darb.ketyov.com

Caveat lector: This blog is where I try out new ideas. I will often be wrong, but that's the point.

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29.3.10

TEDxBerkeley

In a few days I will be giving a talk at TEDxBerkeley. If this were any other talk I wouldn't be too worried; I've done lots of these kinds of things before. However this one will have 700 people in the audience watching live, and they estimate a minimum of 100,000 people watching the live stream online. And who knows how many more will download these talk to watch them later, especially if it makes it to the TED.com main page.

But even these things aren’t that bad.

What gives me pause is the emphasis on telling not only an interesting story, but a compelling and personal story that emphasizes the narrative of how I came to do the work I do. That story is quite a personal one. I don’t have a problem telling my friends about it, but to get up in front of hundreds or thousands of strangers to tell that story is a bit more difficult.

This whole process has been a bit strange and surreal. It started when I first saw some posts online about the upcoming conference. A few minutes after hearing about it I chatted with Curtis online to tell him about it and to say that we should go. I jokingly said I should do a brain talk. It turned out that he’d previously met the person organizing the conference, Jessica, and he asked her if she needed any more speakers. A few hours later I was sitting with her going over my talk ideas, and then I was in. Now I'm meeting with a professional media consultant in a few days to tighten up my talk and go over the slides and narrative.

So here I am, writing out my talk, organizing my slides, and feeling pretty much more nervous than I have about any other talk before. I want it to be personal, and funny, and interesting, and exciting. But I feel a bit weird, because I still technically haven’t done a whole lot professionally. I’m still just a grad student, and yet I keep finding myself in these situations where I feel like I’m asked to do something well about my current “station”. Professionally this feels like a good thing, but I don’t want to just be a speaker, I want to be a scientist and I’m itching to get my work out.

But then again, there’s no real rush, and so I’m going to try and enjoy the ride while I can rather then fret about how safe the ride will be or where it might take me.

28.3.10

PubMed Tips

Okay, this is a totally specific post for my neuroscience friends about some cool tips that have helped me search better using PubMed. I've encountered some folks who have a lot of trouble with PubMed, and these tips genuinely seem to help. So, if you need help with PubMed, look no further!

Searching:

To give an example of some of the search difficulties, if I want to to find a paper published in Science by my advisor Robert Knight, I might enter the search term:

knight r science

However this is quite non-specific and returns (as of this writing) 57 results. Not too bad, but his name isn't quite as common as others'.

What I'm really asking, though, is to find papers by an author with a specific name (R Knight) published in a specific journal (Science). Thankfully, PubMed lets you establish search qualifiers. Thus, to make my search more specific, I could instead write:

knight r[au] science[jo]

where [au] tells PubMed that the term to the left is an author name. [jo] then tells PubMed that everything to the left is the journal name. The reason it knows that the journal isn't named "knight r science", is that whenever it encounters another set of brackets (in this case, the [au]) it knows that what's to the left of that is now a new term unrelated to the [jo] criterion.

This new search returns only 10 items; now I can quickly and easily scan the page for the paper I'm looking for.

The most useful tags that I use regularly are:
  • [au] - author: e.g., Voytek B
  • [1au] - first author
  • [lastau] - last author
  • [dp] - date published (year): e.g., 2010
  • [ti] - words in the manuscript title: e.g., hemicraniectomy electrophysiology
Automatic Searches:

If you're a professional researcher, I can't imagine how you could efficiently keep up with the literature without having PubMed do some automatic searches for you. Every Monday morning I receive some emails from PubMed alerting me of publications of interestWell, technically, I now receive updates via RSS, but it's the same basic idea. To do this, you first need to create an account. This is super easy, free, etc. and well worth doing.

Once you have an account with a linked email address you can set up automatic searches. I'll give a few examples that I find helpful here.

Let's say for the sake of argument that you think I'm an awesome researcher (true) and you want to know every time I publish a paper (which you should). Using the tags I showed you above, enter:

voytek b[au]

into the search bar. Once you complete the search, you'll see some options above the search bar including "RSS" and "Save Search". If you click on RSS, it will ask how many items you want sent via RSS and it will create a personalized XML link for you to enter into your RSS reader of choice (I use Google Reader). If you want to set up an email digest instead, click on "Save Search".



This gives you the option to name your saved search and establish an email schedule (e.g., every Monday morning send a maximum of 20 articles fulfilling my search criteria). You can access saved searches later by clicking on "My NCBI" in the upper-left corner.

Now, you can also get a bit more fancy. For example, I'm very interested in studies looking at the effects of prefrontal lesions. So I might run a search with the terms:

(prefrontal AND lesion*)

where the asterisk indicates to search for any words starting with "lesion" such as "lesion", "lesions", "lesioned", etc.

But let's say you work in a very active field with a lot of new research generated every week. You might want to only see the most important and influential papers. Now, granted, there is always controversy about how meaningful the actual publication journal really is, but sometimes you really need to limit your search criteria, and it's not always an awful metric. So let's say you want to only search a limited set of what you perceive to be more "influential" journals instead of getting hundreds of new publications every week. In this case, you could establish a search such as below:

(annu rev neurosci[jo] OR brain[jo] OR cell[jo] OR cereb cortex[jo] OR curr opin neurobiol[jo] OR eur j neurosci[jo] OR j cogn neurosci[jo] OR j neurophysiol[jo] OR j neurosci[jo] OR j physiol[jo] OR nat neurosci[jo] OR nat rev neurosci[jo] OR nature[jo] OR neural netw[jo] OR neuron[jo] OR neuropsychologia[jo] OR neuroscience[jo] OR plos biol[jo] OR plos comput biol[jo] OR pnas[jo] OR prog neurobiol[jo] OR science[jo] OR stroke[au] OR trends cogn sci[jo] OR trends neurosci[jo]) AND (prefrontal AND lesion*)

This will miss many publications of course, and you'll want to tailor it to your own needs, but you get the idea. For example, I have weekly searches such as above, but I might make a more broad search that emails me ALL the papers once a month instead of weekly.

In the above example, I name all my journals of interest in the first set of parentheses, to tell PubMed to search for all papers published in any of those journals. Then I have another Boolean connector, "AND", and a second set of parenthesis with "prefrontal AND lesion*" inside. This tells PubMed to take all the articles published in my journals of interest and only return those that have the term "prefrontal" and "lesion*" in them somewhere (title, abstract, keywords, or... if there was an author with the last name lesionopoloi, even that, too).

Alright, there you go! I might add more tips later if people are interested, but for now, these are the biggest time-savers and annoyance-reducers for me.

11.3.10

Project completion and academic rejection

When I started my PhD I was lucky to already have a few papers published from when I was working as a full-time RA. Granted, I was nth author on most of those papers (where n > 1), but I was first author on one of them.

That was totally cool. I had an idea, tried it out, and it worked! I wrote a really short paper and got it published! The whole process was easy, but it skewed my idea of what scientific publishing was like.

You see, I really care about my thesis research... it's not a side project or a neat data analysis idea. It matters to me. And now that my papers are starting to get rejected I've come to realize that I need to rethink my notion of "finished".

When I started grad school, here's how I thought the academic scientific process worked:
  1. Have awesome idea.
  2. Do awesome research and be most excellent.
  3. Write well and present your data clearly.
  4. Send to journal.
  5. Get reviewed.
  6. Get helpful feedback from your peers.
  7. Nature paper!
 What I'm coming to realize is that it can work a bit more like this:
  1. Have awesome idea.
  2. Do awesome research and be most excellent.
  3. Write well and present your data clearly.
  4. Send to coauthors.
  5. Rewrite... and iterate...
  6. Finally send to journal.
  7. Get reviewed.
  8. Get helpful feedback from your peers.
  9. Have editor reject you anyway.
  10. WTF?
  11. Send to daughter journal after addressing reviewer's comments and reiterating with coauthors again.
  12. Don't get reviewed!?! Argh!
  13. Send to another journal.
  14. Get reviewed! Phew!
  15. Get helpful feedback from your peers.
  16. Have editor reject you anyway but leave the door open to keep your hopes up. GRR!
  17. Get a real job where you get paid more than what you'd be making if you went on unemployment and actually see a project to completion in less than a year.
Okay, I'm not actually doing step 17, but it is pretty sad that most PhD students make less than unemployment...

Anyway, my point here is that previously I thought that, as soon as I did all the "hard" work of data analysis and writing, I would be done. But there's a lot of steps after that. There is a lot of extra work that needs to be done before a project is really finished. It's very frustrating to do so much work only to have to rework it so many times.


Nevertheless, it's still amazing to me that I get paid to think and have good ideas. I keep my own hours for the most part, and I really enjoy the work I do. I really can't complain that my papers aren't getting accepted into the top scientific journals--not all my work can be that awesome--but when you put so much time into something you do want to see it succeed.


It's the waiting to hear back that's the worst, though.