Announcing September BEMC Talk

Dear Berlin-area Epidemiological Methods Enthusiasts,

You are invited to our next BEMC Talk on Wednesday, September 4th. Please note the location — CVK, Forum 3, Hörsaal 3, 13353 – Campus Virchow Clinic. 

BEMC Talk: Wednesday, September 4th, 2019 @ 4pm

“An introduction to precisely and ggdag: Tools for modern methods in R” – Malcolm Barrett, California

  • Please register online:
  • Description: “Modern epidemiology gives us insight into study planning and causal inference, but the success of these approaches require friendly and accessible software. I will discuss two R packages for modern methods in study design and causal inference: precisely and ggdag. precisely is a study planning tool to calculate sample size based on precision rather than power. Calculating sample size based on precision focuses on the width of the confidence interval instead of statistical significance. precisely is a fast and flexible R implementation of the work by Rothman and Greenland on this subject, including a Shiny web app for calculating sample size. ggdag is a toolkit for working with causal directed acyclic graphs (DAGs), a central tool in causal inference. DAGs help identify many types of bias, such as confounding, selection bias, and measurement error, as well as tell us how to correct for it. ggdag makes it easy to create, analyze, and plot DAGs in ggplot2.
  • **Location change: CVK, Forum 3, Hörsaal 3, 13353 – Campus Virchow Clinic

Upcoming Berlin Epi Events:

  • September 18th – BEMC JClub – Paper posted online
  • October 2nd – BEMC JClub – Paper will be posted online
  • Wednesday, October 23rd – IPH Lecture Partner event– John Gill from Vancouver
    • Charite Mitte Campus, COO starting at 4pm
  • November 6th – BEMC Talk – “The causes of the causes in context: confronting the burden of proof in lifecourse and social epidemiology” – Michelle Kelly-Irving, Toulouse
  • November 20th – BEMC JClub – Paper will be posted online
  • December 4th – BEMC Talk – Uwe Siebert, Hall in Tirol
  • December 18th – BEMC JClub – Paper will be posted online

Interested in other Institute of Public Health events? Visit our calendar to check out upcoming conferences & short courses!

Follow BEMC on Twitter and leave questions for our speakers: @BEMColloquium

Announcing September BEMC Talk

Dear Berlin-area Epidemiological Methods Enthusiasts,

We hope you had a great summer break!
We look forward to seeing you again at our September BEMC Talk in a few short weeks…
BEMC Talk: Wednesday, Sept. 4th, 2019 @ 4pm ·

“An introduction to precisely and ggdag: Tools for modern methods in R” -Malcolm Barrett (US)
**IMPORTANT: Location change: Forum 3, Hörsaal 3, Campus Virchow Klinikum (CVK) in Berlin-Wedding, 13353** ·
Please register here

Description: “Modern epidemiology gives us insight into study planning and causal inference, but the success of these approaches require friendly and accessible software. Malcolm will discuss two R packages he has developed as tools for implementing modern methods in study design and causal inference: precisely and ggdag. precisely is a study planning tool to calculate sample size based on precision rather than power. Calculating sample size based on precision focuses on the width of the confidence interval instead of statistical significance. precisely is a fast and flexible R implementation of the work by Rothman and Greenland on this subject, including a Shiny web app for calculating sample size. ggdag is a toolkit for working with causal directed acyclic graphs (DAGs), a central tool in causal inference. DAGs help identify many types of bias, like confounding, selection bias, and measurement error, as well as tell us how to correct for it. ggdag makes it easy to create, analyze, and plot DAGs in ggplot2.”

Other upcoming Berlin-area epi-related events:
Sept. 18th BEMC JClub article posted here ·
Early Oct no BEMC Talk!
Join us for the IPH lecture on Oct. 23rd · “Understanding and communicating risk of rare but serious health complications – an example from living kidney donation” – John Gill (Vancouver) ·
Oct. 16th, BEMC JClub article posted here ·
February 20-22nd, 2020: REWARD/EQUATOR Conference in Berlin (co-hosted by BIH-QUEST). Details & abstract submission here: https://www.reward-equator-conference-2020.com/

July Talk: Student summary

“Thick” and “Thin” Branches in Epidemiology – a Student Summary from Ana Sofia Oliveira Goncalves

On the 3rd of July 2019, Suzanne Cannegieter held a lecture on ““Epidemiology as a Toolbox to Benefit the Patient”. She graduated as a MD, did a PhD focused on anticoagulant therapy in patients with artificial heart valves, and then completed a Masters in Epidemiology. Throughout her career, she has done numerous studies focused on venous thrombosis. During her lecture, she used venous thrombosis examples to clarify her toolbox, this toolbox can be applied on other diseases as well. She started by highlighting the difference between “thick” and “thin” branch research using a tree as a metaphor. In thick branch research, discoveries are scientific relevant but with little clinical effect. Many other discoveries can come from thick branch research as it leads to further unanswered questions. On the other hand, thin branch research is clinically relevant but holds little scientific influence. Compared to thick branch research, thin branch research is more relevant for patients. She used venous thrombosis as an example for the main study design types: case-control studies, matched case-control studies, self-controlled case series and RCTs. She pointed out that for “thicker” studies, case-controls are the most appropriate study designs, while for “thinner” studies, RCTs are the best option. During the discussion, participants questioned Suzanne whether research can both be “thick” and “thin”, to which her answer was positive. She thinks that it is ideal to be a specialist in a specific disease and a generalist in terms of methods. She also mentioned that scientific research follows trends and some study designs are used less often compared to others.

Announcing July BEMC Talk

Dear Berlin-area Epidemiological Methods Enthusiasts,

You are invited to our next BEMC Talk on Wednesday, July 3rd.

BEMC Talk: Wednesday, July 3rd, 2019 @ 4pm

Title: “Epidemiology as a toolbox to benefit the patient” – Suzanne Cannegieter, Leiden, Netherlands

  • Please register online: https://docs.google.com/forms/d/e/1FAIpQLSf55CFowWvqWsFVlITF8DrGP0aMBj9XbhrOphPx3xSmL9IFMQ/viewform?usp=sf_link
  • Description: “In this lecture, I will discuss how the methods and techniques that we have learned as epidemiologists are applied to many different aspects of medical science. It is, however, not always clear how individual patients benefit from the large number of studies that are performed. From examples of my own research and the literature I will demonstrate how such knowledge eventually evolves from etiologic research into risk factors, via prognostic research in which all this knowledge is combined, toward therapeutic research in which optimal preventive or treatment strategies are developed. Finally I will discuss some pitfalls, and the effects they can have on this type of epidemiologic research.
  • Location: Seminar room 3 (of the Neurology Clinic); Bonhoefferweg 3 entrance, Charité – Campus Mitte

Upcoming Berlin Epi Events:

  • July- no JClub!
  • August 2019 – no BEMC Talk or JClub
  • September 4th – BEMC Talk – Malcolm Barrett **Location change for September BEMC Talk: Campus Virchow Clinic**
  • September 18th – BEMC JClub – Paper will be posted online
  • October 2nd – BEMC JClub – Paper will be posted online
  • Wednesday, October 23rd – IPH Lecture Partner event– John Gill from Vancouver

Interested in other Institute of Public Health events? Visit our calendar to check out upcoming conferences & short courses!

Follow BEMC on Twitter and leave questions for our speakers: @BEMColloquium

June JClub

Don’t miss our June JClub! As usual, it will be held at 4pm on the 3rd Wednesday of the month in the usual location (Bonhoefferweg 3, Charité Campus Mitte Berlin, Neurology Seminar room).

June 19th

  • Tipton E, Pustejovsky JE, Ahmadi H. A history of meta-regression: Technical, conceptual, and practical developments between 1974 and 2018. Res Synth Methods [Internet]. 2018 Dec 27. https://www.ncbi.nlm.nih.gov/pubmed/30589224

PS: BEMC fashion is really taking off! 😉

bemcfashion

Announcing June BEMC Talk

Dear Berlin-area Epidemiological Methods Enthusiasts,

You are invited to our June BEMC events:

BEMC Talk: Wednesday, June 5th, 2019 @ 4pm

  • “Cool new applications in R for epidemiologists: optimize your programming”– Jochen Kruppa (Berlin)
  • Please register here
  • Description: ““The programming language R was original invented and written late in 1993. Since then, many new applications and packages have been added to the core code of R. The R Studio environment has been developed and helps the users to code in R. Still, R sometimes seems to be slow and very unstructured. The problem is twofold. First, young R scripts should be compatible with old R scripts, written a long time ago and second, users are not able to improve the R core code but to add packages to the R environment. In my talk, I will give an overview of the new implementations of faster and efficient programming in R. The focus will not be on pure applications, such as loading packages or running analyses; instead, I will focus on the crafting of R programming. Nowadays, R offers the possibilities to pipe code through functions and allows us to run parallel calculations in an easy manner. Writing and reading of code into R from different sources is very easy and can be plugged into the tidyverse. The talk will give a broad overview, introduce the R packages, and offer code chunks. The Rmarkdown script of the presentation will be sent to the audience. In an ideal world, you will be able to program better and have new ideas to improve your code after participation in my BEMC Talk.”
  • Location: Seminar room of the Neurology Clinic; Bonhoefferweg 3 entrance, 3rd floor, Charité – Campus Mitte

BEMC JClub: Wednesday, June 19th, 2019 @ 4pm

  • Paper will be posted online by June 1st
  • Location: Seminar room of the Neurology Clinic; Bonhoefferweg 3 entrance, 3rd floor, Charité – Campus Mitte

Other upcoming Epi happenings in Berlin:

  • July 3rd – BEMC Talk – “Pragmatic trials and lessons from venous thrombosis” – Suzanne Cannigieter, Leiden
  • July 19th – BEMC JClub
  • August – Summer Break – check out the summer 2019 BSPH short courses in advanced epi methods, medical informatics, applied digital health and mastering R.

 

Check out our website (bemcolloquium.com) for the full schedule of all BEMC JClub and Talk events.

Follow us on Twitter and leave questions for our speakers: @BEMColloquium

Please note: Magdalen Gallagher, part of our BEMC organizing team, left the Charité at the end of May. We thank her for all her help behind the scenes to make the BEMC happen and wish her the best for the future! Please use our online contact form for any BEMC-related inquiries.

May BEMC Talk- Student summary

Dear BEMCers,

We are pleased to be able to share a summary prepared by a student. A warm thank you to the anonymous student for letting us share this recap.

On May 8th, Christoph Lippert, a Professor in the area of digital health and machine learning at the Hasso Plattner Institute and at the University Potsdam held a lecture on “Machine Learning for Population-Based Health Studies”. The starting point of this lecture was to show a graphical representation of a typical patient flow through a health care system. This includes a patient’s contact with the health care system due to some symptom. Later on, some tests will be carried out by a physician and, after a lengthy period, the patient will receive an invasive treatment. It can also be the case that it will eventually be too late for any treatment. The current procedure was compared with what it is expected to be a patient flow in the future, where an individual undergoes continuous monitoring for diseases (e.g. through genetic risk assessment). Thus, it is expected that an individual will constantly receive early warnings, which lead him/her to involve a doctor at an early stage. Christoph highlighted how machine learning has the potential to help moving from the current patient flow to a better one, where people know early on their risks for developing certain conditions and can act accordingly. He highlighted how genetic differences across individuals can shed light on an individual’s risk factors for diseases, thus allowing for better and more individualised treatment options. Christoph proceeded by explaining basic concepts about genome-wide association studies and their goal of finding causal variants and/or markers that explain variance. He provided several examples, such as how phenotypes and population structures are correlated. The discussion was heated and insightful. Several attendees pointed out the need to consider the ethical implications of using genetics to predict health conditions. It was also mentioned how genome testing is cheap but, on a population level, this data does not provide meaningful information (i.e.. on a public health perspective). Furthermore, a question left hanging in the air concerned the degree of impact of lifestyle factors versus genes on an individual’s health status.

Announcing May BEMC Talk

Dear Berlin-area Epidemiological Methods Enthusiasts,

You are invited to our next BEMC Talk on Wednesday, May 8th.

BEMC Talk: Wednesday, May 8th, 2019 @ 4pm

“Machine learning for population-based health studies” – Christoph Lippert, Potsdam

  • Please register online: https://docs.google.com/forms/d/e/1FAIpQLSe2EfMPM2lXX1etpLblhLzDcfM0In9wLoTc3wUSWHD3Q5iVGw/viewform?usp=sf_link
    • If the registration link does not work for you please send us an email at bemcolloquium(at)charite.de with your full name and email address and short note that you’d like to be added to the registration list. Thanks!
  • Description: “In my talk, I’ll introduce our research at the interface of machine learning and statistics towards new methods for large-scale epidemiologic studies. We are working on models and algorithms that allow us to analyze high-dimensional genotypes and phenotypes from imaging and sequencing at scale. I’ll be talking about our work on mixed models for confounder correction, quantitative phenotyping using deep learning, as well as our works on novel statistical tests on deep learning embeddings of images.”
  • Location: Seminar room of the Neurology Clinic; Bonhoefferweg 3 entrance, 3rdfloor, Charité – Campus Mitte

Upcoming Berlin Epi Events:

  • May 15th – BEMC JClub – Paper posted online
  • June 5th – BEMC Talk – “Cool applications in R for epidemiologists” – Jochen Kruppa, Berlin
  • June 19th – BEMC JClub – Paper will be posted online
  • July 3rd – BEMC Talk Suzanne Cannigieter, Leiden, Netherlands
  • July 19th – BEMC JClub – Paper will be posted online in late May
  • August 2019 – no BEMC Talk or JClub
  • September 19th – BEMC JClub – Paper will be posted online in late July
  • October 2nd – BEMC JClub – Paper will be posted online in late August
  • Wednesday, October 23rd – IPH Lecture Partner event– John Gill from Vancouver

Interested in other Institute of Public Health events? Visit our calendar to check out upcoming conferences & short courses!

Follow BEMC on Twitter and leave questions for our speakers: @BEMColloquium

Pamela Rist, “One Size Does Not Fit All: Teaching Introductory Epidemiology” — Student summary

Dear BEMCers,

We are pleased to be able to share a summary prepared by three students who are currently earning credit for participating in the BEMC. A warm thank you to the three anonymous students for letting us share a compilation of their summaries!

As a reminder, we will be having BEMC JClub next Wednesday. A link to the article is available under JCLUB.

On Wednesday, April 3rd, Pamela Rist, Assistant Professor of Medicine at the Harvard Medical School and Assistant Professor of Epidemiology at the Harvard T.H. Chan School of Public Health, held a lecture about different ways to teach introductory courses in epidemiology. She teaches intro epi classes for medical staff and public health professionals, at undergraduate, postgraduate and doctoral levels.

Rist started her lecture by presenting how she first introduces the concept of confounding in her classes. Touching only the most basic aspects, the concept is simple to understand. However, it becomes inaccurate when moving on to more complex causal relations: It does not consider (open) backdoor paths, for instance. This, according to Rist, illustrates the difficulty of teaching: One has to introduce topics in a way that is understandable to the audience but does not cause problems later on for those who progress to substantial classes. Ultimately, there can be a trade-off between an intuitive and a correct definition.

She further explained that what should be thought of in an epidemiology introductory course depends on the type of audience, the skill set they need to learn in their career tracks, the goals of the course and structural issues. This appears to be particularly challenging since these courses are usually characterized by a considerable audience heterogeneity: students have different backgrounds, different coursework and different degrees of interest.

A successful technique to capture an audience’s attention, and to let students understand the importance of the epidemiology in their own field, might be to use different examples and papers based on the audience’s field of interest. In addition, Rist stated that even the way epidemiological concepts are explained should be flexible: using not only medical but also general knowledge examples to explain complex concepts (she provided a striking example explaining the Selection Bias using NBA players as subject).

Lastly, Rist introduced different teaching forms she uses: seminars, online lectures, inverted classrooms and discussed possible advantages as well as drawbacks. Seminars are a good learning environment, however small groups are required for discussion. Therefore, several rooms need to be available as well as teaching assistants to lead the seminars. If the setting does not allow this, Rist advised including live polls in large lectures and polling twice: The first time the students answer the question alone, the second time after discussion with neighbors. In this way, an active element can be incorporated into the lectures and students can learn from one-another. Rist also gave voice to her concern that setting up online lectures for the first time requires intensive preparation.

Discussion:
Q: Where do you find the papers for the discussion with students?
A: Science and Health sections of Times, JAMA, NEJM, Lancet. Talking to family and friends about current issues.
Q: Do you discuss good or bad papers?
A: I try not to focus only on poorly written papers. Sometimes I use also older papers to discuss the constraints of older methodology.
Q: What role does the student evaluation play for your next course?
A: Our course evaluations are done externally and anonymously, but I do read them. I find them to be useful and definitely try to adjust based on feedback where possible.
Q: How do you measure the success of your teaching? Do you have a special format for the exams (multiple choice etc.)?
A: Formally, the school measures the success of the lecture on 1-5 scale (teachers must score at least 3.5 to be allowed to teach the following semester). Informally, by student reactions. In terms of exams: we use tests with multiple choice, true/false, and fill in the blank questions for Master’s students (the class size is quite large and there isn’t much time between the final exam and when grades are due) and essays for PhD students.