Archive for August, 2007

The mind-cancer survival question

August 25, 2007 at 4:41 pm · Filed under Open Access ·Tagged

There has been much interest in the controversial possibility that psychosocial interventions might be used to prolong the survival of cancer patients. See, for example: The mind – body connection and cancer: Can support groups help me live longer? (Oral Cancer Foundation, undated). Excerpt:

Groups have become popular as a means of support among patients. They got an enormous boost in 1989 when Dr. David Spiegel, a psychiatrist at Stanford University, reported a ten-year study showing that women receiving standard treatment for metastatic breast cancer who had participated in group therapy lived longer by an average of eighteen months. The study was not originally designed to look at survival, and the women were never told that group sessions might influence their survival. Published in the British medical journal Lancet, this study created a great stir in the medical community and among patients. …

This topic is of great interest to lay readers. For example, a search of the Breast Cancer Mailing List Archives for the key words ‘David Spiegel’ yielded almost 200 messages. [A sidebar: research involving messages sent to such mailing lists raises issues of Internet research ethics about ‘list mining‘].

In view of the great interest (especially from a lay perspective) in research on psychosocial oncology, one might hope that a high proportion the relevant research articles would be OA. They aren’t.

One example: the Journal of Psychosocial Oncology isn’t an OA journal. (However, according to information available via the section on ‘Preprint Distribution Rights’ of the Publication Agreement of Haworth Press, Green OA is permitted – that is, authors can archive the preprint, and can replace it with the final draft post-refereeing. A summary of this policy is also available via the SHERPA/RoMEO website).

Another example is provided by the article mentioned in the above excerpt. It’s: Effect of psychosocial treatment on survival of patients with metastatic breast cancer, by Spiegel D, Bloom JR, Kraemer HC, Gottheil E, Lancet 1989(14 Oct); 2(8668): 888-91. Only the Abstract is freely accessible, via the Elsevier Article Locator.

The first author, David Spiegel, is a member of the Stanford Cancer Center. A list of publications provides access to the abstracts of each published article (but not to the full text).

A PubMed search for articles authored by David Spiegel yielded a set of 109 articles. Of these, 8 were identified by PubMed to permit, at present, free access to the full text. Of the most recent 20 articles, only one is identified as providing free access to the full text. Of these first 20 articles, Google Scholar and Google searches yielded free access to the full text of one additonal article (2/20 = 10%).

However, articles co-authored by Janine Giese-Davis can be accessed via the publications of Janine Giese-Davis, after a login/password for a downloadable publication has been obtained from the author via email.

The current version of her webpage hasn’t been updated yet to include access to a recently-published article, “Effects of supportive-expressive group therapy on survival of patients with metastatic breast cancer : a randomized prospective trial”, by David Spiegel, Lisa D. Butler, Janine Giese-Davis and colleagues, Cancer 2007; 110(5): 1130-38 (Epub Jul 23). A PubMed abstract is available, but a subscription is required to access the full text. An excerpt (Conclusions):

The earlier finding that longer survival was associated with supportive-expressive group therapy was not replicated. Although it is possible that psychosocial effects on survival are relevant to a small subsample of women who are more refractory to current hormonal treatments, further research is required to investigate subgroup differences.

A news release about this publication is: Support groups don’t extend survival of metastatic breast cancer patients, Stanford study finds, Stanford University Medical Center, 22 July, 2007.

A commentary about this same article is: Group Therapy Fails To Improve Breast Cancer Survival, by David Sampson, Director, Medical & Scientific Communications, American Cancer Society (23 July 2007).

How about access to relevant recent reviews? There’s a recent OA review: The effect of psychosocial factors on breast cancer outcome: a systematic review, by Matthew E Falagas and five colleagues (Breast Cancer Research 2007; 9: R44). It’s identified as a ‘highly accessed‘ OA article. Excerpt (Conclusion):

Most of the studies show a significant relationship between psychosocial factors and survival, but the actual psychosocial variables related to survival are not consistently measured across studies and the findings for many of the psychosocial variables with survival/recurrence are not consistent across studies. Thus, more research is warranted regarding the role of social support, marriage, minimizing and denial, depression and constraint of emotions on breast cancer survival.

Another recent review isn’t OA. It’s:What is the state of the evidence on the mind-cancer survival question, and where do we go from here? A point of view, by Joanne Stephen, Michelle Rahn, Marja Verhoef, Anne Leis, Support Care Cancer 2007(Aug); 15(8): 923-30. Epub 2007 Jun 26. This is a Springer journal, and only the Abstract is freely accessible. (See also the Abstract in the BioInfoBank Library).

An excerpt from the Abstract:

Some researchers view the mind-cancer survival question as resolved and negative, whereas others identify conceptual and methodological challenges and view the possible impact of psychosocial factors on survival as simply unproven. We take the position that the question is unanswered.

It seems likley that there will be additional attempts made to answer the question. Those who attempt to do so should be encouraged to provide open access to their peer-reviewed publications.

Still uncertain about how to do this? For a brief summary of several options that are available, see an item in Biology Library News, Washington University in St. Louis (23 August 2007). This news item includes a link to a summary of the relevant issues. The options that are listed don’t explicitly include the ‘request a login/password’ approach built into the publications page of Janine Giese-Davis.

Not all of these options provide optimal access. However, they are compatible with the goal of John Willinsky’s book: ‘incremental advances in the circulation of knowledge’.

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Cancer stem cells for breast cancer research

August 16, 2007 at 5:43 pm · Filed under Open Access ·Tagged ,

A news item, Newly created cancer stem cells could aid breast cancer research, by Alyssa Kneller, Whitehead Institute for Biomedical Research (13 August 2007) is about an article, “Transformation of Different Human Breast Epithelial Cell Types Leads to Distinct Tumor Phenotypes”, Cancer Cell 2007(14 Aug); 12(2): 160-170. The authors are Tan A. Ince, Andrea L. Richardson, George W. Bell, Maki Saitoh, Samuel Godar, Antoine E. Karnoub, James D. Iglehart and Robert A. Weinberg.

The full text isn’t freely accessible from this Cell Press journal. (For previous posts to this blog about Cell Press journals, see: Paying a fee for Green OA, and Stem cell research). Only the Summary is accessible without a subscription:

We investigated the influence of normal cell phenotype on the neoplastic phenotype by comparing tumors derived from two different normal human mammary epithelial cell populations, one of which was isolated using a new culture medium. Transformation of these two cell populations with the same set of genetic elements yielded cells that formed tumor xenografts exhibiting major differences in histopathology, tumorigenicity, and metastatic behavior. While one cell type (HMECs) yielded squamous cell carcinomas, the other cell type (BPECs) yielded tumors closely resembling human breast adenocarcinomas. Transformed BPECs gave rise to lung metastases and were up to 10[power]4-fold more tumorigenic than transformed HMECs, which are nonmetastatic. Hence, the pre-existing differences between BPECs and HMECs strongly influence the phenotypes of their transformed derivatives.

The corresponding author is Robert A. Weinberg, a senior cancer researcher who is the author of a well-received book, Biology of Cancer (Publisher: Garland, 30 June 2006).

A PubMed search for articles authored by RA Weinberg yielded a set of 301 articles. (The article cited above hadn’t been indexed by PubMed yet). Of these 301 articles, links to free full text were provided via PubMed for 108 (36%). Of the most recent 20 articles, 6 have PubMed links to free full text (30%). Searches via Google Scholar and Google quickly revealed free full text versions of 7 of the 14 other articles in the 20 most recent articles indexed by PubMed, for a total of 13/20 (65%). Usually, these latter free full text versions were available because an embargo period had elapsed.

In subsequent posts, I hope to provide more examples of this kind. My reason for an interest in such examples? It’s the leading researchers in various fields of research and scholarship who serve as role models for their more junior colleagues.

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More on BioMed Central memberships

August 10, 2007 at 11:44 pm · Filed under Open Access

The message from Ann Okerson, R. Kenny Marone and David Stern of the Yale University Library, Library drops BioMed Central’s Open Access membership (3 August 2007) has generated some interest. See, for example, an article by Andrea Gawrylewski, Yale dumps BioMed Central, The Scientist (August 9, 2007), and the comments that are posted at the end of the article. An excerpt from a comment posted by Matthew Cockerill of BioMed Central:

One angle that is unfortunately missing from The Scientist’s article is the perspective of a research funder. As discussed in BioMed Central’s public response to Yale, funders are now playing a key role in helping libraries to cover the costs of open access, at least in a transitional phase while the bulk of libraries budgets remains continues to pay for subscriptions.

For another response, see: Yale Drops It’s Pre-Pay Membership to BioMed Central, posted by Katie Newman (9 August 2007) to Scholarly Communication (University of Illinois at Urbana-Champaign). Excerpt:

It should be noted that BMC’s Institutional Membership program, whereby universities (usually the library) pre-pay all or most of the author’s article fees is not the only way in which the institution can show it’s support for the BMC flavor of open access. BMC also offers a “Supporting Membership” which is not tied to the number of articles submitted from an institution; it offers a modest (usually 15%) reduction in the article publication charge.

See also: BioMed Central: Supporters Membership and List of members.

Of the 28 Canadian Members, 20 are “supporter members“. There are 3 Canadian “Former Members”.

As is pointed out by Katie Newman, for researchers whose institutions are “supporter members” of BioMed Central, a discounted article processing charge is payable by the author. Excerpt from Supporter Members:

Supporter Members pay a flat rate annual Membership fee based on the number of biology, chemistry, physics and medical researchers and graduate students at the institution. Members of the institution are then given a 15% discount on the APC when publishing in our journals.

Very small institution (21-500 faculty and postgraduate students in biology, chemistry and medicine): £1120 [US$1994, €1698].

Very large institution (5001-10000 faculty and postgraduate students in biology, chemistry and medicine): £5596 [US$9967; €8494].

Some statistics about “Number of Faculty” and “Number of Graduate / Postgraduate Students” for various Universities can be obtained via the www.topuniversities.com website. However, the data are totals, not numbers in biology, chemistry and medicine.

A relevant previous post (2 March 2007) was: Scenarios about paying for OA. Excerpts:

One focal point for the debate has been on revenues from academic institutions (a major source of support for knowledge dissemination), relative to revenues from funding agencies (a major source of support for knowledge generation). …

…

More evidence-based analyses of a variety of scenarios are needed.

What does seem clear is that the perspectives of those involved in subscription-based publishing, in fee-based OA publishing, in library acquisitions and in the provision of support for knowledge generation, will all differ. Whose perspectives will prevail in the longer term? One hypothesis: the points of view that will prevail will be those of the researchers and scholars whose work turns out to have had the greatest impact. (Unfortunately, this isn’t a very useful hypothesis, because it can’t be tested easily or quickly, and because the results seem likely to vary from discipline to discipline, and even across subdisciplines).

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Trustworthiness of Wikipedia entries

August 6, 2007 at 12:12 pm · Filed under Open Access ·Tagged

A recent commentary by Brock Read, Software Weighs Wikipedians’ Trustworthiness (Chronicle of Higher Education blog, 3 August 2007) is interesting. An excerpt:

A Wikipedian with a distinguished record of unchanged edits is declared trustworthy, and his or her contributions are left untouched on the Santa Cruz team’s color-coded pages. But a contributor whose posts have frequently been changed or deleted is considered suspect, and his or her content is highlighted in orange.

One of Peter Suber’s comments (see Color-coding Wikipedia entries by trustworthiness,Open Access News blog, 4 August 2007):

Some bad entries go uncorrected because few people read them. Hence, I’d trust an entry more if it had a low rate of overwrites and a high rate of readership. Could the algorithm take the extra variable into account?

I wondered: might Google and Google Scholar be helpful?

A webpage at the UCSC Wiki Lab provides details about the software. The demo currently contains only a few hundred pages from Wikipedia. Once there, one can click on ‘Random page‘ on the left-hand side to get to other pages.

So, yesterday (Aug 5) I selected a ‘random page‘. Then I used the results obtained as key words in Google Scholar (GS) and Google (G) searches, and noted the number of results for each search. Finally, I examined the results of the Google search for links to entries in Wikipedia and in Encyclopaedia Britannica. My results for the first series of 10 consecutive ‘random pages’ were:

Page 1 was: Corrado Gini (little of the text was highlighted in orange).
GS: about 725 results for “Corrado Gini”.
G: about 22,300 results for “Corrado Gini.
G result #1: Corrado Gini – Wikipedia.
G result #3: Corrado Gini – Britannica.

Page 2 was: Clark Ashton Smith (little orange).
GS: about 65 results for “Clark Ashton Smith”.
G: about 172,000 results for “Clark Ashton Smith”.
G result #3: Clark Ashton Smith – Wikipedia.
[No Britannica entry found in the first 100 results]

Page 3 was: Corcovado (little orange).
GS: about 2,600 results for Corcovado.
G: about 1,550,000 results for Corcovado.
G result #1: Corcovado – Wikipedia.
G result #16: Mount Corcovado – Britannica.

Page 4 was: Chaparral (little orange – noted that the word has multiple uses).
GS: about 17,300 results for Chaparral.
G: about 4,680,000 results for Chaparral.
G result #5: Chaparral – Wikipedia.
G result #73: Chaparral – Britannica.

Page 5 was: Donegal fiddle tradition (some orange).
GS: 3 results for “Donegal fiddle tradition”.
G: about 2,470 results for “Donegal fiddle tradition”.
G result #1: Donegal fiddle tradition – Wikipedia.
[No Britannica entry found in the first 100 results]

Page 6 was: Caribbean Sea (little orange).
GS: about 17,900 results for Caribbean Sea.
G: about 1,890,000 results for Caribbean Sea.
G result #1: Caribbean Sea – Wikipedia.
G result #8: Caribbean Sea – Britannica.

Page 7 was: CCC (mostly orange – the term has various meanings).
GS: about 478,000 results for CCC (e.g. initials of an author).
G: about 28,300,000 results for CCC (e.g. stock symbol for a company).
G result #24: CCC – Wikipedia.
[No Britannica entry found in the first 100 results]

Page 8 was: Canton (mostly orange – the word has various meanings).
GS: about 131,000 results for Canton (e.g. surname of an author).
G: about 38,500,000 results for Canton.
G result #4: Canton – Wikipedia
[No Britannica entry found in the first 100 results]

Page 9 was: Commodore 64 (little orange).
GS: about 1,350 results for Commodore 64.
G: about 2,220,000 results for Commodore 64.
G result #1: Commodore 64 – Wikipedia
[No Britannica entry found in the first 100 results]

Page 10 was: Collection (mostly orange – the word has various meanings).
GS: about 7,570,000 results for Collection.
G: about 471,000,000 results for Collection.
G result #2: Collection – Wikipedia
[No Britannica entry found in the first 100 results]

Although only a very small sample of 10 pages was examined, some interesting findings were:

1) Nine of the 10 pages were about entries beginning with the letter “C”.

2) The pages that showed the most obvious orange highlighting were those for key words that had multiple meanings.

3) Google Scholar yielded results for all 10 searches. However, #7 (“CCC”) and #8 (“Canton”) were identified by Google Scholar as authors’ initials (for “CCC”) or surnames (for “Canton”).

4) For all 10 key words, Wikipedia entries were ranked higher by Google’s ranking algorithm than were entries in Encyclopaedia Britannica.

Hence, it appears that searches using Google and Google Scholar may serve as useful adjuncts to any assessments of the trustworthiness of entries in Wikipedia.

And, I agree (as noted by Matthew Cockerill, BioMed Central blog, 16 March 2007) that Wikipedia and OA are a “natural match“. Just as the OA movement can do much to contribute to the further development of Wikipedia, so can Wikipedia help greatly to foster awareness of the benefits of OA. See also: John Willinsky, What open access research can do for Wikipedia, First Monday 2007(Mar); 12(3).

On the basis of this sample of 10 entries, Wikipedia and Google are also a “natural match“.

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On the commons (and MaRS)

August 1, 2007 at 11:18 pm · Filed under Open Access ·Tagged

MaRS (a not-for-profit corporation founded in 2000 and located in Toronto’s downtown “Discovery District”) hosts a blog. A recent post in the ‘Today’s Picks‘ category of the blog is Valuing the commons, by Kathryn Fitzgerald, 24 July 2007. An excerpt:

The idea of a commons encompassing both tangible natural resources and intangible assets like information is gaining ground in contemporary discourse. The concept has been used to support diverse goals, from the regulation of carbon dioxide to open access to information. In business, the idea of the commons drives the corporate social responsibility movement, and is the inspiration behind entrepreneur Peter Barnes’ recent book, Capitalism 3.0: A Guide to Reclaiming the Commons.

Also, links are provided to:

Creative Commons

and

Science Commons

What’s MaRS about? As noted in the webpage Explore MaRS,

MaRS is a convergence innovation centre dedicated to accelerating the commercialization of new ideas and new technologies by fostering the coming together of capital, science and business.

So, MaRS can be regarded as a Canadian example of a contemporary approach to science policy. (See also some comments about science policy in the previous post, Open Access Science and Science Policy).

For more information about MaRS, see:

MaRS Discovery District (via the website of the Office of the Premier of Ontario)

Visit MaRS (via the website of the Innovations Group, University of Toronto)

MaRS Phase 2 (John Barber. Globe & Mail, 19 June 2007, via the SkyscraperPage.com Forum)

MaRS Discovery District (from Wikipedia)

One of the MaRS Centre tenants is the Ontario Institute for Cancer Research (OICR). On 30 May 2007, I attended an event at the MaRS Center (I’m grateful to the OICR for the invitation). This is a news item about the event: Canada and California team up in fight against cancer. Might this latter collaboration involve, as it develops, some “open access science”? I hope so.

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