We need to talk about TED

Couldn't have said it better myself: http://www.theguardian.com/commentisfree/2013/dec/30/we-need-to-talk-about-ted.  Thanks to Roberta Buiani for posting this on her Facebook page.

Paper Published: Carotid Bifurcation Geometry Is an Independent Predictor of Early Wall Thickening at the Carotid Bulb

This paper, just published online by Stroke, is the culmination of nearly a decade's worth of effort (e.g., see here, here, here, and here) trying to answer a deceptively simple question: can carotid bifurcation geometry be considered an additional risk factor for atherosclerosis.

As it turns out, the answer is "yes, but".  "Yes", because we did tease out a significant and independent association between early wall thickening and bifurcation flare & curvature geometric parameters; "but", because the association was relatively weak.

An equally interesting aspect of the study was the care we had to take to exclude secondary effects of thickening on geometry.  Had we not done so -- and as we showed -- the associations would have been even weaker or, worse, significantly stronger but inverse to what they should have been.

WANTED: PhD or Postdoc in Art-Inspired Visualization and/or sonification

Click here for PDF

Google me this: What's wrong with this picture?

Whither Peer Review?

Er, thanks(?) to former BSL postdoc Yiemeng Hoi for sending me this depressing story about the ugly side of open-access publishing: http://scicomm.scimagdev.org/.

Not that traditional journals are exempt.  There are simply too many journals, and good peer-reviewers are overworked, meaning that a lot of stuff gets relegated to potentially unqualified reviewers. And the pressure to publish N papers per year has led to a "let's throw it at the wall and see if it sticks" attitude to journal article submission. Science suffers from all of this noise, and we have only ourselves to blame for falling into the bibliometric trap set for us by the bean-counters.

Which makes me wonder.  Should I review articles from groups I know and trust to be careful and honest, and nit pick their papers to make sure they are rock solid and bullet-proof?  Or should I spend time instead reviewing for lesser journals and novice authors, where the reviewer is implicitly being asked to teach the authors how to write a paper, to make sure that crap doesn't inadvertently make it into the system?

Paper accepted, Am J Neuroradiol

I never know what is the embargo policy for specific journals, but since the printer has delayed the processing of our paper (accepted almost three months ago), I think it's fair that we share the good/bad news about a study led by BSL postdoc Kristian Valen-Sendstad, entitled: "Mind the gap: Impact of CFD solution strategy on prediction of intracranial aneurysm hemodynamics and rupture status indicators".  Here's the abstract, paper (hopefully) coming soon:

Background and Purpose: Computational fluid dynamics (CFD) has become a popular tool for studying intracranial aneurysm hemodynamics, demonstrating success for retrospectively discriminating rupture status; however, recent highly-refined simulations suggest potential deficiencies in solution strategies normally employed in the aneurysm CFD literature. The purpose of the present study was to determine the impact of this gap.
Materials and Methods: Pulsatile flow in 12 realistic MCA aneurysms was simulated using both high resolution (HR) and normal resolution (NR) strategies. Velocity fields were compared at selected instants via domain-averaged error. Wall shear stress (WSS) fields and various reduced hemodynamic indices were also compared: cycle-averaged mean and maximum WSS; oscillatory shear index (OSI); low shear area (LSA); viscous dissipation ratio (VDR); kinetic energy ratio (KER).
Results: Instantaneous differences in flow and WSS patterns were appreciable, especially for bifurcation aneurysms. Linear regressions revealed strong correlations (R2>0.9) between HR and NR solutions for all indices but KER (R2=0.25) and OSI (R2=0.23); however, for most indices the slopes were significantly less than one, reflecting a pronounced underestimation by the NR simulations. Some HR simulations were highly unstable with fluctuating WSS, reflected by the poor OSI correlation.
Conclusion: Typical CFD solution strategies may ultimately be adequate for augmenting rupture risk assessment based on certain highly-reduced indices; however, they cannot be relied upon for predicting the magnitude and character of the complex biomechanical stimuli to which the aneurysm wall may be exposed. This impact of CFD solution strategy is likely greater than that for other modelling assumptions or uncertainties.

NYT rakes our prime minister, er, over the coals

Your correspondent is back after a long absence. Apologies for the copyright violation, but this New York Times editorial is too "good" not to share, although I'm sure it will be dismissed as commie pinko propaganda.  Dark Age Ahead, my friends. Or, to put it more colloquially, "money talks, bullshit walks".

Silencing Scientists

By Verlyn Klinkenborg

Published: September 21, 2013

Over the last few years, the government of Canada — led by Stephen Harper — has made it harder and harder for publicly financed scientists to communicate with the public and with other scientists.

It began badly enough in 2008 when scientists working for Environment Canada, the federal agency, were told to refer all queries to departmental communications officers. Now the government is doing all it can to monitor and restrict the flow of scientific information, especially concerning research into climate change, fisheries and anything to do with the Alberta tar sands — source of the diluted bitumen that would flow through the controversial Keystone XL pipeline. Journalists find themselves unable to reach government scientists; the scientists themselves have organized public protests.

There was trouble of this kind here in the George W. Bush years, when scientists were asked to toe the party line on climate policy and endangered species. But nothing came close to what is being done in Canada.

Science is the gathering of hypotheses and the endless testing of them. It involves checking and double-checking, self-criticism and a willingness to overturn even fundamental assumptions if they prove to be wrong. But none of this can happen without open communication among scientists. This is more than an attack on academic freedom. It is an attempt to guarantee public ignorance.

It is also designed to make sure that nothing gets in the way of the northern resource rush — the feverish effort to mine the earth and the ocean with little regard for environmental consequences. The Harper policy seems designed to make sure that the tar sands project proceeds quietly, with no surprises, no bad news, no alarms from government scientists. To all the other kinds of pollution the tar sands will yield, we must now add another: the degradation of vital streams of research and information.

So long, Flanders!

We are sorry to see Jonathan Mynard leave the BSL to return down under to complete his postdoctoral research back home.  However, as a parting memento, he has left us with this startlingly accurate rendering of his friends at the BSL.  So long, Jonathan, it's been, er, ehhhhx-cellent, having you here!

SBC2012 CFD Challenge published in J Biomech Eng

It was a lot of work, but worth it. The results of the ASME 2012 Summer Bioengineering Conference's CFD Challenge are finally out in a special issue of J Biomech Eng. Thanks to everyone who participated so enthusiastically!  Future challenges are in the works (although not necessarily tied to SBC).

Payam Bijari, freshly PhD'd

Congratulations to BSL's Payam Bijari, who this morning successfully defended his PhD thesis, on "Investigation of Arterial Geometry as a Local Risk Factor for Carotid Atherosclerosis", before an eminent line-up of examiners including UofT's Richard Cobbold, John Sled and Myron Cybulsky; and George Tech's Don Giddens, who wisely declined our offer of a free mid-winter trip to Toronto!

Ignatius J. Reilly, Gene Hunter?!?

Recently Dolores and I received a link to Viruses on Time, a blog post about virology-themed covers of Time magazine, sent to us via a mailing list we joined as part of an ESF Conference on Truth and Trust in Images, which we attended and presented at last fall. While the virus nerds were probably pondering the ethics and aesthetics of the portrayals, I was struck by the March 9, 1981 cover featuring Genetech's Herbert Boyer.  My soft-and-squishy-but-bonily-encased pattern recognition engine leapt immediately into action, and reported (and I paraphrase): "Holy Crap, that's Ignatius J. Reilly".

For those who don't know, Reilly is the protagonist of one of my favourite novels,  A Confederacy of Dunces, introduced to me by my 12th grade English teacher, who could clearly spot a misfit when she met one. Maybe it's a coincidence, but Confederacy won the Pulitzer Prize in 1981 (posthumously, another interesting, but sad, story), the same year as that Time cover.

Maybe the cover artists were one in the same (unlikely).  Or maybe the Time's cover artist was a fan of the book (possible).  Or maybe it was just "in the air".  I'd like to think it was the latter, since it faintly echoes our (and many others', of course) belief that scientific visualizations are, extricably, a product of the broader culture in which they are created.

Velocity profile skewing and Doppler ultrasound

Congratulations to BSL postdoc Jonathan Mynard, who has two papers coming out about the practical impact of velocity profile skewing in "straight vessels" (see our previous work here and here).  The first paper, in press with published by Ultrasound in Medicine & Biology, shows that it may not always be reasonable to infer flow rate waveform shape from maximum Doppler velocity traces, particular using a Poiseuille assumption. The second paper, accepted published by Atherosclerosis, highlights the substantial errors that can arise when trying to infer wall shear stresses from Doppler velocities under the common assumption of fully-developed flow.

Paper Published: High-resolution CFD detects high-frequency velocity fluctuations in bifurcation, but not sidewall, aneurysms.

Congratulations to BSL postdoc Kristian Valen-Sendstad on the publication of "High-resolution CFD detects high-frequency velocity fluctuations in bifurcation, but not sidewall, aneurysms".  Admittedly we faced some challenges getting this paper published, in part owing to our early (over)enthusiasm about the apparent association between velocity fluctuations and rupture status, but also because of our unavoidable conclusion that the bulk of published aneurysm CFD model studies may not be sufficiently resolved. This latter conclusion may be easy to dismiss because our simulations were carried out under steady inflow conditions (albeit at peak systolic flow rates), but not for long...

Paper Published: . Impact of T2 decay on carotid artery wall thickness measurements

Another paper from our collaborators at Johns Hopkins, this one looking at the choice of MRI acquisition parameters can affect artery wall thickness and tissue characterization.  With the help of BSL Master's student Alex Martinez, we used an analytic MRI simulation approach, which Luca Antiga and I had previously used to characterize wall thickness artifacts due to slice resolution and orientation, to confirm that decreased wall thickness measurements with increased echo time is the result of adventitial signal decay.

Paper Published: Helical flow in carotid bifurcation as surrogate marker of exposure to disturbed shear

Congratulations to BSL collaborators Diego Gallo and Umberto Morbiducci, from Politecnico di Torino, on the publication of "Helical flow in carotid bifurcation as surrogate marker of exposure to disturbed shear."  This is one of the first outcomes of work that Diego Gallo started during his stay at the BSL while he was completing his PhD (and congratulations to now-Dr. Gallo!).  

The paper shows that one can anticipate the burden of disturbed wall shear stress via cleverly constructed bulk flow parameters based on helicity, which is a measure of the way flow swirls.  A key advantage of this is that 3D (well, 4D) velocity fields can be measured directly in vivo by MRI, from which data it is (relatively) straightforward to compute helicity, whereas it's much trickier to derive wall shear stress maps from such in vivo data.

Paper Published: Comparison of carotid plaque ulcer detection using contrast-enhanced and time-of-flight MRA techniques

Congratulations to Maryam Etesami from the lab of long-time BSL collaborator Bruce Wasserman, on the publication of "Comparison of carotid plaque ulcer detection using contrast-enhanced and time-of-flight MRA techniques."  Led by former (but then current) BSL postdoc Yiemeng Hoi, our main contribution here was to employ CFD simulations to help explain the observation that some carotid plaque ulcerations, notably ones pointing "downwards", may be more difficult to spot on time-of-flight MR angiography. As shown to the left, this has a lot to do with how blood flows -- or in this case, doesn't flow -- in such ulcers.  See animations here and here.

Welcome John Harvey and Andrew Tubelli

Among Dolores' and my attempts to bring more art into the science of blood flow visualization, about two years ago we began a collaboration with Peter Coppin at OCADU, which grew to include OCADU's Bill Leeming. Now, with some seed funding from The Centre for Innovation in Information Visualization and Data Driven Design (CIV-DDD), we have added some part-time assistance from two talented graduate students, biomedical illustrators John Harvey (OCADU) and Andrew Tubelli (UofT).  Cool things are happening, will keep you posted.

Youtube channel

In my quest to bring our lab into the 21st century, I have started porting more of our videos onto BSL's YouTube channel.  Please subscribe if you are wont to subscribe to such things. We'll try to keep adding our visualizations, both old and new, as time and energy permit.

Been a long time, been a long time, ...

Well, six months later and it's time to update the blog.  As I suspect many in the blogosphere have found, the novelty of maintaining a blog soon wears off, particularly when other time (and writing) commitments rear their ugly heads.  Which I guess explains the popularity of the 140-char tweet, which seems much less daunting than a blank page. (In the not too distant future I imagine I will move our lab updates to twitter, and spare you my verbosity.)

In the meantime, I will soon post some blog, er, posts updating you on recent developments -- and by developments I mostly mean papers we've published.  These will trickle out in not any particular order, but as they come to mind.