Latest Article Alert from BMC Public Health

The latest articles from BMC Public Health, published between 19-Apr-2012 and 26-Apr-2012

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Study protocol
Weight gain prevention among black women in the rural community health center setting:

Today is the day!

Today is the day, our Right to Research Coalition Day of Action in support of the Federal Research Public Access Act!

If you haven’t already, please take a few moments to draft an op-ed or letter to the editor explaining FRPAA and how it would benefit you and your campus community, then submit it to your local newspapers. These articles are very effective advocacy tools and demonstrate to your representatives and your local community the importance of this issue and this legislation. Furthermore, you will help raise awareness of the bill and inspire others to contact their representatives, providing a significant boost to FRPAA and its chances to become law.

You can find more details in our post announcing the day of action as well as talking points and tips for writing to your newspaper.

We’re excited to see pro-FRPAA articles appear in campus and local newspapers across the country over the next week, and don’t forget to send a link to nick [at] arl [dot] org when your story is run.

Thanks for your help in making the FRPAA Day of Action a success and bringing FRPAA one step closer to becoming law!

Observing World Malaria Day 2012: Sustain Gains, Save Lives

Today is the fifth annual World Malaria Day, commemorated every April 25 to recognize and encourage global efforts to control malaria. This year’s theme, “Sustain Gains, Save Lives: Invest in Malaria,” alludes to the many important advances against the malaria parasite that have been achieved in recent years, but also includes a warning: we must continue to invest in malaria research and maintain our vigilance to ensure that painstakingly earned gains are not surrendered to complacency.

Based on the 251 malaria-related PLoS ONE papers published since last year’s World Malaria Day, it’s pretty clear to us that the research community is maintaining its commitment to this disease. Instead of trying to provide an overview of all of these articles, which cover perspectives as diverse as public health, ecology, and microbiology, we decided to observe the day by highlighting a single article that, like this year’s theme, emphasizes the importance of continued research as the parasite proves itself to be a constantly evolving target.

The study, published last October, monitors drug resistance in the causative parasite Plasmodium falciparum in Mozambique over five years, from 2006 to 2010, as the recommended drug treatment was adjusted. The researchers, led by Jaishree Raman of the South African Medical Research Council, found that the incidence of parasitic resistance to the originally recommended drug regimen increased significantly over the course of the study, from 56.2% at the start up to 75.8% in 2010. This approximately 20% leap in resistance suggested that the preferred treatment at the time would become much less effective as its use increased.

However, the Mozambican Ministry of Healthy preempted this scenario by changing their recommended front-line drug treatment in 2008. The authors weren’t able to study the full impact of this policy change, though, because it was not fully deployed until 2010, at which point the study was winding down – further highlighting the need for continued careful monitoring as new treatments are introduced.

You can learn more about World Malaria Day at Roll Back Malaria and the World Health Organization, and read about some additional malaria papers from last year’s World Malaria day post.

Citation: Raman J, Mauff K, Muianga P, Mussa A, Maharaj R, et al. (2011) Five Years of Antimalarial Resistance Marker Surveillance in Gaza Province, Mozambique, Following Artemisinin-Based Combination Therapy Roll Out. PLoS ONE 6(10): e25992. doi:10.1371/journal.pone.0025992

Image source: eyeweed on Flickr

Advances in Open Access à la Nature Publishing Group

Advances in Open Access à la Nature Publishing Group

With its recent launch of Light: Science and Applications, an open access (OA) physical sciences journal, and several more OA specialist publications planned for this year, Nature Publishing Group (NPG) is moving forward with its plan to include this publishing model in the center of its business. Though not every NPG journal is fair game for open access, it seems – top-tier publications will remain under a subscription-based model – specialist titles may be a place for further expansion as open access continues to develop.

Text-mining the scholarly literature: towards a set of universal Principles; Update and strategy

For some years I have seen the primary literature as an enormous untapped resource of scholarly information. We humans are very good at some aspects of “reading the literature” but there are many areas where machines are better and should be used. These include scale (hundreds of thousands of manuscripts), checking, validation, transformation (e.g. scientific units), deduction (many papers have implicit semantics), aggregation of knowledge, and much more. We are now reaching the time when the technology of “text-mining” is mature enough to deploy and, for example, my group and I have developed among the best tools in the world for mining chemistry. I am now expanding that to other fields which I will describe in later posts.

In general the readers of the scholarly literature (who may include the #scholarlypoor) have been seriously frustrated by the restrictions imposed by publishers and universally agreed by librarians. Most subscriptions to most major journals have terms forbidding readers to mine/crawl/index/extract etc. This is not a consequence of copyright – it is an additional restriction imposed by published and apparently automatically assented to by academic purchasing systems (mainly libraries). This automatic assent has done scholarship a grave disservice, so I give the library community a chance to correct the historical record:

Has any library ever publicly challenged the terms of use [on mining] set by publishers? I haven’t seen any. But I’d be grateful to know public cases, and what happened. My current view is that publishers set conditions and that libraries accept them verbatim, which, unfortunately, means that they don’t have a track record of fighting for text-mining or other freedoms.

Moving on, the UK Hargreaves report has recommended removing these restrictions (which are not legally required) and also modifying copyright law. My grapevine suggests there is a high probability that significant changes will be made and that “text-mining” will become widely available without requiring explicit permission. We should prepare for this, and any responsible publisher and library/purchaser should be preparing for this.

A month ago I and colleagues in OKF submitted cases to the Hargreaves process. As part of that I asked 6 major publishers whether I could “text-mine” their journals. Naomi Lillie of OKF is summarising the results and I will keep you in suspense till then. It’s fair to say some were helpful, some were not and some were fuzzy (for whatever motivation).

A number of publishers said we should discuss it with the library. There is no need for this. I and my group can text mine material by myself – in one week Daniel Lowe extracted 500,000 chemical reactions from the US Patent Office without needing any help. Nick Day has built PubCrawler and extracted 200,000 crystal structures from supplemental information without any help. The only thing I need is:

  • An assurance I won’t be sued for behaving like a responsible scholar
  • An assurance that my institution won’t get cut off for (my) responsible behaviour

In case anyone in the publishing or library communities doesn’t understand what “responsible” means, it means:

  • I do not intend deliberately to re-publish the publishers manuscripts (“the PDF”) in bulk without valid scholarly reason.

I am a responsible scholar. I conform to health and safety. I obey the law of the UK. I do not steal. I can justify the expenditures on my grants. I attempt to value and promote human equality in my scholarship. I try to give credit where it is due. Responsible scholarship is a fundamental principle which I believe applies to almost all readers of the scholarly literature. Occasionally I and others fail – there are ample mechanisms for addressing these without forbidding textmining.

So this post asserts my absolute right as a subscriber to the scholarly literature to carry out textmining and to disseminate the results to anyone. I do not need any other permissions.

A number of details follow which I’ll address in later posts.

At present, therefore, a group of us – under the aegis of the Open Knowledge Foundation – is drafting a set of principles for textmining. They include:

We shall come up with a manifesto/set-of-principles. This will be a statement of our rights and our responsibilities. It is not a negotiation, anymore than Tom Paine or the Founding fathers negotiated in the construction of their declarations. Or, more recently, the BBB declarations of Open Access. Those declaration are priceless – it’s just a pity that there are not enough who believe in them enough to push for their universal acceptance. We shall not make the same mistake with the principles of textmining.


Earth Day, Every Day

Dams sorted by status (existing and planned) and size (2–99 MW, 100–999 MW, and ?1,000 MW capacity).

Although the nationally celebrated Earth Day has just passed, it’s important to consider our impact on the environment every day.  In their recently published article “Proliferation of Hydroelectric Dams in the Andean Amazon and Implications for Andes-Amazon Connectivity,” authors Matt Finer and Clinton N. Jenkins highlight a constant environmental concern; meeting the world’s growing energy demands. Finer and Jenkins developed a strategic ecological impact assessment of planned dams from the Andes to the Amazon. Their findings point to the need for this kind of heightened environmental awareness every day.


Due to rising energy demands and abundant untapped potential, hydropower projects are rapidly increasing in the Neotropics. This is especially true in the wet and rugged Andean Amazon, where regional governments are prioritizing new hydroelectric dams as the centerpiece of long-term energy plans. However, the current planning for hydropower lacks adequate regional and basin-scale assessment of potential ecological impacts. This lack of strategic planning is particularly problematic given the intimate link between the Andes and Amazonian flood plain, together one of the most species rich zones on Earth. We examined the potential ecological impacts, in terms of river connectivity and forest loss, of the planned proliferation of hydroelectric dams across all Andean tributaries of the Amazon River. Considering data on the full portfolios of existing and planned dams, along with data on roads and transmission line systems, we developed a new conceptual framework to estimate the relative impacts of all planned dams. There are plans for 151 new dams greater than 2 MW over the next 20 years, more than a 300% increase. These dams would include five of the six major Andean tributaries of the Amazon. Our ecological impact analysis classified 47% of the potential new dams as high impact and just 19% as low impact. Sixty percent of the dams would cause the first major break in connectivity between protected Andean headwaters and the lowland Amazon. More than 80% would drive deforestation due to new roads, transmission lines, or inundation. We conclude with a discussion of three major policy implications of these findings. 1) There is a critical need for further strategic regional and basin scale evaluation of dams. 2) There is an urgent need for a strategic plan to maintain Andes-Amazon connectivity. 3) Reconsideration of hydropower as a low-impact energy source in the Neotropics.

Panton Fellows, Principles in Japanese, #pantonscience



It’s been an exciting week in Pantonia. I have been very active with our new Panton Fellows ( Last Monday Ross Mounce came over to Cambridge and we looked in depth about liberating information about phylogenetic trees. This is exciting and keeps me up at night and active on train journeys. And yesterday I took the train to Oxford to visit Sophie Kershaw who’s putting together a radically different course for Graduates, with emphasis in reproducible computing. I’m deliberately downplaying both of these here, as they’ll be telling you all about what they are doing.

Part of yesterday was an evening meeting run by Jenny Molloy – a new Open Science groups with about 12 of us in the Oxford eResearch Centre (OeRC) where we met Dave de Roure who took us out the dinner in the Royal Oak. While there we discussed in some depth what need to be done for text-mining including Diane Cabell and Dave Shotton. It’s really great to see critical mass in this way. I will have a LOT to write about textmining.

So today I met with Ayumi Koso (above) from Tokyo. Ayumi works with the Japanese government in Tokyo on the National Bioscience Database Centre (NBDC). She has already translated the Panton Principles into Japanese ( ). She’s staying in Cambridge and so today has a chance to meet some OKF people. Here’s our visit to the Panton Arms, preceded by a visit to Hinxton/Sanger Centre to visit Tim Hubbard (OKF advisory). And this afternoon Laura Newman will be coming round to meet.

I am really fortunate to be living in the middle of all this.

(We’ve decided today that the Panton hashtag is #pantonscience)


Unlock our knowledge about alternative energy and renewable technologies – now!

It is scandalous that much of our collective knowledge about alternative energy and renewable technologies is kept locked behind an Elsevier paywall! This is one area where clearly everyone anywhere on the planet with the inclination to read about the possibilities and push for solutions, whether through developing more basic knowledge or transferring knowledge to the business sector, should have immediate, barrier-free access. This is one area where the need is too great to permit for ANY embargo period.

Science works in step-wise fashion, like a detective mystery. One scientist discovers a clue; another builds on the discovery, until we have a new body of knowledge or real-world implementations, or both. If a useful discovery sequence takes six steps, with about 6 months of research for each step, then with no embargoes, the process takes 3 years. With a one-year embargo at each step, the whole sequence takes 9 years (3 years for research, 6 years for embargoes). Consider the impact of 6 more years of increasing greenhouse gases on climate change, and it is easy to see why the public good of rapid advancement in this area far outweighs an outmoded, print-based business model.

Here are the 29 journals Elsevier publishes in this area, from this page:

Algal Research
Applied Energy
Biomass & Bioenergy
Bioresource Technology
Current Opinion in Environmental Sustainability
Electric Power Systems Research
Energy and Buildings
Energy Conversion and Management
Energy Strategy Reviews
Fuel and Energy Abstracts
Fuel Cell Virtual Journal
Fuel Cells Bulletin
Fuel Processing Technology
Geographical Abstracts: Human Geography
International Journal of Electrical Power & Energy Systems
International Journal of Greenhouse Gas Control
International Journal of Hydrogen Energy
Journal of Power Sources
Journal of Wind Engineering & Industrial Aerodynamics
Ocean Engineering
Renewable & Sustainable Energy Reviews
Renewable Energy
Renewable Energy Focus
Solar Energy
Solar Energy Materials & Solar Cells
If funders are considering different embargoes for different fields, let’s argue for immediate open access in this one – and let’s call on the editors and authors of these journals to revolt and move to an open access publisher and model.

Total impact: a critical perspective

Total impact is a set of alternative metrics for scholarship. Total impact looks at a number of factors, including social networking tools such as Facebook and Twitter. As a research tool, Total Impact has a lot of potential, to explore how works are used and what impact they have. As an alternative metric to evaluate the quality of scholarship – an alternative to impact factor – there are a number of potential serious problems to consider.

First, there is the question of whether the current push towards quantitative metrics makes any sense at all. I have talked about the problems of this kind of instrumental rationality is my book chapter, The implications of usage statistics as an economic factor in scholarly communication (In brief, usage stats are likely to have significant negative impacts, from discouraging use to discouraging important but not necessarily popular entire fields of research); and the second chapter of my draft thesis (search for irrational rationalization).

One example, from an interview study of scholarly monograph publishers I did recently, is the impact of pushing scholars to publish more books to obtain tenure. This pressure is not consistent with the time it takes to write books that are really worth publishing and reading; so in this instance, we have a quantitative metric intended to improve quality and productivity (of our academic staff) which appears to be lowering quality (more mediocre books, more book production when the problem for all of us is not enough reading material, but rather not enough time to read).

Research, both quantitative and qualitative, is my recommendation before putting too much stock in Total Impact or other alternative metrics as a replacement for Impact Factor in evaluating the quality of scholarship. Note that I do not recommend retaining Impact Factor, but rather minimizing or eliminating quantitative approaches to evaluating the quality of scholarship.

The use of social networking tools may be particularly problematic. One research area that I recommend is examining the effects of traditional biases. I would hypothesize that social networking tools would be likely to exhibit the following biases prevalent in modern society:

  • men would show more impact than women
  • minorities would have lower impact
  • developing country authors would have lower impact
  • introverts would have lower impact than extraverts
  • authors adept at social networking tools would have more impact than authors less comfortable with these media

In addition, I would suggest that metrics based on social networking tools could easily be manipulated, not only by authors but also by interested others. It doesn’t take much to imagine corporate polluters in favor of climate denial upping the impact of their preferred pseudo-science, or for drug companies to drive up the impact of studies making the drugs that they sell look good.

Another area to consider (for all kinds of tools, not just social networking tools), is the impact of funding considerations. If universities are relying more on corporate funders at a time in society such as today when the political will seems to be on the side of the wealthy who wish to cut spending on social justice, it is reasonable to hypothesize that there will be a smaller proportion of funding for social justice issues. What happens to research on poverty issues and its impact if there is less funding for research and academic positions in this area (hence fewer researchers), at the same time that there is less funding for government services and social workers (fewer potential readers and tweeters), and many of those poverty research is meant to help have lost their homes and jobs and may find it difficult to get internet access?

Accelerating small business in BC: celebrating the success of enterpreneur / philanthropist Irving K. Barber

This week British Columbia is mourning the passing of notable citizen and philanthropist Irving K. Barber. This post celebrates a small part of the achievements made possible by his generosity, the Small Business Accelerator program of the Irving K. Barber Learning Centre.

The Small Business Accelerator program is a highly innovative program and partnership of the University of British Columbia with BC’s public and other libraries and the BC business community.

From the website:

Business success depends on obtaining access to reliable information. The Small Business Accelerator is curated by business librarians and is your gateway to freely available business information, education, and assistance that is both current and trustworthy.

It is my hope that this small token of appreciation will encourage others to consider this model of cooperation, which is also a great model to illustrate how libraries and the business community can work together cooperatively, making use of open access resources, to benefit business and local communities (by making business accelerator programs available throughout the province.

[Disclosure: the Irving K. Barber Learning Centre is a key partner of the BC Electronic Library Network where I serve as Coordinator].