Feb 29

Video: Dr. Joshua Schwimmer on Google Book Search

A few weeks ago I mentioned a post from Dr. Joshua Schwimmer about Google Book Search in which he described a time when it proved extremely useful in a clinical setting.

Google must have liked the positive exposure because they interviewed Dr. Schwimmer. The interview (just over two minutes) is embedded below.

If you’re reading this in an aggregator or via email, you may have to visit the site to view the embedded video above

Dr. Schwimmer’s blogs:

Feb 29

Making PubMed “Easy”?

Jon Brassey writes:

I may have missed something, but none of these alternate interfaces allow easy searching of PubMed. Some are wonders of programming, some allow some very neat tricks but none make searching of PubMed easy.

That’s a fair criticism, I suppose. I think that although PubMed has come a very long way in developing tools that make searching the NLM’s databases easier for medical librarians, clinicians and consumers, it still takes some knowledge and skill to perform a really useful search of the primary literature.

Jon continues:

I suppose my biggest issue with PubMed is that doing a search of statins returns 18,491 results. Unpicking that a bit:

* Most research shows search engine users finish looking after 3 pages of results.
* From our own experience with TRIP we also know that most users only use single search terms (e.g. asthma, hypertension).

So what I’m saying is that statins is a realistic search term and that suggests that 18,431 (18491-60) results are superfluous.

Therefore, the two challenges to me are:

* Return fewer results in the first place
* Allow users to easily qualify their searches.

Let’s bring Jon’s challenges to Healia’s PubMed/MEDLINE Search. It isn’t my favorite, but if Jon uses it to search for statins, he’ll see that, at the time of this writing, only 7,731 results are returnedI’m guessing that the reason why PubMed returns 18,431 results and Healia’s PubMed/MEDLINE search returns only 7,731 is that Healia’s search is only looking for the string statins.

PubMed, on the other hand, translates statins into “hydroxymethylglutaryl-coa reductase inhibitors”[MeSH Terms] OR “hydroxymethylglutaryl-coa reductase inhibitors”[Pharmacological Action] OR statins[Text Word].

After all, if we search PubMed for “statins” as a string, we get only 7,990 results. and that there are a number of tools for “qualifying” the search right there on the search results page.

You can adjust for date:

You can filter for review articles or for English language articles only:

You can filter by patient demographics:

Healia even recognizes that we’re searching about a class of drugs and gives us tabs so we can filter by Dosage, Usage, or Side Effects:

So let us assume that Jon’s hypothetical user wants to see English-language review articles about the dosage of statins from only the last 5 years. That’s only twelve results. I think this passes Jon’s test.

With that out of the way, I need to add:

Criticizing PubMed for returning too many search results for a query as inadequate as “statins” seems unreasonable to me. A major part of what makes PubMed an amazing tool is its complexity. I believe and hope that new tools will continue to be developed that make the data useful to various kinds of users in various new ways, but I don’t expect that getting exactly what one wants from the primary literature will ever truly be “easy.”

Feb 28

New Online Drug Information Tools

I’m in the middle of a really busy few weeks, so I haven’t had time to properly examine these yet- but I wanted to at least mention them:

By now you’ve probably heard about the NLM’s new drug information portal, but you might’ve missed Healthline’s new drug directory, the features of which are reviewed by (Healthline’s own) Dr. Joshua Schwimmer here.

While on the topic of online drug tools I haven’t properly examined for myself, I should mention PharmaLive Search, marketed as “the only pharmaceutical-industry specific search engine.” AltSearchEngines has a post about PharmaSearch Live that might be a good place to start evaluating its potential usefulness.

If you’ve tried these, please leave a comment and let me know what your impressions were?

Feb 27

Web Geekery in Recent Literature – 2/27/2007

Med Teach. 2008;30(1):10-16.
‘Net Generation’ medical students: technological experiences of pre-clinical and clinical students.
Kennedy G, Gray K, Tse J.
University of Melbourne, Australia.
Background: While institutions have been keen to integrate information and communication technologies into medical education, little is known about the technological experiences of the current cohort of so-called ‘Net Generation’ students. Aims: This study investigated the technological experiences of medical students and determined whether there were differences between pre-clinical and clinical students. Method: In 2006, 207 pre-clinical and 161 clinical students studying medicine at a major Australian university were surveyed. The questionnaire asked students about their access to, use of and skills with an array of technologies and technology-based tools. Results: The results show that access to mobile phones, memory sticks, desktop computers, and broadband Internet connections was high while technologies such as PDAs were used in very low numbers. A factor analysis of students’ use of 39 technology-based tools revealed nine clear activity types, including the ‘standard’ use of computers and mobile-phones, and the use of the Internet as a pastime activity, for podcasting and for accessing services. A comparison of pre-clinical and clinical students revealed a number of significant differences in terms of the frequency and skill with which these students use distinct technology-based tools. Conclusions: The findings inform current technology-based teaching and learning activities and shed light on potential areas of educational technology development.
PMID: 18278643

David wonders: Does “Net Generation” = “Digital Natives” = “GenX/GenY”?


Support Care Cancer. 2008 Feb 22
Internet use by cancer survivors: current use and future wishes.
van de Poll-Franse LV, van Eenbergen MC.
Comprehensive Cancer Centre South (IKZ), Eindhoven Cancer Registry, P.O. box 231, 5600 AE, Eindhoven, The Netherlands, l.vd.poll@ikz.nl.

OBJECTIVE: The objective of this study was to evaluate the extent of internet access and use and patient characteristics associated with internet use. We also aimed to study when and at which sites cancer patients search for information, the self-reported effect on health care use, and patients’ wishes with respect to future internet possibilities. MATERIALS AND METHODS: We drew a sample of 390 patients diagnosed with breast (n = 128), prostate (n = 96), or gynecological (n = 89) cancer or lymphoma (n = 77) in four different hospitals in the period 2002-2004, who were 65 years or younger at diagnosis. These patients were sent a questionnaire that contained 45 questions about demographics and three broad applications of internet use: content, communication, community. RESULTS: Of the 261 (75%) patients who responded, 60% used Internet by themselves, 9% via others, whereas 31% did not use the Internet. High education, young age, and high socio-economic status were all independently positively associated with internet use. Of the patients with complaints but pre-diagnosis, 41% searched the Internet for information about cancer daily to several times a week. After diagnosis, during treatment, and at follow-up, this was, respectively, 71%, 56%, and 4%. Although patients preferred to get reliable information from the Web site of their oncologist (88%), hospital (70%) or Dutch Cancer Society (76%), Web sites that are completely financed and created by pharmaceutical industries were mentioned most as source of information. Patients who used the Internet to find information about cancer felt themselves to be better informed about their disease (72%); only 3% thought that consulting the Internet increased the frequency of visiting their doctor, whereas 20% felt that information from the Internet influenced the treatment decision made by their doctor. Most patients who use the Internet would like to be able to access their own medical file (79%) or test results (81%) if possible. CONCLUSION: Many cancer patients use the Internet to find reliable information about their disease and treatment. Patient information centers from hospitals should be strongly encouraged to improve disease and treatment information facilities on their hospital Web site, especially since most patients view their oncologist still as the most important source of information.

PMID: 18293014

David notes: I suppose that it is good to have a supporting study, but I wasn’t aware that there was any doubt about the fact that a lot of patients in comparatively wired (affluent) nations dealing with any illness “use the Internet to find reliable information about their disease and treatment.”
Take-home lesson for hospital libraries: “Patient information centers from hospitals should be strongly encouraged to improve disease and treatment information facilities on their hospital Web site”


BMC Public Health. 2008 Feb 21;8(1):69
Health information seeking on the Internet: a double divide? Results from a representative survey in the Paris metropolitan area, France, 2005-2006.
Renahy E, Parizot I, Chauvin P.
[Free full text PDF]

ABSTRACT: BACKGROUND: The Internet is a major source of information for professionals and the general public, especially in the field of health. However, despite ever-increasing connection rates, a digital divide persists in the industrialised countries. The objective of this study was to assess the determinants involved in: 1) having or not having Internet access; and 2) using or not using the Internet to obtain health information. METHODS: A cross-sectional survey of a representative random sample was conducted in the Paris metropolitan area, France, in the fall of 2005 (n = 3023). RESULTS: Close to 70% of the adult population had Internet access, and 49% of Internet users had previously searched for medical information. Economic and social disparities observed in online health information seeking are reinforced by the economic and social disparities in Internet access, hence a double divide. While individuals who reported having a recent health problem were less likely to have Internet access (odds ratio (OR): 0.72, 95% confidence interval (CI): 0.53-0.98), it is they who, when they have Internet access, are the most likely to search for health information (OR = 1.44, 95% CI = 1.11-1.87). CONCLUSIONS: In the French context of universal health insurance, access to the Internet varies according to social and socioeconomic status and health status, and its use for health information seeking varies also with health beliefs, but not to health insurance coverage or health-care utilisation. Certain economic and social inequalities seem to impact cumulatively on Internet access and on the use of the Internet for health information seeking. It is not obvious that the Internet is a special information tool for primary prevention in people who are the furthest removed from health concerns. However, the Internet appears to be a useful complement for secondary prevention, especially for better understanding health problems or enhancing therapeutic compliance.

PMID: 18291024

David notes: Inside or outside of the context of universal healthcare, it isn’t at all surprising to read that “access to the Internet varies according to social and socioeconomic status and health status, and its use for health information seeking varies also with health beliefs, but not to health insurance coverage or health-care utilisation.” Are there really people who don’t understand that access to quality information depends greatly on social and economic factors even in the most wired and affluent nations?
Take home lesson for hospital libraries: Again, make your hospital library Web site a gateway to the best available free information.


J Med Internet Res. 2008 Jan 22;10(1):e2.
Impact of web searching and social feedback on consumer decision making: a prospective online experiment. [Free full text]
Lau AY, Coiera EW.
Centre for Health Informatics, University of New South Wales, Sydney, Australia.
BACKGROUND: The World Wide Web has increasingly become an important source of information in health care consumer decision making. However, little is known about whether searching online resources actually improves consumers' understanding of health issues. OBJECTIVES: The aim was to study whether searching on the World Wide Web improves consumers' accuracy in answering health questions and whether consumers' understanding of health issues is subject to further change under social feedback. METHODS: This was a pre/post prospective online study. A convenience sample of 227 undergraduate students was recruited from the population of the University of New South Wales. Subjects used a search engine that retrieved online documents from PubMed, MedlinePlus, and HealthInsite and answered a set of six questions (before and after use of the search engine) designed for health care consumers. They were then presented with feedback consisting of a summary of the post-search answers provided by previous subjects for the same questions and were asked to answer the questions again. RESULTS: There was an improvement in the percentage of correct answers after searching (pre-search 61.2% vs post-search 82.0%, P < .001) and after feedback with other subjects' answers (pre-feedback 82.0% vs post-feedback 85.3%, P =.051).The proportion of subjects with highly confident correct answers (ie, confident or very confident) and the proportion with highly confident incorrect answers significantly increased after searching (correct pre-search 61.6% vs correct post-search 95.5%, P <.001; incorrect pre-search 55.3% vs incorrect post-search 82.0%, P <.001). Subjects who were not as confident in their post-search answers were 28.5% more likely than those who were confident or very confident to change their answer after feedback with other subjects' post-search answers (chi(2) (1)= 66.65, P <.001). CONCLUSIONS: Searching across quality health information sources on the Web can improve consumers' accuracy in answering health questions. However, a consumer's confidence in an answer is not a good indicator of the answer being correct. Consumers who are not confident in their answers after searching are more likely to be influenced to change their views when provided with feedback from other consumers.
PMID: 18244893

David wonders: The fact that study participants were undergrad students is pretty significant, isn’t it?

Feb 26

Medical Librarian Treating Information Overload (Nurse.com)

Medical librarian Anne Ludvik takes a proactive approach to helping busy staff nurses solve patient care problems and get up-to-date health information at the San Francisco Veterans Affairs (VA) Medical Center.

“It’s difficult for nurses to get to the physical library, so we work to bring digital resources to them,” Ludvik says.

[Read the rest]

Feb 26

MScanner: a classifier for retrieving Medline citations

MScanner: a classifier for retrieving Medline citations
Graham L Poulter, Daniel L Rubin, Russ B Altman and Cathal Seoighe
BMC Bioinformatics 2008, 9:108doi:10.1186/1471-2105-9-108
Published: 19 February 2008

Free full text: [PDF]

Article is about a third-party PubMed/MEDLINE tool that I have not been able to make work, MScanner.

[Other posts about third-party PubMed/MEDLINE tools]

Feb 25

Why Slate is Wrong About “the myth of Web 2.0 democracy”

Chris Wilson’s article in Slate last Friday argues that social media like Digg and Wikipedia aren’t really “democratic”.

Phil Bradley sums up the article really nicely:

1% of Wikipedia users are responsible for about half of the sites edits.

In 2007 the top 100 diggers submitted 44% of the sites top stories, and in 2006 it was 56%.

The point really is that it’s not the wisdom of the crowds, it’s a gentle dictatorship of the chaperones.

“At both Digg and Wikipedia,” the article says, “small groups of users have outsized authority.”

Well…yeah. Y’know why?

Digg and Wikipedia’s elite users aren’t chosen by a corporate board of directors or by divine right. They’re the people who participate the most.

Right. Those who are most active in the process develop over time a hugely disproportionate influence. How exactly does that differ from democracy in the United States?

But it’s the next bit that really bugs me:

Despite the fairy tales about the participatory culture of Web 2.0, direct democracy isn’t feasible at the scale on which these sites operate. Still, it’s curious to note that these sites seem to have the hierarchical structure of the old-guard institutions they’ve sought to supplant.

First, direct democracy is absolutely feasible at the scale on which these sites operate. In fact, I believe direct democracy that is (more or less) as democratic as the process by which we elect American presidents is happening on these sites. Just as in life and politics, those who posses the necessary desire and resources cultivate a disproportionate influence.

I don’t think it is that these sites have built a hierarchical structure into their source code- it is that human behavior is still human behavior whether it takes places in presidential primaries or on Digg. That behavior forms a hierarchy.

The United States isn’t a populist utopia, and no social site ever will be either. Why? Because they’re run by fallible people operating from positions of widely varying resources who care in greatly varying degrees.

Anyone with the requisite smarts and time to invest has the opportunity to become influential on these sites- and that’s what makes these sites democratic.

Feb 25

Rachel Walden on Replacing LIS Journals with Blogs

In response to this post about Marcus Banks’ assertion that Professional Librarian Journals Should Evolve into Blogs, Rachel Walden (a medical librarian, a blogger and an editor at the JMLA) left the following comments:

…I tend to agree with T. Scott on these mattersDavid’s footnote: See T. Scott’s comments here, for several reasons. I don’t see any reason why librarianship journals as blogs should be singled out as a specialty (goose, gander, etc.) in this discussion, so I’ll talk about this more generally.

1) I believe there is value in having a final version of a manuscript on the record. Getting things out quickly isn’t the only goal in publishing a paper, or shouldn’t be. A larger goal is to contribute to the body of knowledge on a topic, in a way that can be cited and referred to and built upon in the future. If the idea is that authors would post their work to a blog and solicit comments, presumably that manuscript is in a constant revisional state, forever and ever, unless the authors finally shut down comments (at what point is the amount of critique enough?) and post a “final” version. This is perhaps more important when large flaws are detected, and it is nice to have a record of the final version of the manuscript. When citing it, are you citing the final version, or some version in which the author tweaked something in the post? If you cite it, will changes happen later that render your reference irrelevant? I think this process would make it harder to talk about what a given author said or did, and it also puts a tremendous amount of trust in the authors not to change things in a way that is dishonest or unethical. With an official “final” version, the author is officially on the record, and I think that’s an important concept.

2)”The argument for pre-publication peer review is that it filters out poor research.” Marcus seems to believe that this isn’t an issue for library research, or at least that the stakes aren’t high enough to matter. I would ask whether librarians seeking tenure and professional respect are really willing to hang themselves out there like this, simply assuming that what they’ve done is good enough for public consumption. Like Scott, I believe this simply isn’t true. Librarians are perfectly capable of producing research that, in its initial state, would be ripped to shreds by competent reviewers. I suspect that many would prefer that critique to happen more privately, to give them a chance to rethink their assumptions and presentation before opening themselves up to professional criticism and embarrassment.

3) Peer review takes work. When a committed board of peer reviewers exists with a demonstrated interest in the process and a deadline for providing feedback, and an editor does the work Scott mentions prior to publication, it is a certainty that an author will receive feedback. Blog comments are an unreliable thing. Commenters may never hit on the one true major flaw of a manuscript, may not have the expertise to critique to manuscript, or may simply not have time to digest a full manuscript in its raw form and suggest all of the appropriate revisions. The manuscript and the professional body of knowledge may suffer from this, as its not just the shiny, catchy papers that need feedback and critique.

4) Related to #3, it would be important to determine whether a manuscript was just open to whoever felt like commenting (or not), or if peer reviewers would be assigned drop by and comment. Would they be allowed to do so anonymously? Could an editor comment anonymously? If not, would the editor continue to make the needed comments Scott mentions about organization and content? I know some have advocated for peer review that is not anonymous, but I suspect that harsher, yet needed, criticisms might be held back if they had to be publicly written with a name and IP attached.

I’m not saying it couldn’t be done. These are just a handful of issues I see as barriers that would have to be considered. Ultimately, I think part of the question is whether we’re so determined as authors to put our unfiltered thoughts out there as fast as possible, or whether we’re really interested in being accountable and on the record and contributing to the professional knowledge base in a substantial way, even if it takes a little longer. I want to think about this a little longer.

The first of Rachel’s four points made me think about wikis. Since most articles on most wikis lack “final versions,” they might have the same problem that Rachel describes here. Imagine we have a wiki for an academic discipline where contributors are vetted professionals in their disciplines, where the administrators are transparently listed, where rigorous editorial policies are strictly enforced, and where there is an active community of revision that seeks to constantly improve entries. In this hypothetical, we’ll also imagine that the wiki is, for these reasons, considered an authoritative resource by most academics in the discipline it serves. In this hypothetical, how would such a resource be cited when, as Rachel points out, there may not be a “final” version? As it turns out, this isn’t really very hard because good wiki software includes a revision history for every pageHere’s an example of a history page from Wikipedia. Wikipedia itself suggests how it can best be cited in a way that clearly indicates what revision the citing author is referring to by including in the citation the date on which the information was retrieved from the Web. Where blogging software would fail to solve this problem is in that most blogging platforms do not have a convenient way of tracking revision history. Developers: Could we please have a WordPress plugin for “versioning” posts?

Getting it out quickly

When it comes to technology topics, I think that getting the information out quickly is especially important because the technology changes so dang quickly.

For a while there, I thought about TechEssence as kind of informal, blog-based journal on technology topics of interest to LIS people. It went without being updated for long periods and in recent months Roy Tennant has been the only person posting to it, but it is a good concept, isn’t it?

I think that library technologists would probably be mostly comfortable throwing their work onto the Web for immediate criticism and would, in fact, rely on their peers to examine their work critically. I mean, have you ever seen technologists discuss technology books? Most geeks I know seem to have a compulsion to get out the red pen and start correcting what they see as flaws.


So if Marcus moves forward with his goal of making a blog-based LIS journal (something I’m still not entirely convinced is a good idea), I’d suggest making technology its focus and developing a revision history plugin for WordPress.

Feb 24

National Medical Librarians Month: Mark Funk Video

Not new, but seemingly new to YouTube:

Please join us in congratulating in Loretta Merlo, Head of Circulation, on her award-winning video display screen promotion celebrating the contributions and importance of health sciences information professionals. The promotion highlighted Mark Funk, Head of Resource Management-Collections, who is currently the President of the Medical Library Association (MLA) and other Weill Cornell librarians. A record number of libraries submitted entries for the National Medical Librarians Month (NMLM) Creative Promotions Award which were judged for creativity and innovation in library marketing. View our second place winning video.

You’ll want to view the video above at full-screen size in order to see all the detail.

Feb 23

Calculating the Value of Your Library

I had planned just to blog about the calculator posted by the MidContinental Region of the National Network of Libraries of Medicine, but before I got to it, The Krafty Librarian did much more by pointing to a whole bunch of calculators. Go check out Michelle’s post and see if one (or more) of these tools will help you prove the value of your library.

Feb 22

A Social Network (and other tools) for Radiologists

Welcome. radRounds is a new professional networking tool for radiologists, created by radiologists. Think LinkedIN, Facebook, or MySpace but just for us radiologists. Connections matter – enrich your clinical or academic career by joining our rapidly growing radiologist-focused community.

radRounds is built on the Ning platform, so anyone who has used a Ning network social network will be familiar with its features.

While I’m thinking of it, here’s a run-down of the various radiology sites that have been mentioned previously on this blog:

Feb 21

Nitpicks: CNN’s “Tips for savvy medical Web surfing”

Blame Rachel. She started it by offering a critique of CNN’s Tips for savvy medical Web surfing:

In this section about searching for articles in the major medical literature database, PubMed, Guthrie advises reading just the beginning and end of the study, stating that “The conclusion will tell you whether the treatment they studied was effective, moderately effective, or not at all effective.”

This is simply not true as an absolute, and it is the exact opposite of how many expert medical librarians are trained to read papers. The abstract, introduction, conclusion and discussion sections of a paper most reflect the way the authors want to present their data, and may exaggerate findings or make statements that are not supported by the methodology and data. These are the very sections in which authors attempt to make their case for why their work matters – they tell you what the authors think their findings mean, but don’t actually prove it definitively.

Rachel is right. Her criticism moved me to re-read the article with a more critical eye. Here are some nitpicks:

The CNN article says:

To get rid of the junk, use a search engine that looks only at reputable sites that have been vetted by health professionals. Dirline, run by the National Library of Medicine, is one such engine, as are medlineplus.gov and Imedix.com. Healthfinder.gov searches for information on government health Web sites.

First, neither Dirline or MedlinePlus are search engines. Dirline is a searchable directory of organizations in healtthcare, MedlinePlus searches only its own content, including links to external reputable resources. (See? Nitpicking.)

Second and more importantly, it is ridiculous to compare iMedix to MedlinePlus and to describe iMedix as a resource that looks “only at reputable sites that have been vetted by health professionals.” iMedix’s own About page says:

Whether you’re looking for symptoms, diseases, treatments, or simply general health information, you will be searching together with many other people. Members of the iMedix community assist each other by sharing their experiences and ranking medical content in order to make health information personal, organized and accessible to any individual.

[My emphasis]

Translation: The information on iMedix isn’t vetted by health professionals- it is vetted by other laypeople.

It shows, too. I tried searching for Crohn’s. Here are the top results:

High-quality links vetted by health professionals? Comparable to MedlinePlus in any way? No.

Feb 21

Guesses About The Future of Online Social Networks for Clinicians

I read something interesting the other day on a blog about social media.

I believe Facebook will transform networking on the web from a largely social, recreational activity to one that has serious implications for business.

I enjoyed reading this belief about the future and decided I’d try one of my own.

I don’t believe Facebook will transform networking on the web from a largely social, recreational activity to one that has serious implications for business- but I think its bastard descendants might. The social-network-as-an-application-platform model is going to spread and be adopted elsewhere. Many individual social networks seem to be hot for a while and are then abandoned for the next, cooler one (think Friendster -> MySpace -> Facebook).

I think professional associations and other large organizations will have their own Facebook-like networks/platforms that are available in their full-featured versions only to members. It’ll be a serious and significant membership benefit…sort of like a members directory, except lots more useful.

The trick is that some users will be members of multiple (often related) organizations. A cardiologist, for example, might be a member of the ACC and of the AMA), each with its own Facebook-like networks/platforms- and re-creating their profiles and relationships in each one would be so much of a pain in the butt as to make building one’s profile in either platform less appealing.

The two social networks/platforms might be interoperable if they are built by the same third-party vendor, but broad interoperability would only be possible if there was a virtual monopoly of a third-party vendor providing the social networks/platforms to organizations- and monopolies aren’t good for innovation or pricing.

How much better would it be if all such networks could share data in a common format and by a common standard of information exchange. Imagine that you could sign up for a new social network and establish your profile and relationships there by just telling it to copy your data from another social network…or if you could see your friend on network ‘B’ from your profile on network ‘A’- even though you don’t both have accounts on the same social network.

THAT’S why tools like OpenSocial are important- even if they do get off to an iffy start.

Feb 20

Human Brain Atlas

From Michigan State University’s Brian Biodiversity Bank, The Human Brain Atlas looks like just the cool sort of thing that anyone with an interest in neuroanatomy would like to play with.

In this atlas you can view MRI sections through a living human brain as well as corresponding sections stained for cell bodies or for nerve fibers. The stained sections are from a different brain than the one which was scanned for the MRI images. Furthermore, for the stained sections, the brain was removed from the skull, dehydrated, embedded in celloidin, cut with a sliding microtome, passed through several staining and differentiating solutions, and mounted on glass slides. Each step of these procedures changed the shaped of the brain and of the sections. Therefore the stained sections will be quite a different size and shape than those of the MRI sections. Nevertheless, comparing MRI images with stained sections from approximately the same level can greatly increase understanding of the internal architecture of these brains.

Still images:


Feb 19

Article about Anne O’Tate (3rd Party PubMed/MEDLINE Tool)

Free full text article (PDF) from the Journal of Biomedical Discovery and Collaboration on Anne O’Tate.

In this paper, we present Anne O’Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the “most important” words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles.

(Hat tip: ResourceShelf)

You can find other posts about 3rd Party PubMed/MEDLINE tools here.

Feb 19

MLA “Web 2.0″ Webcast

Web 2.0 Principles and Best Practices: Discovering the Participatory Web
MLA’s Educational Webcast
Wednesday, March 5, 2008, 1:00 p.m., central time

As a part of this Webcast, I get to present about 30 minutes of practical tips with Michelle Kraft (which is a real treat because Michelle’s was one of the first blogs I ever subscribed to). Fun!

I have already asked Michelle not to wear a crushed red velvet A-frame dress (because it would embarrassing for us to to be taped wearing the same thing). Michelle has been kind in agreeing to accommodate me in this.

For those who plan to view the Webcast: Are there particular tools or subjects you’d like to see covered (or are there any in particular you’d prefer to have skipped?) Aside from cross-dressing (no, not really), what can presenters do to make this Webcast especially worth your time? Answer anonymously if you need to, but please share your opinions!

Feb 18

New JEAHIL: Semantic Web Applications in Biology and Medicine

The Journal of the European Association for Health Information and Libraries has a new issue out.

On page 41 of the PDF, check out an article by Ioana Robu (“Semantic Web applications in biology and medicine”) that updates “An introduction to the Semantic Web for health sciences librarians” (J Med Libr Assoc. 2006;94(2):198-205.) with information about semantic Web applications.

While you’re in that PDF, also consider checking out:

  • Benoit Thirion recommends recent literature starting on page 45.
  • Starting on page 47, Oliver Obst’s “Web 2.0″ column makes notes on developments on the Web since the previous issue of the JEAHIL.
Feb 18

OvidSP RSS Tutorial

From the Yale University School of Medicine’s Cushing/Whitney Medical Library comes a nice screencast tutorial on generating search-based RSS feeds from OvidSP.

You can download the tutorial (mp4) or watch the streaming version.

Be sure to check out the rest of the tutorials from this blog of video tutorials and consider subscribing to its RSS feed.