed when over 60% of journals (including the top journals in most fields) already endorse immediate, unembargoed Green (and “Almost OA” is available for the remaining 40%)?

Is RCUK trying to encourage publishers to increase their Green OA embargoes?

Stevan Harnad

Women’s Health and Fitness Series Part V: Pregnancy

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In this last post of the Women’s Health and Fitness Series, we delve into the mother of all topics: pregnancy. As one of the few health topics that truly only affects women, pregnancy is highly stressful on for women’s bodies, but amazingly, they know exactly how to respond to this event. In addition, many of the issues previously raised in the series continue to carry weight when discussing pregnancy.

One aspect of pregnancy that carries a lot of weight is exactly that: the amount of weight a pregnant woman gains. Obesity in pregnancy is associated with a long list of medical complications for a mother and child, including gestational diabetes, pre-eclampsia, infection and many others.  A PLOS ONE study published in July 2012 investigates the link between healthy weight during pregnancy and the associated risks when the term “eating for two” is taken too liberally. Obesity in pregnancy is associated with a long list of medical complications for a mother and child, including gestational diabetes, pre-eclampsia, infection and many others.

The authors, from the University of Ulster in Ireland, wanted to see if regimented diet and physical activity was an efficient intervention to reduce excess gestational weight gain (GWG). They reviewed 5 studies that had examined a total of 971 pregnant women with a mean BMI of 26. They found that setting goals through 1-on-1 diet and lifestyle counseling was the most successful strategy to help women gain appropriate amounts of weight during pregnancy. The researchers also note that while weight is a primary concern, and behavior modification is an effective way to address the problem, more research is required “to target women’s psychological needs as well as their emotional and physical needs”.

Pregnancy is a unique experience for the female gender, as well as for each individual woman.  Much like we’ve discussed throughout the series, health incorporates a balance of many factors, like nutrition, weight, emotional well-being, and should be tailored to each person.

With that, happy Women’s Health and Fitness Day, and we hope this month’s series has been informative and inspirational!

Image Credit: makelessnoise on Flickr CC-by license

Citation: Brown MJ, Sinclair M, Liddle D, Hill AJ, Madden E, et al. (2012) A Systematic Review Investigating Healthy Lifestyle Interventions Incorporating Goal Setting Strategies for Preventing Excess Gestational Weight Gain. PLoS ONE 7(7): e39503. doi:10.1371/journal.pone.0039503

 

 

 

 

SCOAP3 Gold OA "Membership": Unnecessary, Unscalable & Unsustainable

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1. High Energy Physics (HEP) already has close to 100% Open Access (OA): Authors have been self-archiving their articles in Arxiv (both before and after peer review) since 1991 (“Green OA”).

2. Hence SCOAP3 is just substituting the payment of consortial “membership” fees for publishing outgoing articles in place of the payment of individual institutional subscription fees for accessing incoming articles in exchange for an OA from its publisher (“Gold OA”) that HEP already had from self-archiving (Green OA).

3. As such, SCOAP3 is just a consortial subscription price agreement, except that it is inherently unstable, because once all journal content is Gold OA, non-members are free-riders, and members can cancel if they feel a budget crunch.

4. Nor does membership scale to other disciplines.

5. High Energy Physics would have done global Open Access a better service if it had put its full weight behind promoting (Green OA) mandates to self-archive by institutions and research funders in all other disciplines.

6. The time to convert to Gold OA is when mandatory Green OA prevails globally across all disciplines and institutions.

7. Institutions can then cancel subscriptions and pay for peer review service alone, per individual paper, out of a portion of their windfall cancelation savings, instead of en bloc, in an unstable (and overpriced) consortial “membership.”

How Open Is It? Draft Document for Open Access- Feedback Please!

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Not all Open Access is created equal. To move beyond the seemingly simple question of “Is it Open Access?” PLOS, SPARC and OASPA have collaborated to develop a resource called “HowOpenIsIt?” This resource identifies the core components of open access (OA) and how they are implemented across the spectrum between “Open Access” and “Closed Access”. We recognize there are philosophical disagreements regarding OA and this resource will not resolve those differences. 
 
We are seeking input on the accuracy and completeness of how OA is defined in this guide. Download the open review draft and provide feedback below in the comment form on SPARC’s website. In its final form, this guide will provide an easily understandable, comprehensive, and quantifiable resource to help authors make informed decisions on where to publish based on publisher policies.
With this guide we aim to provide greater clarity regarding its definition and components. All suggestions will be considered and a final version will be released during Open Access Week (October 22 -28, 2012). The comment period will close on Monday, October 8, at 5:00pm (EST).

Woman’s Health and Fitness Series IV: Ovarian Cancer

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In the last few weeks, we have discussed a range of topics that influence woman’s health and fitness, including obesity, cardiovascular disease and anorexia.  Today, in honor of Ovarian Cancer Awareness Month, we would like to share some research about ovarian cancer, a disease that affects 20,000 women in the United States every year.  In order to best treat and understand the causes of ovarian cancer, researchers continue to dig deeper into this serious woman’s health issue.

For example, we are aware that our environment affects our health, but did you know that the environment your grandmother lived in could affect you as well? This year, researchers at Washington State University published a study in PLOS ONE that found that ovarian cancer may result from previous generations’ exposure to environmental chemicals.  The researchers exposed pregnant rats to various compounds, including a fungicide, a pesticide mixture, a plastic mixture, dioxin, and a hydrocarbon mixture, to investigate the role of environmental exposure in ovarian disease.  They found that the compounds caused epigenetic changes, which are chemical modifications to DNA that affect how the DNA is used in a cell. In both the first and third generations, the results showed significant impact after the toxin exposure.

This study helped further our understanding of the causes of ovarian disease, but what about the treatment?  In another PLOS ONE article published this year, researchers studied the defects in DNA repair pathways in sporadic ovarian carcinomas, a particular type of ovarian cancer, which may influence the effectiveness of treatment.  Through this investigation, the researchers concluded that patients with high levels of three specific proteins were at a higher risk for treatment resistance and cancer reoccurrence.  This finding may have important implications for ovarian cancer diagnosis as well as treatment.

Diagnosis of this disease is particularly important, because treatment is most effective when it is diagnosed in its early stages.  In the spirit of Women’s Health and Fitness Day and Ovarian Cancer Awareness Month, it is important to remember the impact our environment has on our health, as well as the importance of early disease detection.

Please remember to check in later this week for our last blog post of our Women’s Health and Fitness Series, where we will discuss pregnancy.

Citation: Nilsson E, Larsen G, Manikkam M, Guerrero-Bosagna C, Savenkova MI, et al. (2012) Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease. PLoS ONE 7(5): e36129. doi:10.1371/journal.pone.0036129

Citation: Wysham WZ, Mhawech-Fauceglia P, Li H, Hays L, Syriac S, et al. (2012) BRCAness Profile of Sporadic Ovarian Cancer Predicts Disease Recurrence. PLoS ONE 7(1): e30042. doi:10.1371/journal.pone.0030042

Image Credit: cc-by license by Summer Skyes 11 on Flickr.

Disambiguating RCUK’s Open Access Policy Statement

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The Two Tweaks Needed 
to Disambiguate RCUK OA Policy


The Research Councils will recognise a journal as being compliant with their policy on Open Access if:

1. [GOLD] The journal provides via its own website immediate and unrestricted access to the publisher’s final version of the paper (the Version of Record), and allows immediate deposit of the Version of Record in other repositories without restriction on re-use. This may involve payment of an ‘Article Processing Charge’ (APC) to the publisher. The CC-BY license should be used in this case.

Or

2. [GREEN] *REMOVE* Where a publisher does not offer option 1 above,*REMOVE* the journal must allow deposit of Accepted Manuscripts that include all changes resulting from peer review (but not necessarily incorporating the publisher’s formatting) in other repositories, without restrictions on non-commercial re-use and within a defined period. In this option no ‘Article Processing Charge’ will be payable to the publisher. Research Councils will accept a delay of no more than six months between on-line publication and a research paper becoming Open Access, except in the case of research papers arising from research funded by the AHRC and the ESRC where the maximum embargo period is 12 months.

ADD: “Where a journal offers both suitable green (2.) and suitable gold (1.) options the PI may choose the option he or she thinks most appropriate” .

For those with patience for logic, here is how the ambiguity crept into the RCUK Open Access Policy, where it resides, and why it is all the more important to set it right promptly, before it takes root:

The RCUK fundee is actually faced with not one but two semi-independent choices to make in order to comply with the RCUK OA mandate: the between-journals choice of a suitable journal, and the within-journal choice of a suitable option. 

These two semi-independent choices have been (inadvertently) conflated in the current RCUK policy draft, treating them, ambiguously, as if they were one choice.

Both choices are nominally GREEN versus GOLD choices. 

Let’s quickly define “GREEN” and “GOLD,” because they mean the same in both cases. I will use a definition based on the current RCUK policy draft:

GOLD means the journal makes the article OA with CC-BY (“Libre OA”), usually for a fee.

GREEN means the author makes the article OA (“Gratis OA”) by depositing it in a repository, and making it OA within 0-12 months of publication.

These two definitions are not what is in dispute here.

But now the GREEN versus GOLD choice applies to two different things: 

(1) the author’s choice of which journal is an RCUK-suitable journal to publish in (this is the between-journalschoice) 

and then, if the journal offers both the GREEN and GOLD option: 

(2) the author’s choice of which option to pick (this is the within-journal choice).

A perfectly clear and unambiguous way to state the intended policy would be:

An RCUK-suitable journal is one that offers 
(i) GREEN only or (ii) GOLD only or (iii) BOTH (i.e., hybrid GREEN+GOLD).

An RCUK author may choose (i), (ii) or (iii).

If the choice is (iii), the RCUK author may choose GREEN or GOLD.

That would dispel all ambiguity.

But what the current RCUK policy actually states instead is:

An RCUK-suitable journal is one that offers (i) GOLD, or, if it does not offer GOLD, then an RCUK-suitable journal is one that offers (ii) GREEN OA.

The possibility that the journal offers (iii) both (i.e., hybrid GREEN+GOLD) is not mentioned, and the between-journals choice of journal is hence left completely conflated with the within-journal choice of option.

So the conclusion the RCUK fundee draws is that GREEN can only be chosen if GOLD is not offered: “GREEN IF AND ONLY IF NOT GOLD.”

When a policy so fully conflates two distinct, independent choice factors, it is extremely important to disambiguate it so as to undo the conflation.

Dropping the 9-word — and completely unnecessary — clause 

“Where a publisher does not offer option 1 above” [i.e., does not offer GOLD]

would remove the conflation and the ambiguity.

To make this even more transparent, the statement from Mark Thorley, interviewed by Peter Suber, could also be added:

“Where a journal offers both suitable green (2.) and suitable gold (1.) options” [i.e., hybrid GREEN+GOLD] , “the PI may choose the option he or she thinks most appropriate” 

This would make it perfectly clear that if a hybrid GREEN+GOLD journal is chosen, the author is free to choose either its GREEN or GOLD option.

It is not clear why the clause  “Where a publisher does not offer option 1 above” was ever inserted in the first place, as the logic of what is intended is perfectly clear without it, and is only obscured by inserting it. 

(The only two conceivable reasons I can think of for that gratuitous and misleading clause’s having been inserted in the first place are that either (a) the drafters half-forgot about the hybrid GREEN+GOLD possibility, or (b) they were indeed trying to push authors (and publishers!) toward the GOLD option in both choices: the between-journal choice of GOLD versus GREEN journal and the within-journal choice of the GOLD versus GREEN option — possibly because of Gold Feverinduced by BIS’s Finch Folly.)

The RCUK OA Policy can be fixed very easily (and without any fanfare) by doing the two tweaks highlighted at the beginning of this posting — the first for disambiguation, the second for clarification.

Once that is done, we can all unite in support of the RCUK policy and do everything we can to make it succeed. (There is still a lot of work to do in the implementation details, to provide a reliable fundee-compliance-assurance mechanism.)

If these two essential tweaks were not made, however, then the RCUK OA policy would not only fail (because of author resistance to constraints on journal choice, resentment at the diversion of scarce research funds to double-pay publishers, and outrage at the prospect of having to use their own funds when the RCUK subsidy is insufficient): It would also handicap OA policies by funders and institutions all over the world, by giving publishers worldwide the strong incentive to offer hybrid Gold OA (which, for publishers, is merely a license change, for each individual double-paid article) and — to maximize the chances of increasing their total revenues by a potential 6% (the UK share) at the expense of UK tax-payers and research funds — lengthen their Green OA embargoes beyond RCUK limits to make sure UK authors must choose paid Gold. 

The failed RCUK policy would not only mean that the UK fails to provide OA to its own research output, but it would make it harder for the rest of the world to mandate and provide (Green) OA to the remaining 94% of worldwide research output. The perverse effects of the UK’s colossal false start would hence be both local and global.

PLooS, or contemplating new IJPE series: poking fun at CC-BUY

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I am debating starting a new series on IJPE: poking fun at CC-BUY (a reference to those who confuse the Creative Commons Attribution-Only license with open access.

Where to start? Perhaps

PLooS U.S.
Open to Ridicule

This is a fine example of a derivative, with appropriate attribution (the PLooS link takes you right back to the source, fulfilling my obligations under the Attribution element!). I think one might argue that this violates the moral rights of PLoS – but PLoS US is in the country where arguing moral rights under circumstances like this would be a very tricky moral battle.

Future issues of the series could include such exciting novelties as PLooS PAYWALL (because after all none of the CC license require that CC licensed works be made available for free to anyone. Or, maybe we can explore the odds that any true blue CC-BUY devotee has actually READ THE LICENSE  – which doesn’t say anything at all about open access.

This is one series I really hope I don’t actually need to write.