Mr Epidemiology

No, I'm not a skin doctor


better know an epidemiologist

Hot time summer in the city (Legionnaires Disease)

1976 was a busy year in Philadelphia. They were holding the Bicentennial celebration, commemorating the two-hundredth anniversary of the Declaration of Independence. As part of the year-long festivities, the city had become a hub for events, hosting the championship game of the NCAA Final Four, as well as the all-star games for baseball, basketball and hockey. On the 4th of July, around 2 million people descended on the city for the celebrations, which featured a five hour parade with over 40,000 marchers and floats from every state. But it was to be a small, 2000 person event that would go down in history.

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Image courtesy Flickr user DaveZ

Going to #CPHA2014

The 2014 CPHA conference will be held in Toronto, ON | Picture courtesy Wikimedia

Next week, I (Atif) will be heading to the Canadian Public Health Association Conference, where I’ll be presenting at two different points.

I’ll be chairing a session titled “Youth Injury Prevention in Canada – Where should we direct our intervention resources.” It promises to be an interesting presentation, where we’ll be discussing injury in Canada, and where to start tackling the problem of injury. This session is scheduled for Wednesday, May 28th from 1:30pm – 3:00pm.

Injury represents one of the most important negative health outcomes experienced by young people in Canada today. Injuries inflict a large burden on children and adolescents and their
families and communities. Injury events are costly in so many ways, whether measured in premature mortality, or the pain, disability, lost productivity and emotional consequence of non-fatal events.

This panel will be made up of child injury researchers and advocates who will make their case for different forms of injury prevention intervention. At the end of this panel, delegates will: understand more about the burden of youth injury in Canada; be aware of at least four different avenues for injury prevention intervention (primordial intervention, context-level interventions, safe sport and peer-influence interventions); have identified the rationale, strengths and limitations of each intervention approach; and have learned more about ways to undertake and gain support for youth injury prevention (from the CPHA conference program).

Click to go to the conference website

My second presentation is one of the studies from my PhD, titled “The influence of location of birth and ethnicity on BMI among Canadian youth.” This is a study that’s in press (woo!), and represents my own research focus. This one will be in the Kenora Room, on Thursday May 29th 2014, from 11:00am to 12:30pm.

Body mass indices (BMI) of youth change when they immigrate to a new country. This occurs by the adoption of new behaviors and skills, a process called acculturation.

We investigated whether differences existed in BMI by location of birth (Canadian vs foreign born) across 7 ethnic groups, both individually and together. We also examined whether time since immigration and health behaviors explained any observed BMI differences.

Data sources were the Canadian Health Behaviour in School-Aged Children Study and the Canada Census of Population. Participants were youth in grades 6-10 (weighted n = 19,272). Sociodemographic characteristics, height, weight, and health behaviors were assessed by questionnaire. WHO growth references were used to determine BMI percentiles.

Foreign-born youth had lower BMI than peers born in Canada, a relationship that did not decrease with increased time since immigration. Similarly, East and South East Asian youth had lower BMI than Canadian host culture peers. Finally, Arab/West Asian and East Indian/South Asian youth born abroad had lower BMI than peers of the same ethnicity born in Canada. These differences remained after controlling for eating and physical activity behaviors.

Location of birth and ethnicity were associated with BMI among Canadian youth both independently and together.

Our findings stress the importance of considering both ethnicity and location of birth when designing and implementing interventions. While currently either one or the other is addressed, our study shows there is heterogeneity in BMI by specific ethnic groups depending on whether they were born in Canada or not.

As always I’ll be trying to livetweet the conference. I’ll be using the #CPHA2014 hashtag, so feel free to follow along online! As always, there are a wide range of presentations and workshops, so I’m excited to attend.

If you’re attending the conference, leave a comment with details of your own presentation so that other readers can attend your talks. And if you see me at the conference, be sure to say hi!

This was posted simultaneously on my blog PLOS Blogs Public Health Perspectives

So you want to be an Epidemiologist…

Last week, my Gradifying co-author Amanda highlighted how her degree is structured. Today, I’ll be talking about the degrees offered by the Department of Public Health Sciences.

There are six factors that differentiate programs: the degree structure, courses, comps, research project requirements, teaching and timelines.


The degree itself

In my program, research projects are wildly different in terms of substantive research area, and students come in with very different backgrounds. My lab buddy in my Masters had a degree in engineering, I had a background in Psychology, another colleague had a degree in political science. With these different interests comes different theses. I’ve seen students do molecular projects that are most similar to biochem/bio projects, students who have either obtained or are in the process of obtaining their MD that are clinical in scope (note: clinical research projects are also performed by non-clinicians), and then there are projects like mine that draw heavily from psychology and sociology. The intricacies are driven by the interests of the student and the supervisor. There is also the Master’s of Public Health program that is a course-based, professional degree offered within the Department of Public Health Sciences.


Courses requirements

For the MSc in Epidemiology program, students have to take 4 core courses, and 3 elective courses. Usually, students will complete all but one elective in their first year, and will take one elective in their second year. Core courses include biostatistics and research methods, both of which become vital to your career as an epidemiologist. In addition to this, they are expected to complete a Masters Research Thesis.

The Masters of Public Health program is structured as a professional program where students get a broad background in public health. Students in this program take seven core courses and three electives, as well as a skills class (that I have guest lectured). Finally, they complete a 16 week practicum over the summer after their first year.

The PhD is completely different. We have one full-year seminar course, and one advanced biostatistics course. The course requirement is relatively light in that regard – if you want further, specific, training, you can seek that out yourself.



As I walk through the valley of the shadow of comps, I will fear no evil …

In the PhD Epi program, comps are scheduled to occur in the summer of your first year. They consist of a 4 hour open-book written exam that covers basic epidemiology principles. Following this, you are given a paper in your substantive area, and given two weeks to prepare two presentations. This forms the oral exam portion of the comps process, and is given to three professors in the department. For the first, the candidate is expected to present a 20 minute presentation where they summarize and critically evaluate the paper. Following this, they are asked questions about the paper and how the authors evaluated core epidemiology concepts. The second part of the exam requires the student to design and present an appropriate follow up study, addressing the shortcomings of the previous paper. The process takes between 90 minutes and 2.5 hours.

Typically, comps occur in late-June to early-July. The cohort of PhD students will typically study together from around April onwards, and there’s a certain solidarity that develops from going through this process together.


Research Project Requirements

For the MSc Epidemiology program, students are required to submit a 2 page outline of their project. Upon approval of the outline, they then prepare and submit a 20 page proposal. The proposal forms the basis of an open oral defence, where peers can ask questions. There is also a designated faculty member who acts as a reviewer for the project. Once the student passes their oral proposal defence, they can then continue with their project. Finally, they have a Masters thesis defence, where they present their work to an examining committee, consisting of 1) a professor external to the department, 2) one internal to the department, and 3) the department head (or someone in their stead).

The PhD in Epidemiology follows a very similar process, except everything is bigger. Students submit a 5-6 page outline, followed by a 20 page proposal of the project. Again, the proposal is followed by an oral exam, with two faculty members acting as reviewers as opposed to one in the Masters program. Once approval has been granted, the candidate now proceeds with their project, culminating in a PhD dissertation. This is defended to a committee consisting of a professor external to Queen’s in addition to the members of the Masters defence committee.

At both the outline and proposal stage, students are given feedback that they can consider with their supervisors as they move forward. Due to the variability in projects, there are no expectations around the number of manuscripts that you should produce, although I’ve seen Masters students produce 1-2 from their thesis work, and more if they did RA work. Doctoral candidates aim for 3-4 core manuscripts, and again, produce more if they work as an RA. These can be written while in the program, which results in a “manuscript-style” thesis (see mine here), or a “traditional” thesis, where, after defending, the student will prepare manuscripts for publication. My Masters was a manuscript based thesis, and my PhD will be as well, but this really varies on the project and whether this is feasible for you. My PhD fits nicely into four self-contained projects, and so publishing as I go was the best way to approach my PhD (you can read more about the first study from my PhD here, and the Queen’s press release here).


Teaching and Supervising

There’s no undergraduate program in epidemiology, and so teaching opportunities are limited. That being said, there are lots of opportunities to be a TA for graduate courses, and there are undergraduate courses that are offered. Many of the TA positions include opportunities to lecture and lead small group tutorials, which makes them a lot of fun and rewarding. Perhaps the most fun is the ability to really tailor your tutorials and classes to your own style and interests – I’ve taught several classes using data from the NHL to illustrate basic statistical concepts (what are the average number of goals scored, what’s the modal number of goals scored, why are they different).



This is really left up to the student and supervisor – the department asks for progress reports by semester, but the onus is on the student and the supervisor to stick to the timelines set out in the proposal. I meet with my supervisors as required, and so we have gone 2-3 months without meeting in person if I’ve been working on a specific aspect of the project, and more often if I need feedback from them as I’m working through something. However, we touch base by email often, and this works well for us. Your mileage may vary – other students and supervisors work best with regularly scheduled meetings.


So while this is my experience in graduate school, I would suggest meeting with the department and potential supervisors if you are interested in joining the Department of Public Health Sciences. These are some of the core requirements and expectations, but these do change over time, and so if you’re finding this a year or more from now, be sure to check what the current requirements are.


This post was originally published on Gradifying

Life in Grad School: A day in the life of Atif

The editorial staff at Gradifying decided that this month we would describe our experience in graduate school, especially given how different our experiences are. Last week, Amanda discussed her experiences as a graduate student, describing her “field season” and “the outdoors” and “early mornings.” My life is completely different. While Amanda spends her days knee deep in mud, I spend mine exploring databases. While Amanda is taking an ATV through abadoned fields and forests, I’m traversing the internet for PDFs and programming code. While Amanda is worried about mosquitos and horseflies, my biggest health concern is bad posture from being hunched over a keyboard all day.

My desk: Where the science happens!
My desk: Where the science happens!

So lets talk about a regular day for me. Three of my projects use data housed at KGH that I can access 24/7, and so my schedule is completely up to me. There are no external forces at work – I can work all day and all night if I want to, or I can leave for weeks at a time. The only limitation is that I can’t take my data off site, and so I need to work in my office. As you can imagine, this means I have to be SUPER DISCIPLINED. When nothing mandates I be in the office, I have to be that force. While many people would hate working with data all day every day, I love it. Trance/techno/dubstep (courtesy, a large double-double and a database? That’s a pretty awesome day in my books.

In addition to my main database, this year I started working with another database housed at the Research Data Centre (RDC) at Stauffer Library. The RDC is an excellent resource for those interested in using Statistics Canada data, and provides you access to very detailed data about the health and behaviours of the Canadian population. However, this level of information comes with serious security. Since the data available have individually identifying information available, you need Government of Canada Security Clearances to access these data. The Centre is not connected to the outside world through the internet, so if you don’t know something, you have to leave the facility to check or Google it. Finally, no electronics are allowed inside the RDC, which includes MP3 players. So if you’re one of those people who likes to listen to music while they work (see trance music comment above), you can’t unless you can get your hands on a Walkman or Discman somehow. In addition to these levels of security, the Centre is only open from 10am to 4:45pm Tuesday through Thursday. So when it’s open, you need to maximise your time there.

Simba and the Happy Hack(ey sack) give me company while I'm analyzing data.
Simba and the Happy Hack(ey sack) give me company while I’m working.

One thing I decided when I started my PhD was that I never wanted to bring work home. I’ll work late in the office, but, to paraphrase the great urban poet Kei$ha, once “I leave for the night, I ain’t coming back.” So I settled into a pattern of working from 9am to 5/6pm in the office every day, then hitting the gym and heading home, thus leaving my evening free for writing, watching sports (Go Sens! Go Texans!), whatever I want. I’m fortunate in that I can treat my PhD like a job, and can work those hours. The only time I’ll bring work home is if I have a presentation, and then it’ll just be practising it once or twice in the evening in my living room to see how it flows. One suggestion for those who need motivation to go to the gym: Purchase “greys” from the ARC. For around $18 /month, you get your own locker, as well as clean socks, shorts, t-shirt and a towel from the gym every time you go. If you leave shoes there, then there’s really no excuse to not go to the gym. You just show up and it’s all there. I highly recommend it.

Lego Batman reminds me that EVERYTHING IS AWESOME!
Lego Batman reminds me that EVERYTHING IS AWESOME! (except for the angle of this photo, which I can’t figure out how to rotate) (Thanks Kim!)

Outside of grad school, I keep myself busy with various other activities. As you know, I write for Gradifying, but I also am the Editor for PLOS Blogs Public Health Perspectives as well as a Science Writer for PLOS Blogs Sci-Ed. The former focuses on Public Health and issues related to the health of societies, while the latter is focused mainly on science communication – how do we, as scientists, communicate to the public and explain complex ideas in ways that resonate with them. When I’m not writing, I’m usually playing ultimate frisbee through Kingston Ultimate, which takes up most of my free time through the spring/summer, between practice, training and games. If you’re ever walking through City Park on a Sunday morning and see a bunch of people doing laps, wind sprints and various other crosstraining activities, that would be us.

If you have any questions, let me know!


This piece was originally published on Gradifying!

Book Review: Deadly Outbreaks: How Medical Detectives Save Lives Threatened by Killer Pandemics, Exotic Viruses, and Drug-Resistant Parasites

Deadly Outbreaks: How Medical Detectives Save Lives Threatened by Killer Pandemics, Exotic Viruses, and Drug-Resistant Parasites | Click image to go to CSTE website

Anyone who follows my writing knows that I’m a big proponent of using stories to talk about science. We’ve discussed how you can use science fiction teach science, zombies to talk about disease outbreaks, and my TEDx talk discussed using principles of storytelling in how we discuss science. So when I was asked to review (see disclaimer below) Dr Alexandra Levitt’s new book “Deadly Outbreaks: How Medical Detectives Save Lives Threatened by Killer Pandemics, Exotic Viruses and Drug-Resistant Parasites,” I jumped on the opportunity.

The CDC has a program known as the Epidemiologic Intelligence Services, where individuals trained in fields such as epidemiology, medicine, statistics and veterinary sciences come together to identify causes of diseases. For an overview of the EIS, check out this review of “Inside the Outbreaks” by Travis Saunders over at Obesity Panacea. The EIS was set up Alexander Langmuir, who has been profiled on the blog, and their work has been instrumental in learning about, and thus containing, disease outbreaks all over the world. Dr Levitt is well positioned to speak on these issues, having worked at the CDC since 1995, although it should be noted that this was written in her free time, not as part of her position at the CDC.

To continue reading, click here!

Featured Interview with the Queen’s University School of Graduate Studies

Friend of the blog Sharday Mosurinjohn recently interviewed me for a profile on the Queen’s University School of Graduate Studies website. The first paragraph of her (very flattering) interview is below, and follow the link provided for the whole thing.

Atif Kukaswadia – AKA Mr. Epidemiology – is here to help you understand the science that’s important to your life. As a PhD candidate in Queen’s Department of Public Health Sciences and a science writer for the Public Library of Science (PLOS) blogs network, Kukaswadia is immersed in creating and reporting on scientific knowledge of direct relevance to the public, and he wants to share the wealth.

Kukaswadia moved to Canada in 2002 with his family from the UK. He started his undergraduate degree in Biology at Carleton University, where he focused on ecology and studied caterpillars, butterflies and mud shrimp. The thing Kukaswadia most enjoyed about ecology was how “everything was interconnected – you never study one squirrel in isolation. You study the whole environment and how elements of the environment interact.”

While he enjoyed Ecology, he realized that studying butterflies and caterpillars wasn’t for him. So he started a second degree in Health Psychology. Using his background in ecology, he began looking at humans the same way he had been trained to look at non-human animals and, specifically, at how the environment affects humans. This combination of interests led him to Queen’s, and the Department of Public Health Sciences.

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Guest Post: Dear (Food) Diary …

Mr Epidemiology: Today, I’m welcoming Natalie Causarano to the blog. You can find out more about Natalie at the end of this post.

The summer is finally on its way, bringing us BBQs, cottages, and …wait for it…the often dreaded BATHING SUIT SEASON! That moment of truth when we must face the effects of our winter hibernation (which might make us want to stay in hibernation).

Vanity aside, the benefits of maintaining a normal weight is a long-championed public health message. Yet the combined effects of increased portion sizes and our increasingly sedentary lifestyle are making it difficult for us to maintain a healthy weight. So, where should we start to lose? The diet industry seems to be growing as fast as the obesity epidemic and the price of weight loss products is even more discouraging.

One inexpensive weight loss strategy is to self-monitor with a food and / or exercise diary, which has been found to be an effective weight loss strategy by numerous studies (1). I know what you’re thinking, there’s no more room in your purse or murse for a food journal!

Fear not, the internet has the solution!

Continue reading “Guest Post: Dear (Food) Diary …”

A Mr Epid-inar: 3MT – The Three Minute Thesis Contest!

Mr Epid-inar’s are short talks delivered by Mr Epidemiology at various venues; classes, conferences, speaker series’ etc. They should not be confused with the leafy green vegetable (French humour! Le woohoo!)

3MT is a public speaking contest started at the University of Queensland back in 2008. In three minutes, you have to describe your PhD and why it is important. You are judged on your communication style, comprehension and how well you engage the audience. Oh, and you are only allowed one (static) PowerPoint slide. Recently, Queen’s University decided they wanted to host a 3MT contest, and send out an email asking for participants.

Well, that sounds difficult. And a little ridiculous – I’m supposed to condense my PhD into 3 minutes, without any slides, and still do it justice?

Very well. Challenge accepted!

3MT Talk from Mr Epidemiology on Vimeo.

Some thoughts on 3MT. I found the contest to be absolutely incredible. As an audience member, the presentation aspect was fun and novel, and I probably learnt more about what my colleagues were doing in that 90 minute session than I have in the last 2 years I’ve been at Queen’s. The variety of research was great, and because people were told to make it accessible for those outside of their area, they really worked hard and making the concepts clear. I think this, combined with PechaKucha 20×20, are great ways to break up the existing research paradigm and inject some life and energy into conferences.

As a presenter, I found the experience invaluable. Being forced to really ask what is important for the audience to know helped me distill my thesis down to its core components. Also, trying to come up with an exciting and novel way of presenting it was fun. If you have the opportunity to enter a 3MT contest near you, I strongly recommend doing it!! If you’ve been to a 3MT talk, let me know your experiences in the reply!

Special thanks to Anne G, Lindsay K, Kim F, Raymond F, Katie K, Rebecca B, Julia N and the rest of the Clinical Research Centre for their feedback on previous drafts of my 3MT talk. Also thanks to Jess S, Michelle D, Alison Y and all my Epi and Kinesiology friends who showed up to support me on the day. Finally, thanks to Colette Steer and all the organizers and judges of the 3MT contest!

Congratulations to Dylan Wykes, M.Sc (Epidemiology) for qualifying for London 2012!

Dylan Wykes qualified for the Olympics after crossing the finish line with a time of 2:10:47!! Way to go Dylan! Photo courtesy Alan Brooks

They say graduate school is not a sprint, it’s a marathon. Dylan Wykes might have something to say about that.

Dylan is a graduate of the Queen’s University M.Sc. Epidemiology program, and a marathon runner. He just qualified for the London 2012 Canadian Olympic Team with a phenomenal time of 2:10:47.

We’re all incredibly excited for Dylan, and will be cheering him on when he goes to London this August to represent Canada at the 2012 Olympics! Way to go Dylan!!

You can follow Dylan’s adventures on Twitter, or at You can also help support Dylan’s training at Runner Choice Kingston.

History of Epidemiology: Patient Zero and Typhoid Mary

ResearchBlogging.orgBetter Know An Epidemiologist/History of Epidemiology is an ongoing feature where Mr Epidemiology pays tribute to people and studies that have set the stage for his generation of epidemiologists. All of the articles are listed here.

Gaetan Dugas, Air Canada flight attendant and one of the first diagnosed cases of HIV

EDIT 10/01/12: I had indicated (incorrectly) that Typhoid Fever was a viral disease. It is in fact due to a bacterium instead. Thanks to Mike the Mad Biologist for pointing that out!

EDIT 10/01/12: As Brett Keller points out in the comments, Gaetan Dugas was not Patient Zero for HIV. While he contributed to the spread of the virus, he wasn’t the first known case of it, and so the label of Patient Zero is unfairly applied to him.

Patient Zero is a common infectious disease epidemiology term. It refers to the first known case of the disease of interest, and is useful when tracking disease outbreaks. Knowing where the disease starts allows us to track not only the spread of the disease, but also how it spreads – through water, air, person-to-person contact etc.

I heard an absolutely phenomenal podcast through WNYC’s RadioLab podcast about Patient Zero, and that formed the inspiration for this post. I highly recommend listening to it when you have a chance – either through iTunes, on their website. They cover several different “Patient Zero’s,” including Typhoid Mary and Gaetan Dugas (pictured above).

Today, I’ll be talking about Typhoid Mary. To listen exclusively to the Typhoid Mary segment of the RadioLab podcast, click here.

Click the image to go to the RadioLab podcast about Patient Zero.

Continue reading “History of Epidemiology: Patient Zero and Typhoid Mary”

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