Grand Round 5.41 up at Edwin Leap

30 06 2009

This weeks Grand Round, the weekly rotating carnival featuring the best medical blog posts, is up at the blog of Edwin Leap, a practicing emergency physician. As announced in the previous post, the theme is ‘What would you like to say to future physicians?’ This theme was chosen, because today, June 30th, is the day before the start of the ‘residency’.

Alas, my post (about PubMed tips) didn’t make it to the carnival because it was submitted after the Grand Round was published. 😉
But you can always read my  tips here.

Far more interesting are the tips given in Edwin Leap’s compilation. Most of the advice is not merely useful for residents.

For instance Clinical Cases and Images blog reminds us to write for ourselves, not for anyone else’s benefit (even Twitter and Facebook ‘use’ those who write for them, in a sense.) We should share our unique perspectives by independent blogging.

Isn’t that true for every blogger?

Please read other tips here

Next round will be hosted by Pharmamotion





10 + 1 PubMed Tips for Residents (and their Instructors)

30 06 2009

The next Grand Round, the weekly rotating carnival featuring the best medical blog posts, will be hosted by Edwin Leap, a practicing emergency physician. Because the  Grand Rounds are on June 30 -one day before July 1st, which is the traditional start of that thrilling and harrowing journey called ‘residency,’- Edwin decided to make the following theme: ‘What would you like to say to future physicians?’

I’m sure doctors will give plenty advice on the skills that are most important (i.e., see here). But what advice can I give them? I’m not a doctor. I could give them some examples of “how not to behave”, but I’m sure that will be covered well by fellow patients, and probably also by blogging nurses (i.e. see the perfect Intern Survival Guide by Mother Jones RN).

So I will stay with my expertise: searching. And to make it workable, I will restrict myself to PubMed, the platform that offers free  access to 18 million citations from MEDLINE and other life science journals. 18 million, that is a tremendous amount of literature! And that is one of the main problems: the sheer amount makes it very difficult to “pick the needle from the haystack”.

Of course, literature searching is not a primary skill for doctors. It is far more important that a doctor is knowledgeable, handy, and a good communicator (!). But at one time or another, he/she has to look things up or wants to check whether current practice is the best way. Or at the very least, doctors have to stay on top of the best and  latest information. And that’s when they need to search for medical information.

Below are some tips for beginning as well as more advanced PubMed searchers. Obviously, these are only tips, this post is no tutorial and I give but a few elaborate examples. However, I plan to show entire searches in future posts. Perhaps you can help me by sending in examples or asking questions/propose cases.

Here are the 10 PubMed tips:

Tip 1 : Look before you leap.
Before even thinking of going to the PubMed site, consider whether this is the most obvious source to begin with. First decide whether you have a back- or a foreground question.
A background question asks for general knowledge and/or “facts” (questions often starting with who, what, when, why, which). “How can one  diagnose appendicitis?” “Which treatments are available for advanced prostate cancer?”  These questions can be best answered by textbooks, handbooks and certain databases. UpToDate is usually perfect for these kind of questions. A question like “Which dose of drug X should I prescribe to a woman of 65 kg with disease Y.” looks very specific, but can generally be looked up in a Pharmacopeia (“general knowledge”). Some subjects are covered by in-house protocols or specialist guidelines.

When you have a foreground question it is often better (especially for those “new” to the subject) to search evidence in aggregate or pre-filtered resources, like National Guideline Clearinghouse, the TRIP-database and/or the Cochrane Library. This will save you time, because it lowers the number needed to read: individual studies have been sought, selected, appraised and summarized for you.

Besides PubMed there are also so called 3rd party Pubmed/MEDLINE tools, which can be handy for certain questions or approaches. I’m in the middle of writing about these tools, so keep in touch. Meanwhile you may want to read an excellent overview of many of these tools and more on the blog of Mike Cadogan: Medical search for physicians. Earlier I also wrote about the handy use of PubReminer and GoPubMed to analyze text words and MeSH-terms.

Although very useful and intuitive, most of these 3rd party PubMed tools don’t have the power of PubMed and are not suitable for elaborate searches.

Tip 2: A review article from PubMed.
PubMed can be useful for quickly finding good reviews.
Below is one such example. A few months ago, Bertalan Mesko (intern then) asked advice on twitter, because his professor had difficulties finding the cause of recurrent acute pancreatitis in a young adult. Considering this was a background question- I just did a quick and dirty search as follows:

  • Go to PubMed: www.pubmed.gov
  • Type acute pancreatitis in the search bar (pancreatitis may be ‘safer’, but will yield more results).
  • Click the Limits Tab and tick off the following options:
    • Facultative: Links to free full text (if you have no subscriptions/access to the medical library)
    • Facultative: Added to PubMed in the last 5 years (or read the first few hits)
    • Subsets: Core Clinical Journals
    • Type of article: Review
    • Tag-Terms: Title.
  • Click: Go

28-6-2009 12-12-32 PubMed acute pancreatitis  sonder language restr

So you search for acute pancreatitis in the title of review articles in core (English) clinical Journals. There are just 28 results in the last 5 years, including reviews in the Lancet and NEJM.

28-6-2009 12-38-45 results acute pancreatitis kort 4 vd 28 its

The Lancet review gives me a good suggestion:

In most patients, acute pancreatitis is caused by gallstone obstruction or alcohol, and no genetic testing is needed. However, unexplained recurrent acute pancreatitis might be associated with known genetic mutations in the cationic trypsinogen gene protease serine 1 (PRSS1), SPINK1, or CFTR. Mutations in the PRSS1 gene are seen in most patients with hereditary pancreatitis. In the most frequent mutations, the function of trypsinogen is increased, causing premature enzyme activation and autolysis of acinar cells.

Note that I didn’t limit on age and I didn’t add recurrent to the search, as I’m looking for a review that may discuss many forms of this disease in all age categories. Recurrent or young adult may not be mentioned in the abstract (nor in the MeSH), so I may miss important overviews if I add these terms to my search.

If you get to many hits,  you may always narrow the search later.

A similar approach has been used by drW to search for review articles on heparin induced thrombocytopenia (part 1 and 2).

UpToDate is a good source as well, ..and clinical experience. Ves Dimov responded on Twitter that he had described a similar hereditary pancreatitis case on his blog.

Note that at the end of the summer Limits will be under the Advanced Search.#

Tip 3: PubMed is just one NCBI-database.
As you may infer from the official web address of PubMed: http://www.ncbi.nlm.nih.gov/, PubMed is (just) one of the (freely available) databases of NCBI (National Center for Biotechnology Information) . If you click on the NCBI-logo (in PubMed) you reach the Entrez cross-database search page. Most databases are particularly suited for genetics, genomics and proteomics. Several of the residents I know are also involved in research  and may make ample use of GEO (gene expression database) and/or other databases.

If you type for instance acute pancreatitis in the search bar, you see the hits per database, including the PubMed and MeSH database. In this case OMIM seems the most interesting of the genetic databases. OMIM is the “Online Mendelian Inheritance in Man” database. It contains full-text, referenced overviews with information on all known Mendelian disorders and over 12,000 genes and is intended for intended for use primarily by physicians and researchers.

29-6-2009 2-58-03 NCBI acute pancreatitis

There are 33 hits in OMIM which we could limit further (using the Limit Tab) to for instance the chromosome. Hits 3-5 describes the genes mentioned in the Lancet review and gives references to relevant studies. There is even an overview of labs performing certain tests (see for instance here)

29-6-2009 23-53-39 OMIM 12

In stead of going to Entrez, you can also directly search OMIM from the PubMed database (see Figure)

30-6-2009 11-18-27 3x oMIM

Tip 4: Looking up Citations
One of the recent alterations to PubMed is that you can just type the title in PubMed’s search bar to find a specific article. You can also type in other specifications or an entire reference. But it doesn’t always work. When you type Lancet acute pancreatitis you get too many papers (if you would look for a primary study) but if you copy the following reference from Google: Frossard JL, et al. Acute pancreatitis Lancet 2008; 371(9607) you will get zero results. This is because different Journals have different reference-styles (order, initials, punctuation) and people often make mistakes while citing.

Another possibility, much loved by librarians because of its versatility, is the Single Citation Matcher in the blue side bar. # You can fill in any field you like and some fields like “author name” have an auto-fill function.

In this case I searched for the “Author name” Frossard JL (tick “only first author“) and the First page: 143.

I get exactly 1 paper: the correct one.

30-6-2009 1-06-47 SCM

Tip 5: Saving your search and making alerts: RSS and MyNCBI
It is important for a doctor to keep up with the new developments in your field. There are ample possibilities in PubMed. One is RSS. A previous post descibes how it can be created in PubMed.

Another possibility is MyNCBI. Old fashioned? Not at all. In PubMed, I find it more useful and easier than RSS. You can find MyNCBI at the upper right or in the blue side bar#.

You have to create a free account. Once you do that, you can save searches (single searches or set numbers, but NOT the entire Search History). You can immediately save a search after performing it [1] or you can left-click the set number in the History, in this case #14, and a pop-up with options appears [2]

30-6-2009 2-02-47 save search

Searches can be saved, and executed/adapted at later timepoints or can be used to create an alert. Alerts can be mailed at any frequency you like. If searches overlap it is good to combine them, so you don’t read the same items twice (or more).

Other possibilities are: “Save Collections” (individual articles), make filters (see Tip 1) and share them.
The Save function also works in some other NCBI-databases

A nice gadget: under preferences, you can activate a highlight function: When logged in, the terms you search for are highlighted in the desired colors. That’s why acute pancreatitis and review are highlighted yellow in the PubMed search shown above.

For more information see the FAQ

30-6-2009 2-45-29 myncbi2

Tip 6: Stop Googling PubMed: why you find too much or too little

O.k. this is something you may not want to give up, because you’re from the Internet generation and you’re used to intuitive interfaces and searching by trial and error. You’re used to just take a glance at the first few hits out of thousands of records ranked by “relevance” , that exactly match the terms you entered.

This is not what you should aim for in PubMed: finding a paper because the authors use exactly the same words as you search for – and looking at the first few hits (there is no ranking in PubMed, hits are shown chronologically) do not necessarily mean it is the most relevant to you.  It only matters if the study answers your question (for your particular patient), and if it is of good quality.

Thus, don’t aim for wording similarities, aim to find the papers that provide you (and your particular patient) with the best answer.

How do you do that?

It depends on your question, but generally speaking it is not the best thing to type a whole sentence or the entire PICO in the search bar.

Usually it is best to search per term and start with the most important term first and leave out the terms that do not really matter.

So how would you search for the following question?

Does  spironolactone (anti-androgenic) effectively reduce hirsutism in a female with PCOS? Is it safe and is it comparable to Cyproterone acetate?

Some people type: PCOS hirsutism spironolactone treatment cyproterone acetate and add gender and age as well. This yields a few results which are on the topic, but yet you may miss the most relevant ones.

A better way is to search for the two most important concepts: hirsutism AND spironolactone and to look for systematic reviews and RCT’s because these provide the best evidence (see TIP 9). If necessary PCOS can be added afterwards.

Treatment is usually a superfluous term. It is (usually) better to look for RCT’s or -second best “cohort studies” (because these are the best study designs assessing effectiveness of interventions). Also take care not to apply unnecessary limits.

Always ask yourself: is this word crucial? And does adding this word/limit reduce the chance that I find a relevant paper?

Tip 7: Use Details to see how PubMed interpreted (mapped) your search

Whether you use tip 6 or not, at the very least, check the translation of your search by clicking the Details Tab. Yes, your search is interpreted or ‘mapped’, didn’t you know? That is usually a good thing, because PubMed’s keywords (MeSH) are automatically found, if you use terms that PubMed considers as synonyms for certain MeSH. This can enhance your search, but sometimes the translation is either wrong or you didn’t use the correct word (according to PubMed).

So if you check the search PCOS hirsutism spironolactone you will see that hirsutism and spironolactone are correctly mapped to a MeSH, whereas PCOS is not. Seeing this you must be alarmed, because it is very likely that there is a MeSH for such a common disease. The correct MeSH is polycystic ovary syndrome. But in this case you might as well leave PCOS from the search.

30-6-2009 4-05-06 details pcosSometimes your term is wrongly translated. If you search for (early) mobilization (of patients), PubMed will translate this as: “metabolism”[MeSH Terms] (as well as “metabolism”[subheading], that is a qualification of a MeSH term). You can imagine that this may easily result in many irrelevant papers. Rather you should use MesH terms like early ambulation and/or the opposite: immobilization. (How, I will tell you in advanced Tips, to be published later)

By taking ONE second to check Details you become aware of wrong translations and can do something about it. Exclude the term or modify the search. Or you can see that the translation is ok and leave it like that.

Tip 8: MeSH or textwords?

There are people who merely use MeSH and people who swear by textwords. I use them both.

MeSH are keywords, added by indexers to the record. It would be a pity if you would miss relevant MeSH-terms, because this will inevitably lead to missing relevant articles.

MeSH are incredibly useful for finding a group of diseases. Suppose I would like to search for the usefulness of exercise to lessen fatigue in cancer patients (no matter which cancer). If I just type cancer in the search bar, this term is not only translated into the MeSH neoplasms, but it is also automatically exploded, which means that all narrower terms (terms lower in hierarchy) are also searched for. Thus papers are found whether they are indexed with neoplasms, lymphoma or breast neoplasms.

On the other hand, if you use only MeSH you will miss new non-indexed papers or ‘wrongly’ indexed papers, while some terms may not even have an appropriate MeSH.

Therefore I usually use both MeSH and free textwords.

In the above example it is sufficient to search for hirsutism AND spironolactone. By checking “Details” you know you’re searching for the right MeSH as well.

If the MeSH is very different from the textwords you may search for both , thus: in case of early mobilization you may search:

early ambulation[mh] OR immobilization[mh] OR early mobili* (* means that you truncate the term and find early mobilised/mobilized, moblisation(s) etc. =Note that when you use an asterisk there is no longer any mapping with the MeSH!!).

Tip 9: Searching for Evidence: Clinical Queries or other search filters

When u search for the best evidence, Clinical Queries may be very handy. These are prefab search filters that aim to find the best evidence.

It is best to first search aggregate evidence by using the systematic review filter, which is really much broader because it also searches for reviews of clinical trials, evidence-based medicine and guidelines.

You just can type some terms in the Search box, but I prefer to make a basic search in PubMed’s main page first (to check the terms) and to fill in the set number, i.e. #9, later. (see Figure)

30-6-2009 13-33-33 Clinical Queries

30-6-2009 13-41-52 SR spironolactoneYou only get 10 very relevant hits, including one synthesis of evidence in Clinical Evidence, several Cochrane Reviews and other systematic reviews. Since these are all very recent papers you may decide to stop here.
If you like, you can check for individual trials as well by searching by Clinical Study Category (choose the default: therapy narrow and enter search #9 again). This gives 24 hits.

One word of caution: Not all filters are that good. The Systematic Review Filter and the Narrow Therapy filter are quite good for a quick search though. Tip: you can adapt the filters yourselves.

Tip 10: Search Logic (and Boolean operators)

What do you think you search for if you type: hand OR arm AND foot?

You probably mean to search for (hand or arm) AND foot, but Pubmed follows another logic, depending on the order of the words. In this case it puts (invisible) brackets round arm and foot, not hand or arm. Result: you find far more (irrelevant) articles, because you retrieve every(!) article using the word “hand” and a few extra with (arm and foot).

29-6-2009 1-44-31 hand foot pubmedYou can keep it under control by placing the brackets yourselves.
With complex searches I rather combine synonyms with OR and  concepts with AND using the history. It looks like this:

30-6-2009 14-17-36 foot arm history(when you don’t add operators PubMed uses the AND-operator, thus #8 #9 means #8 AND #9).
You can add another term to the search as well, or apply a clinical query or limit. The final search you can save in MyNCBI. It shows the search with the appropriate brackets when you execute it.

Besides OR (synonyms) and AND (narrowing) you have the boolean operator NOT.

Please, generally do not use NOT to get rid of articles that are irrelevant, but rather try to select positively. Why? Because by using NOT you might exclude relevant articles.

Suppose you want to find articles about nosebleeds in children by using NOT adults. Then you also exclude articles about adults AND children.

NOT can be very handy however to subtract searches from each other. Suppose you have screened 100 articles (#1) and you get a brilliant idea using another word, which gives set #5. You can go through 120 articles, but you can also subtract the two searches from each other: #5 NOT #1 : and you only have to check 20 instead of 12o records.

Extra Tip (10+1): Use your library and librarian

As an extra tip, this final and probably most useful tip.
Follow library courses if you didn’t do so already during our internship, ask your librarian to help setting up a search for an automatic alert and to deduplicate results from different databases (i.e. MEDLINE and EMBASE) and ask the help of your librarian if you want to perform exhaustive or difficult searches or if you just want some advice. It is no shame to go to your librarian. We’re there for you.

Let me end with a statement of a fellow librarian (Suzanne Bakker, freely adapted):

“Doctors learn what a Hb-test is, but that doesn’t mean that they have to do the lab test themselves, each time a patient needs a test?! The same applies to searching. It is good that doctors learn the basic stuff, and understand some pitfalls, but they need not become information specialist”

You don’t need to become an information specialist to become a very good doctor…

———————————————–

#Some functionalities may move from the current page (tabs and blue side bar) to the advanced search this summer

Note: Thanks to Edwin Leap who had the patience to await my post, while it was going out of hand and getting much bigger than intended…





LoL: Stop Following Me!

28 06 2009

This picture is so cool.
First seen at ScienceRoll of Bertalan Mesko (@berci); this print is from a T-shirt of Zazzle.
More t-shirts and other prictures can be seen here





LOL: NCBI ROFL

28 06 2009

The last few days various people on Twitter (first: DoNotGoGently) tweeted about a hilarious website: NCBI ROFL (http://ncbirofl.blogspot.com/).

At first site this looks like a contradiction in terminis: NCBI (National Center for Biotechnology Information – that houses Pubmed) and ROFL (slang for Rolling On the Floor, Laughing). However, NCBI ROFL is exactly what it is: Rolling on the floor laughing about real scientific papers cited in PubMed. Hence the subtitle: “Real Articles, Funny Subjects”.

NCBI ROFL is the brainchild of two Molecular and Cell Biology graduate students. But everyone is invited to send in new ROFLs.

What are the articles everybody is ROFLing about? A few examples:

And what a coincidence. One of the first ROFL’s was the following:

mj

Kinematic analysis of facial behaviour in patients with schizophrenia under emotional stimulation by films with “Mr. Bean”.Kinematic analysis of facial behaviour in patients with schizophrenia under emotional stimulation by films with “Mr. Bean”.





MEDLIBs ROUND 1.4 ànd Call for Submissions!

25 06 2009

The fourth MedLibs round, with a selection of superb posts in the field of Medical Librarianship, is up at Eagle Dawg blog, the blog of Nicole (Nikki) Dettmar.

Nikki has chosen  the theme PubMed, which is one of several databases in the the National Library of Medicine’s (NLM) Entrez life sciences search engine developed by the National Center for Biotechnology Information (NCBI), and third party functionalities.
You can read the compilation here. *

Since there have been a few delays in publishing, in part because there were too few submissions on the subject, we’re now running short in time for the next issue, which is due July 7th. Nevertheless, I would like to try to adhere to this scheme.

Thus, you’re invited to submit your blogpost the coming week.

  • Submission deadline: July 4th (and I may accept July 5th in the morning)
  • NO theme, as long as it is related to medical librarianship, medical information retrieval etc.
  • Submission is open to librarians, doctors, students, scientists and health care workers (so no restrictions)
  • Submit the permalink of your post (already written on your blog) here at the Blog Carnival.
  • (See here for the Announcement. The FAQs can be found here and  the Archive  here.

I’m pleased to announce that we also have a host for August: Flavio Guzmán of Pharmamotion has offered to host the MedLibs Round on his blog. This is memorable, because it will be the first (and I hope not the last) time that a MD will host this Medical-Library-related blog carnival.

There are still vacancies for September, October and November. Please let me know if you would like to host a future edition. We really need you to make the best out of this blog carnival!

—————————————–

* You can await a contribution on this blog as well. I was not able to finish it due to congresses and work-related deadlines.





Web 2.0 Tools to Inspire … Teachers and others

16 06 2009

Judy O’Connell pointed out an interesting Slideshare presentation called “Web 2.0: Tools to inspire”.

It contains a lot of suggestions, especially in the field of education, like

Apart from the Social Networking Tools, there are many new suggestions. The tools seem particularly useful in the class room or in spare time.

For other free learning tools see a previous post:
Google Reader and other free (learning) tools.

Here is the entire presentation.

** tip of my daughter: http://www.picnik.com/ online photo editing (free)

* my tip: Snag-it (professional screen capture -can’t do without) <





Grand Rounds 5.39 at ACP Internist

15 06 2009

shutterstock_1387084-786145-latest-newsGrand Rounds, the weekly roundup of the best of medical blog posts, is now live at ACP Internist, a newspaper serving internal medicine.

“We’re paying tribute to the daily newspaper. Read on for the latest headlines, opinions, features and even the funnies.”

Clearly, the editor of this “newspaper” is used to tight deadlines: no themes, deadline expiring at 8 am and the newspaper is already delivered…. Please enjoy reading all headlines here.

Next weeks edition of the Grand Rounds will be hosted by Florence dot com, the blog of Barbara Olson.





An Online Birthday Party!

15 06 2009

15-6-2009 18-05-22 BD poes kaart kleinToday is my birthday. And although I stayed home with a headache and other small complaints, and although I don’t really celebrate it any longer (except for the real round figures, like 50-60), the day started out pretty bright just around midnight with all kinds of virtual birthday wishes.

It started with an e-card (left) from Ramona Bates, plastic surgeon and quilter from the USA (hence her blog Suture for a Living), followed by many other birthday wishes.

Robin of Survive the Journey was so kind to send a song via blip.fm and then to organize a “twitter-party” by using the twitter-tool QuoteURL I had just reviewed on my blog (see here).

The start of the Twitter party  is shown below. Here is the link: http://www.quoteurl.com/r1e27

Suture for a Living

  1. rlbates
  2. drval
    drval Happy Birthday to @laikas, our favorite Dutch medical librarian. 🙂
  3. Ves Dimov, M.D.
  4. Deirdre
  5. Vijay
    scanman @laikas Happy Birthday Jacqueline 🙂
  6. Laika (Jacqueline)
    laikas @scanman: @laikas Happy Birthday Jacqueline 🙂 Thanks vijay. Wish we could have a Twitter birthday party with cake or so.
  7. Marilyn Mann
  8. Laika (Jacqueline)
    laikas @MarilynMann thanks Marilyn. It is very nice to begin your birthday with all those kind birthday-twishes.
  9. Robin
    staticnrg @Laikas Oh, happy birthday!! Hope it is a wonderful one!! ♫ http://blip.fm/~88du0
  10. Laika (Jacqueline)
    laikas @staticnrg: “@Laikas Oh, happy birthday!! Hope it is a wonderful one!!” – Well the start is all right – thnx! ♫ http://blip.fm/~88e8a

this quote was brought to you by quoteurl (pity that WordPress transforms the style)

Later I received more birthday and get-well wishes from Twitter, Hyves, Facebook, and Fabulously 40 (and beyond). I even received a e-card with “happy birthday” in Chinese!happy-birthday in chinese

Although my friends are virtual (?) and the cards and wishes are virtual, it feels like I’m having a real birthday party with real friends. The only thing that was missing was real coffee, cake or wine. 😉

15-6-2009 18-29-23 tweet rlbates





#CECEM Bridging the Gap between Evidence Based Practice and Practice Based Evidence

15 06 2009

cochrane-symbol A very interesting presentation at the CECEM was given by the organizer of this continental Cochrane meeting, Rob de Bie. De Bie is Professor of Physiotherapy Research and director of Education of the Faculty of Health within the dept. of Epidemiology of the Maastricht University. He is both a certified physiotherapist and an epidemiologist. Luckily he kept the epidemiologic theory to a minimum. In fact he is a very engaging speaker who keeps your attention to the end.

Guidelines

While guidelines were already present in the Middle Ages in the form of formalized treatment of daily practice, more recently clinical guidelines have emerged. These are systematically developed statements which assists clinicians and patients in making decisions about appropriate treatement for specific conditions.

Currently, there are 3 kinds of guidelines, each with its own shortcomings.

  • Consensus based. Consensus may be largely influenced by group dynamics
    Consensus = non-sensus and Consensus guidelines are guidelies.
  • Expert based. Might be even worse than consensus. It can have all kind of biases, like expert and opinion bias or external financing.
  • Evidence based. Guideline recommendations are based on best available evidence, deals with specific interventions for specific populations and are based on a systematic approach.

The quality of Evidence Based Guidelines depends on whether the evidence is good enough, transparent, credible, available, applied and not ‘muddled’ by health care insurers.
It is good to realize that some trials are never done, for instance because of ethical considerations. It is also true that only part of what you read (in the conclusions) has actually be done and some trials are republished several times, each time with a better outcome…

Systematic reviews and qualitatively good trials that don’t give answers.

Next Rob showed us the results of a study ( Jadad and McQuay in J. Clin. Epidemiol. ,1996) with efficacy as stated in the review plotted on the X-axis and the Quality score on the Y-axis. Surprisingly meta-analysis of high quality were less likely to produce positive results. Similar results were also obtained by Suttorp et al in 2006. (see Figure below)

12066264  rob de bie CECEM

Photo made by Chris Mavergames

There may be several reasons why good trials not always give good answers. Well known reasons are  the lack of randomization or blinding. However Rob focused on a less obvious reason. Despite its high level of evidence, a Randomized Controlled Trial (RCT) may not always be suitable to provide good answers applicable to all patients, because RCT’s often fail to reflect the true clinical practice. Often, the inclusion of patients in RCT’s is selective: middle-aged men with exclusion of co-morbidity. Whereas co-morbidity occurs in > 20% of the people of 60 years and older and in >40% of the people of 80 years and older (André Knottnerus in his speech).

Usefulness of a Nested Trial Cohort Study coupled to an EHR to study interventions.

Next, Rob showed that a nested Trial cohort study can be useful to study the effectiveness of  interventions. He used this in conjunction with an EHR (electronic health record), which could be accessed by practitioner and patient.

One of the diseases studied in this way, was Intermittent Claudication. Most commonly Intermittent Claudication is a manifestation of  peripheral arterial disease in the legs, causing pain and cramps in the legs while walking (hence the name). The mortality is high: the 5 year mortality rates are in between those of colorectal cancer and Non-Hodgkin Lymphoma. This is related to the underlying atherosclerosis.

There are several risk factors, some of which cannot be modified, like hereditary factors, age and gender. Other factors, like smoking, diet, physical inactivity and obesity can be tackled. These factors are interrelated.

Rob showed that, whereas there may be an overall null effect of exercise in the whole population, the effect may differ per subgroup.

15-6-2009 3-06-19 CI 1

  • Patients with mild disease and no co-morbidity may directly benefit from exercise-therapy (blue area).
  • Exercise has no effect on smokers, probably because smoking is the main causative factor.
  • People with unstable diabetes first show an improvement, which stabilized after a few weeks due to hypo- or hyperglycaemia induced by the exercise,
  • A similar effect is seen in COPD patients, the exercise becoming less effective because the patients become short of breath.

It is important to first regulate diabetes or COPD before continuing the exercise therapy. By individually optimizing the intervention(s) a far greater overall effect is achieved: 191% improval in the maximal (pain-free) walking distance compared to for instance <35% according to a Cochrane Systematic Review (2007).

Another striking effect: exercise therapy affects some of the prognostic factors: whereas there is no effect on BMI (this stays an important risk factor), age and diabetes become less important risk factors.

15-6-2009 3-35-10 shift in prognostic factors

Because guidelines are quickly outdated, the findings are directly implemented in the existing guidelines.

Another astonishing fact: the physiotherapists pay for the system, not the patient nor the government.

More information can be found on https://www.cebp.nl/. Although the presentation is not (yet?) available on the net, I found a comparable presentation here.

** (2009-06-15) Good news: the program and all presentations can now be viewed at: https://www.cebp.nl/?NODE=239





QuoteURL: a new Twitter Tool to Quote, Save and Publish Tweets

14 06 2009

Ever tried to catch and publish a twitter conversation? Hard, isn’t it, especially at WordPress.com where the lay-out is often difficult to control, if you just copy and paste.
Tweets also tend to disappear after approximately 3-4 weeks.  Thus if you want to capture them you should do it (relatively) soon after they have been tweeted.

A month ago I gave a presentation where I showed medical students a real fancy twitter-application with tweets of  doctors, patients and nurses giving them advice on how to use web 2.0 tools in medicine. Now the tweets have all gone….14-6-2009 0-13-00 Qoute URL logo

But the new Twitter Tool QuoteURL, developed by Fabricio Zuardi, offers a perfect solution.

It is a very intuitive and easy tool that allows you to collect several tweets, for instance answers to a question. A maximum of 4 tweets per quote are allowed for unregistered tweeps and 10 after free registration. The 10-tweet limit is only meant to keep Twitter API quotas under control, but you can twitter @fczuardi or email fabricio at fabricio dot org to ask for an exception (source: comment of Fabricio at onlinejournalismblog.com)

You can collect tweets in two ways:

1. Enter the Twitter status URL or ID (click on the date or on “view tweet”, depending on the interface). For instance http://twitter.com/laikas/statuses/2115296397. You can easily gather the tweets in a text or word file, till you need them. This is for instance suitable for the series Top of the Tweets, where I collect funny tweets over time.

14-6-2009 15-27-56 CECEM tweet 12

Method 1: copy/paste permalink

2. Drag or drop the tweet-URL’s from a split screen that shows pop-ups of  Twitter Home or Twitter Search in a separated window. Perform a search (figure) or go to your Twitter home page to drag permalinks into the text-field. Just drag the line that would show the url when you click on it.

Method 2. Drag and drop from spilt window

Method 2. Drag and drop from split window (click to enlarge)

QuoteURL arranges tweets chronologically, so you can drag them in in any order.

After you have collected the tweets you press the Save button and the permalink is created. To embed the Quote in your blogpost just copy the <!– QuoteURL styled embed start –> (lower right) in the HTML-view of your blog and the code appears)

Summary.

  • Tweets can be collected by copy-pasting of the tweet URL’s or by dragging and dropping.
  • Tweets are ordered chronologically
  • The Quote can be saved as a permalink
  • You can mail the URL to someone or you can post it directly on your blog by copy-pasting of the embedded code
  • The individual tweet-URL’s can still be produced (click on dates).

Below is an example of a Quote made with QuoteURL. I thought it would be nice to show a recent discussion with the maker of QuoteURL @fczuardi. The permalink is: http://www.quoteurl.com/by608
WordPress.com shrinks the lay-out after saving. Other hosts may let the style intact. Still I find the result pretty awesome.

  1. laikas @fczuardi Hi, I like your Quoteurl – although the lay-out becomes less when saved on WordPress. Questions: can you add tweets (days) later??
  2. laikas @fczuardi Q2: do the quotes remain stable over time? (tweets normally disappear after 3-4 weeks) ; and the avatars?
  3. fczuardi @laikas regarding the layout on wordpress, you can get the unstyled version of the embed code and use your own CSS
  4. fczuardi @laikas the avatars breaking later is a known issue, the right thing to do would to cache those images, but the code does not do it yet

this quote was brought to you by quoteurl

The video gives more details about the whole procedure.

Vodpod videos no longer available.

more about “QuoteURL“, posted with vodpod





#CECEM David Tovey -the Cochrane Library’s First Editor in Chief

13 06 2009

cochrane-symbolThis week I was attending another congress, the Continental European Cochrane Entities Meeting (CECEM).

This annual meeting is meant for staff from Cochrane Entities, thus Centre Staff, RGC’s (Review Group Coordinators), TSC’s (Trial Search Coordinators) and other staff members of the Cochrane Collaboration based in Continental Europe.

CECEM 2009 was held in Maastricht, the beautiful old Roman city in the South of the Netherlands. The city where my father was born and where I spend many holidays.

One interesting presentation was by Cochranes’ 1st Editor in chief, David Tovey, previously GP in an urban practice in London for 14 years and  Editorial Director of the BMJ Group’s ‘Knowledge’ division (responsible for BMJ Clinical Evidence and its sister product Best Treatments, see announcement in Medical News Today)

David began with saying that the end user is really the key person and that the impact of the Cochrane Reviews is most important.

“How is it that a Senior health manager in the UK may shrug his shoulders when you ask him if he has ever heard of Cochrane?”

“How do we make sure that our work had impact? Should we make use of user generated content?”

Quality is central, but quality depends on four pillars. Cochrane reviews should be reliable, timely, relevant and accessible.

Cochrane Tovey wit

How quality is perceived is dependent on the end users. There are several kinds of end users, each with his own priorities.

  1. doctor: wants comprehensive and up-to-date info, wants to understand and get answers quickly.
  2. patient: trustworthiness, up-to-date, wants to be able to make sense of it.
  3. scientist: wants to see how the conclusions are derived.
  4. policy and guideline-makers.

Reliable: Several articles have shown Cochrane Systematic Reviews to be more reliable then other systematic reviews  (Moher, PLOS BMJ)*

Timely: First it takes time to submit a title of a Cochrane Review and then it takes at least 2 years before a protocol becomes a review. Some reviews take even longer than 2 years. So there is room for improvement.

Patients are also very important as end user. Strikingly, the systematic review about the use of cranberry to prevent recurrent urinary tract infection is the most frequently viewed article,- and this is not because the doctors are most interested in this particular treatment….

Doctors: Doctors often rely on their colleagues for a quick and trustworthy answer. Challenge: “can we make consulting the Cochrane Library as easy as asking a colleague: thus timely and easy?”

Solutions?

  • making plain language summaries more understandable
  • Summary of Findings
  • podcasts of systematic reviews (very successful till now), .e. see an earlier post.
  • Web 2.0 innovations

Key challenges:

  • ensure and develop consistent quality
  • (timely) updating
  • putting the customer first: applicability & prioritization
  • web delivery
  • resources (not every group has the same resources)
  • make clear what an update means and how important this update is: are there new studies found? are these likely to change conclusions or not? When was the last amendment to the search?

I found the presentation very interesting. What I also liked is that David stayed with us for two days -also during the social program- and was easy approachable. I support the idea of a user-centric approach very much. However, I had expected the emphasis to be less on the timeliness (of updates for instance), but more on how users (patients, doctors) can get more involved and how we review the subjects that are most urgently needed. Indeed, when I twittered that Tovey suggested that we “make consulting the Cochrane Library as easy as asking a colleague”, Jon Brassey of TRIP answered that a lot has to be done to fulfill this, as the Cochrane only answers 2 out of 350+ questions asked by GPs in the UK, a statement that appeared to be based on his own experience (Jon is founder of the TRIP-database).

But in principle I think that Jon is correct. Right now too few questions (in the field of interventions) are directly answered by Cochrane Systematic Reviews and too little is done to reach and involve the Cochrane Library users.

13-6-2009 15-43-17 twitter CECEM discussion

click to enlarge

During the CECEM other speakers addressed some of these issues in more detail. André Knottnerus, Chair of the Dutch Health Council, discussed “the impact of Cochrane Reviews”, and Rob the Bie of the Rehabilitation & Related Therapies field discussed “Bridging the  gap between evidenced based practice and practice based evidence”, while Dave Brooker launched ideas about how to implement Web 2.0 tools. I hope to summarize these (and other) presentations in a blogpost later on.

*have to look this up

NOTE (2009-11-10).

I had forgotten about this blank “citation” till this post was cited quite in another context (see comment: http://e-patients.net/archives/2009/11/tell-the-fda-the-whole-story-please.html) and someone commented that the asterisk to the “the amazing statement” had still to be looked up,  indirectly arguing that this statement thus was not reliable- and continuing by giving an example of a typically flawed Cochrane Review that hit the headlines 4 years ago, a typical exception to the rule that “Cochrane systematic reviews are more reliable than other systematic reviews”. Of course when it is said that A is more trustworthy than B it is meant on average. I’m a searcher, and on average the Cochrane searchers are excellent, but when I do my best I surely can find some that are not good at all. Without doubt that also pertains to other parts of Cochrane Systematic Reviews.
In addition -and that was the topic of the presentation- there is room for improvement.

Now about the asterisk, which according to Susannah should have been (YIKES!) 100 times bigger. This was a post based on a live presentation and I couldn’t pick up all the references on the slides while making notes. I had hoped that David Tovey would have made his ppt public, so I could have checked the references he gave. But he didn’t and so I forgot about it. Now I’ve looked some references up, and, although they might not be identical to the references that David mentioned, they are in line with what he said:

  1. Moher D, Tetzlaff J, Tricco AC, Sampson M, Altman DG, 2007. Epidemiology and Reporting Characteristics of Systematic Reviews. PLoS Med 4(3): e78. doi:10.1371/journal.pmed.0040078 (free full text)
  2. The PLoS Medicine Editors 2007 Many Reviews Are Systematic but Some Are More Transparent and Completely Reported than Others. PLoS Med 4(3): e147. doi:10.1371/journal.pmed.0040147 (free full text; editorial coment on [1]
  3. Tricco AC, Tetzlaff J, Pham B, Brehaut J, Moher D, 2009. Non-Cochrane vs. Cochrane reviews were twice as likely to have positive conclusion statements: cross-sectional study. J Clin Epidemiol. Apr;62(4):380-386.e1. Epub 2009 Jan 6. [PubMed -citation]
  4. Anders W Jørgensen, Jørgen Hilden, Peter C Gøtzsche, 2006. Cochrane reviews compared with industry supported meta-analyses and other meta-analyses of the same drugs: systematic review BMJ  2006;333:782, doi: 10.1136/bmj.38973.444699.0B (free full text)
  5. Alejandro R Jadad, Michael Moher, George P Browman, Lynda Booker, Christopher Sigouin, Mario Fuentes, Robert Stevens (2000) Systematic reviews and meta-analyses on treatment of asthma: critical evaluation BMJ 2000;320:537-540, doi: 10.1136/bmj.320.7234.537 (free full text)

In previous posts I regularly discussed that (Merck’s Ghostwriters, Haunted Papers and Fake Elsevier Journals and One Third of the Clinical Cancer Studies Report Conflict of Interest) that pharma-sponsored trials rarely produce results that are unfavorable to the companies’ products [e.g. see here for an overview, and many papers of Lisa Bero].

Also pertinent to the abovementioned discussion at E-patient-Net is my earlier post: The Trouble with Wikipedia as a Source for Medical Information. (references still not in the correct order. Yikes!)

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#EAHIL2009 Web 2.0 and Health Information – Chris Mavergames

4 06 2009

2-6-2009 23-11-41 EAHIL 2009

I’m in Dublin to attend the EAHIL workshop 2009.
The EAHIL is the European Association for Health Information and Libraries.

The EAHIL -workshop 2009 really started Wednesday afternoon. Tuesday morning, as a foretaste of the official program I attended a Continuing Education Course, namely the Web 2.0 and Health Information course by Chris Mavergames.

Chris Mavergames is currently the Web Operation Manager/Information Architect for the Cochrane Collaboration. Before, he worked in the field of information and library science.

So Chris and I are really colleagues, but we didn’t realize until we “met” on Twitter.

On this hot day in June I was pleased that the workshop was held in the cool Berkeley Library of Trinity College.
They have chosen real good locations for this EAHIL workshop. Most presentations are in the Dublin Castle, another place at the Heart of the Irish History.

The workshop took approximately 3 hours and consisted of two presentations, followed by short Q&A’s and an open forum afterwards.

The presentations:

  • Web 2.0 and Health Information“,
  • A case study of the experiences of implementing and using these technologies in a large, non-profit organization (Cochrane Collaboration).

Eighteen people could attend. Each of us had a computer, which raised expectations that they were needed during the workshop. They were not, but they were handy anyway to look up things and to draft a post. And.. I could post this message on Twitter before Chris loaded a photo of his class on TwitPic.  LOL.

4-6-2009 9-46-55 chris is making a photo

10848362 class chriss mavergames

Web 2.0 versus web 1.0
Chris began with asking the audience how many people either have used ..or at least have heard of Facebook, LinkedIn or any other social networking service. And then he asked which tools were being used. Afterwards he admitted he had checked everyone’s presence on various social bookmarking sites. Hilarious.

To my surprise, quite a number of people were familiar with most of the web 2.0 services and sources. Indeed, weren’t librarians the first to embrace web 2.0?

I got the impression Twitter was the least well known/appreciated tools. Most people were either on Facebook or Linkedin, not on both. This presumably has to do with separation of professional and personal things.

Chris first explained the difference between Web 1.0 and Web 2.0: Web 1.0 is a one way interaction, static. Web 2.0 is: “more finding or receiving, less searching”. It has a dynamic aspect: there is more interaction, the possibility to ‘comment, subscribe, post, add, share or as Chris puts it: “Web 2.0 allows you to have information “pushed” at you vs. you having to “pull”.

Another characteristic of web 2.0 is that technology has become easier. It is now more about content.

As an example he showed the Cochrane website from 2004 (web 1.0) and the current website. The first was just a plain web site where you could search, browse and email, the second has social bookmarking tools and is more dynamic and active: you can add comments, post on websites etc.. In addition the Cochrane Collaboration is now on Twitter and Facebook and produces podcasts of a selection of systematic reviews.

Another example of web 2.0 interfaces are MyNCBI of PubMed (for saving your searches) and i-Google.

Social Networking services
These services allow you to create an online profile so that you can interact with others, share and integrate.

Examples are Facebook, LinkedIn and 2 Collab. What is used most, differs around the world. Linkedin is more a professional site, an “online resume” and Facebook is for more general stuff. “You’re mother is on facebook too, so..”. Most young people don’t realize what others can read. However, Facebook offers the possibility to select precisely who can see exactly what.

Twitter
Twitter is a microblogging system, that allows a 140 chracter message (tweet). At first, Chris wasn’t very much interested. He only knew Twitter through the automatic updates on Facebook, but “wasn’t really interested in a  friend in New York eating a scrambled egg.”

It is as easy to subscribe to one’s updates as it is to unsubscribe. Chris uses Tweetdeck to filter for keywords that are of interest. But as he showed me later, he uses the i-phone to easily catch what people (he follows) are tweeting.

Although Twitter was created as a social tool it is now much more than that. It creates a so called “ambient awareness” and as such it is a perfect example of “push” technology: you won‘t see every tweet, but you will l be ambiently aware of the conversation (of your “friends” or the subject you follow). Twitter is also very useful for getting a real fast answer to your question. This is how Chris learned the value of Twitter. He had a question at a meeting. Someone said: just put it on Twitter with the hashtag of the congress (an agreed upon keyword with #in front, like #EAHIL2009). He did it and within 3 minutes he got an answer. Twitter is also very useful for sharing and finding links.
There are many “Twitter apps” around. Just search Google for it.

For professional use within a company the twitter look-alike Yammer can be a useful alternative, because only people in the company are able to follow the updates.

My personal experience is also very positive. Twitter and other web 2.0 tools can work synergistically, dependent on your Twitter community and how you use it.

Social bookmarking:
Although librarians aren’t always very happy with user generated tagging, social bookmarking tools are and easy way of allowing users to share a collections of links.
Links used (directly or indirectly) for his presentation are available at del.icio.us/mavergames under the tag EAHIL.

Blogs, Wiki’s
A blog can give a good summary of interesting articles in a particular field. Chris began a blog 2 months ago (http://mavergames.net) about  a very specific subject he is involved in: Drupal. For him is it just an open notebook: a platform to share your ideas with others.
It is possible receiving updates via RSS (push).

Wiki’s are a very powerful knowledge gathering tool,  a way to collaboratively create a resource, based on the principle of “Crowd sourcing” (The Wisdom of Crowds).

Examples of the two are:

  1. https://laikaspoetnik.wordpress.com/ (this blog)
  2. http://scienceroll.com/ (of the Hungarian Medical Student Bertalan Mesko)
  3. http://www.medpedia.com/ (not yet fully developped medical wiki)
  4. http://twictionary.pbwiki.com/ (a fun wiki with the Twitter Vocabulary)
  5. cochrane.org/ideas
  6. http://mavergames.net (Chris’s blog on Drupal)

Subscription services: RSS
Via RSS Really Simple Syndication you can push information from a variety of sources:

  • Podcasts, for instance cochrane.org/podcasts
  • Saved searches, like in PubMed
  • News feeds cochrane.org/news
  • Updates to sites
  • Updates to collections of bookmarks
  • Updates to flickr photos
  • Etcetera

Platforms can vary from Google Reader, Yahoo, Bloglines, but you can also use i-Google or a specilized medical page where you can find links to all kinds of sources, like blogs, podcasts and journals. Perssonalized Medicine (http://www.webicina.com/rss_feeds/) is especially recommended.

Somebody from the audience added that Medworm is a good (and free) medical RSS feed provider as well. For an overview of several of such platforms, including Medworm, i-Google and www.webicina.com see an earlier post on this blog:  Perssonalized Medicine and its alternatives (2009-02-27).

A typical Web 2.0 scenario:

  1. Chris visits Laika’s MedlibLog and reads Cochrane PodCasts are available.
  2. He finds it interesting , goes to the Cochrane website and subscribes to the Cochrane podcasts with RSS.
  3. He want to share this finding with others, so he decides to tweet that Cochrane podcasts are available.
  4. He gets a response: Hé do you know the Cochrane is on Facebook, so he visits Facebook joins and posts the news on facebook again. And so on.

Not only did Chris give a nice overview of Web 2.0 tools, but there was ample opportunity for discussions and remarks.

The two most common questions were: [1] When can you find time for this? and [2] what can you do when the IT-departments don’t allow access to web 2.0 tools like YouTube, Facebook, RSS? It really seamed the main barrier for librarians from many countries to the use of web 2.0. Nevertheless, Chris engaging presentation seemed to encourage many people to try the tools that were new to them at home. Afterwards I only heard positive comments on this workshop.

The slidecasts of the two presentations are now online on http://www.slideshare.net/mavergames.

The slidecast I’ve reviewed is below.