Scientists, Foundations, Libraries, Universities, and Advocates Unite and Issue New Recommendations to Make Research Freely Available to All Online

 

Those of you who follow my blog know this is one of my passions!

From the press release

September 12, 2012   Information Program

Scientists, Foundations, Libraries, Universities, and Advocates Unite and Issue New Recommendations to Make Research Freely Available to All Online

FOR IMMEDIATE RELEASE: September 12, 2012

CONTACT: Andrea Higginbotham, SPARC, andrea@arl.org; 202-296-2296

Amy Weil, Open Society Foundations, aweil@sorosny.org; 212-548-0381

WASHINGTON—In response to the growing demand to make research free and available to anyone with a computer and an internet connection, a diverse coalition today issued new recommendations that could usher in huge advances in the sciences, medicine, and health.

The recommendations were developed by leaders of the Open Access movement, which has worked for the past decade to provide the public with unrestricted, free access to scholarly research—much of which is publicly funded. Making the research publicly available to everyone—free of charge and without most copyright and licensing restrictions—will accelerate scientific research efforts and allow authors to reach a larger number of readers…

Related articles

• Ten Years After Budapest Open Access Initiative New Recommendations Released (infodocket.com)
• Whither Science Publishing? (the-scientist.com)
• Open access for development: a battle not yet won (scidev.net)
• UK government to make all publicly-funded scientific research freely available (rawstory.com)
• UK reseach to be freely available (bbc.co.uk)
• New open access recommendations ten years on from Budapest Open Access Initiative (okfn.org)
• Academic journals face a radical shake-up (economist.com)
• You: Free access to British scientific research to be available within two years (guardian.co.uk)

 

“Too much ownership of data and secrecy involved”

From the 21 March 2012 article by Gary Schwitzer at HealthNewsReviews.org

That’s what one author writes in a series of papers published in Circulation: Cardiovascular Quality and Outcomes this month addressing issues involving the integrity of research data.

Yale’s Harlan Krumholz writes: “Patients facing a decision deserve information that is based on all of the evidence.”  Further excerpt:

Every day, patients and their caregivers are faced with difficult decisions about treatment. They turn to physicians and other healthcare professionals to interpret the medical evidence and assist them in making individualized decisions.

Unfortunately, we are learning that what is published in the medical literature represents only a portion of the evidence that is relevant to the risks and benefits of available treatments. In a profession that seeks to rely on evidence, it is ironic that we tolerate a system that enables evidence to be outside of public view. Those who own data, usually scientists or industry, have the choice of what, where, and when to publish. As a result, our medical literature portrays only a partial picture of the evidence about clinical strategies, including drugs and devices. Experts have recently drawn attention to this issue, including contributions in this issue of our journal, but there is resistance to change….

The article goes on outline how sharing of clinical trial and research data could be shared for the common good.

Read the entire article here

Related articles

• Bias and error are rampant in medical literature (kevinmd.com)
• Data sharing as a moral imperative (Marilyn Mann’s blog)
• Open Science and Data Sharing in Clinical Research
  Basing Informed Decisions on the Totality of the Evidence (Circulation)
• Strengthening and Opening Up Health Research by Sharing Our Raw Data (Circulation)
• The Importance of Clinical Trial Data Sharing (Circulation)
• Scientific evidence (sixpointnineme.wordpress.com)
• Many NIH-funded clinical trials go unpublished over 2 years after completion (eurekalert.org)

European scientists call for greater integrity, openness, clarity and public engagement

From the 18 February Eureka News Alert

European-based speakers representing the fields of nuclear energy, genetically modified organisms, and harm reduction science in tobacco made the plea on 18 February at the Annual Meeting of the American Association for the Advancement of Science held in Vancouver, Canada. The panelists, each with pertinent experience of real-life scientific support to policy-making, offered first-hand advice on best practices and pitfalls when architecting science policy on both sides of the Atlantic. The 18 February symposium, titled “Exploding Myths on Reactor Security, Harm Reduction, and Genetically Modified Organisms,” featured a call for greater integrity, openness, clarity and public engagement on difficult to communicate issues of global significance. A key message was that science and policy do have a crucial relationship. But scientists should not think that they are policy-makers. Equally, science must remain independent. ‘Bad science’ and spin must be challenged more. Science coming out of industry must be trusted more. The symposium was moderated by the Irish Chief Scientific Advisor and Champion of EuroScience Open Forum 2012, Professor Patrick Cunningham….

…

Irish Chief Scientific Adviser, Professor Patrick Cunningham, in summing up, said that: “In policy decisions, important factors beyond the reach of science are often involved: fear, hype, ignorance, profit, resentment, economic and political advantage. And science does not always have clear answers. However, science and scientists have a special claim to be heard, provided they are committed to:

 

• Integrity: to uphold the inherent honesty of scientific enquiry and debate
• Openness: to keep the lab door open, and making clear any special interests
• Clarity: to speak in terms the public can understand
• Engagement: to demonstrate that we take our duty to society seriously.”

 

He added: “At the same time, policymakers should encourage scientists to speak out even when their research or assessment may be unpopular. Scientists should learn to stand up, shout up and when necessary, shut up. The voice of the rational middle ground should be louder.”

Related articles

• Europe needs a ‘RESCUE’ revolution (eurekalert.org)
• How AAAS Scientists View the Public, the Media, and the Political Process (bigthink.com)
• First E.U. Science Adviser: ‘We Are Sitting On a Goldmine’ (news.sciencemag.org)
• Collaboration: Expanding the very model of a modern major scientist (eurekalert.org)

NIH Launches Research Program to Explore Health Effects from Climate Change

 

Image via Wikipedia

NIH Launches Research Program to Explore Health Effects from Climate Change.

Excerpts from the Environmental News Bits Blog item

A new research program funded by the National Institutes of Health will explore the role that a changing climate has on human health. Led by NIH’s National Institute of Environmental Health Sciences (NIEHS), the program will research the risk factors that make people more vulnerable to heat exposure; changing weather patterns; changes in environmental exposures, such as air pollution and toxic chemicals; and the negative effects of climate change adaptation and mitigation efforts.

In addition to better understanding the direct and indirect human health risks in the United States and globally, one of the program’s goals is to determine which populations will be more susceptible and vulnerable to diseases exacerbated by climate change. Children, pregnant women, the elderly, people from low socioeconomic backgrounds, and those living in urban or coastal areas and storm centers may be at elevated risk. This program will also help to develop data, methods, and models to support health impact predictions.

“Governments and policy makers need to know what the health effects from climate change are and who is most at risk,” said John Balbus, M.D., NIEHS senior advisor for public health and lead for NIEHS’ efforts on climate change. “The research from this program will help guide public health interventions, to ultimately prevent harm to the most vulnerable people.”

The funding program is an outgrowth of two previous efforts led by NIH. A December 2009 workshop, sponsored by a trans-NIH working group, brought leaders in the field together to begin identifying priorities for NIH climate change research. NIH then led the ad hoc Interagency Working Group on Climate Change and Health in developing an outline of research needs, which are described in a report available atwww.niehs.nih.gov/climatereport.

Using Social Media to Enhance Your Research

Excerpts from Using Social Media to Enhance Your Research, at the Krafty Librarian blog

Daniel Hooker posted some nice slides on Using Social Media to Advance Your Research that he presented to a group of PhDs and post-docs at the UBC Faculty of Medicine.  I gave a similar presentation to World Health Interest Group at Case Western Reserve University.  I spoke about using blogs, Twitter, wikis, etc. in scientific research.

During my presentation some of the attendees got hung up on the tools and technologies as toys and the idea of communicating was lost.  Social media is just one method people can use to communicate, share ideas, protocols, methods, lab notes, etc. In the very broadest of terms, email is sort of social media.  You can email many people who can then pass that discussion along to others. Listservs are a perfect example of this.  But email has been around with us for such a long time that there is no real discussion about its communication potential.  Yet, email was once a new fangled communication toy.

Read this abstract from Science 1982. 12;215(4534):843-52.

Computer networks are an integral part of the rapid expansion of computing. Their emergence depends both on evolving communication technologies, such as packet-switching and satellites, and on diverse experiments and innovations in the software tools that exploit communications. The tools provide computer users with facilities such as electronic mail, access to remote computers, and electronic bulletin boards. Scientists can both adapt and extend tools to meet the communication needs of their work, and several networks are developing to serve particular scientific communities.

……

Blog examples:

• Useful Chemistry  -Chronicles research involving the synthesis of novel anti-malarial compounds. Closely tied to Useful Chemistry wiki

• Cold Spring Harbor Protocols –Discusses current events in biology with emphasis on lab techniques, protocols are highlighted & discussed in detail

• HUGO Matters  –Discusses topics relevant to human genetics and genomics

Lab Notes blogs:

• Cameron Neylon http://biolab.isis.rl.ac.uk/camerons_labblog

• Michael Barton http://www.michaelbarton.me.uk/research/

 Wiki examples:

• UsefulChem wiki –Synthesis of novel anti-malarial compounds, including experiments. It is completely open.

• OBF wiki –Open Bioinformatics Foundation focused on supporting open source programming in bioinformatics

• OpenWetWare –Promotes sharing of information, know-how and wisdom among researchers & groups working in biology & biological engineering. It is partially open.

• WikiPathways –Dedicated to the curation of biological pathways

• Yeast Genome wiki –Everything yeast including protocols, methods, reagents, strains

Lab or Research Group wikis:

• Kochlab notebook wiki –DNA unzipping data analysis. It is semi public.

• Rosania Research Group wiki –All lab notebooks of Department of Pharmaceutical Sciences at University of Michigan College of Pharmacy

 Twitter feeds:

• NatureNews

• NEJM

• NIHforFunding

• FASEBopa

• CellPressNews

Lists of scientists and researchers on Twitter:

• 100 Amazing Scientists You Should Follow on Twitter -organized according to discipline

• Biomedical Twitter People and Lists – List of people, companies, publishers, etc

The easiest way to have a rich and informative Twitter feed is to follow the people the leaders in your field are following and branch off from there.  By the way, Twitter’s site is ok for learning, but it really stinks for following any sort of conversation AND you always have to refresh the page (annoying). I highly recommend using Hootsuite or TweetDeck to monitor your Twitter feeds.  The thing I like about TweetDeck is that a little message pops up in the corner of my computer screen with the tweet. I can read it quickly and decide whether I want to ignore it, comment, or click on their link. Using Twitter on TweetDeck this way is very similar to how I use email because my email pops messages to my main screen too.

Really you need to sit down and figure out what your information needs are and the leaders in your field to follow.  This might be hard, but I bet there might be somebody in your field who is already doing it, so ask them, build off of what they are doing and tweek it to fit your needs.

Journal of Visualized Experiments

The Journal of Visualized Experiments is a peer reviewed, PubMed indexed journal devoted to the publication of biological, medical, chemical and physical research in a video format.

The editors believe that videos of techniques and procedures will greatly aid scientists in learning and keeping abreast of new advancements in scientific methods. They will be able to focus their time and thought more on other experimental aspects and thus speed up the process from hypothesis generating to publication.

Medical Research Article: Lies, Damned Lies, and Medical Science

Excerpts from the Atlantic October 20 article by David H. Freedman

[Summary] Much of what medical researchers conclude in their studies is misleading, exaggerated, or flat-out wrong. So why are doctors—to a striking extent—still drawing upon misinformation in their everyday practice? Dr. John Ioannidis has spent his career challenging his peers by exposing their bad science.[end of Summary]

…..wasn’t it possible, he asked, that drug companies were carefully selecting the topics of their studies—for example, comparing their new drugs against those already known to be inferior to others on the market—so that they were ahead of the game even before the data juggling began? “Maybe sometimes it’s the questions that are biased, not the answers,”[Flahiff’s emphasis] he said, flashing a friendly smile. Everyone nodded. Though the results of drug studies often make newspaper headlines, you have to wonder whether they prove anything at all. Indeed, given the breadth of the potential problems raised at the meeting, can any medical-research studies be trusted?….

…..

[Biostatistician and physician] Ioannidis was shocked at the range and reach of the reversals he was seeing in everyday medical research. “Randomized controlled trials,” which compare how one group responds to a treatment against how an identical group fares without the treatment, had long been considered nearly unshakable evidence, but they, too, ended up being wrong some of the time. “I realized even our gold-standard research had a lot of problems,” [Flahiff’s emphasis] he says. Baffled, he started looking for the specific ways in which studies were going wrong. And before long he discovered that the range of errors being committed was astonishing: from what questions researchers posed, to how they set up the studies, to which patients they recruited for the studies, to which measurements they took, to how they analyzed the data, to how they presented their results, to how particular studies came to be published in medical journals.[Flahiff’s emphasis]

This array suggested a bigger, underlying dysfunction, and Ioannidis thought he knew what it was. “The studies were biased,” he says.

…….He chose to publish one paper, fittingly, in the online journal PLoS Medicine, which is committed to running any methodologically sound article without regard to how “interesting” the results may be. In the paper, Ioannidis laid out a detailed mathematical proof that, assuming modest levels of researcher bias, typically imperfect research techniques, and the well-known tendency to focus on exciting rather than highly plausible theories, researchers will come up with wrong findings most of the time. Simply put, if you’re attracted to ideas that have a good chance of being wrong, and if you’re motivated to prove them right, and if you have a little wiggle room in how you assemble the evidence, you’ll probably succeed in proving wrong theories right. His model predicted, in different fields of medical research, rates of wrongness roughly corresponding to the observed rates at which findings were later convincingly refuted: 80 percent of non-randomized studies (by far the most common type) turn out to be wrong, as do 25 percent of supposedly gold-standard randomized trials, and as much as 10 percent of the platinum-standard large randomized trials. [Flahiff’s emphasis]
The article spelled out his belief that researchers were frequently manipulating data analyses, chasing career-advancing findings rather than good science, and even using the peer-review process—in which journals ask researchers to help decide which studies to publish—to suppress opposing views. “…

….he peer-review process often pressures researchers to shy away from striking out in genuinely new directions, and instead to build on the findings of their colleagues (that is, their potential reviewers) in ways that only seem like breakthroughs…

…He looked at three prominent health studies from the 1980s and 1990s that were each later soundly refuted, and discovered that researchers continued to cite the original results as correct more often than as flawed—in one case for at least 12 years after the results were discredited…..

…he’s concerned that, like many patients, he’ll end up with prescriptions for multiple drugs that will do little to help him, and may well harm him. “Usually what happens is that the doctor will ask for a suite of biochemical tests—liver fat, pancreas function, and so on,” she tells me. “The tests could turn up something, but they’re probably irrelevant. Just having a good talk with the patient and getting a close history is much more likely to tell me what’s wrong.”[Flahiff’s emphasis] Of course, the doctors have all been trained to order these tests, she notes, and doing so is a lot quicker than a long bedside chat….

…

 

 

Making Scientific Research Accessible to All

 

Melissa Hagemann. Photo: Laura Brahm for the Open Society Foundations

 

 

[Related to recent posting here Access to Knowledge for Consumers]

Excerpts from the interview with Melissa Hagemann about the Open Access Movement.
She is program manager in the Open Society Foundations Information Program. She’s also on the advisory board of theWikimedia Foundation, which operates Wikipedia

What is “Open Access”?

Open Access refers to the free online availability of research literature. It was first defined at a meeting organized by the Open Society Foundations in 2001, which led to the Budapest Open Access Initiative.  This initiative outlined two strategies for developing OA:

• Open Access Journals, which are journals, freely available worldwide, which do not rely upon the traditional subscription-based business model to generate their revenue; and
• Open Repositories, or archives where all scholarly research articles published by those associated with a university or within a discipline can be deposited.

In 2003, we added a third strategy, which is to advocate for public access to publicly funded research.

What are some of the most notable accomplishments of the open access movement so far?

Probably the single most important victory was a mandate adopted by the U.S. Congress which stipulates that all research funded by the National Institutes of Health (about $29 billion annually) be made freely available online.

While the NIH is the largest funder of research in the world, the OA movement has worked with governments and universities throughout the world to adopt similar mandates, and today there are 230 of them. In addition, there are over 5,500 OA journals and over 1,700 open repositories.

What major obstacles does the movement face at this moment?

As Open Access is so new, one of our main challenges is simply raising awareness of it and explaining the benefits of this new model.  At the same time, you can imagine that many within the publishing industry haven’t always been keen supporters of OA.

But I’m curious: How can the publishing industry benefit from Open Access? Wouldn’t they say they need the money to continue publishing? How do you persuade them that OA is a good thing?

While OA journals are freely available online, about half of them charge a processing fee (anywhere from $500 to $3,000 or so) per article. So there are commercial OA journal publishers which are doing quite well. Actually one of the largest OA publishers, BioMed Central, was purchased by Springer (the second largest scientific journal publisher) in 2008, and Springer pledged to keep all of the journals OA.

How can others get involved in advancing the issue?

Participating in an event during OA week is a great way to start! Then I would suggest learning more about OA, and OASIS is one of the best resources for information on the OA movement.

• If you’re a student, I recommend connecting with the Right to Research Coalition.
• If you’re an academic, you can self-archive copies of your research articles in your institutional repository or submit your article to anOA journal. You can also advocate for your institution to adopt an OA mandate at your university; 230 mandates have been adopted worldwide (see www.eprints.org/openaccess/policysignup).
• If you’re in a developing or transition country, the EIFL Open Access Program offers a wealth of support and services for librarians, academics, policymakers, and funders in these countries to tap into.
• If you’re based in the United States, you can support the Alliance for Taxpayer Access, which advocates for public access to publicly funded research in the U.S.

 

 

 

 

 

 

Surgeons fail to disclose big payments to journals

From a Reuters Health Information news item

Nearly half of surgeons who earned more than $1 million from companies that make orthopedic devices did not disclose it when they published medical journal articles, U.S. researchers said on Monday.

“The findings raise troubling questions about undisclosed payments or royalties and other fees from medical device companies that could lead to biased scientific conclusions,” said David Rothman of the Institute on Medicine as a Profession, a think tank based at Columbia University in New York.

Members of Congress including Senator Charles Grassley, an Iowa Republican, have been pushing to limit the influence drugmakers have over the practice of medicine in the United States after investigations revealed that Harvard University psychiatrist Dr. Joseph Biederman and others failed to fully disclose payments from drug companies.

Rothman’s team used a public database to check the accuracy of surgeons’ financial disclosure statements.

They focused on five companies: Biomet; DePuy Orthopedics, a unit of Johnson & Johnson; Smith & Nephew; Stryker and Zimmer.

These companies made a total of 1,654 payments that amounted to $248 million in 2007 for consulting, honoraria or other payments for services, the team reported.

How to Read a Research Paper (and also Understand Health News Research Items)

Biomedical research results are increasingly available to the public. However, caution is urged in interpreting results. For example, be very careful to not confuse causation with association.

(A recent news item about insulin use and cancer is very controversial. Some say insulin use can cause cancer, while others insist insulin users are predisposed to cancers.)

The MedlinePlus Topic Page Understanding Medical Research has links to tutorials, overviews, and more

A sampling of links

**Increasing Knowledge — How to Read a Research Paper(Lewy Body Dementia Association)

** Clinical Research & Clinical Trials(National Institute of Child Health and Human Development)

**Making Sense of Medical News (Nemours Foundation)

Related Blog Items

“Summaries for Patients” and other plain language summaries help patients and others understand medical studies and guidelines

Related articles

• NLM released several exciting enhancements that improve users’ ability to share and consume MedlinePlus content: (jflahiff.wordpress.com)
• Improving Health Care Decisions By Putting Research Into Practice (jflahiff.wordpress.com)

Transforming Discovery into Health

Excerpts from a recent interview with NIH (National Institutes of Health) Director Dr. Francis S. Collins

Revolution in Cancer Research

NIH-funded research has revolutionized how we think about cancer. A decade or two ago, cancer diagnosis was based on the organ involved and treatment depended on broadly aimed therapies that often greatly diminished a patient’s quality of life. Today, basic research in cancer biology is moving treatment toward more effective, less toxic therapies tailored to the genetic profile of each patient’s cancer.

Shortening the Pathway to Health

Whatever the disease, be it depression, diabetes, or something much rarer, NIH’s emphasis will be on translating basic discoveries into new diagnostic and treatment advances in the clinic. For many disorders, there are new opportunities for NIH to shorten and straighten the pathway from discovery to health.

This expectation is grounded in several recent developments: the dramatic acceleration of our basic understanding of hundreds of diseases, the establishment of NIH-supported centers that enable academic researchers to use such understanding to screen thousands of chemicals for potential drug candidates, and the emergence of public-private partnerships to aid the movement of drug candidates identified by academic researchers into the commercial development pipeline.