ScienceRoll

Life Hacks for Doctors: Slideshow

Bertalan Meskó — Sat, 17 May 2008 10:03:31 +0000

Joshua Schwimmer, the author of the Efficient MD Blog and the Efficient MD wiki, came up with a fantastic slideshow about life hacks for physicians. According to Wikipedia:

The term life hack refers to productivity tricks that programmers devise and employ to cut through information overload and organize their data.

What’s on the web (2008 May 15)

Bertalan Meskó — Thu, 15 May 2008 20:26:36 +0000

Hackers’ posts on epilepsy forum cause migraines, seizures (AP)

Greetings from Games for Health 2008 (Resilient Ambassadors of Change)
Defining Health 2.0 - Debate Rages On (Health Management Rx)
Web 2.0 Business Trends (Health2Zero (Health 2.0))
Introducing The Efficient MD Wiki (The Efficient MD): Visit the Efficient MD Wiki at http://wiki.efficientmd.com.
Wikiversity interview: Do you know what Wikiversity is?

X-Prizes for Health and Medicine?

Bertalan Meskó — Wed, 14 May 2008 17:21:44 +0000

Have you ever heard about the Ansari X Prize that resulted in constructing the world’s first privately developed spacecraft?

Source

Have you ever heard about the Archon X-Prize for Genomics? It will lead us to a new generation of genome sequencing methods.

What about an X Prize for Health and Medicine? Students at the Massachusetts Institute of Technology came up with some interesting ideas.

Of the specific proposals, one team suggested a prize for a major milestone in dealing with the problem of TB, which remains endemic in 22 nations and costs 1.7 million lives every year. Effective treatments exist, but the testing is relatively expensive and often misses active cases. So they proposed a $10 million prize for a new cheap, fast and accurate diagnostic system that could reach most of the 50 percent of cases that now go undiagnosed. Winning the prize would require not just laboratory demonstrations but field tests on 1,000 patients to show that it really works under difficult conditions.

The second proposal was for a simple, portable system that could be used by community health workers to carry out initial diagnostic evaluations for the 10 most widespread fatal, transmissible diseases. Such screening could lead to prescriptions of drugs or treatment for some conditions or referral to a doctor or nurse for conditions that require skilled care or more difficult diagnosis.

What do you think? An X Prize for Health and Medicine would be a good idea? Which medical specialty would be your choice?

Scientific Research and Medicine in Second Life

Bertalan Meskó — Tue, 13 May 2008 21:35:46 +0000

David Pescovitz at BoingBoing had an interesting post about scientific research in Second Life, the virtual world:

This week’s Science News discusses several real scientific research projects inside Second Life. For example, Drexel University neurobiologist Corey Hart is building a virtual frog to study the neural pathways involved in hopping. Meanwhile, Robert Amme, a physicist at the University of Denver, is modeling a nuclear reactor as a training tool. Indeed, many research institutions are leveraging the simple sim tools of SL to create immersive science learning experiences.

This is a great example about how to close the gap between real science and the virtual world. You may also know about our medical exercises at the Ann Myers Medical Center where they train medical students (just like me) with case presentations. Now here is a tool with serious potential that could help us do it even better:

Text files, images and videos in one place. The aim is to create virtual patients with virtual medical conditions. Why is it beneficial for medical students?

The entire medical education is about case presentations. We move forward clinic by clinic during our studies and listen to case presentations all the time. That’s what we can do in Second Life but with even more educational material and without time or geographical restrictions.

According to DusanWriter, there are pharmacy patient case studies as well in Second Life.

The school has started to use SL as a training module, and has created a virtual version of Greensboro’s Moses Cone Family Practice Center, a local medical center. Students create an avatar and move through the center either as a student interviewing a patient, or as a patient. At the end of the simulation, the student takes a quiz to test his knowledge of the case history and of the practice center.

If you want to know everything about Second Life & Virtual Worlds for Academic Healthcare & Education, check out the slideshow of Patricia F. Anderson.

And if you don’t have a computer at home, let’s use a mobile to enter Second Life:

Further reading:

Gene Genie #31 at Adaptive Complexity

Bertalan Meskó — Sun, 11 May 2008 07:21:51 +0000

The 31st edition is up at Adaptive Complexity. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Michael White, for hosting Gene Genie.

Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine.

Many thanks to Ricardo Vidal for the logo!

The next edition is due to be published on the 25th of May but has no host at this time. If you are interested in hosting Gene Genie, drop me a mail. Don’t forget to submit your articles via the official page.

Here are all the issues of Gene genie:

The 21st Century in Medicine: What will it look like?

Bertalan Meskó — Sat, 10 May 2008 21:37:30 +0000

Jeffrey Dach used one of my recent posts (Personalized Medicine: Real Clinical Examples!) as a reference in his article describing the future of medicine. It’s a quite detailed and comprehensive essay about several fields of medicine and he doesn’t forget to mention personalized medicine and its impact on the future of healthcare:

Personalized Medicine is the combination of these two new powerful forces, Orthomolecular Medicine and Genetic Testing. In the future, Personalized Medicine will expand and ultimately play a dominant role in medicine. Example: Warfarin Genetic Testing allows improved calibration of coumadin dosage to avoid bleeding complications. Drug metabolism testing allows for personal modification of drug dosage.

Orthomolecular and personalized medicine together?

We will be able to sequence the entire genome of an individual human in milliseconds. The cost will be minimal and within the means of the average person.

Individuals will have ability to reprogram our own sperm and eggs. One will be able to buy new genes on the internet based on desired traits and features, and use these genes to make one’s own children as easily as buying a copy of Microsoft office.

My comment: If the government gets involved, then this sounds a lot like Aldous Huxley’s, Brave New World.

Example of this new biotechnology: Human genes are inserted into microbes to make insulin. We will see a dramatic increase in gene therapies and treatments.

Well, I think and hope many of these will never come true, but it’s interesting to see how others predict the future. This fantastic video tries to show us some plans and projects that can really shape this century:

If you would like to know more about the future,

check out some of the presentations at TED

or follow CNN Future Summit

My Medical Career: Serving Medical Students

Bertalan Meskó — Sat, 10 May 2008 21:00:36 +0000

My 5th year exam period is just about to begin, and I still need one more year to graduate from medical school as medical education takes 6 years in Hungary. I’ve been studying genetics for years and I’ve been trying to find good opportunities through my blog for more than a year now so I really know how hard it is to build a medical career. A new Australian service now aims to help medical students:

My Medical Career is an online career planning portal for Australian medical students and junior doctors. Our goal is to guide you through the process of selecting and achieving a career which best suits your interests, skills and lifestyle needs.

You start with

Self-assessment through personality tests
Specialty profiles: it helps you decide which medical specialty should be your choice
Options: activities that can be undertaken during your student and junior doctor years
Career plan: how to write a résumé, what to expect in an interview
News and conferences in your field of interest
Useful resources: websites, blogs, forums, etc.
And a whole community is ready to answer your questions.

The idea is fantastic, I can’t wait to see something similar in Europe as well.

What’s on the web (2008 May 9)

Bertalan Meskó — Fri, 09 May 2008 12:25:16 +0000

Web 2.0 101 (My MD Journey): Videos about RSS, wikis, podcast or blogs:

Telemedicine could eradicate many expensive ED visits (huliq.com):

A community-wide study in upstate New York found that nearly 28 percent of all visits to the pediatric emergency department could have been replaced with a more cost-effective Internet doctor’s “visit,” or telemedicine, according to investigators from the University of Rochester Medical Center.

The new medical bloggers’ list is up at Medblog.nl. Check it out!

Talking Up A New Role For Cell Phones In Telemedicine (ScienceDaily): Two recent studies by other researchers showed that cell phones can be used to acquire and transmit images of wounds and rashes to off-site locations for diagnosis, he notes.

Prescription Drugs, Health 2.0 and the eDrugSearch.com Community - Cary Byrd (The Health 2.0 Blog)

Slidesonline.org is a great resource of medical slideshows. You can download the presentations as well.

Personalized Genetics: Privacy and the Virtual Gene

Bertalan Meskó — Wed, 07 May 2008 08:35:20 +0000

Here is the regular post about the recent improvements of individualized medicine. This week, T. Ryan Gregory at Genomicron attempted to define the term genome. While The New York Times tried to redefine disease, genes and all.

Daniel MacArthur at Genetic Future reported the low technical error rates for personal genomics companies: Of the 560,299 sites analysed by both companies (23andMe and DecodeMe), just 23 showed a different result between the two scans! Funny number, isn’t it?

Another privacy threat: personal genome projects (Kyose Blog):

What if a unauthorized person get access to the 23andme database? He will have a lot of information about many people. Ok, they can use strong encrypting algorithms but we know there is no 100% secure system. Maybe providing a anonymous service as Keyose this problem could be nearly totally prevented.

But this is not the only problem. Not at all!. What if I just take some of the spit of my new partner or my employee and send it to 23andme pretending to by my own spit? Then I could access to the genomic information of a third person without his/her permission. That sounds not really funny!

Google and Microsoft together on medical health records:

Steve Murphy, our gene sherpa, commented a Lancet article in his Osteoporosis and Gene Tests post.

Would you like to download your own genome’s data? It looks like that:

And if you’re fed up with these news about the personalized genetic companies, send a virtual gene to your friend in Facebook.

More here.

Medicine 2.0 carnival at Canadian Medicine

Bertalan Meskó — Wed, 07 May 2008 07:00:38 +0000

The 23rd edition is up at the Canadian Medicine! Check out the many posts and news about the world of medicine 2.0 and health 2.0. I’m thankful to the whole Canadian Medicine Team, and especially Sam Solomon, for hosting Medicine 2.0!

Medicine 2.0 editions so far:

The next edition is due to be published on the 18th of May 2008 at My MD Journey.

Submit your blog article to the next edition of medicine 2.0 using our carnival submission form.

And read about this interesting and emerging field here.

NextBio: Life Sciences Data Search Engine

Bertalan Meskó — Mon, 05 May 2008 13:55:10 +0000

Almost a year ago, I wrote NextBio was just like using Pubmed but in a more dynamic way. Now the public version was launched so it’s free for everyone.

With NextBio, in just one click users can search through thousands of studies with billions of data points spanning across different experimental platforms, organisms and data types. It also searches across millions of publications to help find new articles pertaining to your search query. NextBio’s data and literature search engine makes massive amounts of disparate biological, clinical and chemical data from public and proprietary sources searchable, regardless of data type and origin, empowering researchers to quickly understand their own experimental results within the context of other research.

I gave it a try by searching for psoriasis and it looked impressive as it offered me the subtypes of psoriasis to search for (auto-complete list).

There were some genes that can play a role in the pathogenesis of the disease and some groups as well. It would be interesting to see how and why it shows only these genes (take a look at Gene2Mesh for a clearer example).

And one more thing:

We process the world’s publicly available high-throughput data through a semi-automated analysis pipeline which involves comprehensive quality control steps and the manual review of studies by our experienced scientific team to ensure the highest quality final output. NextBio correlates gene ontology, pathway and other functional information within the context of the world’s experimental data.

I still need time to get used to this system but looks quite useful and can really ease the job of a scientist. Give it a try!

Further reading:

New business models for life science content (BBGM)

4 in 1: Video, podcast, photo and Pubmed

Bertalan Meskó — Mon, 05 May 2008 12:50:24 +0000

There are nearly 25 sites and services focusing on medical videos and animations on my list I’ve been working on for months. Here is the newest addition, The DAVE Project - Gastroenterology:

The DAVE Project, an acronym for the Digital Atlas of Video Education, is a collection of teaching tools. The project consists of a gastrointestinal endoscopy video atlas and medical lectures and presentations. The most recent additions to the collection are displayed below. Physicians are encouraged to submit material, for consideration, new entries to enrich and expand the atlas.

We can watch the videos or download them; listen to the podcast; see some related photos or do a Pubmed search in that specific field of interest.

DAVE stands for Digital Atlas of Video Education Gastroenterology…

Internal Medicine Journal Search: Personalize Your Searches!

Bertalan Meskó — Sat, 03 May 2008 18:20:17 +0000

Have you ever heard about Google Co-op? According to Wikipedia:

Google Co-op is a platform provided by Google that allows web developers to feature specialized information in web searches, refine and categorise queries and create customized search engines, based on Google Web Search.

Flavio Guzmán created his own search engine, the Internal Medicine Journal Search where we can search on the top 5 medical journals: JAMA, NEJM, BMJ, AIM and Lancet.

This is a great example on how to create a customized search engine. Another example is the Scienceroll Personalized Search Engine where you can choose which databases to search in. More about it here.

Gene2MeSH: Automated Literature Based Genome Annotation

Bertalan Meskó — Sat, 03 May 2008 17:37:58 +0000

Some weeks ago, I mentioned on Twitter how hard it is to find proper gene-disease associations in Pubmed, the database of health-science data. Some days later, P. F. Anderson sent me this link: Gene2MeSH.

According to her:

Gene2MeSH was described 2 me as mapping various terms used 2 describe the same gene, or genes assoc w/ medical term

I gave it a try and made a search for psoriasis:

It looks like an interesting and useful idea, while the MeSH heading column seems to be totally unnecessary, for example.

I will keep on using it and will let you know how it goes.

Further reading:

NCBI Introduction to Molecular Biology Information Resources

What’s on the web (2008 May 3)

Bertalan Meskó — Sat, 03 May 2008 16:57:05 +0000

Video: “I Wanna Be a DNR” Sung to Rockstar by Nickelback (Clinical Cases and Images):

What does DNA mean to you? #3 (Eye on DNA): It was my turn. Thank you, Hsien, for the opportunity!

QuizMD - practice exam questions (Medical Education Blog): I must try it now.
X-Games Athletes have Modified Anatomy (Street Anatomy):

New TED Talk: Ernest Madu talks about Bringing world-class health care to the poorest

Medical Bloggers’ Panel: Anyone interested?

Bertalan Meskó — Fri, 02 May 2008 13:12:14 +0000

We are currently recruiting bloggers who would be interested in participating in a Medical Bloggers’ Panel during the Medicine 2.0 Congress taking place in Toronto, Canada this September, 4-5.

Some details:

Panels are 45-60 min presentations or debate sessions of a group of leaders in a field discussing a broad issue of general interest from various perspectives.

Please note that normally we will not be able to cover the registration fee, travel and accommodation for any of the panelists.

The abstract should contain up to 500 words, containing a short overview of the common issues and 1-2 sentences per presenter about the contribution of each panelist.

So far we have:

Jen McCabe Gorman - Health Management Rx
Sam Solomon - Canadian Medicine Blog
Berci Mesko - ScienceRoll

If you’re interested, please send me an e-mail (berci.mesko at gmail.com) so we could submit our abstract in the next couple of days.

Also check out Jen’s post about it.

Health News in Second Life: Virtual Conference

Bertalan Meskó — Thu, 01 May 2008 18:39:13 +0000

Second Life is a virtual world with more and more educational resources and in this series, I try to keep you up-to-date about these.

Second Life, Education: Health Science Endeavors in Second Life? Always growing! (EBM and Clinical Support Librarians@UCHC):A really comprehensive compilation of what we have now in Second Life in the medical field.

Search in Second Life Opens Up! (Health & Medicine in Second Life): The new build-in browser in SL opens up massive opportunities to search in web-based resources out there on the Web.

The site of Second Nature on Nature.com is quite impressive:

International Virtual Association of Surgeons (iVAS) Conference in Second Life (Resilient Ambassadors of Change):

No travel arrangements, no hotel, no last minute flight hassles, no cost, no jet lag–in no time I’m at an international conference with surgeons and experts in virtual patients, telerobotics, and using eye tracking to separate the novice from expert surgeons.

Please join the debate! (A Sexual Health SIM in Second Life® (University of Plymouth)):

Why 3D? Web conferencing: 2D vs. 3D (or both), or ‘Why conduct events and meetings in Second Life?’

The Mission of Navigenics: Interview

Bertalan Meskó — Thu, 01 May 2008 18:16:30 +0000

Navigenics is a company focusing on personalized genetics and it launched its service just weeks ago. Dr. Dietrich Stephan, a human geneticist at Navigenics, agreed to answer some of my questions. And many thanks to David Harley who helped me a lot to get this interview done.

As a co-founder, why did you take part in constructing such a service?

My mother died of breast cancer when she was in her early 30’s due to a missed lump. This shaped my career and guided me toward developing effective early diagnostics and new knowledge-based therapies for human disease. I have been working in academia for the last 15 years to identify gene variants that cause human disease.

My group has been involved in identifying the genetic basis of a dozen monogenic diseases that now allows early genetic testing following the established principles of medical genetics and genetic counseling. While crucial to the families afflicted with these diseases, they remain rare on a population-wide basis.

Approximately 5 years ago I charged into the field of deciphering complex genetic disorders using ultra-high density SNP genotyping arrays and case-control study designs. We published the first paper using more than 500,000 SNPs (in Science), established new risk alleles for Alzheimer’s disease, amyotrophic lateral sclerosis, progressive supranuclear palsy, and half have dozens more projects ongoing. I believe we are still the only group that makes our raw genotype data freely available on-line for any scientist to download and use .

These risk alleles that we have been finding have effect sizes that are on exactly the same order of magnitude scale as the environmental risk factors that we, as a community, accept as robust and communicate to members of our community on a daily basis (for example “you are obese so you are going to get a heart attack”, or “you smoke so you are going to get lung cancer”). The risk communication for environmental risk factors does not require a testing lab because we can see or sense the exposures in most cases, and the method of communication is quick and crude in that we do not communicate effect sizes or interactive models between risk factors.

As my group continued to define allelic imbalances that are predisposed to human disease, I looked for a place where we could genotype individuals to assess their risk. There were no monogenic testing facilities that we felt comfortable performing the genotyping tests and interpreting the results. Additionally, there were no genetic counselors or physicians who felt comfortable in using genetic risk information to work with their patients proactively to prevent disease based on a holistic understanding of their risk. It is critical to remember that all human disease has a genetic component.

I started Navigenics with my partner David Agus, who is a clinical oncologist, to build the appropriate infrastructure to allow widespread assessment of genetic risks so that we, as a global community, could have a chance at effective prevention strategies to stave off a global health-care crisis in the next 50 years. The concept revolved around encouraging focused prevention, early screening, and early intervention to compress the burden of morbidity to the end of like and balance it with lifespan.

Will you perform SNP analysis or whole-genome sequencing on patient samples?

We will perform both - starting with genotyping for common variants for common diseases and ending with whole-genome resequencing. You will see an exciting product line evolution over the coming year.

Based only on SNPs, how can we tell patients about their disease-specific risks? Even if I have some SNPs that indicate a serious risk for coronary heart disease, there can be other SNPs, we don’t know yet, which lower my risk. So can you really tell the patient about their risks?

The SNPs we are reporting on are valid associations (based on thorough validation) and are independent risk factors in population-wide studies. Most of our interpretations are based on studies for which a whole-genome scan has been performed and we know that there are no other large effect size SNPs lurking in the genome. We are making the assumption that independent risk factors when present do not cancel each other out, rather they compound risk. We have seen no validated exceptions to this assumption in the literature. As we become aware of exceptions to this assumption we can modify our reporting. We are providing the current state-of-the-art associations and informing members that their risks may refine themselves over time. Take the example again of environmental risk factors - the more you have the higher your likelihood of disease - but we know that we can’t predict with certainty an outcome.

What kind of role will web 2.0, the new generation of web, play in your service?

Web2.0 features will be employed primarily to ensure data privacy, but also to assist in visualizing very complex data sets and results so they are understandable to members and physicians.

Why will people choose Navigenics instead of the other genetic companies?

Quality. Data will be complete with all risk genotypes being called. Genotypes will be generated in a CLIA-certified diagnostic environment. On staff genetic counselors assist in interpreting this information any time of the day or night. We will not give risk information on associations that are wrong. Our ethics, policy, clinical, scientific, and business advisory boards are experienced and made up of individuals who want to ensure this type of sensitive information is used correctly and accurately. For example we are sponsoring an industry standard-setting meeting in conjunction with the personalized medicine coalition this fall. When making health decisions you need to be able to trust the quality of the information you base those decisions on.

What do you expect to see in the field of personalized genetics in the next few years?

Full resequencing of the genome, copy number analysis, and methylation status assessment where all of that data is run through the Navigenics interpretation engine to provide a rank-ordered list of health risks so that a focused prevention plan can be devised along with the physician, and a focused biomarker monitoring program for early detection is implemented. Early intervention equals better outcomes.

Further reading:

Anatomical Theatre

Bertalan Meskó — Tue, 29 Apr 2008 19:32:06 +0000

I found this on BoingBoing:

Anatomical Theatre is a photographic exhibition documenting artifacts collected by and exhibited in medical museums throughout Europe and the United States. The objects in these photos range from preserved human remains to models made from ivory, wax, and papier mâché. The artifacts span from the 16th Century to the 20th, and include examples from a wide range of countries, artists, and preparators.

Further reading:

How Not to Give a Presentation!

Bertalan Meskó — Tue, 29 Apr 2008 19:24:16 +0000

This slideshow, I found at Clinical Cases and Images, is one of the best ones I’ve ever seen. It focuses on how not to give a presentation:

I’m a medical student so I know exactly what it is like to sit and watch plenty of bad and long presentations while I still believe even the worst and most boring subjects could be visualized properly on a well-structured slideshow.

I’ve given dozens of slideshows about web 2.0 and medicine and they changed a lot after my US trip this February. I realized the aim is not to transmit all the information you have, but to persuade your audience to search for your project or your work after your presentation. You can clearly see the difference if you take a look at my old and the new slideshows.

Now I

use images (many many images)
talk instead of inserting all the texts I have on the slides
make comparisons (e.g. between the old and new form of web)
present only a slice of the whole story (I used to talk about all the axes of medicine 2.0)
try to avoid “overhyping” the importance of web 2.0
tell more stories (like this one about Second Life)

What are your tips?

Let’s finish with a funny video about the same topic:

Further reading:

How not to give a presentation: Richard Smith, editor; BMJ