Category: Student Experience

Parent category for student posts

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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

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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:
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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…
 
 
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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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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

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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
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All the World’s a Stage

For journalists, authors, bloggers and tweeters, sharing articles has never been easier. Indeed, the public expects to be able to read articles about world events almost in real-time. For example,
the New York Times Twitter account was updated nine minutes ago, and National Geographic tweeted three minutes ago. This expectation of speediness applies equally to scientific advances as it does to international affairs.
As an avid reader of online news, I would be the last to complain about being able to access such a vast amount of information. But there is something particularly noteworthy about information presented by a visible human. Perhaps that explains the persistence of televised news in the age of Twitter. 

Maybe it also explains the popularity of other media sources like TED talks, which often explain complex ideas in an engaging and understandable format. A personal favourite is “The best stats you’ve ever seen” by Hans Rosling. In his talk, Rosling explains the importance of little-known global public health data that shows the progress (or lack thereof) made by different countries over the past few decades. 

A more recent talk on a similar topic is also informative. One would be hard-pressed to find a paper or article that presents the same information with as much clarity and appeal.

In addition to numerous (maybe too numerous?!) TED talks, I have recently experienced the value of human-to-human information transfer. At the beginning of my ROP project in September, I was lucky to be able to hear about previous students’ research in person. I think it helped address the complexity of the work, but also conveyed its importance and the effort that had gone into it. Thanks Kiersten!
I’m not sure if information is generally more effective this way, but it is almost certainly more memorable. In any case, it has definitely worked for the 3.5 million subscribers to CrashCourse’s YouTube channel, where one can learn about anything from astronomy to macroeconomics.
For me, learning more about how researchers give and receive qualitative information to and from their subjects has allowed for a more well-rounded understanding of information transmission in the digital age.  But I think researchers andthe media have a lot to learn from each other. Communication is key for both, so understanding how others best absorb and respond to information can be instrumental.
That’s all for now, Julia!
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Kiersten Thomas – Summer 2015 ROP at UofT: Another great student experience… part deux!

Kiersten Thomas – ROP summer 2015

Hello, I’m one of Professor Pascal Tyrrell’s summer ROP students and a second year Immunology Specialist student at the University of Toronto. I have just completed my summer research project investigating the cost-effectiveness of using MRA to evaluate asymptomatic carotid artery stenosis. 


I learned a lot and had an amazing time conducting research with Dr. Eli Lechtman and my ROP partner Indranil Balki. Using TreeAge Pro to create and analyse decision trees, we demonstrated that the additional information gained from an MRA/IPH scan increases the effectiveness of MRA when imaging carotid artery stenosis. 


Our research suggests that the additional information of the presence of intraplaque hemorrhage (IPH) would lead to better patient care, reducing long-term stroke risks. This means that MRA/IPH can be cost-effective or even dominant when compared to the current imaging strategy that uses standard ultrasound as a first-line imaging modality, for evaluating all degrees of asymptomatic carotid artery stenosis. Take a look at my timeline to see some of the highlights of my summer!


Thank you Dr. Pascal for this wonderful summer. 


Kiersten Thomas

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Indranil Balki – Summer 2015 ROP at UofT: Another great student experience!

Indranil Balki – ROP Summer 2015

 

I am one of Dr.Pascal’s 2nd year ROP students at the University of Toronto.  This summer, I had an amazing experience into the realm of research working with my partner Kiersten Thomas, mentor Dr. Eli Lechtman, and supervisor Prof. Pascal Tyrrell. This timeline-cum-infographic highlights some of the especially memorable moments of this journey.
Our main project was focused on constructing a computer simulation to model the effect of choosing either MRI or US as a first line imaging modality to diagnose and treat patients with Carotid Artery Disease. This project involved comprehensive literature search, discussions with experts (including the “Trip to Cambridge”), learning computer software and presentations!
Our team’s models’ main finding was that MRI can be both more effective and no more costly than US as a first line diagnosing tool in measuring carotid artery disease.
 

Thanks to Dr. Pascal for allowing me to share my experience on his blog and I hope you enjoy the read!
 
 
Indranil Balki