Blog Archives

A MR Imaging primer through analogy with Guitar playing

Thanks to my colleague Jerry Battista from the University of Western Ontario, understanding the basic MR pulse sequence (a not so obvious topic especially if you have to design such a sequence) is now easier than ever. For those who do not know Prof. Battista also developed a mini-CT scanner (using non-ionizing radiation!) to teaching the basic of medical imaging from high-school all the way to university. We are using this scanner in our undergraduate laboratory.


So, check out this wonderful and accessible teaching YouTube Video: Understanding an MRI Pulse Sequence using a Guitar.

An interesting resource for PhDs, postdocs and early career researchers

I recently came across the following document by Professor Alan M Johnson, which appears to be distributed freely by Elsevier and entitled “Charting a Course for a Successful Research Career: A Guide for Early Career Researchers – 2nd edition“.

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The status of science… 450 years after Galileo!

“A quarter of American adults do not know that the Earth goes round the sun. Half think that antibiotics kill viruses and almost as many believe electrons are larger than atoms” Stephen Luntz – I Fucking Love Science.

In an earlier post, I reported that a majority of young adult in the US thought that astrology was a science. Similar numbers and others can be found in a biennial survey from the USA National Science Foundation. A round up can also be found here, with link to the said survey and a link to the Science and Engineering Indicators.

Meanwhile the 450th anniversary of the birth of Galileo, who was persecuted for something that is now proven without the shadow of a doubt (for those who may wonder, I refer you to the first sentence of the quoted text above 😉 ), was just a few days ago.

The failure of an education system is happening when…

The majority of young adults think astrology is a science –

The tyranny of the top science journals?

Are journals like Science, Nature and the like giving too much importance to themselves to the point of distorting the scientific process? A Nobel prize winner seems to think so (from The Guardian)

Carl Sagan’s Cosmos documentary available

Just recently rediscovered the must see documentary Cosmos: 13 episodes of 1 hour each, all available for free here.

“The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.”

― Carl SaganCosmos

Massive Open Online Course (MOOC) in Scientific Writing

Want to get better and more effective at writing scientific manuscripts? Stanford is hosting a free MOOC course on the topic. The content look very interesting:

Week 1 : Introduction; principles of effective writing (cutting unnecessary clutter)
Week 2 : Principles of effective writing (verbs)
Week 3 : Crafting better sentences and paragraphs
Week 4 : Organization; and streamlining the writing process
Week 5 : The format of an original manuscript
Week 6 : Reviews, commentaries, and opinion pieces; and the publication process
Week 7 : Issues in scientific writing (plagiarism, authorship, ghostwriting, reproducible research)
Week 8 : How to do a peer review; and how to communicate with the lay public

LINK:  Writing in the Sciences | Coursera.

Are you at an exciting phase of your thesis project?

If we knew what it was we were doing, it would not be called research, would it?

– Albert Einstein

How do you know for sure that you are at a particularly interesting stage of your thesis project?

When the excitement spread to your supervisor, fellow students and the extended team (collaborators and others). When you present at a meeting and peoples come talk to you with that look in their eyes. When you are asked by scientists or other students unrelated to your project if you have published/submitted your results.

The flip side of that coin is that the pressure is on you (and your supervisor) to convert in a timely fashion to peer-reviewed publications 😉

Laptop multitasking hinders classroom learning…

With the start of the a new semester approaching fast, here is an interesting study on the effect of laptop in university classroom both on the person of interest and the surrounding peers. Based on my teenagers behavior at home, it seems obvious that multitasking  in the form of (homework, Facebook, music, Skype) or (TV, Facebook, texting) never really worked.

The manuscript is by Sana et al in Computers & Education entitled “Laptop multitasking hinders classroom learning for both users and nearby peers” is demonstrating the (significant) effect in the classroom.

Abstract: “Laptops are commonplace in university classrooms. In light of cognitive psychology theory on costs associated with multitasking, we examined the effects of in-class laptop use on student learning in a simulated classroom. We found that participants who multitasked on a laptop during a lecture scored lower on a test compared to those who did not multitask, and participants who were in direct view of a multitasking peer scored lower on a test compared to those who were not. The results demonstrate that multitasking on a laptop poses a significant distraction to both users and fellow students and can be detrimental to comprehension of lecture content.

Thanks to those who have pointed out this study on LinkedIn.

Practice, practice, practice

“Practice is the best of all instructors”
Publilius Syrus (Roman author, 1st century B.C.)

Back from the AAPM scientific meeting, and kudos’ to the organizers for an excellent meeting. Over the past few years, they have set-up a “Best in” category regrouping the 5 highest scored abstracts in each 3 broad categories of the meeting. Not only do they get oral presentations but they also deserved a special poster viewing session. An extremely interesting and exciting session!

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Big week at the 2013 AAPM meeting

Our group is well represented at this year AAPM meeting. 2 Faculty and 7 graduate students for a total of 11 oral presentations and 2 posters.

For a number of these students, it will be their first experience presenting at such a big event (over 3000 participants). Also for many of them, it will be their first scientific presentation in English. Hours of preparation and rehearsing for 5 minutes (snap oral) or 8 minutes (regular oral) presentations. While, I do tell them that the shorter the talk the more time (usually many hours!) is needed to select and organize the visual materials (aka slides), they do not realize it until we do the general repetition during our weekly group meeting.

For each talk, we can spend between 10 to 30 minutes going over the slides, suggesting modification, addition, removal, asking questions such as: what are you try to say? What is your main message? What do you want the audience to remember from this or that slide, …

Of course, senior grad students have it easier as they already know what to expect and prepare their presentations accordingly 😉

For my friends and colleagues in the medical field, see you in Indy.

The best job is …

Choose a job you love, and you will never have to work a day in your life.


My two teenagers have started their summer jobs as instructor and assistant instructor in specialized summer camps. This reminded me that when my son started his first summer job (last year), I asked him at the end of his first week how it was, if he liked it?

His reply was, I am having lots of fun and their paying me to for it!

This is a very important feeling, maybe the most important one when it comes to employement. I told him never to loose that feeling because whatever he choses to do later on in life, this how it should feel.

I also told him that this is exactly how I feel everyday in my line of work: scientific research and university teaching. Yes it is tought to get such a position, even thougher to thrive due to the highly competitive nature of publishing manuscripts and getting research grants. At the same time, I get to chose what I am working on and the perks are very satisfying in the end.

The best job is the one that does not feel like it 😉

Writing Your First Scientific Paper, Part I: The “Data/Story Flow”

You’ve been working hard, around the clock to get all the data out. You might even have submitted an abstract about your current to the great scientific meeting of your field (and maybe got to travel and present it). Now is time to plant the flag, leave your mark i.e. publish!

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Journal Impact Factor: why you should not care… too much

I have been publishing scientific manuscripts for the past 22 years. My educated comments with regard to journal impact factor has always been the same (If you do not know what JIF is, please have a look at this Wikipedia entry). First order, you should publish in the most important journals for your field. If their JIF are low, who cares as long as your work is important to your field and well cited. For example, the scientific discovery of 2012 according to Science (very high JIF) is the publication of the experimental finding of the Higgs boson… in Phys Lett B (low JIF relative to Science)!

Do not forgot that from an historical perspective, we are awfully bad at predicting what will be the next important discovery down the road. A number of fundamental discoveries and early engineering feats were discarded at first. Similarly there are numerous example of scientists having had tremendous issues in getting those game-changing results published, even those ending up winning Nobel prizes. Karry Mullins’ PCR work is one of many examples of work was rejected by journals having top JIF but for which the application of this very technique was published in Science and Nature and the citations counts of these second generation papers also receiving higher numbers than the original, award-winning work!)

Now, you do not have to agree with this lone scientist opinion but certainly you should have a look at the The San Francisco Declaration on Research Assessment or DORA petition, which is supported by the “big boys” (no discrimination intended). The declaration statement is actually a very interesting read and it covers the historical origin of the JIF (which was not for evaluating researchers at all) and further call for dropping journal-based metrics in assessing scientific productivity for funding and promotion. Over 240 organizations and 6000 individuals have already signed the declaration.

In conclusion, do not loose a good night sleep over your favorite journals’ impact factors…

Has the Canadian Government declared war on science?

A post by John Dupuis on Science Blogs seems to think so and it started over 7 years ago: The Canadian War on Science: A long, unexaggerated, devastating chronological indictment – Confessions of a Science Librarian.

That being said, do not forget that Canada’s Sciences Minister is actually a creationist; It is sad.

NOTE ADDED [May 25th]: The Science, Technology and Innovation Council just publish its 3rd public report on the performance of Canada in Science and Technology. Between 2008 and 2012, Canada’s ranking in term of expenditure decreased significantly from 16th out of 41 OECD member countries to 23rd.

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