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Happy New Year and Enjoy Some AR&R…

Or Attributable Risk Reduction…

First let me wish you all a fantastic New Year! Last year was crazy and I think this year is looking like it will be more of the same…


So in a previous post called Risky Business: Is It All Relative? we started talking about risk. We agreed that in lay terms a risk is generally associated with a bad event. However, a risk in statistical terms refers simply to the probability (usually statistical probability value between 0 and 1) that an event will occur, whether it be a good or a bad event.


We also defined the risk of “smartphone thumb” as the number of new cases of smartphone thumb (the outcome) in a given period of time divided by the total number of people who own a smartphone (the exposure) and are at risk. This was called the cumulative incidence or absolute risk. Now what if we wanted to compare this risk to people who did not receive a smartphone for their birthday or Christmas for that matter? Let’s look at the results in a contingency table:


So, the absolute risk of smartphone thumb is A/(A+B) and similarly for those sad people without a smartphone their risk is C/(C+D). Now your chances of developing smartphone thumb are not necessarily 0 as maybe you are an avid gamer and play a little too much Xbox on the weekends. The reduction in risk can be expressed as the risk difference (also called the attributable risk reduction – ARR) and can be calculated as RD = A/(A+B) – C/(C+D). We can also estimate the proportion of cases of smartphone thumb among smartphone users that can be attributed to smartphone use by calculating the attributable risk percent: [RD/ A/(A+B)] x 100.


Let’s say 20% of smartphone users develop smartphone thumb whereas only 10% or non-smartphone users do. The RD is then equal to 10% (0.2 – 0.1 *100). The reduction in the chances of experiencing smartphone thumb who own a smartphone is the AR% which in this case is 50% (0.1/0.2*100).

That was easy. What’s next? Well, what if we want to know how many times more likely is it for a smartphone user to develop smartphone thumb than for a non-smartphone user? Let’s talk about that next post.






For now, decompress listening to “Under my Thumb” by the Rolling Stones. Classic…




See you in the blogosphere,


Pascal Tyrrell
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MiDATA hosts “Hour of Code” at the University of Toronto

What hour of code? What code?

The Hour of Code is a global movement reaching tens of millions of students in 180+ countries. The purpose is to to demystify “code”, to show that anybody can learn the basics, and to broaden participation in the field of computer science. Please see here for more info.

I belong to Code.org a non-profit dedicated to expanding access to computer science, and increasing participation by women and underrepresented students of color.

On Wednesday, December 7th at 10AM we will be hosting the inaugural

“MiDATA Hour of Code at UofT”

What is the purpose of this event?

To engage young minds and help them see the exciting possibilities computer programming can offer them in their future careers.

Who is coming?

Over 100 students (grades 7 to 11) from Central Toronto Academy (TDSB), St Francis Assisi and St Ignatius of Loyola (TCDSB).

Who will be engaging them (so far)?

University of Toronto:
MiDATA (Data Science unit from the Department of Medical Imaging)
*Prof Pascal Tyrrell – Director, Data Science

*Prof Anne Martel – Medical Biophysics (Machine Learning)

*John Harvey – Information Architect

MiNE (Medical image Network Enterprise, Sunnybrook Health Science Centre)
*Dr Mariam Afshin – Research Physicist
*Rasha Mahmood – VBIRG

Department of Medical Imaging
*Dr Alan Moody – Radiologist and Chair of the Department

Department of Statistical Sciences
*Prof Jamie Stafford – Statistician and Chair of the Department
*Prof Paul Corey – Senior Biostatistician

Translational Research Program /Institute of Medical Science
*Prof Joseph Ferenbok – Program Director

Department of Computer Science
*Prof Francois Pitt

Faculty of Engineering
*Prof Naomi Matsuura – Department of Materials Science & Engineering

Industry:
IBM Watson Health and Merge Healthcare
*Steve Schudlo – Executive Director, Strategic Alliances, IBM Watson Health Imaging
*Marwan Sati – VP of Development, Clinical Speciality Solutions, Merge Healthcare
*Aditya Sriram – Developer, Watson Health Imaging, IBM

Microsoft (Big Data and Analytics)
*Mark Godfrey – Cloud Architect, TSP – Cloud & Data Center, Microsoft Canada

AceAge
*Spencer Waugh – CEO AceAge
*Sam Campbell – CTO AceAge
*Dylan Horvath – Cortex Design President

SAS Canada
*Mark Morreale – Lead, Academic Program

Community:
Ladies Learning Code – Yaa Otchere

Tyrrell lab students and Computer Science undergraduates will be acting as ambassadors.

Where and when will the event be held…exactly?

University College Media Room (RM 140 and RM148) from 10 AM to 1 PM

University College, University of Toronto
15 King’s College Circle
Toronto, Ontario

 

Interested in participating? Contact me at pascal.tyrrell@utoronto.ca!

See you all there,

Pascal Tyrrell

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Engaging Primary Care in Research: Not Always an Easy Task

Stella Song ROP Summer 2016

I am Stella Bing Xin Song, currently a second year student studying pharmacology and psychology at University of Toronto. I was fortunate to be a part of the 2016 Research Opportunity Program (ROP) supervised by Dr. Pascal Tyrrell in the Department of Medical Imaging at University of Toronto. 


My ROP project focused on evaluating the feasibility of using MRI as the primary imaging modality for carotid artery stenosis diagnosis and assessment (not sure what we are talking about? See previous posts here and here). Along with Ginni Ting, a student volunteer in Dr. Tyrrell’s lab, we surveyed physicians in the Niagara region of Ontario to learn about their perspectives on this proposal. Our community partner in this research was Heart Niagara – a fantastic local organization that has been guiding advances in cardiac health education and services since 1977.

Most of the responding physicians saw approximately 2000 or more patients per year. Physicians expressed a variety of care-related decisions for carotid artery stenosis patients, especially for those where diagnosis was less obvious with less than 70% stenosis. Most responding physicians would consider MRI over Ultrasound as the first-line diagnostic imaging modality, because of its ability to detect IPH yielding more pertinent information. IPH is bleeding within the plaques, which causes them to become more vulnerable (see vulnerable plaque). There is a 6 times greater risk of stroke in people with IPH! For those who were reluctant to consider it, they expressed that it was mostly due to their concerns for the relative cost and current wait time for MRI. 



Unfortunately, the response rate for this online survey was very low. Reasons given for the reluctance to participate were that physicians were on a tight schedule and were busy with their patients. Feedback from participants was that the online survey seemed long. Nevertheless, from the responses received, we were able to learn more about physicians’ perspectives of using MRI for carotid artery stenosis diagnosis and assessment.


In the end, it was an exciting and valuable experience to plan out and execute this research project. Most importantly, I had the pleasure to join Dr. Tyrrell’s lab and meet his team. I am grateful for all the help and support which I have received throughout my time at the lab. I look forward to continuing to work as a member of Dr. Tyrrell’s lab.

Stella Bing

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Risky Business: Is It All Relative?

Now this movie takes me back a few years. Tom Cruise’s first big movie Risky Business. His underwear dance scene is pretty famous (haven’t scene it yet? Have a gander here). 


So what does Tom Cruise in underwear have anything to do with our blog? Well it is the concept of risk that interests me today. David Streiner was a fantastic professor of mine and is the author of many great stats publications. He talks about risk here. I will endeavor to do the topic justice with his help over the next few posts.


What do we mean when we talk about risk? In lay terms a risk is generally associated with a bad event. However, a risk in statistical terms refers simply to the probability (usually statistical probability value between 0 and 1) that an event will occur, whether it be a good or a bad event. 


Now that you are clear on that, you are probably wondering what are the best ways of describing risk or – better yet – comparing estimates or risk between groups (wondering what a statistical estimate is? See my earlier post here).  




Let’s say that you have just received the latest and greatest smartphone for your birthday and you can’t wait to text everyone you know to tell them about it. This would be considered the exposure: your smartphone. The outcome would be “smartphone thumb”: a painful thumb resulting from smartphone overuse (don’t believe me? See here). We can define the risk of smartphone thumb as the number of new cases of smartphone thumb (the outcome) in a given period of time divided by the total number of people who own a smartphone (the exposure) and are at risk. This is also called the cumulative incidence or absolute risk. 


As you have an inquisitive mind, you are now wondering what would be the difference in levels between conditions: people with a smartphone compared to people without. Well this can be expressed as absolute differences in risk or relative changes in risk and I will have mercy and address this in more detail… next post! 


For now, decompress by listening to the Barenaked Ladies singing Pinch me (believe it or not this song has something in common with Tom Cruise from Risky Business. Get it yet?).


See you in the blogosphere,




Pascal Tyrrell

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Sharing Medical Images for Research: Patients’ Perspectives

Michelle Cheung – YSP 2nd Place Award

Michelle was our second YSP student this summer and did a great job at particpating in one of our studies in looking at patients’ willingness to share their medical images for research. This study is also part of the MiNE project.

Here is what Michelle had to say:

“My name is Michelle Cheung and I am a rising senior at Henry M. Gunn High School in Palo Alto, California. In my free time, I love to bake, read, travel with family, and take Barre classes. I also enjoy volunteering with friends at local charitable events and the Key Club at school. I am very interested in human biology and hope to study genetics and biotechnology next fall.

I really enjoyed the three weeks with the YSP Research Program. I learned so much about medical imaging modalities and had the amazing opportunity of helping research assistants survey patients at the Sunnybrook Hospital for the MiNE project. At first, it was a little daunting, but over time, I became more confident and comfortable interacting with patients, and grew to love surveying. The continuous surveying each day highlights the aspect and importance of repetition in conducting scientific research. Above all, it was an absolute pleasure getting to know the MiDATA and VBIRG lab. I’m grateful to my mentors and the lab members for exposing me to a whole new lab world I never thought existed beyond the traditional wet labs.”

Great job Michelle!

Have a peek at Michelle’s award winning poster and…

… I’ll see you in the blogosphere.

Pascal Tyrrell

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Wow! What a Busy Summer….

Jenny Joo – YSP 2016

Over 20 students in the lab this summer beavering away at some great projects. Last week my two Youth Summer Program (University of Toronto) students finished their three week stay with us. 


Jenny and Michelle both did fantastic work.


Today Jenny will show you her poster entitled:“Comparing Healthy and Unhealthy Carotid Arteries”


Jenny Joo is from Richmond Hill, Ontario, entering her senior year of high school. She plans on studying life science at the University
of Toronto in the future. She spent the last 3 weeks in U of T’s YSP Medical
Research program, where she was placed in two different medical imaging labs: The
MiDATA lab of U of T and the Vascular Biology Imaging Research lab at
Sunnybrook Hospital. 

Jenny chose to do research on the
MRI scans of the carotid artery because it focused on both research and
clinical aspects and had this to say about her experience with us: “It has been an enriching 3 weeks working with my PI, Pascal
Tyrrell, my mentors, John Harvey and Moran Foster, and the rest of the research
group.” 

Great work Jenny Joo!


Have a peek at her poster and…

… I’ll see you in the blogosphere.


Pascal Tyrrell
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MiDATA – Enabling Medical Image Research at the University of Toronto

Poster to be presented at the Department of Medical Imaging Resident Achievement Day 2016

Where have a I been you ask? At my desk putting this program together! I apologize for being MIA for the past month or so but I it has been a busy time nurturing this fledgling program of MiNE (pun intended!).

Here is the premise:

Bridging the gap between clinical expertise and the science of managing and analyzing medical imaging data is challenging. To provide direction for data management as well as the analysis and reporting of research findings, we are in the process of introducing a data science unit – MiDATA – offering users an environment geared towards a “soup to nuts” approach to medical imaging research methodology and statistics. The Department of Medical Imaging of the University of Toronto is one of the largest in North America with a clinical faculty of more than 184 faculty, 60 residents and 80 fellows based at nationally and internationally renowned hospitals conducting cutting edge clinical research in the greater Toronto area. The challenge of any successful research and educational program is bridging the “know-do” gap. The goal of MiDATA is to facilitate impactful research through the efficient and creative use of a mentored learning environment.

Shout out to our collaborators the Division of Biostatistics from the Dalla Lana School of Public Health!



Tomorrow is the official unveiling at the 2016 Department of Medical Imaging Resident Achievement Day. I thought I would share with you our poster as a sneak peek…



Once you have digested its contents have a listen to Paper Planes by M.I.A. to decompress and…

… I’ll see you in the blogosphere (or at tomorrow’s event!)


Pascal Tyrrell


Posted on

Engaging Primary Care in Research: Not Always an Easy Task

I am Stella Bing Xin Song, currently a second year student studying pharmacology and psychology at University of Toronto. I was fortunate to be a part of the 2016 Research Opportunity Program (ROP) supervised by Dr. Pascal Tyrrell in the Department of Medical Imaging at University of Toronto. 
My ROP project focused on evaluating the feasibility of using MRI as the primary imaging modality for carotid artery stenosis diagnosis and assessment (not sure what we are talking about? See previous posts here and here). Along with Ginni Ting, a student volunteer in Dr. Tyrrell’s lab, we surveyed physicians in the Niagara region of Ontario to learn about their perspectives on this proposal. Our community partner in this research was Heart Niagara – a fantastic local organization that has been guiding advances in cardiac health education and services since 1977.
Most of the responding physicians saw approximately 2000 or more patients per year. Physicians expressed a variety of care-related decisions for carotid artery stenosis patients, especially for those where diagnosis was less obvious with less than 70% stenosis. Most responding physicians would consider MRI over Ultrasound as the first-line diagnostic imaging modality, because of its ability to detect IPH yielding more pertinent information. IPH is bleeding within the plaques, which causes them to become more vulnerable (see vulnerable plaque). There is a 6 times greater risk of stroke in people with IPH! For those who were reluctant to consider it, they expressed that it was mostly due to their concerns for the relative cost and current wait time for MRI. 

Unfortunately, the response rate for this online survey was very low. Reasons given for the reluctance to participate were that physicians were on a tight schedule and were busy with their patients. Feedback from participants was that the online survey seemed long. Nevertheless, from the responses received, we were able to learn more about physicians’ perspectives of using MRI for carotid artery stenosis diagnosis and assessment.

In the end, it was an exciting and valuable experience to plan out and execute this research project. Most importantly, I had the pleasure to join Dr. Tyrrell’s lab and meet his team. I am grateful for all the help and support which I have received throughout my time at the lab. I look forward to continuing to work as a member of Dr. Tyrrell’s lab.

Stella Bing

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U of T Research Opportunity Program – Clare Sheen

Clare Sheen is an undergraduate student at the University of Toronto, in process of completing her Bachelor of Sciences in Genomics and Microbiology/Molecular Genetics. She was a 2015-6 Research Opportunity Program (ROP) student working on designing the Medical Image Network Enterprise (MiNE) interface for Dr. Pascal Tyrrell from U of T’s Department of Medical Imaging. She is currently a social director on the Life Science Student Network exec team and a volunteer at U of T’s Agrawal Lab where she helps with Drosophila experiments. She continues to seasonally work as a student camp teacher in the summer.

At the Research Opportunity Program (ROP) fair on March 3rd, U of T ROP students from different departments came together to share their research. A mock-up of the MiNE interface was presented in PowerPoint with the goal of increasing user engagement and encouraging the development of a medical imaging research community. Some features of the interface are presented below.

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MiWORD of the day is… Mop-top!

Ahhh, the mop-top! I sigh not because I miss the hairdo but because I miss my hair – all of it. In the mid-60s this hair style was made famous by The Beatles. Don’t know who they are (shame on you!) have a listen here for instruction.


Well the mop-top was made popular because the 4 guys who sported the hairdo were crazy successful musicians from England. Their recording company, Electrical Musical Industries (EMI), was also very happy and successful because of the overwhelming record sales (music was sold to listeners on vinyl records back then).


So, what does any of this have to do with medical imaging? Lots actually. The money generated by record sales enabled the EMI basic science researchers (another division of the company) to work in a prosperous cash-rich environment. One of those researchers was Sir Godfrey Hounsfield, an electrical and computer engineer. 


In 1967, he started his work on what would soon become the first CT scanner. By directing x-ray beams through the body at 1 degree angles, with a detector rotating in tandem on the other side, he was able to measure the attenuation of x-rays. These values were then analysed using a mathematical algorithm and a computer to yield a 2-D image of the interior of the body. The production of CT scanners by EMI started in the early 1970s and their monopoly ended by 1975 when companies like DISCO (not even kidding) and GE entered the arena.


Interestingly, in the 1960s Dr Allan Cormack of South Africa had also independently showed similar results to Housfield. In the end, Cormack was cited for his math analysis that led to the CT scan and Housfield for its practical development. They shared the Nobel prize in Physics and Medicine in 1979. Cool.

Now for the fun part (see the rules here), using mop-top in a sentence by the end of the day:

Serious: Who would have thought the success of the mop-top Fab Four would be instrumental in the development of the CT scanner?

Less serious: Hey Bob, I went for my head CT scan today and something weird happened. I went in bald and came out with a mop-top! Is that normal?…

Listen to With a Little Help from My Friends from The Beatles to decompress and…

…I’ll see you in the blogosphere.

Pascal Tyrrell