Archive for November, 2008

Grants support OA journal in 2009

The OA journal Ethics & Global Politics was launched in 2007 and published its first issues in 2008. A recent Announcement (November 15, 2008):

Publishing in Ethics & Global Politics is free in 2009 due to generous grants by the Swedish Council for Working Life and Social Research and Swedish Research Council.

This journal provides an example of a peer-reviewed OA journal that does not charge authors an article-processing fee. (There are many others. See, for example, Bill Hooker, Open Reading Frame, December 2, 2007).

The journal uses, as its publishing system, Open Journal Systems

An example of a recent article: Borders on the mind: re-framing border thinking by John Agnew, Ethics & Global Politics 2008; 1(4), 2008: 175-191. The last two sentences of the Abstract:

Thinking about borders should be opened up to consider territorial spaces as ‘dwelling’ rather than national spaces and to see political responsibility for pursuit of a ‘decent life’ as extending beyond the borders of any particular state. Borders matter, then, both because they have real effects and because they trap thinking about and acting in the world in territorial terms.

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Information session: CIHR’s public access policy

See: “Access to Research Outputs“, Geoff Hynes, November 4, 2008 (PDF version of his PowerPoint presentation at the University of Ottawa. Presentation notes are included).

Found via: uOttawa Library LibGuides section on CIHR Policy. See also the section on Open Access.

Added November 26, 2008: The link to the presentation hasn’t been stable, so it’s been archived by WebCite® at (on November 26th, 2008).

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Redesigning primary care in the USA

There’s a section in the November 13 edition of NEJM that’s currently gratis OA: Perspective roundtable: redesigning primary care, by Thomas H Lee, Thomas Bodenheimer, Allan H Goroll, Barbara Starfield, and Katharine Treadway, N Engl J Med 2008(Nov 13); 359(20): e24 [PubMed Citation] [HTML]:

U.S. primary care is in crisis. Primary care physicians must care for more and more patients, with more and more chronic conditions, in less and less time, for which they are compensated far less than subspecialists. They must absorb increasing volumes of medical information and complete more paperwork than ever, as they try to function in a poorly coordinated health care system. As a result, their ranks are thinning, with practicing physicians burning out and trainees shunning primary care fields. In a roundtable discussion moderated by Dr. Thomas Lee, four experts in primary care and related policy — Drs. Thomas Bodenheimer, Allan Goroll, Barbara Starfield, and Katharine Treadway — explore the crisis, as well as possible solutions for training, practice, compensation, and systemic change.

[Video]; Transcript of video [PDF]; [Comments].

For some additional comments, see: The doctor is out? by Cervantes, Stayin’ Alive, November 18, 2008.

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On enabling OA

A few thoughts on the heels of Berlin 6 by Cornelius Puschmann, CorpBlawg, November 15, 2008. Excerpts:

There is still the belief among many involved in financing, supporting and disseminating research that those who undertake it have both the ability and the motivation to “move to open access” by themselves. I don’t believe that this is true. Many junior researchers who might be in favor of OA cannot choose freely where they want to publish, because the wrong choice is a risk to their career. Many senior researchers who have the influence and standing in their discipline to drive a paradigm shift do not embrace OA because the formats, publishing channels and procedures involved are unfamiliar and appear unreliable to them. But at the core, neither of these issues is decisive.

The pivotal problem is that most researchers, regardless of where they stand on the career ladder, are not impacted personally by whether or not something is Open Access, and that their perspective as individuals, and not the common good, shapes their views.


I believe that one very effective way of enabling OA in the long term is to push for entirely new forms of publishing, forms that are ‘OA by nature’, such as blogs and wikis. The entrenched forms are conceptually associated with the entrenched system and it will probably be harder to disassociate the one from the other than to popularize entirely new forms of science communication (i.e. ‘journal’ and ‘article’ are conceptually associated with ‘paper’, ‘commercial publisher’ and ’subscription’, while ‘blog’ and ‘wiki’ aren’t).

New forms of scholarly communication that have novel advantages over existing forms will be adopted not because they are open (because, as outlined above, by itself that hardly matters) but because they offer specific benefits to the individual scholar. Obviously they will exist side by side with established forms. But they could act as a catalyst that raises awareness among researchers for the benefits of Open Access, because the reach and openness of hypertext publishing is what makes it so attractive.

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Finding articles on CSC via OAIster or PMC

A mentioned in a previous post, in addition to this OA-oriented blog, I’m currently also editing another blog, Cancer Stem Cell News. I recently, using OAIster, searched the “entire record” field for the phrase “cancer stem cell*”. The search for articles about CSC was limited to resource type “text”, and the results were sorted in “date descending” order. This search yielded 167 records. Of these 167, 136 (81%) were obtained from 5/29 (17%) of the contributors. These 5 were: PubMed Central (PMC) [41 records]; CiteBase [39]; HighWire Press, Stanford University [20]; BioMed Central (BMC) [19] and Defense Technical Information Center (DTIC) Repository [17]. The remaining 24/29 contributors (83%) provided 31/167 (19%) of the records. Perhaps, another example of the Pareto principle (for many events, 80% of the effects come from 20% of the causes)?

The most recent article, dated 2008-06-09, was Mammosphere culture of metastatic breast cancer cells enriches for tumorigenic breast cancer cells by Matthew J Grimshaw, Lucienne Cooper, Konstantinos Papazisis, Julia A Coleman, Hermann R Bohnenkamp, Laura Chiapero-Stanke, Joyce Taylor-Papadimitriou and Joy M Burchell.  Publisher: BMC. PubMed Citation: Breast Cancer Res 2008; 10(3): R52. Epub 2008 Jun 9. (The full citation for this article isn’t included in the OAIster record).

This same article can also be accessed via PMC. The Conclusion section of the PMC Abstract:

This paper shows, for the first time, that mammosphere culture of pleural effusions enriches for cells capable of inducing tumours in SCID mice. The data suggest that mammosphere culture of these metastatic cells could provide a highly appropriate model for studying the sensitivity of the tumorigenic ‘stem’ cells to therapeutic agents and for further characterisation of the tumour-inducing subpopulation of breast cancer cells.

Comment: A search of PMC for the phrase “cancer stem cells” yielded access to articles published more recently than the one cited above. For example, a search limited to articles added to PMC in the last 30 days (done on November 9) yielded 3 citations, all published in November 2008.

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Ethics and access to databases

This publication has attracted attention: Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays by Nils Homer and 9 co-authors, including David W Craig, PLoS Genet 2008( Aug 29);4(8): e1000167 [PubMed Record].

See, for example: NIH Limits Access to GWAS Databases Due to Privacy Concerns by Charles P Clayton, Alliance for Academic Internal Medicine, September 5, 2008. Excerpt:

The National Institutes of Health (NIH) announced new procedures for researchers to access previously public databases from genome-wide association studies (GWAS) in light of recently published research …

See also: NIH Tackles Privacy Concerns for GWAS, NIAID Funding News, September 17, 2008. Excerpts:

On August 25, 2008, NIH removed files of aggregate GWAS data from the public portion of its databases while keeping summary information public.

You will still be able to share and use these data. As an investigator, you must now apply for access and agree to protect confidentiality. This process matches the one NIH has required all along for individual-level data.

Read more about NIH’s new policy for accessing GWAS data at Modifications to Genome-Wide Association Studies (GWAS) Data Access.

Excerpts from NIH’s new policy:

The NIH developed a two-tiered access policy for GWAS data. The first level is the public posting (open access) of summary-level information and aggregate genotype data, including allele frequencies by case-control status, association tests odds ratios, and p values for each SNP in the scan. The second level is controlled access to individual-level data (genotypes and phenotypes). The controlled access data are available to investigators from scientific institutions who submit Data Access Request (DAR) packages that are reviewed and approved by the NIH Data Access Committees (DACs).

New statistical techniques for analyzing dense genomic information make it possible to infer the group assignment (i.e., case or control) of an individual DNA sample if one has access to high-density genomic data for that specific individual from another source and the allele frequencies for the case and control groups from publicly available aggregate datasets. …..

Two recent publications about research ethics in the genomics era:

Ethical and Practical Issues Associated with Aggregating Databases by David R Karp and 14 co-authors, PLoS Med 2008(Sep 23); 5(9): e190 [PubMed Record]. Excerpt:

Box 1. Recommendations

1. Determine whether initial consent and ethical approval will allow secondary research.
2. Ensure that there are appropriate data security mechanisms and review bodies to protect privacy interests in aggregated databases.
3. Informed consent should take into account the potential incorporation of data into aggregated databases.
4. Address special challenges of using data obtained from existing databases.
5. Pursue efforts directed at standardization of data.
6. Establish data sharing rules, including attribution of contributions.
7. Adopt “best practices” to avoid identifiability of the data.

And, Informed Consent in the Genomics Era by Deborah Mascalzoni, Andrew Hicks, Peter Pramstaller, Matthias Wjst, PLoS Med 2008(Sep 16); 5(9): e192 [PubMed Record]. Summary Points:

* Genetic cohort studies storing biological materials hold great promise for medical research, but also present new problems that are profoundly different from the classical clinical trial for which informed consent was developed.
* The classical risk/benefit analysis of physical harm doesn’t take into account new threats to the individual such as uninsurability, unemployability, genetic discrimination, or disruption of family relationships.
* Traditional informed consent may therefore no longer be appropriate when dealing with long-term studies using biological materials.
* Informed consent should be seen as an ongoing process between researcher and participant, and not just as a once-and-for-all decision.
* Research following the initial storage of samples needs to be likewise explained and may be announced using new communication methods.

The publications cited above are all in PLoS journals, and are OA.

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