Silly Sunday #43 Know Your Numbers

As I touched upon in Grand Rounds 8.5 the Mayo Clinic Center held the 3rd Social Media’s Health Care Social Media Summit a few weeks ago. Lots of good information and resources were shared, including the video below. The video has already gone viral (it has been viewed appr. 24,000 times), but most important is that its message gets viral.

The song is a parody of 867-5309/Jenny, produced by the Mayo Clinic Center* to promote healthy heart awareness, especially among women:

Heart disease is the number one killer of men and women, but most women aren’t aware of this.

You need to know your numbers, don’t let them get too high: blood pressure, lipids and BMI

I love it & remember, know your numbers!

Go to http://knowyournumbers.me/ to calculate your heart risk (BMI and LDL-cholesterol) and see how you can lower it.

You can become a fan of Mayo Clinic at Facebook:
http://www.facebook.com/MayoClinic

* For this purpose, the band of Ron Menaker, the administrator for the Mayo Clinic Division of Cardiovascular Diseases, was renamed to “Tommy and the Heartbeats” (see The  Making of  Know Your Numbers) .

Hattip: Scott Hensley (Facebook)

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• Mayo’s Parody Video Invites You to Know Your Numbers: Blood Pressure, Lipids, and BMI (Sing to the tune of Jenny 867-5309) (managemypractice.com)
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Friday Foolery #42 So You Think You Can Dance Your PhD Thesis?

It’s hard to explain your research to non-scientists. My PhD defense was preceded by a slide show (yes, that was once-upon-a-time that we didn’t use Powerpoint). It was the only part the public could follow a bit. But it is too long, static and detailed.

That cannot be said of these videos, where PhD’s from all over the world interpret their graduate research in dance form.

The videos below are the winners of the 2011 edition of the Dance your PhD contest. For the 4th year, this contest is organized by Gonzolabs & Science. See http://gonzolabs.org/dance/

There are 4 categories—chemistry, physics, biology, and social sciences

The overall winner of 2011 was Joel Miller (category physics), a biomedical engineer at the University of Western Australia in Perth. Miller apparently compensated his poor dancing skills and the lack of a video by applying stop-motion animation (stringing together about 2,200 photos to make it look as though his “actors” were dancing). His video shows the creation of titanium  alloys that are both strong and flexible enough for long-lasting hip replacements.
I love the song by the way. It fits perfectly to the dance scene.

You can see all winning videos here and all 2011 (this years) PhD videos here. You can also check out the 2010 and the 2009 PhD dances.

The other winners of 2011 were  FoSheng Hsu (chemistry category) who guides viewers through the entire sequence of steps required for x-ray crystallography,  Emma Ware (social science) who studies the traditional ‘stimulus-release’ model of social interaction using pigeon courtship (a beautiful pas a deux) and Edric Kai Wei Tan (biology) with the funny dance about Smell mediated response to relatedness of potential mates, simply put “fruit fly sex”.

Being Dutch, I would like to close with the Dutch winner of the biology category in 2010, Maartje Cathelijne de Jong who dances her PhD, “The influence of previous experiences on visual awareness.”

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• Friday Foolery #41. A Special Offer for the Major [#4square] (laikaspoetnik.wordpress.com)
• Ph.D Dance of the Day (geeks.thedailywh.at)
• Physics Wins Dance Your Ph.D. Contest (cenblog.org)
• Ph.D. dance-off makes science sexy (cosmiclog.msnbc.msn.com)
• BLOG: So you think you can dance, PhD candidates? (cbc.ca)
• Dance Your Ph.D.: When Science People Shake A Tail Feather, Everybody Wins (npr.org)
• Winnaar dans je proefschrift speelt een beetje vals  (weblogs.nrc.nl) [Dutch]

Ten Years of PubMed Central: a Good Thing that’s Only Going to Get Better.

PubMed Central (PMC) is a free digital archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health (NIH), developed and managed by NIH’s National Center for Biotechnology Information (NCBI) in the National Library of Medicine (NLM) (see PMC overview).
PMC is a central repository for biomedical peer reviewed literature in the same way as NCBI’s GenBank is the public archive of DNA sequences. The idea behind it “that giving all users free access to the material in PubMed Central is the best way to ensure the durability and utility of the electronical archive as technology changes over time and to integrate the literature with other information resources at NLM”.
Many journals are already involved, although most of them adhere to restrictions (i.e. availability after 1 year). For list see http://www.ncbi.nlm.nih.gov/pmc/journals/

PMC, the brain child of Harold Varmus, once the Director of the National Institutes of Health, celebrated its 10 year anniversary earlier this year.

For this occasion Dr. Lipman, Director of the NCBI, gave an overview of past and future plans for the NIH’s archive of biomedical research articles. See videotape of the Columbia University Libraries below:

Vodpod videos no longer available.

more about “Ten Years of PubMed Central | Scholar…“, posted with vodpod

The main points raised by David Lipman (appr. time given if you want to learn more about it; the text below is not a transcription, but a summary in my own words):

PAST/PRESENT

• >7:00. BiomedCental (taken over by Spinger) and PLoS ONE show that Open Access can be a sustaining way in Publishing Science.
• 13:23 Publisher keeps the copyright. He may stop depositing but the content already deposited remains in PMC.
• 13:50 PMC is also an obligatory repository for author manuscripts under various funding agencies mandates, like the NIH and the UK welcome trust.
• 14:31 One of the ideas from the beginning was to crosslink the literature with the underlying molecular and other databases. For instance NCBI is capable of mining out the information in the archived text and connecting it to the compound and the protein structure database.
• 16:50 There is a back issue digitization for the journals that are participating, enabling to find research that you wouldn’t have easily found otherwise.
• PMC has become international (not restricted to USA)
• The PMC archive becomes more useful if it becomes more comprehensive
• Before PMC you could do a Google Scholar search and find a paper in PubMed, that appeared funded by NIH, but then you had to pay $30 for it in order to get it. That’s hard to explain to the taxpayers (Lipman had a hard time explaining it to his dad who was looking for medical information online). This was the impetus for making the results of NIH-sponsored results freely available.

PRESENT/FUTURE

• 23:00 Discovery initiative: is the use of tracking tools to find out which changes to the website work for users and which don’t. Thus modifications should lead to alterations in users behavior (statistics is easy with millions of users). Discovery initiative led to development and improvement of sensors, like sensors for disease names, drug names, genes and citations. What is being measured is if people click through (if it isn’t interesting, they usually don’t) and how quickly they find results. Motto: train the machine, not the users.
• 30:37 We changed the looks of PMC. Planning to make a better presentation on the i-phone and on broad monitors.
• 31:40. There are almost 2 million articles in PubMed Central, 585 journals fully participate in PMC
• 32.30 It takes very long to publish a paper, even in Open Access papers. Therefore a lot of people are not publishing little discoveries, which are not important enough to put a lot of time in. Publishing should be almost as easy as writing a blog, but with peer review. This requires a new type of journal, with peer review, but with instant feedback from readers and reviewers and rapid response to comments. The Google Knol authoring system offers a fast and simple authoring system where authors (with a Google profile) can collaborate and compose the article on the server. Uploading of documents and figures is easy, the article updates are simple and fast, there is a simple workflow for moderators. After the paper is accepted you press a button, the paper is immediately available and the next day PMC automatically gets the XML content. There is also a simple Reference Manager included to paste citations.
• Principle: How you can start a journal with this system (see Figure). Till now: 60 articles in PLOS Currents Influenza. There are also plans for other journals: the CDC is announcing a Systematic Reviews journal, for instance.

QUESTIONS (>39:30):

• Process by which “KNOL-journal” is considered for inclusion in NLM?
  • Decide: is it in scope?, implicit policy (health peer review being done), who are the people involved, look at a dozen articles.
• As the content in PMC increases, will it become possible to search in the full text, just like in Google Scholar?
  • Actually the full text is searchable in PMC as apposed to PubMed, but we are not that happy with the full text retrieval. Even with a really good approach, searching full text works just a little bit better than searching PubMed.
    We are incorporating more of the information of PMC into PubMed, and are working on a separate image database with all the figures from books and articles in PMC (with other search possibilities). Subsets of book(chapter)s (like practice guidelines) will get PubMed abstracts and become searchable in PubMed as well.
• Are there ways to track a full list of our institutions OA articles in PMC (not picking up everything in PubMed)
  • Likely NIH will be contacting offices responsible for research to let them know what articles are out of compliance,  get their assistance in making sure that those get in.
    
  • Authors can easily update the electornic My Bibliography (in My NCBI in PubMed).
    
  • Author ID project, involves computational disambiguation. Where you are asked if you are the author of a paper if you didn’t include it. It may also be possible to have automatic reporting to the institutions.
• What did it took politically to get the appropriation bill passed (PMC initiative)?
  • Congress always pushed more open access, because it was already spending money on the research. Most of the initiative came more from librarians (i.e. small libraries not having sufficient access) and government, than from the NIH.
• Is there way to narrow down to NIH, free full text papers from PMC?
  • In PubMed, you can filter free full text articles in general via the limits.
    
• Are all the articles deposited in PMC submitted the final manuscript?
  • Generally, yes.

HT: @bentoth on Twitter

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Friday Foolery #24 Social Media Revolution 2, Right Here Right Now

People who still think Social media is a fad, should watch this video…..

Social Media Revolution 2 is an update of the original video with compelling social media statistics.

Social Media Revolution was created by the author Erik Qualman to promote his book Socialnomics: How Social Media has changed the way we live and do business.

The music from Fat Boy Slim (“right here, right now”) is electric (might be another reason to watch it).

Hattip: my colleague René Spijker, seen on the Salt Magazine page on Facebook

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How a Flu-Virus Invades your Body: An Animation

I’ve seen “viral invasion, replication and spread” more elaborately and scientifically explained, but nothing comes near a clear visual and audible presentation of what happens on a micro-scale.

Here is a video on a Flu Attack that stirs the imagination.

And one thing or another, those kind of videos get really viral on Twitter and blogs as well.

When seeing the video you at least understand why CDC’s motto is: Cover it!

Although the above video has the tags “swine” and “flu” and alludes to H1N1, it gives no specific information on H1N1 (Swine flu), but could be about any influenza virus. For information on H1N1 go to:

• the CDC H1N1 page: http://www.cdc.gov/h1n1flu/
• Flu.gov: http://www.flu.gov/
• Medline Plus: H1N1/Swineflu
• Highlight Health for some specific articles on H1N1
• Informatie van de Rijksoverheid over Nieuwe Influenza A (H1N1): http://www.grieppandemie.nl/
• An up to date map tracking the progress of H1N1 swine flu at: http://flutracker.rhizalabs.com/

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Friday Foolery #7 Play Doh World, the Safe and Unexpected

Seen at the Loom of Carl Zimmer: using Play Doh, Sophia Tintori and Cassandra Extavour talk about multicellularity and the specialization of reproductive cells.

The video, made by the evolutionary biologist Casey Dunn, is from Creature Cast, a collaborative blog produced by members of the Dunn Lab at Brown University. The Dunn Lab investigates how evolution has produced a diversity of life. On this newly evoluted “Creature Cast” you can find short, original and  good quality posts on zoology in the broad sense often with beautiful photos or videos. You can now subscribe to the CreatureCast video podcast through Brown University at  iTunes U.

Vodpod videos no longer available.

more about “CreatureCast Episode 2 on Vimeo“, posted with vodpod

Work provided under a Creative Commons Attribution-Noncommercial-Share Alike license.

Another example of a great post on Creature Cast is the Tale of two holes about why some animals have one hole and others two. Does the single hole in one-holed animals correspond to the mouth or anus of animals with two holes?  Apparently the same sets of genes appear in many different contexts within and across species. In this case there are two distinct modules for mouth and blastopore (the first hole developed in animals during their development) and they can be decoupled. Again there is a terrific photo made by Dunn showing a sea anemone with a single hole for eating, excreting, and shedding eggs and sperm, and an annelid worm with two holes.

This is a Friday Foolery post, thus permit me to show me something completely different: a successful Play-Doh ad-campaign started in Singapore (what a coincidence, the city I left 26 h ago). These ads talk to parents directly, reminding them about the thousand of possible things you can make with the product, but even more so about how safe it is to play with it. (although someone commented: “what if kids eat those pills? Although Play-Doh is non-toxic…)

From: Play Doh Ads Make Crying Out For Help Fun [Weird] (consumerist.com) and A campaign with an edge (uglydoggy.com)

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Educational Videos about Library Stuff

Yesterday @alisha alerted me to a post of Sheila Webber at the information-literacy blog about a wonderful series of YouTube videos by Llordllam with hand puppets as actors. The videos are a mix of educational videos aimed at librarians, information scientists and library readers. The leading actors are Goose the librarian and Professor Weasel the academic (patron).

The following YouTube video is really superb as well as hilarous. With a typical british sense of humor it tries to make you understand Academic Copyright. Prof Weasel struggles to understand the problems with the traditional journal publication system. Look how he is fooled by the publisher rat.

And for librarians and librarian users this one is a must. Boolean operators explained. Think the jam/bread example will work better than my epistaxis/child example, so who knows I will adapt my slides.

And finally the video “Your Library: A User Centric Experience”. This feels very familiar (the user becomes the king, see also the Flikr pictures in the side bar of our library)

More video’s of Goose and Weasel see page of llordllama on youtube.com and  a facebook page for fans of the video Randy Weasel, Kooei Goose and others

—-

Now, not a Llordllam/Goose/Weasel production, but a very useful video (by paulrobesonlibrary) to illustrate to students the (unusefulness) of Wikipedia as their primary research tool.
Seen at Phil Bradley’s Weblog (No, you can not lower the speed)