Friday, January 30, 2009

Friday Foolery #19: Bacon Bunn

Here is Coffee Central in our office, and I'd like to introduce our brand new baby Bunn. Oh, how I love our Bunn. 10 cups of piping hot non-bitter coffee in 3 minutes! The bling I've brought to the wall decor is the BACON! pennant, the jaw bra (voted best swag from the AAOMS conference), and this curiousity.

Does anyone out there know Russian to verify that this says 'SHHH!'?

Edit: Thank you Guus! Also from Soviet Power and the Media

During the “Ne boltaj!” (“Do Not Chatter!”) campaign of the late 1940s, Soviet
propaganda posters urged citizens to use the telephone only very cautiously as the enemy
might always be listening in.

Thursday, January 29, 2009

PubMed Update - SCR Recording & Guide

The National Network of Libraries of Medicine, South Central Region (NN/LM SCR) posted about their January 21st PubMed update.

The recording, at, is in Adobe Connect which can be a little quirky if you've not used it before on your computer. The recording can and probably will take a while to load even if you're on a high speed connection. If you have either no audio at all or the participants sound like Mickey Mouse on speed, run this system check that will guide you to fixes.

I'm a big fan of indexes and guides (I am a librarian, after all) for anything I'm not an active participant in that lasts more than 15 minutes. As I did for the Medical Library Association 2008 presentation, without further ado...

  • 01.00 - Advanced Search intro, including 'the tabs will be going away & watch for announcement'
  • 01:55 - Where in Advanced Search to do a Single Citation Matcher-esque query
  • 02:30 - Sensor in PubMed can pick up citation info from main search box
  • 04:02 - Queries at the bottom of Advanced Search mostly the same as in left sidebar of PubMedPubMed page (MeSH & Journals Databases, Special & Clinical Queries)
  • 05:10 - New MEDLINE tag - Young Adults
  • 06:40 - Demo of a search in Advanced Search
  • 07:00 - Note that in Citation view article titles are now hyperlinked, display is title then authors, other features. This isn't the case in AbstractPlus view.
  • 07:40 - Explanation of what's going on in the right side boxes
  • 08:20 - Just what is 'Recent History'?
  • 08:50 - Recent History crosses different NCBI databases
  • 10:00 - Test: does Recent History pick up MeSH Database search at the moment?
  • 11:10 - Please email your feedback in because frequency counts [or try #pubmed on Twitter!]
  • 11:50-13:10 - View when logged in to customized MyNCBI vs. not logged in citation view
  • 13:55 - Right hand side discussion, Related Articles & Recent Activity
  • 14:45 - Other things may pop in here (Discovery Panel?) as things are tested
  • 15:18 - Related Articles and Recent Activity are being used, so they're there
  • 15:50 - Details tab will be going away, available at top of Advanced Search
  • 16:00 - The question mark icon is the Help screen, will be updated soon
  • 16:33 - Automatic Term Mapping (ATM) - effect of changes during Summer 2008
  • 19:50 - Saved search parameters have changed in MyNCBI
  • 21:00 - May need to create new search if no tags, save under new name, delete old one
  • 23:50 - If you previously saved the search with tags, the saved search should be fine except if it was around September 25, 2008
  • 26:00 - Create date & Entrez date are two different things
  • 30:50 - Watch for Skill Tips and Search Clinic announcements in NLM Technical Bulletin

The rest of the recording is mostly region-specific discussion, questions & answers except

  • 36:00 - Yes really, the Single Citation Matcher search will be disappearing soon


  • 40:20 - Send in your feedback to NLM and a history lesson about AbstractPlus

Monday, January 26, 2009

PubMed Advanced Search: MeSH & Single Citation Matcher

Kay Deeney at the National Network of Libraries of Medicine, Pacific Southwest Region (NN/LM PSR) gives a great question & answer session about some of the recent and upcoming changes in PubMed including

Can you show where Single Citation Matcher will be?
  • In Advanced Search, you can select Click here! to Add More Citation Search Fields. This gives you Title, Volume, Issue, and Pagination as shown in the screen shot below. Author and Journal are part of the defaults. The drop down boxes will allow you to change any field. This is a substitute for the Single Citation Matcher.


Will we have access to the MeSH details with Advanced Search?
  • Through the Search by Author, Journal, Publication Date, and more, you can select MeSH Terms. The Index will show you terms you can select. Details will also be available at the top right of the page.
So the MeSH Database option will remain in the redesigned search database?
  • Yes. See the bottom of the Advanced Search page for links to Clinical Queries, Topic-Specific (Special Queries), the MeSH and Journals Databases.

Most of the NN/LM regions have already or are soon scheduled to give PubMed updates via free web conferencing.

Pacific Northwest Region - March 25th (hopefully changes will be live)
Pacific Southwest Region - Done, more scheduled when changes are live
MidContinental Region - January 28th
South Central Region - Done earlier this month
MidAtlantic Region - February 11th

Friday, January 23, 2009

Friday Foolery #18: A hat we can believe in

Thursday, January 22, 2009

A tweet for change: #Pubmed

The official communication portal for your feedback to the National Library of Medicine (NLM) about PubMed is 'Write to the Help Desk' at the bottom of each PubMed page or via email to This mechanism is helpful for NLM to have trackable data, much like the tickets that are generated by calls to the hospital IT services help desk, however this format doesn't allow for others to see what insights and challenges their colleagues are having.

Medical information professionals have multiple channels of communication ranging from international to regional, state & association listservs, reading each others' blogs, and social networking tools such as Twitter. We can and do share among ourselves! However, each of these communication methods can carry high levels of noise, or information that is neither concise nor relevant to what we are looking for in terms of helpful input.

As I previously explained in my PubMed and the Discovery Initiative post, behind-the-scenes work for the past few years is now manifesting itself in visible changes with PubMed. The main channel for communication from NLM regarding these changes is the NLM Technical Bulletin, where you can quickly browse PubMed-specific entries.

A thought I had for a quick, easy-to-contribute, low-noise feedback mechanism for everyone to see, participate in, and track via a webpage or RSS regarding PubMed is the use of hashtags on Twitter by including #pubmed in your tweet. The hashtagged word works for both a regular message (such as the one from me) and a reply, or @, message (such as the one from dial_m)

Going to
currently brings up the results since I pitched this idea to medlibs, a group Twitter account that David Rothman started & I now moderate:

The RSS feed is #pubmed - Twitter Search

Caveat 1: The 'hashtags' I'm referring to in my tweet is, where currently nothing is displayed. It should since there is reciprocal following of @hashtags on my Twitter account, which displays your hashtags even if you have a private Twitter account. Maybe their system is currently lagged when it comes to new entries?

Caveat 2: If you have a private Twitter account or are sending a group tweet message (such as on medlibs), your #Pubmed tag won't appear on the Twitter search results.

If all of the above didn't make much sense, check out Alison Aldrich's post on the Dragonfly for a great Twitter 101 introduction.

If it did make sense, please contribute your #pubmed thoughts on Twitter separate from your usual discussion of Pubmed (which is still searchable here)! To my knowledge there is not an official NLM presence on Twitter, but I will share this with NLM and encourage them to consider this as a type of social network feedback that is targeted and concise so they won't have to wade through a bunch of noise to get to the point.

Wednesday, January 21, 2009

University of Washington Library Research Award for Undergraduates

Are (or were) you a University of Washington student with an awesome research project between the Spring 2008-2009 quarters who knows and shows the significant resources of the UW Library system in your work? Perhaps you're a faculty member who has a student or otherwise know of a UW student who does?

I encourage students to apply for the Library Research Award for Undergraduates with faculty support if so. The deadline is May 18, 2009 and the project doesn't have to be 100% complete right now in order to begin the application process.

Even if you're not in the UW community check out the great Faculty Toolkit on how to design effective research assignments that include strategies for lifelong best practices for research. I certainly fell in the 'trial and error' undergraduate research category and it was only by chance I received some helpful advice along the way from my professors.

By the time they are ready to graduate, many students have learned new research strategies through trial and error in several different courses. They learned that the research process is recursive---looking forward to analysis, back to the research questions, then returning to the data/readings. But students tell us that this learning could have occurred more smoothly, and earlier, if they'd gotten experienced researchers' help with three challenges posed by the research task:

  • constructing an inquiry's focus;
  • making sense of the chaos of data or readings; and
  • composing the report of findings or the argument.

Full disclosure: I had heard of but not known the details about this award until I received an email from the award's co-chairs that included "Librarians who teach, write blogs or newsletters, or meet with faculty and students have been key to encouraging students to apply and faculty to get involved, too." How cool is that acknowledgment of the value of librarian bloggers?

Friday, January 16, 2009

Friday Foolery #17: How to pee in Antarctica

Two of my best/lifelong friends include a scientist at the Diamond synchrotron in Oxfordshire and executive administration at the European Climate Foundation in The Hague. Then there's me with a marriage, mortgage & medical librarianship career in Seattle.

Among the other expats I'm friends with is Gifford Wong, who is working at the West Antarctic Ice Sheet (WAIS) Divide in Antarctica on a National Science Foundation project studying the past 100,000 years of deep ice core. Here's where WAIS is & more on what they do there.

I've been fascinated by their WAIS Divide Outreach group blog since Giff announced he was on his way back to the ice in November (remember that it's summer down there) because how else can I live life vicariously in Antarctica doing extremely important work to study climate change?

However, I was particularly intrigued by one of the latest entries from Logan regarding something I've never previously considered: how does one pee in Antarctica?

There are two options for going to the bathroom here at WAIS: You can go to one of the outhouses if you need to sit down, or you can pee at the pee flag... Now, as you can imagine, if lots of people pee in the same spot in snow, you can make quite a hole. (People here joke that this is called “hot water drilling”)
What I wanted to know and they didn't share is if there is actually a yellow cloth on a pole posted nearby for the pee flag. Given that this is the case at McMurdo (also in Antarctica) per my research, I'm thinking the answer is yes:

The one closest to the Galley that sees the most traffic was about 6” in diameter and a maybe a couple of feet deep.
This is particularly impressive because Logan decided it would be fun to connect two of them yet cautions us about the hazards of doing so:

This is quite a delicate task since the area around the pee holes is solid ice and if you pee on flat ice you will splash all over the place (including your shoes) which is not cool. You have to hit right at the rim of the hole – too far inside it and you don’t make any progress, too far outside it and you are splashing your shoes. It took me a couple of days, but at long last I finally created a channel connecting the two holes!! The channel even had a neat “S” shape to it!
Well, that was obviously major news that needed to be shared with everyone at camp. I'm not surprised Giff was mentioned:
The reactions I got were priceless. When I told Gifford, his face lit up with a huge grin and he said with a laugh “Oh that was you? That’s awesome!”
Yes, my life is indeed quite boring in comparison. I never imagined that studying climate change could be so entertaining, and I have to wonder what scientists 100,000 years in the future will think of the pee holes of Antarctica since there's no way the flags will last that long.

Monday, January 12, 2009

More journalism news: A cup of Google tea with your Brazilian Second Life avatar?

I first learned via Wired Campus that Alex Wissner-Gross, a physicist at Harvard, supposedly claimed that conducting two Google searches produces the same amount of carbon dioxide as bringing a kettle of water to a full boil. Since this was published in the United Kingdom's The Sunday Times (not to be confused with high quality journalism if you're unfamiliar with the UK), I guess they went with the tea aspect to appeal to their audience despite the fact that Harvard's up the road from the Boston Tea Party. Has anyone done an environmental impact study on that one?

I digress. I'll do that a lot with this particular entry, but it's to make a point about the authenticity of journalism when it comes to scientific research. Google replied via their blog that this wasn't the case, a single Google search only generates .2 grams of carbon dioxide.

According to Technology News, Mr. Wissner-Gross spent the majority of Monday trying to state the facts about his research study and how it was reported in The Sunday Times, among them these

One problem: the study's author, Harvard University physicist Alex Wissner-Gross, says he never mentions Google in the study. "For some reason, in their story on the study, the Times had an ax to grind with Google," Wissner-Gross told TechNewsWorld. "Our work has nothing to do with Google. Our focus was exclusively on the Web overall, and we found that it takes on average about 20 milligrams of CO2 per second to visit a Web site."

And the example involving tea kettles? "They did that. I have no idea where they got those statistics," Wissner-Gross said.

Why Google in particular? I think Mr. Wissner-Gross nailed it on the head:

The short answer is, it's a really easy way to sell papers. Google is a very successful company and it's a very easy way to get readership by making grandiose claims about them.
A closer look at the Sunday Times article brings up a familiar hodgepodge journalism style I've had issues with before at Pew Internet: citing research from a respected authority source, then bringing in components of a completely different story and blending it all together as one. The Sunday Times' additional claims:

Nicholas Carr, author of The Big Switch, Rewiring the World, has calculated that maintaining a character (known as an avatar) in the Second Life virtual reality game, requires 1,752 kilowatt hours of electricity per year. That is almost as much used by the average Brazilian.

“It’s not an unreasonable comparison,” said Liam Newcombe, an expert on data centres at the British Computer Society. “It tells us how much energy westerners use on entertainment versus the energy poverty in some countries.”

Though energy consumption by computers is growing - and the rate of growth is increasing - Newcombe argues that what matters most is the type of usage.

If your internet use is in place of more energy-intensive activities, such as driving your car to the shops, that’s good. But if it is adding activities and energy consumption that would not otherwise happen, that may pose problems.

Newcombe cites Second Life and Twitter, a rapidly growing website whose 3m users post millions of messages a month.

Personally, I'm surprised they didn't go after the #1 online bandwidth, energy and productivity-sucker there is according to my completely unscientific research and observation of my colleagues: checking out a suggested YouTube video then nonchalantly surfing the Related Videos that pop up after it.

My apologies if YouTube is blocked at your particular location due to those who have gone before you; and my suggestion on a quick way to make donuts per the embedded video below:

Where did you end up after that, if not at Krispy Kreme or trying not to sing 'b0rk b0rk b0rk' aloud while flinging pens at your colleagues?

Bottom line: Study the original research study publication whenever possible, especially if the soundbite you're picking up via a retweet on Twitter or an RSS headline news blurb is too catchy to be true, and question the credibility of all parties involved.

Friday, January 9, 2009

Friday Foolery #16: The secrets to a healthy, long life

1. Reduce your risk of oral cancer by drinking coffee.

2. Eat an occasional piece of crispy bacon, live to be the oldest person in the world.

Thursday, January 8, 2009

CE 2.0 for Web 2.0 - Check out these free modules!

The Medical Library Association Task Force on Social Networking Software is offering another round of free continuing education classes in January through April. This time they are stand-alone modules covering media sharing, web collaboration tools, wikis and blogs. Check out the details and be sure to register by February 9th for the web collaboration class. Looks great!

My soft spot: Healthcare journalism

With all the current discussion regarding Dr. Sanjay Gupta, CNN's chief medical correspondent, as the nominee for Surgeon General under President-elect Barack Obama, I thought I'd offer a glimpse into my own history for the perspective I'm coming from regarding healthcare and journalism.

In the fall of 1995, I was a young and idealistic student at Sonoma State University and part of Project Censored. Each week we received a stack of paper news media reports to review and match against selection criteria, then discussed them the following week to see if further research (mostly on the Nexis database in the library which contained records of news stories for journalists, quite different from what LexisNexis is now) would be justified to forward it to the much smaller batch of articles a national panel of journalism experts would review & vote to be one of the top 25 underreported stories of the year. The exact criteria and methodology of review have since changed, although so has the news media and the accessibility of information in ways I don't think we could even comprehend over 13 years ago. I was the last class with founder Carl Jensen & am no longer too familiar with the direction Project Censored (now under the Sociology department instead of Communication Studies) has gone since then.

The often-cited 2000 To Err Is Human: Building a Safer Health System report about medical errors being the 3rd highest killer in the United States? Old news to me by 5 years at that point. Two articles that ended up being combined into one and voted #12 for the spring 1996 book (1995 news stories) were in my article stacks: 180,000 Patients Die Annually From Treatment in Hospitals, based in part on a July 1995 JAMA adverse drug events (ADE) study. I apologize for the typos/funky wording in that HTML copy which may be from an optical character resolution (OCR) scan that wasn't post-edited well. I guarantee I used proper grammar in all text I wrote above my name. Can you see my writing style there? I still can. I used way too many commas in my youth and now I only use slightly too many... right? I remember balking at the emphasis on the names and careers of individuals in Chicago but being overridden by higher ups who wanted the personal touch in there.

Investigative journalism and librarianship are not all that far removed in the ability to research with ruthless efficiency under tight deadlines. Where there is a drastic difference between the fields is the pressure in journalism to not have your corporate owners, board members and advertisers look bad and lose revenue as a result of your research. For medical librarians (or any specialization), think about the amount of time you have personally invested in learning the medical and health care field, the information needs in it, and the specialized tools of the trade to be an effective researcher there. Journalists, even those with an MD or focused on health issues, do not usually have such background training nor much time or comprehensive access to the information sources we librarians do. Industry deregulation and the rate of media mergers that was a concern in the 1990s is eclipsed by the extent of the corporate media empires today.

This is why I can't offer an opinion about Dr. Gupta; I never watch CNN. It is hurting greatly in this economy but we always have and will continue to subscribe to a daily & Sunday print newspaper, The Seattle Times, from the independent and family-owned Seattle Times Company. They did an excellent job of researching methicillin-resistant Staphylococcus aureus (MRSA) in the state of Washington that led to the Department of Health announcing they would track MRSA rates as I mentioned in November. It's no longer common to see investigative journalism stories in corporate media since it takes a substantial amount of time and money to do the research for them... and you must also watch your back. This is why I hope people will continue to understand the value in and support independent media sources. They are truly better for our health!

Friday, January 2, 2009

Friday Foolery #15: ..and a Bacon New Year!

With gratitude to OrgMonkey and

Yes, I am indeed bringing home the bacon for 2009 although I'm not English, a man or living in the 12th century.