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in this video I'm going to walk you
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through how to effectively read a
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scientific research article and the
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first thing I'm going to do is introduce
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you to the software that I'm going to be
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using to um walk you through how to read
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a research article and that is afar and
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afar is actually sponsoring this video
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So within afai it's a reference manager
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that has a lot of AI features built in
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so this is the article that I'm going to
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be looking at and I have a different
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video if you want to learn more about
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apari all together before I jump in I
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want to make sure that you know that you
00:00:33
can access afri using the link in the
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description below and you can also use
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this code if you would like to get 10%
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off if you choose to upgrade to the paid
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version of arar so I'm going to double
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click on this article to open it up and
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this is going to open up the file that's
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already saved within my account and then
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I can go through and use f to annotate
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it and to work with AI throughout
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Reading This research article but the
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very first thing we want to do isn't
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about software and it isn't about just
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diving in and starting to read the
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research article the first thing we
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actually want to do is set an objective
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for reading a research article and
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essentially that means why do we want to
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read this research article and there's a
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few different reasons you may want to
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read a research article the very first
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one is that you might need to find or
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learn a method so you've created a
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research question and you know what you
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want to study but you're not quite sure
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how to study that or how to analyze it
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and so you might just want to find a
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method that you can use or learn a
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protocol for a given method and if this
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is what you want to do then all you need
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to do is go into your results find
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whatever method was used to generate the
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result that you want to generate and
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then go back to the methods and learn
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about the method and the protocol that
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was used another use case for wanting to
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read a research article is just to
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identify the key findings so you might
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be trying to get up to date on the
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research in your field or answering a
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very specific questions about what
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results have been found up to this point
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in a certain question and if you're just
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trying to identify the key findings then
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a great way to do that is just to go to
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the results sections and look at the
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different figures that you're interested
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in and identify what their key findings
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were another option is if you're trying
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to find gaps in the literature so you're
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trying to find a new research question
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what should you study a good place to
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start there is to look at the
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conclusions and see what future work is
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suggested and also to look at the
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limitations of a paper and and then the
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big one that we're going to discuss
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today is If you're trying to actually
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understand the research article maybe
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you're initially starting out in your
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field and you're wanting to really
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understand the full research article
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maybe you have to give a presentation on
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it there's a lot of different reasons
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why you actually want to dive in and do
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a deep dive in understanding the full
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research article and that's what we're
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mainly going to get into today but I
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want to talk about one case that really
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doesn't suit well with reading a
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research article and that's if you're
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trying to figure out background
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information on your field if you're like
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trying to figure out what a protein does
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or general background information I want
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you to stop looking at a research
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article and instead try and go find a
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review that really covers that you're
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going to tend to find much better
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quality information if you use a review
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instead of using a research article for
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that General background information so
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whenever you're trying to understand
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your research article in more in depth
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or if you're using any of the other
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objectives I talked about I want to go
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through how to read the different
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articles sections so that you know
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exactly how to approach it so whenever
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I'm looking at a research article the
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very first thing I'm going to do is look
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at the abstract here so you can see this
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abstract goes from about here to here
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and what I'm looking for is just to get
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accustom with what this research article
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is talking about I'm also looking for
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reasons why it may not be a good idea
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for me to spend my time going into deep
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depth into this article maybe it doesn't
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I thought it matched what I was wanting
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to read about but it really doesn't
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match what I was wanting to read about
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and so I just start with the abstract
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and figure out is it really a good fit
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for me and what I want to do after
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reading my abstract what I'm actually
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going to do is jump all the way down to
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the conclusions and you can see here's
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my conclusions here this tends to give a
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little bit more of the results and
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discussion parts of the paper instead of
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more of the introduction methods that
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tends to be in an abstract and so I read
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this to understand again is this
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important to my field and to go ahead
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and understand what are the main key
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findings that they found so I have that
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context as I read through the results
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figures methods and introduction after
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the conclusion what I'm going to do is
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actually look at all of the figures so
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that's a good way to learn the story of
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a paper is just to look through all the
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figures now once you've gone through the
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figures the next thing I would do is if
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you are at a certain figure and you have
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questions about it or you're wondering
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how they got there or anything like that
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I would then go into the results and
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actually read the words but I would
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actually start looking at the visuals
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themselves and that can actually give
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you a lot of information whereas reading
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the words can sometimes get really
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confusing and make you feel a little
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unsure of what they're trying to say so
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if I want to understand the context
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behind some of these results or any
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competing results I would go into the
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discussion that's where I'm going to get
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a lot of why is this happening not just
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what is happening and then the final
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thing I'm going to do is look at the
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methods and introductions but only as
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needed so if I need to understand how
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they generated results I'll look at the
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methods especially if I wanted to
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duplicate the study which I actually did
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I looked at the methods to figure out
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what were they using how did they create
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their Solutions um and what results were
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they getting and then if I'm not
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understanding abbreviations if I'm not
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understanding basic background
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information about something that they're
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talking about I'll go up to their
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introduction and then kind of read about
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what is important and what um that
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abbreviation was or what that background
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information is so this why I don't start
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at my introduction because typically a
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lot of the information from my
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introduction especially if I already
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know my field is really redundant and
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it's kind of a waste of my time to read
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in depth and introduction when it's not
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completely related to what I'm actually
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trying to work on or trying to learn
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from this article so as I'm going
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through reading this article I want to
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talk about how you can annotate your
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article for your future self to really
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thank you and so this is one of the
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things I really like about using arari
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because they actually have a really good
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annotation system that's built in so I'm
00:06:32
going to show you the different ways you
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can use their annotations if you're in a
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different reference manager you can also
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use those annotations but I really like
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the way that they do it within F so the
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very first type of annotation is
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highlight and if you've seen previous
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videos on my channels I basically talk
00:06:46
about how I really don't recommend
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highlighting and apai has actually
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changed this um and how I feel about
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this and the reason why so if I come up
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here you can see I can click on this
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pencil and it's going to do a text
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highlight I can also actually just use
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the keyboard shortcut and hold down S&T
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and you see it brings up that highlight
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there what I like about highlighting
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within F specifically is if I want to be
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able to access information within the
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paper really easily in the future let's
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say I have this statement here without
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addition of any modifiers or salts the
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major ionization species observed for
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each compound included the M plus a and
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the 2 M plus na so this is actually
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something that's really important for us
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to understand is that even without
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adding insults we're still getting this
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sodiated species here and let's say I
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want to I want this to be something that
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I want to remember about this paper is
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that they didn't add in sodium for it
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and they still got this so what I can do
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is I can highlight
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this and it's going to highlight with it
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it with a color and if you have like
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different topics that you are trying to
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work with or something like that or even
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different like maybe red is going to be
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for my result and blue is for my
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background information I want to know
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and green is for future work that I want
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to have easy access for um that's one
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way to categorize it the reason I like
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this because generally if you just
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highlight especially if you highlight on
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paper when you go back to that paper
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especially if you highlight a lot it
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doesn't mean anything anymore it just
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just highlights all over the place and
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nothing really stands out what I like
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about this is it actually extracts the
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text and it puts it in a note so I can
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see this exact text within a note now
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and what that also means is if I look
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for if I
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search M plus na a within this this
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still shows up because it has that note
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within it so if I click on it and go to
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my notes you can see it has that note
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within it now and so this makes it
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searchable now I can take text and
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automatically make it searchable for
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later and that's one of the things that
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I now would use highlighting for even
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though I really discouraged that in the
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past because I hadn't found a software
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that had this specific feature in it the
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next component component of annotating
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is highlighting with comets the way that
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I would use comments with highlights is
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to be able to ask questions or leave
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thoughts about the Highlight that I did
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so for example if I had this highlight I
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might come in and ask the question how
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common is it for sodiated
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species to show
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without sodium added and so that might
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be something for me to investigate later
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but I'm writing all my notes down in
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here so it's easily accessible for me in
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the future the other thing is if I had
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thoughts so if I wanted to um maybe I'm
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going to add another comment and also
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say like
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sodium can be prevalent even
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in
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deionized water and
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potentially causes sodiated species
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something to that effect I can do that
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and so again that's just like a thought
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that I'm having in that moment and so
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that's a way for me to easily write it
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down and it's all available for me and
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searchable the next type of annotation
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is to take notes and so what's nice
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about this is there's two ways that you
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can add notes in you can add a quick
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note just by using the bar down here
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with an apari and you can also add a
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sticky note so if I click on this and
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added a sticky note in here I could add
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my comment in here and so a few ways to
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use notes is overall ideas so like if
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you get a research idea you can do it
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like that comments questions that you
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have overall about the paper and then
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thoughts for a specific purpose so if
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you're like want to include in and then
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talk about what how you want to use that
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um this paper that's another way to do
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notes so if I wrote a note on this
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separation
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differs for different
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species
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of isomer so this is just kind of a
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general note that I might want to add
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it's something that if I need it I can
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search for it and I can come back to it
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later I can also potentially write note
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about research ideas and if you're going
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to write something like about a research
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idea I would have a specific prefix to
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it so like research question and then I
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would add in what my research question
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is so how does group one medals
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affect the separation of isomer the
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reason I'm doing that oh let me press
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enter to actually add it so there it is
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there the reason I'm doing that is if I
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come back in here and I go to my notes I
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can search my notes so I can search for
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what research questions I had um I can
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also change the color of this note if I
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come up here I can make this blue so all
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my blue ones are research questions and
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things like that and I can also if I
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have a lot of papers and I just want to
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see which ones have research questions
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in them that I have created I can also
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include that up here as well and so if
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you also have like uses like I want to
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use this in something I would say use
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and then I would say like introduction
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of group one medals paper something like
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that so having these prefixes within
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your notes especially if you always
00:12:24
start with them is a good way to be able
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to find them later on the two other
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annotation meth methods is first of all
00:12:30
capturing images so let's say this is an
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image I know I'm going to want easy
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reference back to later what I can
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actually do is use the area highlight
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and I'm going to capture this image so
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that whenever I come to this paper I can
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really easily if I exit out of that I
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can really easily see this image here
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and if I want I can make copies of this
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image and just being able to like know
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the different images without having to
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go in and relook at the paper that can
00:12:58
be really helpful the the final way to
00:13:00
kind of annotate a paper is actually not
00:13:03
in The annotation sections it's more of
00:13:05
an organization technique but it's the
00:13:07
ability to add tags so if I wanted to
00:13:09
add a tag I can go into my info click
00:13:11
add a tag and then click on steroids and
00:13:13
go ahead and add that in and specific
00:13:15
ways you can use tags is to Mark out
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methods specific results um analyes
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topics or themes that you're interested
00:13:23
in and even uses for it so I could add a
00:13:25
use for a different paper that I'm
00:13:27
working on that way I can filter down to
00:13:28
just the papers that I'm interested in
00:13:31
working on for like if I'm writing a
00:13:33
specific paper or for my dissertation or
00:13:35
anything like that the final thing I
00:13:36
want to talk about is how can we use AI
00:13:38
to read our papers more effectively and
00:13:40
the very first thing we can do is
00:13:42
actually work with it to explain things
00:13:45
that we don't quite understand either
00:13:47
phrases or anything like that so if I
00:13:49
come up into my introduction here so
00:13:52
let's say take this sentence here so
00:13:55
this says um this is especially true
00:13:57
when dealing with epimers that different
00:13:59
only in their stereochemistry so I'm
00:14:01
going to go ahead and do a highlight and
00:14:03
I'm going to copy that and then I'm
00:14:05
going to click on
00:14:07
it and I'm going to go into my comments
00:14:10
and I'm going to type in at and this
00:14:12
gives me access to the AI chatbots I'm
00:14:15
going to use this one and I'm going to
00:14:17
say can you
00:14:20
explain can you explain this
00:14:25
selection so it talks about epimer so EP
00:14:29
are one type of stereo isomer that only
00:14:31
differ in the configuration at one
00:14:33
specific chyro Center um that means that
00:14:35
the overall thing is very similar it
00:14:37
talks about what ccss are the challenge
00:14:39
with epimers the implications and the
00:14:42
strategies to overcome the challenge and
00:14:44
so that's kind of pulling from the paper
00:14:46
so it gives me a description um of
00:14:49
what's going on and it can kind of
00:14:53
explain a little bit more and and
00:14:54
simplify things for me the other way to
00:14:57
use AI is to get an easy summarization
00:15:01
so if I come in here I'm going to do at
00:15:03
to get the AI model up and then I'm
00:15:05
going to make a note saying please
00:15:08
summarize this article including the
00:15:12
methods key findings and future
00:15:20
work and so you can see this pops up
00:15:25
here and so it gives me the summary the
00:15:28
ad abstract the methods that they used
00:15:31
the key
00:15:33
findings and the future work and a
00:15:35
conclusion so it gives me a really quick
00:15:37
summary of it and now this is now saved
00:15:39
as a note so I don't have to copy and
00:15:41
paste it anywhere it's already saved
00:15:43
within here and the final thing is to
00:15:45
use it to identify limitations or future
00:15:48
work and I kind of did that in my
00:15:49
previous one so it says the study
00:15:51
suggests further exploration um using
00:15:54
dtims to uh provide the analysis of
00:15:57
isomeric steroids and the potential use
00:15:59
of different cat addicts so I might come
00:16:02
in here I have to add in
00:16:05
my AI chatbot so then what are the
00:16:09
limitations of this
00:16:14
study and I can go into its
00:16:18
comment so you see it gives me several
00:16:21
different
00:16:22
limitations um of the study and then I
00:16:25
can take a limitation and make it into a
00:16:27
future work so I I hope that gives you
00:16:29
an idea of not only how to read a paper
00:16:31
but how to also annotate it and organize
00:16:34
it in order to be able to find it easily
00:16:36
in the future and then also to be able
00:16:39
to use AI to make it more smoothly and
00:16:42
be enhance your ability to read it if
00:16:45
you are interested in apari I will leave
00:16:48
a link in the description below you can
00:16:50
also use the code right here to get 10%
00:16:52
off of your purchase for afar if you
00:16:55
would like to upgrade um to get more of
00:16:57
the AI features and more uses of the AI
00:17:00
I hope you enjoyed this video and I look
00:17:02
forward to seeing you in the next one
