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Video: Dissecting a Research Article

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Transcript

Slide 1: Title

Hello, my name is Rebecca Somach and I’m going to talk to you today about dissecting a peer reviewed scientific research article.

Slide 2: What is a peer reviewed scientific research article?

  • But what is a peer reviewed scientific research article?

  • That means it is an article with original research that was reviewed by other scientists, like the one you see on the screen here.

  • The people who wrote the article are the ones who are doing the research and the article should include that research, like these graphs here.

  • That doesn’t include popular science articles in magazines or news stories that report about science.

Slide 3: General tips for reading

Reading articles is not easy when you start, but don’t be discouraged. Before diving in, here are some general tips to keep in mind when you are reading scientific articles.

  • Give yourself the right amount of time. Your goal is to understand the article, not just to finish it. If you need to take an hour, or even a day to read the whole thing, that’s fine. You might have to read the article twice or three times to understand it, and that’s fine too.
  • When you’re stuck, look it up. Scientific authors will often assume the readers already know things about their field of research. They might write about a subject with only a few details because they think they are only talking to experts. If you don’t understand a word, a sentence or a concept, put the article down and look that up. As you read more articles and take more classes, these ideas will become more familiar but there’s no shame in looking things up, it can only help you.
  • Write it down. Keeping a lot of ideas in your head at once can be exhausting. If you just looked up what a word means, write it down on the side of the paper, or on a separate piece of paper. That way you can refer back to it. Scientists like to abbreviate words to make it easier to write papers, but it can make papers harder to read. Write those abbreviations at the top of the page.
  • Ask a friend. If you can’t still understand something, reach out to a friend, teacher or mentor who has experience. Sometimes talking about an article out loud can help you understand it.

Slide 4: Parts of an article

  • Now we will take a look at the parts of a research article
  • These are the parts of a research article in the biological sciences
  • Let’s briefly talk about each section and their purposes.

Section
Purpose
Title and Authors
What the article is about and who did the work.
Abstract
The whole paper in a paragraph- this is not an ‘easier’ version of the paper, it is just shorter.
Introduction
Why is the scientific question important? Tells you what you need to know about this paper.
Materials and Methods
Gives you all the details for how they did the experiments in the paper.
Results
What the experiments showed. Usually includes graphs and figures. This should have no opinions, just facts.
Discussion
What did the authors think about their results? How do their results fit in with other science that has already been done?
References
Where did the authors get their information from?

Slide 5: Before you read, why are you reading?

  • Before you read an article, take a moment to think about why you’re reading it. You don’t always read an article in order, and sometimes you need one section more than others.
  • Let’s try a quick activity. I want you to imagine that you’re a researcher and you are reading an article.
  • What parts of a paper would you look at if:
  • You were new to the topic and wanted some more information?
  • You’re trying to repeat an experiment in your lab?
  • You’re trying to get an overview of what is known in the field?
  • Pause the video now and write down what you think

Slide 6: Trying it yourself

  • Now, we’re going to be looking at a figure from a paper and trying to understand it. If you want an extra challenge, you can pause the video when I show the figure and the title of the paper and you can look it up yourself. Try to understand the experiment that was done, why they did it and the results.
  • You can also keep listening to see how I broke it down.

Slide 7: Tackling the unknown (PART I)

  • When you already know what terms mean, reading papers is a great way to gather information for your own work. For students starting out, one of the hardest parts of reading papers is understanding what is happening when you don’t know much about the field yet. The paper isn’t meant to be confusing, but it might take some more work to understand it. This isn’t just true in the biological sciences, this is true for any type of research paper- including those in physics, chemistry or the humanities. When you don’t know a field it can be hard to jump in, but never impossible.
  • As an example for trying to understand something outside of your knowledge, I am going to take you through a figure (CLICK) from a paper that I didn’t understand from a field of biology I’m not that familiar with and I’m going to show you how I approached it. This paper is talking about treatments in cancer biology.
  • The results of this figure aren’t important, what is important is learning how to understand something when you aren’t familiar with it.
  • This figure is from a paper called High-Affinity GD2-Specific CAR T Cells Induce Fatal Encephalitis in a Preclinical Neuroblastoma Model, Figure 1, parts E and F

Slide 8: Tackling the unknown (PART II)

  • The first thing I did was look at the title of the figure. That is: CAR T cells expressing the original wild-type GD2 CAR display antitumor activity in vitro but not in vivo. I don’t know what some of these terms mean, so I’m going to look them up.
    • The first is what CAR-T cells are. When I search the paper for that term, I see it says that it is a therapy involving removing a patient’s T cells and genetically engineering them... infusing them back into the patient where they find and kill antigen bearing tumors.
    • That tells me, is that CAR-T cells are being used as a therapy to target cancer.
    • Wild type usually means the control type. Or something in its natural state.
    • The next thing I don’t know is what a GD2CAR is.
    • And it also says in the paper that there is ‘effective targeting of GD2’
    • To me, that means that CART cells are targeting GD2 and the GD2 is in the cancer.
    • In vitro means an experiment not done in an animal
    • In vivo means an experiment that is done in an animal
  • If I simplify everything I’ve learned: the title is this: A treatment for cancer worked in cells, but not in animals.

Slide 9: Tackling the unknown (PART III)

  • Now let’s break the figure up, which is a good way to understand it piece by piece.
  • Figure E isn’t showing us a graph or data, so it is showing us the plan that the experimenters used.
  • I see here that these animals are labelled as NOD-SCID GAMMA MINUS MINUS. I don’t know what that is. If I look it up in the paper methods section, it says that they are also called NSG mice. When I look that up online, I can see that the NSG mouse is type of mouse that is immunocompromised, meaning they have no immune system.
  • Why do the experimenters want this? They are testing a type of immune cell here, the T cells, so they don’t want other immune cells to interfere with their results.
  • The next thing I see is that the experimenters injected cells into rodents. The cells are called SY5Y-CBG cells. I don’t know what that is so I looked in the methods section. It says that the cells are from the “Human neuroblastoma cell lines SY5Y”
  • And it also says that “The SY5Y-click beetle green (CBG) luciferase line (“SY5Y-CBG”)”
  • What’s luciferase? Looking it up, it is an enzyme that produces bioluminescence, or a glow.
  • The line on the right, has the words “Day 5” and an arrow pointing to the right. It also has lines pointing down that point to the words “Bioluminescent imaging”. Imaging is when researchers are measuring something and taking pictures of it, usually with a microscope. Here, they’re measuring the bioluminescence, or the glow. On Day 5, they introduce their treatment for the cancer, which are the GD2 CART cells we talked about before.
  • If we put that all together, this is how I can describe Figure E in my own words. The experimenters injected cancer cells that glowed into mice. 5 days later they injected a treatment, the CART cells. Every few days they checked if there was still cancer by checking for glowing.

Slide 10: Tackling the unknown (PART IV)

  • Now that we know how they did this experiment, let’s take at their results.
  • What I can see here is a graph, with time in days on the x axis. On the Y axis, that should be what we’re measuring.
  • Here, I had to look this up. They are measuring the glowing in Flux, which is also also known as Photons per second. That’s a way to measure light.
  • I also see a new term, CD19. The figure legend underneath the figure tells me that these are T cells transduced with an irrelevant CAR. It means that they aren’t actually a treatment, that’s the control. That will tell us if the cancer went away from something that wasn’t actually due to the GD2 CAR treatment, maybe something else that was injected, or maybe that the cancer went away on its own.
  • Now I look at the graph. All the lines are on top of each other. Which means that the GD2 treatment looks the same as the CD19 treatment. If I summarize this figure and its results, it would be this: There was the same amount of cancer cells in these mice with the GD2 treatment as there was with a treatment that was not supposed to work , the CD19.
  • That means that this treatment doesn’t work in this experiment. If you remember, that’s what the title said also, that this experiment didn’t work.
  • To understand this figure, I had to look up terms that were in the paper, in the title, and in the methods, but also terms that were not in the paper at all because the authors expected me to know what they were already. As you read more papers, this will all get faster because you’ll know some of these terms already. Be patient, and look up what you need to. Every scientist has to start with learning the terms in their field. The best way to get faster is with experience.

Slide 11: Critiquing a paper

  • Scientific papers are not sacred. They aren’t the set in stone facts of the universe. They were written by scientists like you. Sometimes articles are written poorly and can have mistakes.
  • You can disagree with what they write and how they did their work.
  • When you read a paper, your first step is to understand what they did. The next step is to ask if you agree with them. Here are some things you can ask when looking at a paper:
    • If I looked at the data by itself without the words, would I also make those conclusions?
    • Did the scientists analyze this in a way I think is correct?
    • Did the way they did their experiments answer their questions?

That’s just the beginning. The way that science gets better is through discussing it which is why people like to talk about papers with other scientists.

Slide 12: Reading is a skill

  • Reading papers is not like reading books. It can be frustrating to think that a 10 page article might take 2 hours to read and understand. Scientific reading is meant to put a lot of information in a small space so you don’t need to read a whole textbook to understand every study.
  • Reading articles is a skill that you have to build over time. With patience and hard work, you will soon be able to read articles and fully dissect them.

Slide 13: Thanks for watching!