Short vs. full RSS feeds

Jonathan of PlagiarismToday posted about the pros/cons of full vs. short feeds and brought up a number of issues that I hadn't really thought about before.

Some feeds I subscribe to use short feeds, and some use the full. As a reader, I prefer the full feed -- I like not having to click to the actual blog to view the full version, only click to the full version if I have a comment to contribute or want to see what others are commenting, and the short feed versions sometimes make it hard to tell what the entry is really about (I have to confess that if I can't tell what it's about from the short feed, I usually just pass by instead of investigating - I'm sure this means I miss useful things, but it just seems inconvenient to have to go to the site).

I'm fairly new to blogging and I was thinking about this last week when looking at my Blogger settings. With my own blog, I contemplated switching to short feeds, because I thought it might give me a better idea of which posts were more "interesting" to those reading my blog and might prompt me to consider topics that aren't always at the forefront of my mind. Because I don't really like the short feed as a reader, though, I decided that it wasn't worth the potential inconvenience (and the burden of trying to make the first few words so great that people couldn't resist clicking to read the full entry!). I also don't feel at great risk of content theft (hadn't even occurred to me until I read the post linked above).

I'm wondering what others are thinking on this issue, as both readers and as blog authors.

Update:
A follow-up Plagiarism Today post about a petition against short feeds (petition launched by an Australian blogger).

Preparing for population-based genetic studies in the US

A recent press release from the National Institutes of Health reports that the National Human Genome Research Institute has awarded ~$2 million to Johns Hopkins University to "conduct a public discussion about future potential large U.S. population-based studies examining the roles of genes and environment in human health."

Possibly coming soon to an area near you...

As part of its two-year, $2 million pilot project, the Washington, D.C.-based Genetics and Public Policy Center will obtain input on issues related to large, population-based studies through a series of focus groups in Jackson, Miss.; Kansas City, Mo.; Middletown and Philadelphia, Pa; Phoenix, Ariz.; and Portland, Oregon. In addition to the focus groups, the center plans to carry out a national web-based survey of 4,000 individuals and will conduct town hall meetings attended by 1,000 people in the five states. Community leaders will be interviewed as well. The grant will also be used to develop educational materials for the participants, providing them with information about large, population-based studies for the focus groups, survey, and town hall meetings.

Collecting public concerns about large-scale projects to gather and analyze genetic information from populations of people in the US seems to be a key step in figuring out how such projects need to be organized to secure public support and participation - demystifying the intent of these projects, understanding how the average person perceives population-based genetic research and where any misunderstandings or misperceptions lie, what key ethical issues arise in such conversations, how people regarding confidentiality and anonymity with regard to this particular kind of research -- it will be very interesting to see what people are thinking about these issues and how they share them with the Hopkins team.

Clinical use of pharmacogenetic data

The American Association for Clinical Chemistry has posted draft guidelines from the National Academy of Clinical Biochemistry for clinical use of pharmacogenetic data, "Guidelines and Recommendations for Laboratory Analysis and Application of Pharmacogenetics to Clinical Practice (PDF; the committee members are listed here).

The guideline objectives:

"... to provide a systematic rigorous assessment of the discipline of pharmacogenetics as it applies to clinical laboratory testing and its application to clinical practice. Issues to be addressed will be: methodological (pre-analytical and analytical) considerations, standardization and quality assurance of testing; selection of appropriate PGx testing profiles; recommended reporting of test results and interpretation; standards needed for demonstration of clinical utility and efficacy; and, regulatory and other recommendations for effective use of pharmacogenetic information in a clinical setting."

The document is still in progress and is currently going through an open-comment phase to solicit outside reaction and opinion about its current direction.

If, like me, you need a quick refresher about what pharmacogenetics encompasses, this definition from the American Association of Pharmaceutical Scientists may help:

"Pharmacogenetics is the study of genetic causes of individual variations in drug response; pharmacogenomics more broadly involves genome-wide analysis of the genetic determinants of drug efficacy and toxicity. Primary candidate genes of interest include those encoding for drug receptors, metabolizing enzymes, and transporters. However, selection of optimal drug therapy may also involve disease susceptibility genes indirectly affecting drug response. Moreover, pharmacogenomics includes the identification of suitable targets for drug discovery and development" (Source).

The topic also has its own Medical Subject Heading and a quick search of pharmacogenetics returns 1000s of documents (e.g. this editorial from the Medical Journal of Australia).

This overview in the NCBI Science Primer also gives a very good introduction to the concept and its potential impact on how drugs are developed and prescribed in the future, exciting stuff.

N-of-1 trials

Biomed Central Family Practice has published an article considering the utility of n-of-1 trials in determining the best management practices for individual patients (full citation: Wegman AC, van der Windt DA, Stalman WA, de Vries TP. Conducting research in individual patients: lessons learnt from two series of N-of-1 trials. BMC Fam Pract. 2006 Sep 19;7(1):54). An n-of-1 trial is basically a randomized crossover trial in an individual patient, to compare two different treatments or treatment and placeboo, to gauge the most effective strategy in that particular patient.

This research design has also been receiving some attention lately for potential application in evaluating complementary and alternative medicine interventions.

Additional material:
- Bandolier definition
- NIH Interactive Textbook on Clinical Symptom Research: Ch. 6: Within-patient studies: crossover trials and n-of-1 studies
- Mahon J, Laupacis A, Donner A, Wood T. Randomised study of n of 1 trials versus standard practice. BMJ. 1996 Apr 27;312(7038):1069-74.
- example trial from clinicaltrials.gov: Randomized Trial Comparing N of 1 Trials to Standard Practice to Improve Adherence to Statins in Patients With Diabetes
- a quick PubMed search for more examples and discussion of this research design.

News: drug marketing and safety, genetic screening, physician-patient email

A few recent highlights from Medical News Today:

- Unexpected Effect Of Direct-to-consumer Drug Ads (also see this previous post)
- Safety Test Results On Children's Drugs Not Always Reaching Physicians Study Finds
- Medical Centers Should Follow Stanford's Lead In Banning Gifts From Drug Companies
- Industry Using Third Parties To Manage Public Concerns About Genetic Screening (also see this previous post)

And from the Center for Studying Health System Change (via Docuticker):
- Physicians Slow to Adopt Patient E-mail

British Library announces intellectual property manifesto

Today at the Labour Party Conference in the UK, the British Library launched their "manifesto," including intellectual property recommendations:

- "Existing limitations and exceptions to copyright law should be extended to encompass unambiguously the digital environment;
- Licenses providing access to digital material should not undermine longstanding limitations and exceptions such as ‘fair dealing'
- The right to copy material for preservation purposes – a core duty of all national libraries – should be extended to all copyrightable works;
- The copyright term for sound recordings should not be extended without empirical evidence of the benefits and due consideration of the needs of society as a whole;
- The US model for dealing with ‘orphan works' should be considered for the UK;
The length of copyright term for unpublished works should be brought into line with other terms (ie: life plus 70 years)."

Links:
- British Library press release
- full text of intellectual property manifesto (PDF)

Commentary:
- Nate Anderson of Ars Technica: "British Library issues copyright manifesto" - "The British Library has the Magna Carta, the Lindisfarne Gospels, and Leonardo da Vinci's notebook, but it's still not happy. Why not? Because it has the intellectual property blues."
- ZDNet UK: quoting Lynne Brindley, chief executive of the British Library, "Unless there is a serious updating of copyright law to recognize the changing technological environment, the law becomes an ass."

Journal financial disclosure policies

Tim Lambert of Deltoid blogged yesterday about financial disclosure policies of scientific journals, including a recent retraction by the Journal of Occupational and Environmental Medicine and a brief item in Environmental Science and Technology.

Also see this previous post from August discussing recent changes by the Journal of the American Medical Association to address financial disclosure issues, as well as integrity of data analysis and results reporting in industry-funded research.

Opposition to open access legislation

Senior academic officials from 10 academic institutions have sent a letter to the two senators (Cornyn, TX; Lieberman, CT) sponsoring the Federal Research Public Access Act (S.2695)

The letter comments:

"The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research...Mandating free dissemination of scientific manuscripts within six months would significantly limit the ability of non-profit and commercial publishers to cover the upfront reviewing, editing, and production costs of creating these manuscripts. Some journals would simply cease to exist. Others would be much less able to support innovation in scientific publishing and archiving. Ultimately, this could lead to a system in which NIH and other federal agencies must sustain a significant portion of the research publishing enterprise, maintaining 100+ years of archival journals, as well as producing new research articles."

The Library of Congress provides several links to further description of the legislation and related documents.

Contrary to the initial focus of the letter, it's hard to see how the following text from the legislation would subvert peer review:
"Each Federal research public access policy shall provide for--

(1) submission to the Federal agency of an electronic version of the author's final manuscript of original research papers that have been accepted for publication in peer-reviewed journals and result from research supported, in whole or in part, from funding by the Federal Government;

(2) the incorporation of all changes resulting from the peer review publication process in the manuscript described under paragraph (1);

(3) the replacement of the final manuscript with the final published version if--

(A) the publisher consents to the replacement; and

(B) the goals of the Federal agency for functionality and interoperability are retained;

(4) free online public access to such final peer-reviewed manuscripts or published versions as soon as practicable, but not later than 6 months after publication in peer-reviewed journals;

(5) production of an online bibliography of all research papers that are publicly accessible under the policy, with each entry linking to the corresponding free online full text; and

(6) long-term preservation of, and free public access to, published research findings

The legislation also explicitly excludes material that is not peer reviewed, including:

(1) laboratory notes, preliminary data analyses, notes of the author, phone logs, or other information used to produce final manuscripts;

(2) classified research, research resulting in works that generate revenue or royalties for authors (such as books) or patentable discoveries, to the extent necessary to protect a copyright or patent; or

(3) authors who do not submit their work to a journal or works that are rejected by journals.

I can see how this may hurt scientific publishing financially, but the text of the proposed legislation seems to be in line with the traditional peer review process. The legislation also seems to parallel similar efforts, already nationally mandated, in the UK to facilitate public access to the results of publicly-funded research (see this previous post).

Update:
T. Scott provides an interesting commentary and suggestions re: the economic aspects of the debate and the potential detrimental nature of partisanship on the issue (i.e. "us vs. them" arguments).

Striking image: potato chips and oil

BBC News reports a few examples from the British Heart Foundation's Food4Thought campaign -- children that eat a bag of potato chips each day (though the estimate is based on a larger bag than a 28 g snack size bag of Lay's chips) end up consuming the equivalent of about 5 liters of cooking oil in a year. Also includes a downloadable PDF poster of the girl-chugging-cooking-oil image.

The Food4Thought site is geared toward adolescents and contains other junk food stats in a "Gross Me Out" section and a health quiz, as well as tips for healthy eating (including celebrity examples) and for exercise and fitness.

MedlinePlus magazine

The National Library of Medicine has posted the 2nd issue of the MedlinePlus magazine, targeted at consumers. The site notes, "NIH MedlinePlus , the magazine, is the free, trusted consumer guide to the vast array of authoritative online health and medical information at www.medlineplus.gov. Published four times a year, the magazine showcases the NIH’s latest medical research and healthcare information."

This issue (PDF, 2.7 MB) features Mary Tyler Moore and her fight with type 1 diabetes, as well as covering the flu, arthritis, vaccine development news, and the Sister Study of breast cancer in families.

You can subscribe to the magazine for free (PDF) and also join the Friends of the National Library of Medicine.

Update:
Donald A.B. Lindberg, M.D., Director of the National Library of Medicine, regularly records a Director's Comments podcast, and today's discusses the MedlinePlus magazine (mp3 file, text transcript).

Self-care

Mary Chimato of medlibrarian.net posted today about a new handout from the American College of Emergency Physicians to aid patients in making decisions regarding how to decide when a symptom etc is severe or serious enough to warrant a trip to the emergency room.

The American Academy of Family Physicians also has a self-care decision making tool on their familydoctor.org site, with simple decision trees organized by key presenting symptom.

The medical literature includes an increasing volume of discussion about how to improve individuals' health and utilization of health care resources through self-care or self-management strategies (a few key Medical Subject Headings below), covering a wide variety of disease-focused and wellness- focused strategies and representing all age groups.

Some examples:
- Bodenheimer T. Planned visits to help patients self-manage chronic conditions. Am Fam Physician. 2005 Oct 15;72(8):1454, 1456.
- Sarkar U, Fisher L, Schillinger D. Is self-efficacy associated with diabetes self-management across race/ethnicity and health literacy? Diabetes Care. 2006 Apr;29(4):823-9.
- Sherman KJ, Cherkin DC, Erro J, Miglioretti DL, Deyo RA. Comparing yoga, exercise, and a self-care book for chronic low back pain: a randomized, controlled trial. Ann Intern Med. 2005 Dec 20;143(12):849-56.
- Herxheimer A. Helping patients take responsibility for their own health. Ann Intern Med. 2001 Jul 3;135(1):51-2.

MeSH terms: consumer participation, self care, patient participation

Publication bias and statistical significance

Chris of Mixing Memory has blogged a great discussion of statistical significance, scientific publishing, and publication bias - the lower likelihood of getting accepted for publication if your study has null results, i.e. fails to show a statistically significant difference.

For more details on publication bias, consider the Cochrane Collaboration description and the results from a quick PubMed search on the topic ("publication bias" has been a Medical Subject Heading (MeSH) term since 1994) .

David Wallace of Fayetteville State University has developed a good description of Type I and Type II statistical errors (PDF file).

Women in the sciences, continued

As a follow-up on yesterday's post about gender bias in the sciences, another Inside Higher Ed artice published today, "Bias or Interest?," discusses preliminary, unpublished results from a study of gender bias in academia

"Unpublished data, however, suggest that most professors don’t agree that discrimination — intentional or otherwise — is the main reason that men hold so many more positions than do women in the sciences. Professors overwhelmingly
think it’s a matter of men and women having different interests.

The data come from a national survey of 1,500 professors at all kinds of institutions in the United States. Two sociologists — Neil Gross of Harvard and Solon Simmons of George Mason University — conducted the survey on a range of social and political issues. While they have not yet finished their analysis, they agreed to release the data on women and science because of the interest generated by the National Academies’ study. "

Richard Smith critique of medical journal publishing

Richard Smith, a former editor of the British Medical Journal, has published a book titled, "The Trouble With Medical Journals" (Amazon record and RSM Press description), based in part on his 13 years of experience as BMJ editor. There's an excerpt from the initial part of the book published in the March 2006 issue of the Journal of the Royal Society of Medicine; this article introduces the series:

"Medical journals, which many imagine to be as dull as telephone directories and twice as obscure, influence the lives of everybody—and not always for the better. Not only do they affect how doctors treat patients and the actions taken by public health authorities, they also influence how we think about birth, death, pain, and sickness. It may therefore make sense for you—the thoughtful but not necessarily expert reader—to pay attention to the ways of medical journals, particularly as many of those ways are deficient and need reform. That is the thesis of this series of articles. "

The full text of other excerpts from the text have been published in the same journal over the last couple of months.

Commentary on the book:
- "Medical Journals Slammed by Former Editor," Life Style Extra (UK)
- "The trouble with medical journals: bias, fraud, and lack of OA," Open Access News
- "How worthy is research?," The Times (UK)
- Royal Society of Medicine press release

Luck and medicine

Today's New York Times has an essay by Barron Lerner of Columbia University about the role of luck in medicine - "In Science-Based Medicine, Where Does Luck Fit In?" The piece considers how clinicians and patients interpret and explain outcomes that are different than expected, how we manage uncertainty despite strong emphasis on assessing the relevant "evidence" for a given clinical case - the broad concept of luck as a catch-all explanation for such situation -

"A more frank acknowledgment of the role luck plays has another virtue: eliminating the tendency to second-guess and blame patients... [R]isk reduction is not risk elimination. Even well-established interventions, like regular screening mammograms in women over 50 and antihypertensive pills for high blood pressure, lower the risk of death by 30 percent at most. That means that plenty of patients who are 100 percent compliant with their doctors’ wishes will still die of breast cancer or complications of hypertension, like heart attacks or strokes. These are the unlucky ones.

And then there are always those patients who constantly disregard medical recommendations and seemingly suffer no ill effects. You guessed it: lucky."

Also some brief commentary on the article at DB's Medical Rants.

Women in the sciences

Inside Higher Ed today profiles a recent National Academies of Science report, "Beyond Bias and Barriers: Fulfilling the Potential of Women in Academic Science and Engineering." Noting the relatively low proportion of women among science and engineering faculty at research institutions, the report notes,

"The representation of women in leadership positions in our academic institutions, scientific and professional societies, and honorary organizations is low relative to the number of women qualified to hold these positions. It is not lack of talent, but unintentional biases and outmoded institutional structures that are hindering the access and advancement of women. Neither our academic institutions nor our nation can afford such underuse of precious human capital in science and engineering. The time to take action is now."

The authoring committee has put together recommendations for transforming academic insitutions to address this issue, including halting attrition during the academic advancement process, revamping models for institutional support, and reducing other institutional constraint factors. In Chapter 6, the report includes a "scorecard" for institutions to use in assessing progress related to each of the recommendations.

The report is also covered in ScienceNOW Daily News, the New York Times, Nobel Intent, Ontogeny, and other popular media outlets.

The issue certainly is not unique to the US, e.g. see Arunn of Nonoscience's "Unsung Heroines" blog entry today about women scientists in India.

Scientific research and development spending: national statistics from Canada

Statistics Canada has published a new report, "Total spending on research and development in Canada, 1990 to 2006, and provinces 1990 to 2004" (PDF).

From the highlights regarding Gross Domestic Expenditure on Research and Development (GERD) in Canada:
- Preliminary estimates for GERD in 2006 suggest that this indicator will continue to grow at a modest pace. Total spending on R&D in Canada is expected to amount to $28.4 billion dollars in 2006, a 4.4% increase over the figures for 2005 ($27.2 billion). Although this increase is slightly below the 4.5% increase in GERD experienced in 2005, it is higher than the meager 1.6% rise recorded in 2002.
- As has been the case since 2004, increases in expenditure on R&D in the higher education sector continue to account for a major proportion of the growth in GERD. In 2006, a 10% ($990 million) increase in expenditure on R&D by higher education institutions is expected to account for 84% of the estimated growth in GERD of $1.2
billion. Business enterprises’ R&D performance dollars are expected to contribute only 16% (or $195 million) to the growth in GERD.
- In 2006, the federal government is projected to be the second largest funder of R&D (behind business enterprises) accounting for $5.2 billion (18%) of the total funding of R&D. This amount represents a 5.0% increase over the figures for 2005 ($5 billion). Business enterprises are expected to account for $13.2 billion (or 47%) of the total funding for R&D in Canada, a 1.9% increase over the amount they provided in 2005 ($13 billion).

In estimates based on conversion to 1997 dollars, GERD spending has almost doubled in Canada from 1990 - 2005 (in millions of 1997 Canadian dollars, from 11,554 in 1990 to 22,970 in 2005).

Benefits of science blogging

Eva of easternblot.net has published an article that includes interviews with several science bloggers in the latest issue of Hypothesis: Journal for the Discussion of Science. The article is titled "Who benefits from science blogging?" (PDF here) --

"Blogging researchers have a chance to expand their casual science-related conversations worldwide, possibly meet other scientists and enhance their teaching skills, while blog reading scientists can informally communicate with their peers through comments. Blog reading non-scientists have access to science stories they might otherwise have missed. Blogging science writers and journalists can use their blogs as a playpen for new ideas, meanwhile giving the rest of the world a well-written piece on an interesting topic. Finally, blogging journal editors can get reader feedback on articles, and read other science blogs for ideas.

So if you’re looking to expand your horizons, read some science blogs!"

Biomed Central articles: international collaboration, research quality

A few interesting articles from the Biomed Central journals:

• Gonzalez Block MA. The state of international collaboration for health systems research: what do publications tell? Health Res Pol Sys 2006, 4:7 - analyzed author information from to evaluate how much international collaboration is going on in research focusing on health systems and policies in developing countries. Concludes "While there is modest health systems research capacity in many developing countries for single country studies, capacity is severely limited for multi-country studies."


• Nieminen P, Carpenter JR, Rucker G, Schumacher M. The relationship between quality of research and citation frequency. BMC Medical Research Methodology 2006, 6:42 - looked at the quality of statistical analysis and results reporting in 4 psychiatric journals. Authors note: "Unclear or inadequate reporting of the research question and primary outcome were not statistically significantly associated with the citation counts. After adjusting for journal, extended description of statistical procedures had a positive effect on the number of citations received. Inappropriate statistical analysis did not affect the number of citations received. Adequate reporting of the primary research question, statistical methods and primary findings were all associated with the journal visibility and prestige."
• Poolman RW, Struijs PAA, Krips R, Sierevelt IN, Lutz KH,, Bhandari M. Does a "Level I Evidence" rating imply high quality of reporting in orthopaedic randomised controlled trials? BMC Medical Research Methodology 2006, 6:44 - examined reporting of evidence levels in the Journal of Bone and Joint Surgery, American Volume, found that the reported level of evidence did not correlate with quality of the corresponding study

Biomed Central survey of funder policies on open access

Biomed Central has released initial results from a survey of major biomedical research funding agencies regarding their support for and policies regarding open access publishing.

Their summary of findings so far (33 responses from 75 funding agencies surveyed):
- 31 funders have confirmed that they are willing to fund article processing charges
- 16 funders are signatories of one of the major international declarations in support of open access
- 15 funders have an official policy in support of open access
- 11 of these funder policies encourage or in some cases require funding recipients to deposit resulting research articles in an open access repository

AbstractPlus view in PubMed

Flags and Lollipops discusses a Greasemonkey script that adds TrackBack links within PubMed, designed to work with the AbstractPlus view.

I really like the AbstractPlus view (sample citation here) -- in a recent search that included mostly case reports, I found some useful citations that otherwise would have likely taken much more "looking" to find. It also has helped me make some connections with related concepts in the literature. (More on PubMed's Related Articles algorithm and the AbstractPlus view)

Also, if you haven't seen Postgenomic yet, it's definitely worth a look - front page notes it "collects data from hundreds of science blogs and then does useful and interesting things with it." It pulls together commentary on different topics, issues, and recently published papers.

News: genetic testing, healthcare in the UK, drug trials

A few stories from Medical News Today over the last couple of weeks:

• "FDA To Begin Requiring Approval Before Genetic Tests Can Be Marketed" and "Claiming Diagnostic Tests For Diabetes Genes Is Misleading, Say Experts, UK" (related to this past post)
• "Put Clinical Evidence Before Cost, Says BMA, U.K." - quoting Dr. Sam Everington from the British Medical Association regarding the new initiative from the UK's National Institute for Health and Clinical Excellence (NICE) to identify ineffective healthcare interventions - "we would not want to see a blanket ban imposed on certain treatments since there may be occasions where individual patients, with specific health needs, would necessitate a particular intervention. Decisions taken by NICE must therefore allow for such treatments to be available for patients whose health outcomes would improve."
• "Five Lawmakers Call For GAO Investigation Into Clinical Trials Comparing New Drugs With Those Already On Market"

Randomized experiments in social research

MDRC has released a guidance statement, "The core analytics of randomized experiments for social research," that may be of interest to those thinking about evaluation of programs/services in the health sciences. The abstract notes, "Its goal is to provide a compact discussion for faculty members, graduate students, and applied researchers of the design and analysis of randomized experiments for measuring the impacts of social or educational interventions."

The paper covers both design issues (e.g. selecting a study sample, randomizing particpants) and analysis issues (e.g. estimating impact in the presence of participant noncompliance, estimating impacts on randomized groups rather than individuals).

The document is part of a broader initiative by the MDRC to aid evaluation efforts: "Launched in 1999, the Initiative is exploring the use of quantitative and qualitative methods in the context of experimental, quasiexperimental and mixed research designs to rigorously study how programs are implemented, the impacts they produce, and how their implementation affects their impacts." Other papers in the series are also available.

The flow of scientific communication

Some graphical representations of current scientific communication dynamics:

Big Monkey, Helpy Chalk: "Scientific Communication" and "Scientific Communication 2.0"

Nonoscience: "Science Communication and the Role of Science Blogs"

Great comments on both blogs too.

Principles of epidemiology course

The Centers for Disease Control and Prevention have a self-study course covering basic principles and applications of epidemiology.

The objectives as described in the full-text of the course materials:
- Describe key features and applications of descriptive and analytic epidemiology.
- Calculate and interpret ratios, proportions, incidence rates, mortality rates, prevalence, and years of potential life lost.
- Calculate and interpret mean, median, mode, ranges, variance, standard deviation, and confidence interval.
- Prepare and apply tables, graphs, and charts such as arithmetic-scale line, scatter
diagram, pie chart, and box plot.
- Describe the processes, uses, and evaluation of public health surveillance.
- Describe the steps of an outbreak investigation.

I haven't worked my way through the whole course yet but it has a great overview of the history of epidemiology and a good description/comparison of the various terms used in epidemiology (e.g. contrasting the various measures of risk, common techniques employed in epidemiology), and how to interpret illustration types commonly used in epidemiology papers (e.g. scatterplots, box plots).

More on word choice in the medical literature

Thinking about the study I talked about in this post made me curious about how often certain words are used in the medical literature. Some quick PubMed searches today (not in any order):

• surprising[tiab] OR surprisingly[tiab] OR surprised[tiab] OR surprise[tiab] retrieves more than 45,000 citations


• startling[tiab] retrieves ~ 500 citations


• astonish*[tiab] retrieves ~ 800 citations


• astound*[tiab] retrieves a puny 200


• amaze*[tiab] OR amazing[tiab] retrieves ~650


• unexpected[tiab] OR unexpectedly[tiab] doesn't quite beat the surprise variations, at ~43,000


• dumbfound*[tiab] only works because of its genetic meaning, at ~20 citations


• and, surprising me because I thought it would be more common than some of the others, maybe too bland? interesting[tiab] retrieves ~40,000 citations
  

Variation in research ethics board decisions

There's a research study reported in this month's Journal of Medical Ethics examining variability in the judgments of 44 research ethics boards (REBs) in reaction to a mock research protocol scenario. Snapshot of the results: "Similar criteria were used by most participating REBs. Yet the project was unconditionally approved by 3 REBs, approved conditionally by 10 and rejected by 30."

Citation: de Champlain J, Patenaude J. Review of a mock research protocol in functional neuroimaging by Canadian research ethics boards. J Med Ethics. 2006 Sep;32(9):530-4.

Commentary by Jim Giles in Nature on the study (subscription required to access full-text):
"'Everyone knows institutional review boards make very different decisions,' says Joan Sieber, a psychologist at California State University, East Bay, who helps to train board members. She argues that it would be unrealistic to expect all boards to reach the same decision, but that the range of answers given shows that ethical norms are being applied in worryingly different ways. 'This shows that something needs to be done'...

Sieber says review boards need to be more rigorous in their risk assessments and decisions, and says they should call in outside experts where necessary. She adds, however, that a more common problem with institutional review boards is not a willingness to allow dubious studies, but an overly cautious approach that comes from ignorance of the experimental methods involved."

EBM instructional support materials

David Rothman has compiled a great summary of books, sites, tutorials, etc to support EBM teaching efforts, also includes an annotated bibliography that includes some really interesting things that I hadn't heard of before and can't wait to check out.

Open access grab bag

A few open access news stories that have been lingering in my "to read" list...

• Medical News Today: "Announcing the launch of Open Access Central" - launched by the producers of BioMed Central, Open Access Central will broaden the group's open access umbrella to mathematics and the sciences


• Oxford University Press: "Demand for open access 'low'" - OUP report examining statistics for author-pay model in its publications indicates slow adoption; notes much of the uptake has been in the life sciences
  
• Nature Publishing Group: Press release announcing open access to all online content before January 2003


• Inside Higher Ed: "Momentum for open access research" - discussing the proposed Federal Public Research Access Act and examining the national open access debate
  

Beyond the journal article in the sciences

The Scientist has an interesting discussion of the limitations of the traditional journal article, "The death of the scientific paper." The suggested solution:

Journals must produce more than just papers. Editors should demand online deposit of data as a requirement for publication, and enforce a unified nomenclature for biology. In addition to the traditional manuscript, authors should deliver structured methods and results sections suitable for computer parsing, a lay-friendly news blurb (like those PLoS Medicine includes), and a single PowerPoint slide summarizing the work. This entire body of information should be peer-reviewed, published en masse, and kept in sync, thereby avoiding the current problem of disconjugate articles and data sets.

Word choice in discussion of research results

From the badscience blog:

"Polish researcher Michael Jasienski reported in the journal Nature recently how he searched for words indicating surprise in 30 million abstracts of English-language scientific papers from the Science Citation Index; he then compared them with 8 million academic articles from the Social Sciences and Arts & Humanities citation indices, and with some samples of standard English.

The word ’surprising’ appeared 12 times more frequently in the natural sciences than in standard English, and 1.3 times more frequently than in social sciences, arts and humanities research; and the word ‘unexpected’ appears 39 times and 2.2 times more frequently in the natural sciences than, respectively, in standard English and in non-science academic writing. Obviously humanities graduates don’t find their “discoveries” as surprising as scientists do. It must be a dreary life."

The study he mentions is reported in a letter to Nature: Jasienski M. It's incredible how often we're surprised by findings. Nature 2006 Apr 27;440(7088):1112; PubMed record (access to full text of letter requires a subscription to the journal).

Risks to healthy volunteers in research studies

Jeffrey Drazen in today's New England Journal of Medicine provides editorial commentary on risks to healthy volunteers in clinical research, prompted by a study also published in today's NEJM (subscription to the journal required to read the full study).

Drazen notes, "Clinical research can be a risky endeavor. In this issue of the Journal, Suntharalingam et al. describe the events that occurred when six healthy volunteers received a dose (0.1 mg per kilogram of body weight) of TGN1412...In all six patients, the cytokine-release syndrome developed, including multiorgan failure. Two of the patients required mechanical ventilation, and all received renal-replacement therapy. All six had severe hypotension, and peripheral ischemia developed in one patient to the extent that surgical treatment was required."

Drazen concludes, "As long as we continue to manipulate biology in new ways, we probably cannot prevent all such events from occurring. We must do what we can to minimize risk, but the future health of the world population demands that we not let adverse events put an end to medical progress. We must treat those at risk with respect and great care, but the work must go on. The troubling fact of the matter is that without people who are willing to place themselves at risk to advance our knowledge, we will be frozen in our current state of understanding. And this state simply may not be good enough to enable us to meet the next unexpected challenge that comes our way."

Further commentary on the rationale for attempting the therapy and why it may have gone wrong in these healthy volunteers is included in a perspective piece by Sharpe and Abbas.

JAMA patient page: evidence-based medicine

This week's issue of the Journal of the American Medical Association has a patient page discussing evidence based medicine.

The reading level still seems somewhat high but they do try to explain some of the terms:
"Systematic reviews of the medical literature, large randomized controlled trials (the best way to assess the efficacy of a treatment), and large prospective studies (followed up over time) are types of research published in the medical literature that can be helpful in providing evidence about tests and treatments. Reports of the experiences of individual patients or small groups usually provide less reliable evidence, although they may provide important clues about possible adverse effects of treatments."

Open access and the American Chemical Society

From Chemical and Engineering News: open access gaining more ground as the ACS launches a new AuthorChoice feature for authors publishing in their journals:

"In October, American Chemical Society journal authors will have the option of paying to immediately provide free online access to their articles on the society's website. Authors will also be able to post electronic copies of their sponsored articles on personal websites and institutional repositories. Fees for the program will range from $1,000 to $3,000 per paper, depending on whether the author is an ACS member or is affiliated with an institution that subscribes to ACS journals."