From YSP to Hanging Out at Stanford: Michelle Cheung

Hello! My name is Michelle Cheung and I am a rising 2nd year student at the University of Toronto. I was one of the Youth Summer Program (YSP) students in Dr. Pascal Tyrrell’s lab in the summer of 2016. During the program, I helped with the Medical Imaging Network Enterprise Project by surveying patients at Sunnybrooks hospital for their perspectives on sharing medical images for research.
Before entering Pascal’s lab in 2016, I took part in YSP the summer before in 2015. It was my two years in the summer program that made me aware of U of T. Being able to live in the dorms, attend classes and labs, and explore the city made me fall in love with the campus, especially the fast-paced metropolitan city life in contrast to the suburban life back home in California. More importantly, through the program, I was exposed to the lab environment. Of course, it was more than the allure of lab coats and micropipettes, but my time in the labs sparked my interest in research, hence am now pursuing genomics and hoping to learn more about hereditary diseases. Thus, when it came down to deciding which college to attend, all these factors placed U of T high up on the list.
Near the beginning of second semester of my first year, I started thinking about what to do over the summer. I couldn’t waste the 4 months and knew I needed the exposure and experience in professional labs if I plan on becoming a genetics researcher, hence started looking for research internships.
I was offered an internship position at the biopharmaceutical company, AbbVie, back in California, and it was quite an interesting experience applying for the position. I thought the first phone interview went decent but I was aware that I didn’t express enough interest in a particular aspect of research associated with the position. A month later, I interviewed a second time. It went really well until the interviewer said, “Let me ask you a challenging question.” I was expecting a deep theoretical question, and it ended up being, “Introduce yourself and your career goals in Cantonese.” In all fairness, my auditory skills are on point and I can understand conversational Cantonese, however, truthfully, my speaking skills had grown too rusty after not speaking it at home anymore. Hence, in my response, I managed to fluently get out my name, age, and school. I tried talking about my hobbies; trying to say “hiking with friends” turned out in me saying “taking walks with friends”, and “baking” turned out to me saying “cooking”. I was stumped when trying to describe my career goals as I blanked on how to say genetics and research and complicated bio words. Least to say, the awkward silence as I tried to come up with the right thing to say was mortifying. Little did I know that the interviewer would become my current manager (great guy), but hey, he hasn’t brought up the mortifying experience and I now have an embarrassing interview story to tell and a lesson learned.
Meanwhile, my parents connected with a family friend who was a scientist at Stanford. She was looking for a student research trainee to help her with her research project studying pulmonary disease, working with mice, and it was a fitting role for me.
I found out I was accepted to the research internship at AbbVie and luckily, the timing works out with my shadowing at Stanford. One internship would give me more practical lab experience while the other would give me a taste of the bio corporate industry. Hence, it’s the best of both worlds this summer – getting to experience both academic and industry research.
All in all, I am here today, about 1.5 months into the research internships, and having a blast. I had a wonderful first year of undergrad, and as I reflect, am very grateful for my time in YSP for bringing me to U of T and exposing me to the medical research world.     
 
-Michelle Cheung

My Past and Future at U of T: Helena Lan’s Perspective

 



Hey everyone, it’s been a while since I posted here. In case you don’t remember me – my name is Helena Lan, and I started in Professor Pascal Tyrrell’s group as a ROP299 student. Fast forward to the present, I have finished my specialist program in pharmacology, and will be graduating with an Honours Bachelor of Science degree later this month! But if you think that I am finally leaving U of T – nope, my journey is not over yet. This August, I will be living my dream of many years as I start my MD training at U of T! As I prepare to begin the next chapter of my life, I wanted to share with you how my involvement in Prof. Tyrrell’s group paved the way for me achieving my goal today.

At the end of my first year of undergrad, I connected with Prof. Tyrrell and took on a project investigating how the choice of non-invasive imaging modality for diagnosing carotid stenosis impacts patient care (check out my experience here http://www.tyrrell4innovation.ca/2014/08/helena-lan-summer-2014-rop.html).
Afterwards, I continued on as a research assistant, where I ­explored the need for statistics and research methodology training in the medical imaging department.  My early research endeavours showed me that research was not just pipetting; there is a diversity of research that can drive innovations and improve patient care. 
That being said, I also wanted to experience working in a wet lab setting. So upon completing my second year of undergrad, I ventured to the Karolinska Institute in Sweden to investigate the tumour killing mechanism of Natural Killer cells (find out more about my project here http://www.tyrrell4innovation.ca/2015/02/who-is-going-to-karolinska-institute.html). After a summer in basic science research, I decided to switch gears into translational research, where I worked on strategies to augment the therapeutic utility of stem cells and enhance the drug delivery platforms at Prof. Jeff Karp’s lab at Brigham and Women’s Hospital, Harvard Medical School. After I returned from Boston, my passion for discovering ways to improve existing treatments for diseases led me to my current work at Dr. Albert Wong’s lab at CAMH, where I am assisting with the characterization of a novel animal model for schizophrenia with the ultimate goal of using it as a screening platform for new anti-psychotics.
In my experiences as a researcher, I’ve always been very excited at the prospect that what I am working on right now may be brought into the clinic sometime down the road and offer benefits to patients. Then one day, I thought to myself, “How rewarding would it be if I can get involved in patient care, where I can directly impact the life of the person sitting in front of me?” With this idea planted in my mind, I decided to shadow a physician. As I observed how a doctor applies their scientific knowledge and the findings from medical research to figure out ways to best help their patients, my attraction to medicine gradually evolved. For a long time, my goal in life has been to make a positive impact on other people’s lives. But after that shadowing experience, I realized that I wanted to do so through taking on the role of a clinician.
I am incredibly grateful to the U of T medical school for giving me the opportunity to pursue my dream, as well as the pharmacology department and New College for their recognition of my undergrad academic achievements with the Dr. Walter Roschlau Memorial award and the Tricia L. Carroll Memorial Prize in the Life Sciences. But more importantly, thank you to U of T for the unforgettable undergrad experience. Not only was I able to immerse myself in fascinating science and interesting research, I was also connected with mentors who provided unconditional support to me along my journey. Even though the ROP project I worked on under the supervision of Prof. Pascal Tyrrell and Dr. Eli Lechtman ended years ago, the two of them have provided invaluable mentoring to me even to this day.
University can seem arduous at times, and it is almost inevitable that we run into obstacles here and there. But no matter how difficult the circumstances may be, never, ever, lose sight of your goal. Surround yourself with people who cheer you on, and invest the work that is necessary to reach your ambition. And one day, your dream will come true!  
All the best,
Helena Lan

Lee Radigan: A Reflection on my (6th) Year as an Undergrad at the University of Toronto

My name is Lee Radigan and I am a non-degree student pursuing admittance to the Biostatistics Masters program at the Dalla Lana School of Public Health.  After returning for my 6th year studying statistics at The University of Toronto, I thought that this was a perfect time to reflect on my progress.
Since September, I have been working under Dr. Pascal Tyrrells guidance on a project aimed at helping the Department of Medical Imaging report agreement in their research.  To do this, I created a flow chart to help guide the reader towards the proper method of agreement.  Along with this, I conducted a simulation looking at a specific question pertaining to the Department.
Initially, I was tasked with combing through various papers on the theory of agreement and making sense of all the different published work that was out there.  There are many different approaches and different ways of looking at reporting agreement, so it was quite difficult to figure out when and where to properly use every single approach.  After reading and re-reading each paper, as well as consulting the MiData team, I started to develop a thorough understanding of what agreement was, why it is important to report it, and how to go about reporting it appropriately.
Next, a flow chart was required to summarize what I had learned from the literature.  This was not an easy task, because it forced me to dig really deep and make sure that every node in my flow chart was well thought out and appropriate.  After many iterations and adjustments, I created a detailed chart that walks the reader from their initial research question up to the required agreement statistic.
My final task was to conduct a simulation that would test the question: Can a group of less experienced student raters be as accurate as a smaller set of more experience expert raters?  And if so, how many students?  And under what conditions?  This was a very fun and informative task for me as I was able to conduct my first simulation.  During this experience, my biggest difficulty was justifying my choices of parameters within the simulation.  When conducting a simulation you have freedom to choose how it is going to work, but you must be careful to be able to back up each and every parameter choice.  The simulation ended up showing that: the larger the disparity between the rating errors of the student and expert raters, the more students it takes to match the accuracy of the experts, confirming my intuition.
There are many things that I wish to expand on with respect to my project in future.  I want to create a user friendly app that will be even easier and more compact than my flow chart.  Additionally, I want to try to get my paper published.  To do this I will need to look further into my simulation and consider a more broad range of student/expert scenarios that likely will occur in practice.  I will also need to further refine my definitions and understanding of each concept of agreement.
This year has truly been the best of my life and I can largely attribute that to Dr. Pascal and the MiData team.  I look forward to contributing to Medical Imaging research and to many more learning experiences.
Time to enjoy the summer as I embark on yet another exciting experience as a student Statistical Analyst at the CAMH Nicotine Dependence Clinic as a summer placement!
Lee Radigan

ROP299 2017-2018: A Medical Imaging Journey from a Humanities Perspective

My name is Samantha Santoro, and I am completing my second year in the English and Biology majors at the University of Toronto, St. George. A rather unconventional combination, when reviewing past students of Dr. Tyrrell’s lab. I was a 2017-2018 Research Opportunity Program (ROP) student in Dr. Pascal Tyrrell’s lab, and my work chiefly consisted of evaluating the internal vessel wall volumes of carotid arteries in a particular cohort of patients provided by the ongoing prospective CAIN study. My ROP was in the field of Medical Imaging. I am the co-president of the student club known as Watsi, with the main chapter based in San Francisco. I am also a special contributor to the Rare Disease Review, along with volunteering at an amalgamation of charity walks and fundraisers.

My ROP project was a turbulent experience – although that word is typically associated with a negative connotation, I regard my ROP299Y1 as one of the most humbling, interesting, and educative experiences that I have had thus far – most definitely not negative. However, to say everything went smoothly would be discrediting the lessons I learned from when things were not idyllic and smooth. My project, as aforementioned, statistically analyzed data provided by patients part of the CAIN study (an analysis that could not have existed without Dr. Tyrrell’s generous and unwavering support). My study determined that patients who were found to have IPH, or what is known as intraplaque hemorrhage, when I analyzed their MRIs, were also found to have increased vessel wall volume. This conclusion is incredibly significant, as IPH is a surrogate marker for atherosclerosis and could potentially be an indicator for patients at risk of future cerebrovascular events (namely, ischemic stroke). As strokes are currently the number three killer in the U.S and Canada alone, and heart disease number one, having a potential indicator for patients at risk of stroke would greatly benefit clinicians in their practice, as well as patients themselves.

As aforementioned, studies similar to my own are currently underway by the Canadian Atherosclerosis Imaging Network, furthering the important research in this field. The VBIRG (Vascular Biology Imaging Research Group) was the lab in which I primarily worked throughout the course of my ROP, at Sunnybrook Hospital. Moreover, I also worked on systematic reviews and reports outside of the focus of my project, in the fields of medical ethics and AI in the radiology workplace – both of which were opportunities provided to me by Dr. Tyrrell, and both of which were incredibly valuable experiences, allowing for me to broaden my knowledge of certain areas of medicine and science that are developing and expanding.

Although my project was littered with its own respective difficulties – a substantial number of drafts throughout each step of the program (more than I had ever made, even being an English student); a reluctant, but later fulfilling, acquaintanceship with the post-processing software VesselMass; and several late nights learning about the field of statistics – it is in light of these difficulties, and at present having overcome them throughout my ROP, that I remember Dr. Paul Kalanithi’s words in his memoir When Breath Becomes Air: “It occurred to me that my relationship with statistics changed as soon as I became one”. He, too, had studied Biology and English. I may not have played a lead role in the statistics I had been working with, but I can now say that understanding what they meant and how they were formulated has generated a deep respect in me for the field of statistics.

My poster was on display at the 2018 Research Opportunity Undergraduate Fair. Special thanks to Mariam Afshin, my supervisor at Sunnybrook Hospital; Bowen Zhang, for answering each question I had while at Sunnybrook; John, and the rest of the lab team; and Dr. Pascal Tyrrell, for answering my email last February and holding my interview on the same day as my Chemistry exam. Never before had I met such an – in a word – outstanding professor, and I dare say that I will never meet one like him throughout the rest of my academic journey.

Samantha Santoro

Lessons Along the Way

https://betakit.com/startupcfo-explains-the-long-windy-road-to-a-closed-funding-round/
 
 
With summer almost here, it’s a good time to reflect on lessons learned from the academic year gone by. Since September, I’ve been working under Dr. Pascal Tyrrell’s supervision on a systematic review (SR) project investigating sample size determination methods (SSDMs) in machine learning (ML) applied to medical imaging. Shout out to the Department of Statistical Sciences where I completed my independent studies course! Here, I share important lessons I learned in the hopes that they may resonate with you.
 
Despite being a stats student (as you know from my previous posts!), I was initially new to ML and confronted with the task of critically reviewing theoretically-dense primary articles. I came to appreciate the first step was to develop a solid background – starting from high-level YouTube videos and lessons on DataCamp, to reading ML blogs and
review articles – all until I was confident enough to evaluate articles on my own. For me, the key to learning a complex subject was to build on foundational concepts and keep things as clear as possible. As Einstein once said: “If you can’t explain it simply, you don’t understand it well enough”.
 
Next, it was time to conduct a systematic search. The University of Toronto library staff were especially helpful at guiding me in use of OVID Medline and Embase, databases with methodical search procedures and a careful search syntax relying on various operators. To be thorough, we also sent a request out to the rest of our research team, who hand-searched through their own stash of literature. Along the way, we garnered support from the university, successfully receiving the Undergraduate Research
Fund grant. The lessons for me here? The importance of seeking expert help where appropriate, and that being resourceful can pay off (literally)! Finally, I valued our strong team culture, without which none of this would have been possible.
 
While working on the SR, I also conducted a subsampling experiment using a medical imaging dataset, testing the effect of class imbalance on a classifier’s performance. Hands-on/practical experiences are critical in developing a more nuanced understanding of subject material – in my case, an understanding that translated to my SR.
 
So now you are probably wondering about the results! The subsampling experiment helped us develop a model for the deleterious effect of class imbalance on classification accuracy and demonstrated that this effect was sensitive to total sample size. Meanwhile in our SR, we observed great variability in SSDMs and model assessment measures, calling for the need to standardize reporting practices.
 
That was a whirlwind recap of the year and I hope some of the lessons I learned resonate with you!
 
See you in the
blogosphere,
 
Indranil Balki
 
A special thanks to Dr. Pascal Tyrrell, as well as Dr.
Afsaneh Amirabadi & Team

A Medical Ethics ROP Journey with Jayun Bae

Jayun Bae – ROP299Y 2016-17
My name is Jayun Bae and I am completing my second year in the Neuroscience and Bioethics majors at the University of Toronto, St. George. I was a 2016-2017 Research Opportunity Program (ROP) student in Dr. Pascal Tyrrell’s lab, working on a study that investigated the ethics of sharing patient data with private organizations (see my timeline above). I am a member of the Hart House Debating Club and an events associate for the Life Science Student Network. 
                                                               
My ROP project was necessitated by the partnership proposed by the Medical image Networking Enterprise (MiNE) that would establish a data-sharing relationship between public and private sector organizations. The ethical concerns with the partnership involved patient consent, privacy, and financial gain – but there were also issues that I
uncovered throughout the project. It quickly became clear that the answers could not be found through an examination of precedence or legal documents, because many of the research actions that would take place (specifically involving private organizations) fell in the grey area between what was legal and what was ethical. For example, the Personal Information Protection and Electronic Documents Act (PIPEDA) and Personal Health Information Protection Act (PHIPA) are two guidelines for organizations to follow when handling patient data – but neither are able to clearly and positively dictate how this partnership should operate.
Therefore, I developed a study that would seek expert opinions through the administration of a survey. I conducted interviews at Sunnybrook Health Sciences Centre and the University of Toronto and performed qualitative data analysis. My ROP project was presented at the ROP Poster Fair and the Victoria College Research Day events. The ROP was an extremely valuable experience in gaining research skills, and I’m grateful to
Dr. Tyrrell for the guidance and mentorship. The project is not yet completed, so I am looking forward to continuing the study beyond the scope of the ROP.   
Please have a look at my poster from the 2017 ROP Research Day below:

MRI, Statistics, Carotid Arteries, and 1000 Cups of Coffee with George Wang

GeorgeWang – ROP299Y 2016-17
I’m George. I have recently completed my 2nd year undergrad at the University of Toronto studying physiology and physics. In the fall-winter term of 2016-17 I had the privilege to work in Pascal’s group, looking into carotid artery MRI and using the volume of the carotid artery vessel wall as a marker for atherosclerosis. Having an acquired interest in medical imaging and a previous summer position working with PET, I saw this as an excellent opportunity to expand my knowledge of the field while having the chance to be exposed to clinical research methods. Above is my account of how the year went in a nutshell.
 
Have a look at my poster from the ROP Research Day below…
 
 

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.

Back to Basics… Midpoint Thoughts from an ROP Student

Reaching new heights? (Source: NYT)

Through the ‘Research Opportunity Program‘ (ROP) for second year students at U of T, I have been working on a project about physicians’ willingness to use MRI as the front-line diagnostic imaging technology for carotid stenosis patients. For a description see here.

After a recent discussion with Dr. Tyrrell (my supervisor), and as I approach the midpoint of my ROP project, I thought it would be a good idea to review some of my background knowledge of carotid stenosis from my work in the Fall term. Having a certain amount of independence while working on this project has been a great experience, but it also means I am responsible for keeping track of my own learning.


So, during the first week of January, I took out my notes, my Physiology textbook, and several articles in order to compile what I have learned so far and highlight areas that need further review.

Review in process!

Begrudgingly, I’ll admit that this ‘self-directed’ review process has shed new light on the usefulness of midterms in other courses. However, I still prefer this project-based review format. It has allowed me to review necessary information to make sure that it is fresh in my mind. Now I feel more prepared to begin the second half of the project. I’m looking forward to a major meeting this month and all the other exciting parts of the project to come.


Julia Robson

Ethics Schmethics?

 

Today, it may seem obvious that the first step of any research project should be to complete a proposal for ethics review. But why do we need ethical standards? While helping to complete an ethics form for a project I’m working on, I wondered if scientists perhaps made more ‘progress’ before ethical considerations became commonplace. Even if this was the case, research is certainly better now, when institutions and procedures protect patients’ and research subjects’ rights. 

It also seems that scientific research in the 18th and 19th centuries tended to be somewhat more haphazard than it is now, and almost certainly less ethical. For example, Dr. Edward Jenner tested his smallpox inoculation hypothesis for the first time on an eight-year-old
boy in 1796, with little preliminary understanding and no certainty that the patient would not be severely harmed.

Scientists were often fairly independent, acting based on their own curiosity to advance knowledge. Fortunately, research standards have evolved significantly since then. Ethics have been a major part of the transition, as ethical standards help to ensure that scientific research does not cause harm to researchers or subjects. The shocking Stanford Prison Experiment, just one example, shows that physical and psychological damage can occur if study participants’ rights are not upheld through ethics. College students with no criminal record were asked to play the role of prisoners and prison guards, the ‘guards’ became brutal and cruel, while the ‘prisoners’ became stressed and depressed. The experiment was terminated early, after only six days.

Fortunately, much has changed since the emergence of modern science in the 20th century. The current structure of research, including working in teams and undergoing peer review, helps to ensure a high standard of practice. Nevertheless, ethical issues in science remain. Researchers who work with human participants can become quite focused on the minutiae of their work, so Research Ethics Boards have an important mediating role. They provide an experienced, unbiased viewpoint that weighs the potential benefits of the research against any harm that may come to participants. Even if an ethical review sometimes slows the pace of scientific progress, it provides an essential foundation and structure for research, to the benefit of participants and researchers alike.  





Julia Robson

2nd year student at U of T