Orphan Works & Mass Digitization: Obstacles & Opportunities [symposium]

Listen to expert speakers and download powerpoint presentations from this two-day symposium held at the Claremont Hotel in Berkeley, California on April 12-13, 2012. Made possible through the efforts of the Berkeley Digital Library Copyright Project and generous support from the Alfred P. Sloan Foundation.


A pictorial Amusement

I dropped in to see our computer officers today – they’ve just had an aircon failure and I was offering sympathy – they have a lot to deal with. While there I noticed this splendid spanner (== wrench/US). I love tools and this one has a majesty of its own in a computer office. It’s about 40 cm long (see ruler) and we guess it’s about 2 kilos.

I naturally assumed it was for something like bolting units to the floor or something like that, but that’s not why it was ordered. The reason is gently amusing – perhaps you can make some guesses).

Meanwhile tomorrow I’ll be blogging about text-mining. I’ve been hacking code furiously over the last 5 days and feeling it. There is a lot I need to write about but textmining is the priority.


Identical twins caught red-fingered

Fingerprints are as unique as snowflakes – or so we’re taught in elementary school. Identical twins, though, provide an interesting caveat to this rule: Not only do they look alike, they are also more likely than non-twins to have similar fingerprint patterns.

These similarities raise potential complications for biometrics-based security systems and crime solvers, but a PLoS ONE paper published Friday suggests there’s no reason to worry.

The study, conducted by an international team of researchers from the Chinese Academy of Sciences and the University of Iowa, looked at fingerprints from 83 pairs of identical twins. They collected each print six times, rather than the single impression that is usually collected, and used two different identification methods, called P071 and VeriFinger 6.1, and novel analytical methods to evaluate the prints. They found that identical twins’ fingerprints had a 74% probability of being the same type (though not identical), as compared to a 32% probability for a random pair of prints, but they also showed that the fingerprints could be distinguished using the sophisticated identification methods.

Based on these results, it looks like identical twins may not be the perfect criminals after all. Nevertheless, they seem to have a leg up on the rest of us – maybe something to keep in mind the next time you’re trying to solve that thorny art heist.

Citation/Image source: Tao X, Chen X, Yang X, Tian J (2012) Fingerprint Recognition with Identical Twin Fingerprints. PLoS ONE 7(4): e35704. doi:10.1371/journal.pone.0035704

Latest Article Alert from BMC Infectious Diseases

The latest articles from BMC Infectious Diseases, published between 28-Mar-2012 and 27-Apr-2012

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Point-of-care detection of lipoarabinomannan (LAM) in urine for diagnosis of

Latest Article Alert from BMC Medical Research Methodology

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An evaluation of the quality of statistical design and analysis of

Open Access Priorities: Peer Access and Public Access

The claim is often made that researchers (peers) have as much access to peer-reviewed research publications as they need — that if there is any need for further access at all, it is not the peers who need it, but the general public.

1. Functionally, it doesn’t matter whether open access (OA) is provided for peers or for public, because OA means that everyone gets access.

2. Strategically, however, it does matter, because currently OA is not being provided in anywhere near sufficient numbers spontaneously by researchers (peers).

3. This means that policies (mandates) from peers’ institutions and funders are needed to induce peers to provide OA to their publications.

4. This means that credible and valid reasons must be found for peers’ institutions and funders to mandate providing OA.

5. For some fields of research — especially health-relevant research — public access is a strong reason for public funders to mandate providing public access.

6. But that still leaves all the rest of research, in all disciplines, funded and unfunded.

7. Most research is technical, intended to be used and applied by peer researchers in building further research and applications — to the benefit of the general public.

8. But most peer-reviewed research reports themselves are neither understandable nor of direct interest to the general public as reading matter.

9. Hence, for most research, “public access to publicly funded research,” is not reason enough for providing OA, nor for mandating that OA be provided.

10. The evidence that the primary intended users of peer-reviewed research — researchers — do not have anywhere near enough access is two-fold:

11. For many years, the ARL published statistics on the journal subscription/license access of US research universities:

12. The small fraction of all peer-reviewed journals that any university can afford to access via subscriptions/licenses has since become even smaller, despite the “Big Deals”:

13. The latest evidence comes from the university that can afford the largest fraction of journals: Harvard University

14. Researchers’ careers and funding as well as research progress depend on the accessibility, uptake and impact of the research output.

15. Open Access maximizes accessibility and enhances uptake and impact.

16. Hence peer access, rather than just public access, is the reason (all) researchers (funded and unfunded, in all disciplines) should provide OA — and the reason their institutions and funders should mandate that they provide OA.

Stevan Harnad
Enabling Open Scholarship


The list of recommendations I made was strategic. The objective was to maximize OA deposits and maximize OA deposit mandates.

The issue is not about how many members of the general public might wish to read how many peer-reviewed journal articles.

The issue is strategic: What provides a viable, credible, persuasive reason for researchers to provide OA and for institutions and funders to mandate providing OA in all fields of research, funded and unfunded, in all disciplines.

My point was that providing access for the the general public is a viable, credible, persuasive reason for providing and mandating OA in some fields (notably health- related research, but there may be other fields as well) — but it is not a viable, credible, persuasive reason for providing OA in all fields, nor for all research.

It is not difficult to find anecdotal evidence of nonspecialist interest in specialized research; one’s own interests often go beyond one’s own area of expertise.

But that is user-based reasoning, whereas providing OA and mandating OA require reasons that are viable, credible and persuasive to providers of research — and not some providers, sometimes, but all providers, for all research.

The only reason for providing OA to research that is valid, credible and persuasive for all research and researchers is in order to ensure that it is accessible to all of its intended users — primarily peers — and not just to those whose institutions can afford to subscribe to the journal in which it was published.

The issue is strategic. It is a great mistake to construe giving priority to reasons for providing peer access over reasons for providing public access as somehow implying that public access should be denied: Public access automatically comes with the territory with OA. So public access denial is not the issue.

The strategic issue is whether researchers (and their institutions and funders) are more likely to be induced to provide and mandate OA by the argument that the public wants and needs access or by the argument that peers want and need access.

Peer access provides research progress and impact. It is an appeal to researchers’ self-interest to stress the beneficial effects of OA on the uptake and impact of their research.

Most researchers of course also have a secret yearning that their research should appeal not only to their peers, but to the general public. But they also know that that is probably just wishful thinking in most cases. And in any case, public access does not have the direct affect on their careers, funding, and research progress that peer access has.

So it is not that the enhancement of public access should not be listed among the reasons for providing OA. It is just that it should not be promoted as the first, foremost, or universal reason for providing OA, because it is not: for many or most researchers, that argument simply will not work.

Ditto for the argument that researchers need to provide OA because journal subscriptions cost too much. The eventual solution to the journal affordability crisis will probably also come from providing and mandating OA. But, like public access, journal affordability is not a sufficiently compelling or universal rationale for providing OA.

The public access rationale for providing OA appeals to politicians and voters. Good. Use it in order to help get OA mandate legistlation adopted by research funders. But the rationale is much less convincing to researchers (peers) themselves, and their institutions.

The journal affordability rationale for providing OA appeals to librarians and institutions, but it is much less convincing to researchers (peers).

In contrast, providing OA in order to maximize research progress and impact, by maximizing researcher (peer) uptake, usage, applications and citations — if backed up by evidence — is the way to convince all researchers, funded and unfunded, in all disciplines, that it is in their own best interests to provide OA to their research.

Stevan Harnad

Happy Arbor Day!

Cross-sections of Q. palmeri stems.

Today’s internationally recognized tree holiday was founded in 1872 by J. Sterling Morton, former Secretary of Agriculture to US President Grover Cleveland, and avid tree enthusiast. The holiday is generally observed on the last Friday in April, and today marks over 135 years of tree planting and conservation efforts across the globe. Highlighted below are some of PLoS ONE’s arboreal related articles. Take a moment to read about the  critical role trees have in our global ecosystem.

Sudden Oak Death, caused by a pathogen introduced to California forests, continues to disturb local oak populations. This research explores the clonal reproductive behavior of the pathogen, Phytophthora ramorum.

Researchers at the University of Toronto have collected samples from Panamanian rainforest tree species to estimate total carbon content in tropical ecosystems. Read more here.

The fascinating colonization of Juniper trees, Juniperus brevifolia, a native species to the Azores archipelago, has been explored in the following article.

Recent analysis indicates that although forested areas have declined globally, the overall tree density in such areas has increased. Read more about how this is important in the sequestration of atmospheric carbon.

Logging practices in wood-producing forests pose risks for many endangered flora and fauna. Managing these areas sustainably could help conserve such species, as well as increase carbon storage. Read more here.

To find ways to get involved, or to learn how to plant a tree in your community, visit www.arborday.org

Image source: Figure 2 (May MR, Provance MC, Sanders AC, Ellstrand NC, Ross-Ibarra J (2009) A Pleistocene Clone of Palmer’s Oak Persisting in Southern California. PLoS ONE 4(12): e8346. doi:10.1371/journal.pone.0008346)

Evolutionary Applications Issue 5.4 is now live!

5_4 coverEvolutionary Applications has now published issue 5.4. As for all the other 2012 issues, this issue is open access – free to read, download and share.

This issue contains two excellent papers on plant-pathogen interactions. The first of these is ‘Genetic structure and local adaptation of European wheat yellow rust populations: The role of temperature-specific adaptation’ by Mamadou Mboup and colleagues. Yellow stripe rust of wheat is a major concern for wheat farmers.  It’s typically thought that variation in the ability of this pathogen to infect different populations of wheat was due to genetic changes among strains of the rust.  This paper shows that differences in the environment can also play a key role in whether or not the rust can infect wheat populations.  

The second highlighted papers is ‘The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley’ by Helen R. Jenson and colleagues. This paper addresses the question of whether it is more important to conserve crop plants on the farm or to store in a seed bank. Although it is seen that seeds conserved on the farm can adapt to changes in genetic strains of parasites, the authors argue that it might be important to store seeds away in a bank because the seeds may contain rare alleles that confer resistance to parasites that farm plants are no longer resistant to. Evidence is given to show that both predictions are seen.

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Latest Article Alert from Journal of Occupational Medicine and Toxicology

The latest articles from Journal of Occupational Medicine and Toxicology, published between 12-Apr-2012 and 26-Apr-2012

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Interferon-gamma release assays for the tuberculosis serial

Latest Article Alert from Breast Cancer Research

The latest articles from Breast Cancer Research, published between 12-Apr-2012 and 26-Apr-2012

For research articles that have only just been published you will see a ‘provisional PDF’ corresponding to the accepted manuscript. Fully formatted PDF and full-text (HTML) versions will be made available soon.

In vivo proton magnetic resonance spectroscopy of breast cancer: a review of the