Wednesday, 20 August 2014

Using Europe PMC’s export options as research funder

Recently Europe PMC released new export format options, to help users get Europe PMC’s wealth of metadata (and our open access papers) into the file formats they like to use.

We’ve already posted about how useful this function is for researchers, but it’s great for research funders too. Funders can convert their carefully constructed search into a tab separated file and use Excel to manipulate the metadata as they wish.

Funders can find out how many papers acknowledging their funding have been made open access, what research areas papers are being published in, or which grants papers are linked to, among other things!

Wednesday, 6 August 2014

New export options now available: use Europe PMC to populate your bibliographic references in EndNote, Reference Manager etc.

Europe PMC has released new export format options, indicated in the image below:

The RIS export format is typically used by Reference Manager and EndNote bibliographic applications for example, so you can now easily import Europe PMC citations.

You can also email citations to yourself, or others, by selecting this destination option from the Export menu and filling in the required address fields.

Identifying articles and populating your reference list now just got easier using Europe PMC.

More information can be found here:

Stay up-to-date with Europe PMC news by following us on Twitter, @EuropePMC_News

Friday, 18 July 2014

Taylor & Francis Open Access Survey: translating values into licences

Guest post from Alex Green, Transformation Project Co-ordinator, Wellcome Trust

Last month saw the publication of the 2014 Taylor & Francis Open Access Survey. Combining responses from just over 7,900 authors who published with Taylor & Francis in 2012 (9% of the total), this represents the opinions of authors from across the world in roughly the proportions they have published with Taylor & Francis – although my inner data geek really wants to get hold of the full dataset to apply some weighting to the under-represented authors of East and South East Asia.

The Taylor & Francis survey shows strong support for open access (OA) publishing by authors and a clear belief in its benefits compared with traditional publication, which has increased from the 2013 survey. 70% of respondents also disagreed or strongly disagreed with the statement ‘There are no fundamental benefits to open access publication’, up 10% from 2013.

However, when read alongside this evidence of increasing widespread positive attitudes to OA publishing, the findings on licensing are striking. In particular, the preference for more restrictive licenses seems at odds with the attitudes and values expressed by authors in response to the Section 1 questions on that topic. For example, in Question 5, 71% of authors were happy for their work to be re-used without prior knowledge or permission for non-commercial gain provided they receive attribution. This is equivalent to a CC-BY-NC licence, but only 18% of authors selected this licence as their first or second choice when answering Question 6 (see graphic below).

Question 5

Question 6

This mismatch between author attitudes and licence preference seems common to nearly all responses. Again in Question 5 authors seem concerned about commercial reuse of their work without prior knowledge, with 65% disagreeing that it is acceptable. However in Question 6, 47% selected Copyright Assignment as their first or second preference for licensing making it the second most popular licence along with Exclusive License to Publish. Having assigned copyright away, authors would have little control over any commercial reuse, not least by the publisher they have assigned the copyright to.

There are several hypotheses we could explore to account for this seeming contradiction. Looking down the results for Question 6 there is a clear drop off towards the bottom of the list for ‘preferred licences’. It would be interesting to know if these options were always presented in the survey in the same order that they are presented in the report. If so, we may be seeing response order effects (Krosnick and Alwyn 1987), but unfortunately full details of the methodology are not openly available along with the report. 

The contradictions between responses may also be partly due to a degree of satisficing, an effect where respondents choose adequate answers rather than optimal answers because it is easier to pick the first acceptable, or most familiar, option than fully evaluate all options (Simon 1957, Krosnick 1991). This could be leading to selection of the more familiar Copyright Assignment and Exclusive License to Publish over the various Creative Commons licence combinations.

Finally, it’s probably relevant to note that the definition boxes provided to respondents at the start of the survey gave explanations of different modes of OA publishing, repositories and text- and data-mining but not the differences between the licences. These aren’t always easy to grasp, especially when completing a survey at speed – I don’t mind admitting that I had to check with a colleague on the exact differences between the various licence options. Perhaps, as Dr David Green, Global Journals Publishing Director said in the Taylor & Francis press release, there is still ‘much work left to do in simplifying our policies and documentation so that our author communities are in no doubt as to what their OA options are’.

Monday, 7 July 2014

The right to read is the right to mine: Text and data mining copyright exceptions introduced in the UK.

New copyright exceptions to text and data mining for non-commercial research have recently come into effect and this is welcome news for UK researchers and research, argues Ross Mounce. Here he provides a brief overview of the past issues discouraging text and data mining and what the future holds now that these exceptions have been introduced. But despite legal barriers being removed, many technical barriers still remain. Furthermore it remains to be decided what formally constitutes ‘non-commercial’ research.

After eight long years including not one but two expert-led reviews of intellectual property; new copyright exceptions, some of which in particular will enable and empower UK academic research came into force on June 1st 2014. All disciplines are set to benefit from this: the humanities, the social sciences, science, technology and medicine.
Of particular interest to myself and other researchers is the ‘Exception for copying of works for use by text and data analytics’. In order to understand why this is so important, let me take you back to how it was before the copyright exception came into force (and how the legal situation still is for researchers in most other European countries):

Content Mining: mining one or more types of media for information; media as data (Image credit: DeclanTM (Flickr, CC BY)
The situation before the copyright exception
Before this exception came into force in the UK, for subscription-access content, you’d essentially have to ask permission from the publisher, before you started analysing. If you proceeded, without permission, to download electronic copies of ‘their’ copyrighted materials (see author’s note - bottomen masse for analysis, you would be infringing ‘their’ copyright – it would be illegal, and they could take legal action against you, even if your analysis was undertaken for non-commercial academic research purposes. Depending on the exact subscription-access agreement held with your institution (of which your institution may not be able to disclose the details of, because of confidentiality clauses!), the publisher could even ask for additional fees to be paid to cover this ‘additional’ type of usage if it is not covered in the subscription agreement. Many agreements did & and still do explicitly prohibit text and data mining.

If one did ask for permission, the process was complex and lengthy, involving many employees, and much bureaucracy, for each publisher. That’s if the publisher agrees to give permission. In a study by the Publishing Research Consortium it was found that “only 35% of the respondents [publishers] state that permission is granted in the majority or in 100% of the cases for all requests” (p. 106) – and that sample of publishers included open access publishers that by definition, allow mining. Thus publishers can and have denied permission for content mining research on ‘their’ works.

The situation after the introduction of the UK copyright exception for TDM
After June 1st 2014, for research conducted in the UK, under the jurisdiction of UK law, for ‘non-commercial’ research purposes (more of which later…), the new copyright exception overrides anything in subscription contracts that prohibits content mining. As Peter Murray-Rust puts it: The Right To Read Is The Right To Mine, and provided you are in the UK, and doing ‘non-commercial’ research that is now true, and legal. This provides welcome and useful protection for researchers against litigious publishers.
No researcher, doing ‘non-commercial’ research in the UK, needs to agree to, nor abide by the terms of any text and data mining ‘licence’ that publishers may wish to impose upon researchers.

Schemes such as CrossRef’s text and data mining services will be heavily advertised to researchers by the major publishers, in order to try and control the way in which researchers do content mining both through legal means (the licencing) and technical means (the API). The use of such services entails agreeing to detailed and lengthy licencing agreements, which many probably won’t read. If you do read the full terms and conditions you’ll find them disappointingly limiting which is why organisations such as LIBER have publicly criticized these terms.

Even with some legal barriers now removed, technical barriers remain
Despite legal barriers being removed, non-trivial technical barriers still remain which can be problematic for content mining. Most websites for instance have rate limits. If you are detected attempting to crawl or scrape too many pages (i.e. research articles) within too short a time-span, your access to that website may be blocked. Publishers such as BioMed Central (BMC) have a crawl rate limit of one article per second which is an acceptable rate limit for researchers. Through Elsevier’s text-mining API there’s a limit of 10,000 articles per week which is equivalent to a rate limit of 1 article every 60 seconds. At that rate limit it would take ~21 years to go through all 11 million articles that Elsevier control access-to through their Science Direct platform – not really feasible! The rate limit imposed is entirely artificial – researchers with good internet connections can crawl many articles per second if they were allowed to. The publisher sets the rate ‘allowed’ and even despite this new copyright exception, to get the rate-limit changed a researcher would still have to beg permission from the publisher, which the publisher is fully within their rights to either grant or not.

Open Access publishers tend to be exceedingly helpful to content miners: BMC, Hindawi, and MDPI to name but a few, make available whole content dumps (i.e. everything they publish), openly available to download by anyone for any purpose which greatly facilitates content mining. For biomedical researchers, the PubMed Central Open Access Subset and Europe PMC also allow downloading of full-text dumps but these are limited to CC BY papers only (another reason of many why CC BY is the preferred licence of open access publishers).

Other less-helpful publishers sometimes pay money to employ external firms like Atypon to populate their websites with booby-trapped links that block access to the entire subscribing institution if clicked. These links called ‘spider-trap’ links, inevitably end-up doing more harm than good as in the recent #ACSgate debacle whereby over 200 institutions had their access to one publisher’s content blocked by people innocently clicking on a DOI-like URL that was openly available on the publisher’s website.

Image Source Shutterstock Copyright: dmitriyGo
Why do these publishers dislike crawling and scraping so much? Scraping the web is a normal, legitimate activity for researchers; even a recent European Commission report says so:
‘Scraping’ the World-wide web for data is today a familiar activity for the digitally literate researcher. (p. 11)

With over 50 million scholarly articles out there, and millions being published each and every year in popular fields like biomedical science; content mining is fast-becoming a necessity. Human-eyes can only read so much. Computers, and computational techniques to help us comprehensively and rigorously mine the literature are a boon for research. One expert report on the state of content mining argues that “European academics are falling behind their Asian and North American counterparts” – this new copyright exception will thus help the competitiveness of UK research in the global sphere.

The only nagging question remaining to address is: what is ‘non-commercial’?
I won’t pretend to give a convincing answer to this. I simply don’t know, and I can see it being a potentially difficult sticking point for many.

For my own research on extracting data from evolutionary tree figures (phylogeny), I can feel safe that this subject and use-case might not readily be definiable as ‘commercial’ but for other researchers I can imagine it may not be so easy to safely & surely classify their research as ‘non-commercial’. Indeed a recent court in case in Germany seemed to indicate that ‘non-commercial’ use was only safely equivalent to personal-use. The consequences, risks and side-effects of ‘non-commercial’ remain largely untested in case law and can prevent much more usage than you might think. Will publishers be eager to sue academic researchers for what they perceive to be commercial mining? I hope not, but sadly it would not surprise me if they did.

Author’s Note: I feel pained to discuss the copyright owned by publishers, over work written by academics hence the inverted commas when discussing ‘their’ copyright. Part of the reason academia got into this copyright-pickle in the first place is that we allowed publishers (and still do for some!), to take copyright away from the authors with completely unnecessary copyright transfer agreements (CTA’s). Publishers do NOT need a CTA to publish your work, so don’t sign them! You can instead retain your copyright over your work, and just give them a non-exclusive license to publish. Keep your copyright!

Disclaimer & Warning: None of this article constitutes formal, vetted legal advice and should not be relied on or treated as a substitute for specific advice relevant to particular circumstances. Academic publishers and even societies can, and do take legal action against research-related activities, if they feel so inclined.

About the Author
Dr Ross Mounce is a BBSRC-funded postdoc at the University of Bath, working on the PLUTo project to liberate phyloinformatic data from the literature. He is working with The Content Mine team to encourage the adoption and use of content mining tools and techniques, including giving a workshop at this year’s Open Knowledge Festival 2014 (Berlin, July). As a keen advocate for open scholarship, you can also find him at OpenCon 2014 (Washington D.C., November) – the student and early career researcher conference on Open Access, Open Education and Open Data.

This piece originally appeared on The London School of Economics and Political Science's Impact Blog under a Creative Commons CC BY license. One of the images has been replaced, and another omitted (please see individual images for copyright restrictions). The article gives the views of the author.

Wednesday, 4 June 2014

Let’s (not) Get Physical: the Effect of Spironolactone on Muscle Strength in the Elderly

Image Source: Serial/Trash

Life expectancy has increased continuously over the past several decades, and with it, a host of new age-related ailments have emerged as contemporary medical issues. Muscle function decreases with age, leaving increasing numbers of elderly people incapable of being physically independent. This not only has devastating personal effects but is also a major public health issue. In a recent study, researchers investigated whether blocking the hormone aldosterone may help counter the effects of physical impairment with age.

Aldosterone is a hormone best known from the role it plays in the regulation of blood pressure, but it has also been associated with muscle weakness. This makes sense, considering that aldosterone also lowers levels of magnesium and potassium – two minerals that are essential for muscle contractility. Thus lower levels of aldosterone may promote restoring muscle function.

How can we keep aldosterone levels low? The production of aldosterone in the body is a complex interplay between hormones and enzymes. Medication can be targeted to interfere with it at different stages. One way to influence aldosterone levels is to inhibit the creation of a hormone that would otherwise stimulate its production. These so-called angiotensin-converting enzyme blockers (ACE blockers) are usually prescribed to treat high blood pressure and heart failure. Interestingly, some studies reported additional positive effects on muscle strength and physical fitness in elderly.  But the results not conclusive: some studies did not find any positive effect on muscle strength. Furthermore, ACE blockers seem to fail at reducing aldosterone levels over longer time periods. However, long-term efficacy is a crucial factor for improving muscle function. 

Image Source: Shutterstock Copyright: Tish1

Another way to interfere with aldosterone is to block aldosterone receptors directly. This is exactly what a drug called spironolactone does. It blocks receptors in the kidneys, heart and blood vessels that are usually targeted by aldosterone. Because aldosterone can only act when it has the possibility to bind to its receptors, any competition for those receptors blocks its action. Recent studies suggest however that blocking the aldosterone receptors by means of spironolactone may be superior to ACE inhibitors when it comes to blocking the specific effects of aldosterone. For example, spironolactone seems to be more effective than ACE inhibitors in keeping magnesium and potassium levels in muscles high – a highly desired effect for improving muscle strength. Spironolactone may thus be a promising medication to counter the decline in muscle function in elderly.

In line with this, physical fitness of heart failure patients improves after they’re treated with spironolactone. However, one must consider that spironolactone is well-known as an effective medication for high blood pressure and heart failure. Therefore, its positive effect on physical performance may simply be caused by better overall health after treatment rather than by a direct effect of spironolactone on muscle strength. To understand whether the intake of spironolactone may have a beneficial effect on muscle strength in elderly who do not suffer from heart failure, a research team from the University of Dundee recruited 120 patients aged 65 and older. The patients had self-reported difficulties in performing daily activities, but did not suffer from heart conditions or high blood pressure. Half of the participants received a daily dose of spironolactone over a period of 20 weeks, while the other half of the patient group received a placebo – a pill that resembled spironolactone but which was medically inert. The researchers considered various factors of interest, including objective and subjective physical function. Subjective physical functioning was measured by self-reports. Objective physical function was assessed by the distance that participants could walk within 6 minutes, a simple but widely-used, reliable measure of exercise performance in the elderly.

The results were surprising: the treatment with spironolactone did not increase the distance that participants could walk within 6 minutes, suggesting that the intake of spironolactone did not enhance their muscle functioning. In contrast to the objective findings, the self-report measures showed another picture: after 20 weeks, only those participants who had been treated with spironolactone reported an improvement in quality of life. Whether this effect was caused by a pain-relieving effect or by other pharmacological benefits associated with spironolactone is not known; further studies are required to clarify these results.

Despite the fact that the results could not confirm any positive effect of spironolactone on muscle strength, this should not be interpreted as a definite exclusion of its efficacy as a counteragent for age-related muscle decline. Rather, the findings demonstrate that spironolactone was well tolerated in participants without heart failure and improved their quality of life. This provides encouragement to test the drug at higher doses and for longer treatment durations. Future studies are needed to determine whether these advanced treatments can cause the desired physiological effects, but the current findings help to define them.

This summary by Jenny-Charlotte Baumeister was shortlisted for Access to Understanding 2014 and was commended by the judges. It describes research published in the following article, selected for inclusion in the competition by the Chief Scientist Office of the Scottish Executive:

PMCID: PMC3695565
L.A. Burton, D. Sumukadas, M.D. Witham, A.D. Struthers & M.E.T. McMurdo.
The American Journal of Medicine (2013) 126(7), 590-597.

Access to Understanding entrants are asked to write a plain English summary of a research article. For Access to Understanding 2014 there were 10 articles to choose from, selected by the Europe PMC fundersThe articles are all available from Europe PMC, are free to read and download, and were supported by one or more of the Europe PMC funders.

Look out here and on Twitter @EuropePMC_news for further competition news and other Europe PMC announcements.