EBM and Clinical Support Librarians@UCHC

Entries categorized as ‘Web 2.0 and Geek Stuff’

News, EBM, Library Resources: JAMA Evidence now available

October 29, 2009 · Leave a Comment

For those interested in learning strategies for practicing evidence-based medicine, check out the latest digital subscription from UCHC Library:

JAMA Evidence

JAMAEvidence
Image Credit: http://www.jamaevidence.com/ - All rights reserved – Copyright 2009

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Produced by American Medical Association editors and publisher McGraw Hill, content from the digital textbook is also available for mobile applications.

I particularly liked the JAMA Evidence glossary.

If off-campus, connect via your UCHC library proxy account.

Categories: EBM/Clinical Decisionmaking · Library 2.0 · News & Medical News · Teaching-and-Learning in Medicine · Web 2.0 and Geek Stuff
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Visualization, PBL: Visit with Wordle Occasionally

October 14, 2009 · Leave a Comment

One aspect of participating in problem-based learning is that by the end of the semester, every student in the group has taken their turn at the group tasks involved, which are:

  • The Reader narrates the case as it is made available online. The written case with any supporting visual materials such as radiology or histology about the patient are posted on Blackboard and are no longer distributed in paper handouts.
  • The Scribe is the person with the marker who listens to the groups’ discussion and synthesis of the pertinent data about the patient such as chief complaint, presentation, past medical history, current labs values, medications, tests to be ordered, treatments to begin, etc.  They are writing down the data, hypotheses, learning issues as they become available.
  • Before every student in the room brought a computer to class — which sounds like the olden days but it was less than 6 years ago — the Scribe may or may not have been the one creating hand-drawn concept maps of that week’s PBL work.  Nowadays, concept maps are created not by drawing on the whiteboard but by using CMap, a free software program from IHMC (Institute for Human and Machine Cognition).  This brings on a new role in the group: Concept Mapper.
  • The Facilitators mostly listen, occasionally asking clinically-oriented questions or providing a bit of background or narrative about a patient, a procedure or a disease without being “teacherly”.
  • Each week, one person bakes and brings in goodies for 9 people.  That is an important function, too.

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On a basic science or biomolecular level, concept maps can get pretty complicated.

Recently I wrote down some of the medical terms, processes or conclusions which were heard during PBL, and made a Wordle map out of them.   Here is what it looks like:

WordleNPC1

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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This week I learned more about the function of Purkinje fibers (oh my duh – I’d never make it through medical school!).

Here are two other Wordles.

This one is based on words found on the EBM and Clinical Support Librarians@UCHC blog:

WordleEBMBlog

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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The last one is formed from words taken from my Delicious account called Onc2009, a set of bookmarks about cancer, that was created for Mechanisms of Disease-Oncology:

WordleOnc2009

Image credit: http://www.wordle.net – All rights reserved – Copyright 2009

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Wordle, an elegant piece of software, was created by Jonathan Feinberg.

Categories: Academic Medicine · EBM/Clinical Decisionmaking · Educational Sites · Instruction · Medical Students · Medicine 2.0 · Other Stuff · Teaching-and-Learning in Medicine · Virtual Environments · Web 2.0 and Geek Stuff
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The Friday Post #38: Strange Posts, Sleepy Chickens and Strange Sports

October 2, 2009 · Leave a Comment

This is the Friday Post #38 for October 2 2009.

Strange?  Define Strange.

As a blog-administrator I get to filter all comments to the page before they are displayed publically.  The majority of the spam is deleted by myself or caught by Askimet, the utility in WordPress that takes care of that function.

On Tuesday, Sept 29 there was a link in my Comments section referring to a post I’d written earlier this week about LigerCat, a new PubMed search tool.  The in-coming link looked like this (screenshot shown below):

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StrangePost#3

Image credit: http://www.wordpress.com - All rights reserved – Copyright 2009

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Intrigued, I clicked on the address of the referring page and below is a screenshot of their synopsis of what I wrote:


StrangePost

PubMed Poke Apparatus grown in 2009?  Heaven help us all

Image credit: http://tiny.cc/I78dS - All rights reserved – Copyright 2009

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Cartoonist Doug Savage writes a blog called Savage Chickens and invented the term “sleepworking” with this post from Aug 28 2008:

SleepworkingSavageChickens

Photo credit: http://www.savagechickens.com/2008/08 - All rights reserved – Copyright 2009

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These videos come with a couple of caveats: Don’t try this at home. Some activities could result in serious bodily injury. Never jump off a roof, no matter what your friends say to you.  In questionable taste.

Getting hit in the eye by a pair of flying sunglasses would be no laughing matter.  These videos should remind us that there is, and will always be, a need for a new generation of Emergency Medicine physicians due in part to the poor coordination (or questionable judgment) of young people when it comes to acting like daredevils on (or with) sports equipment.

However, the young men in question have obviously practiced their sports often, are well-trained in them, and (admit it) it is creepily fascinating to observe their accuracy.

.First:  Sunglasses Catching

Video credit: http://www.youtube.com/watch?v=-prfAENSh2k - All rights reserved – Copyright 2009

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Second:  Pants Jumping

Video credit: http://www.youtube.com/watch?v=pShf2VuAu_Q - All rights reserved – Copyright 2009

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Last:  Laptop Catching is so out of the scope of this blog, I’m not even going to post the URL for it.  You can find it on your own.

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And that’s the Friday Post #38 for Oct 2 2009, folks.  Have a restful, enjoyable weekend!

Categories: Humor · Journalism · News & Medical News · The Friday Post · Videos & Podcasts · Web 2.0 and Geek Stuff
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The Friday Post #37: A Cartoon, Visualize your Persona and a Favorite Med Student Video

September 18, 2009 · Leave a Comment

A timely cartoon from PhDcomics.com called “Brain on a Stick

PhDComics

Source/Credit: http://www.phdcomics.com/comics/archive.php?comicid=1126 – All rights reserved – Copyright 2009

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Next: Professors may see you as a brain on a stick, but how does the Internet see you?

Personas, a specialized data-mining/visualization software program from designers at MIT, attempts to answer that question by scouring the web to collect groups of information on specific named person and then builds it into a graphical “fabric” constructed of the parts of that person’s online presence.

How does it work? Following is an excerpt from the Personas About page:

It is fascinating to watch Personas work to build this collection of an individual’s online presence.  It takes a few minutes.  The timeline is beautifully-rendered.

However, having said that it’s beautiful to watch it work, I ask you to consider how the technology should alert one’s “caution” button.   Meaning, lend some consideration about the depth of pertinent as well as random facts that Google and other search engines have collected about “you” over the years.  If that information available in public domains about “you” is incorrect, or God forbid, you share the identical name with a notorius or criminal person, what recourse would “you” have to delete or rewrite that data?  There is a long, long trail of information connected to “you”… one tool to evaluate that information is Personas.

Here’s a small question: How is the name of the site pronounced — as personas or Person As?

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Next: a Favorite Medical Student Video

Yes, I have posted about this before, but I enjoy seeing it from time to time.   Bravo to a group of medical students (Class of 2010) from the University of Alberta who filmed Diagnosis Wenckebach:



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And that’s the Friday Post for Sept 18, 2009, folks. Enjoy your weekend!


Categories: Humor · Medical Students · Medical Students-Videos · News & Medical News · The Friday Post · Web 2.0 and Geek Stuff
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The Friday Post #36: Bad Clowns, Doggies and a Music Video

August 14, 2009 · 2 Comments

It is my blogo-versary (two years, 3 weeks of blogging, folks – send a comment, please), it’s the depths of summer, the students are on vacation, so let’s take poetic license to post whatever is at hand.  Here they are:

A friend of mine is terrified of clowns in all forms. If you read the novel It by Stephen King, you might not ever walk past a clown (or street gutters) without wincing. The actor Tim Curry (who played Pennywise, the evil clown, in the film version of It) gives me the creeps, too.

Adam Berg in 2009 created a short film funded by Philips to promote their Cinema 21:9 LCD TV. Like a Dada film, one can start and stop watching Carousel – and then start it again – and it all makes about as much sense.

The fictional mayhem in this short film occurs in a hospital.  It won an award at the 2009 Cannes Lions FestivalDada-esque?

Photo credit:  http://stinkdigital.com – All rights reserved – Copyright 2009

For more information about the creation of this interactive work, visit links to Stink Digital and Philips Carousel for Cinema 21:9 TV – How they did it.

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Don’t laugh – I used to live in San Francisco and have eaten once or twice at Doggie Diner, where the food is cheap, fast and good — amusing for the fact that the cooks yell at you if you don’t give your order quick and then move along.  No holding up the customer line!

Thanks to blogger Scott Beale at LaughingSquid for posting about this:

DoggieDinerAwardSFPhoto credit:  http://laughingsquid.com – All rights reserved – Copyright 2009

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Hibi no Neiro” (Tone of everyday) is a music-video by Japanese band SOUR, used to promote the group’s first mini-album, Water Flavor EP.   The 3.5 minute video was created by Masashi Kawamura, Hal Kirkland, Magico Nakamura and Masayoshi Nakamura in June 2009.

It is interesting to watch for both the music and the people (all fans of the band) who collectively filmed it worldwide.  It is one of those videos where, every time you watch it you can see something new in it:

Image source: YouTube.com - All rights reserved – copyright 2009

Thanks to Michael Wesch for twittering about it.

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And that’s the Friday Post #36 for Aug 14 2009.   Hurray – a new academic year begins next week!



Categories: Humor · The Friday Post · Videos & Podcasts · Virtual Environments · Web 2.0 and Geek Stuff
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News, Scientific Literature, Bioinformatics, Search Technologies: MedlineRanker

July 28, 2009 · Leave a Comment

Anyone who works with geneticists and biomedical researchers already knows that learning the language of their science is daunting for a non-scientist to understand. This international community has developed dozens of highly specific databases, data-mining software and cooperative, collective digital libraries for their own use.  In an approximate sense, one could even imagine the mapping of the human genome as one vast wiki.  Clinical care follows the translational research of these investigators.

This month in Nucleic Acids Research, Volume 37-July 1 2009, the Supplement 2: Web Server issue was published, described by Oxford University Press as:

“…the seventh in a series of annual special issues dedicated to web-based software resources for analysis and visualization of molecular biology data. The present issue reports on 112 web servers with a special emphasis on metagenomics, molecular network and pathway analysis, and biological text mining”..


Full-text of the NAR-Supplement 2 is available open-access for anyone in the world to read, on PubMedCentral.

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An article in that special issue attracted my interest, entitled MedlineRanker: flexible ranking of online literature” and written by a group of computational scientists affiliated with the Computational Biology & Data Mining Group of the Max Delbruck Center for Molecular Medicine (MDC) in Berlin.

The six authors describe their project in this way:

We have implemented the MedlineRanker webserver, which allows a flexible ranking of Medline for a topic of interest without expert knowledge. Given some abstracts related to a topic, the program deduces automatically the most discriminative words in comparison to a random selection. These words are used to score other abstracts, including those from not yet annotated recent publications, which can be then ranked by relevance. We show that our tool can be highly accurate and that it is able to process millions of abstracts in a practical amount of time.

Source: Link from Nucleic Acids Research – Vol. 37, Suppl. 2: W141-W146

Please view the four Supplementary Data (note: these open as either Word or Excel documents) that describe search terms used to search  PubMed using the MedlineRanker server.

The illustrations in the article look like a cross between a tag cloud and a Wordle picture.

MedlineRanker is free for use and is available at http://cbdm.mdc-berlin.de/tools/medlineranker.

A list of current research projects from MDC can be viewed at this link.

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In January 2009, Supplement 1 – Datatabase Server Issue was published in  Nucleic Acids Research, Vol. 37 and that is also available online on the PubMedCentral archive.

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The 122 sites listed in the July 2009 NAR supplement will be added to the 1,200 already listed in the Bioinformatics Links Directory which:  “... now expands to almost 1400 unique web servers, databases and resources for computational research in the life sciences. All links are freely accessible to the public, and may be browsed by biological category and research task subcategory. “

For more information on text-mining programs written by scientists from around the world, go to the Bioinformatics Links Directory-Literature: Text Mining page.

Categories: Educational Sites · Medicine 2.0 · News & Medical News · Scholarly Publications · Scholarly Publishing & Open Access · Web 2.0 and Geek Stuff
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News, Scientific Literature, Visualization: Cell Press and Elsevier introduce Article of the Future

July 20, 2009 · Leave a Comment

STM publishers Cell Press and Elsevier ratcheted up the technological ante this month with their announcement on Monday, Jul 20 2009, of a shared project called Article of the Future, which they are funding to provide:

“… an on-going collaboration with the scientific community to redefine how the scientific article is presented online. The project’s goal is to take full advantage of online capabilities, allowing readers individualized entry points and routes through the content, while using the latest advances in visualization techniques“.

Text source: http://beta.cell.com – All rights reserved – Copyright 2009

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Currently available are two “prototypical” articles which the companies have put up in order to solicit feedback about the page and suggestions from the worldwide scientific community about useability and function.

Here’s one nice feature of the demo: “Integrated audio and video [will] let authors present the context of their article via an interview or video presentation and allow animations to be displayed more effectively”.

Below is a screenshot showing visualizations of tables from article Prototype #2, entitled “Identification of Positionally Distinct Astrocyte Subtypes whose Identities Are Specified by a Homeodomain Code” by Christian Hochstim, Benjamin Deneen, Agnes Lukaszewicz, Qiao Zhou and David J. Anderson.

This article was published originally published in the journal Cell (Vol. 133, issue 2 – May 2 2008, p 510-522).

CellPressElesevierJuly 2009collaborationExample

Image Source: http://beta.cell.com/hochstim/inc/hochstim_article.pdf – All rights reserved – Copyright 2009
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Visitors to the Article of the Future page are encouraged to provide direct (anonymous) input about the site using a 10-item online survey.

Thanks to AD for telling me about this.

P.S. This news release was first read on Twitter – Cell Press News around 1oopm today – http://twitter.com/CellPressNews – but the funny thing is, neither of the companies have posted a press release on their official websites yet (as of 3:15pm EST – Jul 20 2009).

Note: Chronicle of Higher Education also wrote about this venture – see entry dated July 20, 2009 at this link.

Categories: Academic Medicine · Educational Sites · Library 2.0 · Medicine 2.0 · News & Medical News · Scholarly Publications · Videos & Podcasts · Virtual Environments · Web 2.0 and Geek Stuff
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The Friday Post #35: Renaissance Medicine at NLM, Harry Potter and 2 Quizzes

July 17, 2009 · 2 Comments

So excited about going to see the fifth movie based on J.K. Rowling’s work, Harry Potter and the Half-Blood Prince, which was released in the U.S. on July 15th at midnight.  I’ve read every book in the series at least twice.

A timely exhibition by the librarians from the U.S. National Library of Medicine features an exhibit (both digital and real) about herbal medicine, mythical beasts and other fantastical arcana in a series called “Harry Potter’s World: Renaissance Science, Magic and Medicine“.

NLMHarryPottersWorldImage credit: National Library of Medicine – All rights reserved – copyright 2009

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American Library Association is co-sponsoring the traveling Harry Potter exhibit, which will stop in the U.S. at twelve libraries starting in the fall of 2009..

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She needs to sort out her priorities!

– Ron Weasley, commenting on Hermione Granger in the first book in the series, Harry Potter and the Philosophers Stone (1997)

Quiz #1

If you’re a big Harry Potter fan, you might want to check out which house in Hogwarts that the Sorting Hat would place you in, which you can do by clicking this link and filling out a 122-item questionnaire:

Hogwarts Sorting Hat Quiz

Said Ravenclaw, “We’ll teach those whose intelligence is surest.”

The sorting hat says I belong in Ravenclaw.

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Quiz #2

Associate editor Jennifer Van Grove on Mashable wrote an article entitled “What Kind of Social User Are You?” (July 15 2009), which links to a brief online quiz from Anderson Analytics entitled “Social Networking Services User Typing Tool” (click here to take it).

After taking the quiz, their assessment ranked my social networking skills as:AndersonAnalyticsSNSImage credit: Anderson Analytics – All rights reserved – Copyright 2009

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Oh man.  Their assessment of my SNS skills is encouraging, but it doesn’t seem to be too accurate.  Because, although the blogging part is going well, in fact…  I’m pretty sure I flunked Twitter.     :roll:

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That’s the Friday Post for Jul 17 2009, folks.  Have a nice weekend!




Categories: Educational Sites · Humor · News & Medical News · The Friday Post · Videos & Podcasts · Virtual Environments · Web 2.0 and Geek Stuff
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Searching Technologies, Cultural Evolution, Web 2.0: Slight Nostalgia for Olden Days, and Don’t Diss Librarians

July 16, 2009 · 3 Comments

Tis far better to be thought a fool than to open your mouth and remove all doubt.

-Quote variously attributed to Benjamin Franklin, Galileo, Socrates and Abraham Lincoln

You get the network that you deserve.

-Written by Brian Morressey

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Being in the library/information business for more than a decade has taught me to take a long-term perspective about new companies or products (and possibly, a somewhat jaded outlook as well). What do I mean by this?

The technologies of Web 2.0/3.0 distribute your website, saves your comments on Twitter, immortalizes your blog-postings, shares your photos (for good or ill), exhibits your conference presentations or business plans, allows you to create an instant survey on Google Docs… each of these become instantly visible by those in your network, or worldwide.  (As YouTube.com famously advises, “Broadcast Yourself”.)  This connectivity has been described as ambient intimacy.

One of the first lessons a new blogger learns is how ridiculously easy it is to trip up online… when you make a mistake in a public and highly-distributed way, such an online event can make one very glad for the solitude of the workplace cubicle (while your face turns a deep, burning and lasting shade of red).  But that’s also a shared experience.  By joining up into the collective “we”,  it is possible to be anonymous yet harder to be invisible.  In digital life, these terms are elastic, relational, relative.  And Google never forgets.

Two recent examples of the downside of all that connectivity come to mind.   In 2008, a PhD student/blogger wrote on her Nature Network blog LabNotes that “I hate PubMed. I hate it with a burning passion.“  As seen in the comments garnered by that post, she was given a mild dressing-down by a variety of scientists, bloggers and medical librarians.  Some of us even offered to teach her how to search the database better.

Another more recent example involves the June 2009 roll-out of a clinically-oriented website named Clinical Reader.com, as medical librarian-blogger EagleDawg describes it, with additional commentary found at The Health Informationist blog.

These events have been Twittered about aplenty. One could take the view that the  company’s response to the librarian was that of a newbie… turn the prism, see it as free publicity.

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By taking the long-range view, it’s not surprising to appraise commercial or non-commercial web sites as they come and go, in a literal sense*. Some sources stay the distance, some disappear quickly, some just can’t deliver a quality array of information, some sites are just plain ugly to use or to teach others to use, some crash frequently (thus losing your data), or are so difficult to navigate for results that users simply give up (and so then turn to Google Scholar).

For librarians, the perspective is a bit different than that of a researcher or medical student.  We are highly concerned with the content, scope and utility of individual information sources for our unique clientele.  That is why the mission of the librarians is to spend funds wisely, distribute the information efficiently along networks, assist those who have questions or problems with “digesting” the data, and to train our users to search well, collect and analyze their data.

Librarians aren’t the end-consumers of the information assembled by our subscriptions; we are more like information brokers and, to some extent, strive for impartiality.

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Talk to almost any librarian with decades of experience, and they will tell you how it was before Google.  It was different.

The first library I worked in after graduate school was an academic library where the database subscriptions were delivered on CD-ROMs and loaded on an IBM server for distribution throughout the local area network.  Each month a new CD-ROM arrived and the old one was either returned to the company or discarded.

If a faculty member or student needed a comprehensive literature search, a librarian would use a dial-up modem to connect to a commercial information services corporation, Dialog, which charged by the minute for connection time, and charged individual fees for seaching a database, displaying citations, and for downloading each and every item.  Before even connecting to the site, the librarian had to check the so-called Dialog bluesheets to learn the scope and arrangement of fields for an individual database (or, which one of 300 individual databases were the best to search?).  It was all too easy to spend $100 of the library’s money on a search which might take 8-10 minutes.  And I still miss SilverPlatter.

Any student doing research had to physically be in the building in order to do any work.  Once the search was completed, they then had to trek around the stacks to locate the individual article in the journal.  They could read it in the building, or make a copy of it to take along for later reading.  After typing up a finished copy, the students handed-in a copy to their professor at the end of the term.  There was no TurnItIn then.

Sounds like ancient history, doesn’t it?

It was an analog world.   Our digital natives wouldn’t recognize the place.

And truly, it is so great in 2009 to offer our users Harrison’s Principles of Internal Medicine online.  What would our residents or students do without their ability to search and access medical information via Up to Date, PubMed or dozens of other sources?

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* To take a brief “time-capsule” look at just how far academic libraries and collections have evolved over a decade can be appreciated by reading this ERIC Digest from 1990.

Finally… getting back to the feeling-jaded comment?  There are some who might feel a bit over-stressed by this always-on technological connecting.  If that applies to you, then check out the 2009 Cultural Dictionary (2nd edition) created by the ad agency Cramer-Krasselt, where the following definition was recently found:

CKCulturalDictionary2009UpdateMandate

Image credit: C-K Cultural Dictionary – Copyright 2009 – All rights reserved

Categories: Blogs or Wikis about Medicine · Journalism · Libraries or Librarians · Library 2.0 · News & Medical News · Other Stuff · Virtual Environments · Web 2.0 and Geek Stuff
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News, Medicine 2.0, Current Awareness: The debut of Clinical Reader

July 9, 2009 · 1 Comment

ClinicalReaderMultimedia

.Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

Clinical Reader, introduced Jun 29 2009 in beta, is getting a lot of buzz* on Twitter, blogs and librarian discussion lists.  Thanks to librarians posting about it on Medlib-L listserv and to Berci for blogging about it.

Following is an excerpt from their About page:

Clinical Reader was brought to life in 2009 by a junior doctor and a small group of forward thinking young tech programmers spread across London and Toronto. The conceptualized idea was to manage clinical information overload and deliver relevant news from an authoritative source on a daily basis.… it is truly quality collection of accessible clinical, scientific and health literature aiming to filter the river of information presented to the online medical community.”

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I noticed that the creators of the site have constructed it using sets of criteria which include journal performance indicators; two of the criteria for inclusion in the site are shown in this screenshot of their FAQ page:

ClinicalReaderFAQ#3and#4

Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

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There are currently about 3,000 readers who subscribe to the Clinical Reader newsletter.  Anyone can use the site, at no cost.

This is a rich and multi-layered site targeted at medical and dental clinicians.  It can be used to read daily health news, journal scans, searching links for training or educational videos, clinically-oriented podcasts and medical specialties. Site content is divided in three sections: News (links to UK-oriented news), Sections and Multimedia.

Below is a screenshot from Virtual Reality Training for Surgeons (8 minute video), featured this week:

ClinicalReaderVirtualRealityTrainingforSurgeonsScreenshotVideo credit:  http://tinyurl.com/n7c4lu

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There is a page for medical students, medical education and dentisty/oral surgery (among many others).

And links to Del.icio.us, Connotea, Digg and (of course) Twitter.  Finally: a hand-picked list of fourteen Medical Blogs is included, which features a Canadian librarian-blogger, Dean Giustini and Scienceroll blogger, Bertalan Mesko ~ woot for that!

ClinicalReaderCircle

Photo credit: http://www.clinicalreader.com – All rights reserved – Copyright 2009

Best wishes to the creators of Clinical Reader.com, who have rolled out a working website designed to meet the information needs of physicians, by physicians. I look forward to watching this site develop over time.

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* Edit: On July 15, after reading posts from other medical librarians (see EagleDawg blog and Steve Lawson (both dated Jul 13 2009), and other discussions who collectively remind administrators at Clinical Reader to proceed with caution in regard to commercial and copyright laws, to intellectual and graphical property, I think I’m going to retract what I wrote on Jul 9 2009 (above).

And ask Clinical Reader folks to take a look at the Creative Commons site at http://creativecommons.org/ and the doctrine of fair use.


Categories: Libraries or Librarians · Library 2.0 · Medicine 2.0 · News & Medical News · Scholarly Publications · Videos & Podcasts · Web 2.0 and Geek Stuff
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