SFN 2009 – so much to see

I apologize for my lack of updates lately.  It turns out that trying to actively learn things and socially interact with other scientists while also reporting on new findings, etc, is extremely difficult.  Though this isn’t exactly what I believe SFN Interactive had planned, I think I’m going to try and only post brief updates for the remainder of the conference (especially on my twitter) and then work on several in-depth posts on cool findings when I return.  I could rush through some things this week while waiting for talks to start, etc, but I’d prefer to give the presenters a good write-up, something I’m not completely confident I could do in a very short time period.  I have no idea how other Neurobloggers are able to keep up – I’m completely overwhelmed, and I still feel like I’m not seeing that much of the conference.

The first day (Saturday) I was presenting all afternoon, which left me too exhausted to return until Sunday around 11.  Since then, I’ve been hanging out at the Theme F poster sessions – these have been unbelievable.  I’ve also attended a large number of the large lectures (including Elizabeth Spelke, Richard Morris, Steven Laureys, Francis Collins, and May-Britt Moser), all of which have been quite enlightening.

Poster highlights thus far include the entire perceptual decision-making session this morning, a poster on a beautiful new tool for controlling social stimuli (truly an incredibly creative idea), a nice poster on neuroimaging children with William’s Syndrome by Dr Tricia Thornton-Wells at Vanderbilt, and an equally-interesting poster on early visual processing of valid currency.  If I can get author permission, expect to hear a great deal more about these in the coming weeks.

This afternoon I’ll be wandering around the poster floor and exhibitor booths.  If you see a poster you think I’d enjoy, or you yourself would like me to come check out your work, feel free to comment below or contact me on twitter (@M_ostlyHarmless, hashtag #sfn09).  I’m looking forward to providing more complete and satisfying coverage when I return later this week.

View your OASIS itinerary for SFN on your mobile device

For all those who are organized enough to have an itinerary planned out for SFN next week using the online Neuroscience Meeting Planner (a rather archaic tool that is only marginally useful, linked from the meeting homepage above), you may be interested in how you can use your mobile device (like iPhone, blackberry, etc) to explore your schedule.  I’ve been looking all afternoon for a way to automatically export the OASIS itinerary to outlook or Google Calendar, but nothing seems to work (though if you like using Excel to plan your events, they’ve got that covered).  An ambitious student with more time than appropriate on his or her hands could cook up some Applescript to generate iCal events from the rows of the .xls file, but I unfortunately won’t be much help there.

Once you’ve signed in to the OASIS meeting planner and have picked out a reasonably nice itinerary, you can view it on your mobile device in two ways:

1) create a pdf of the printable version of the itinerary and put this in your Dropbox folder or Evernote notebook (if you don’t use Dropbox or Evernote, drop what you’re doing and sign up – these are fantastic, infinitely useful services).  If you use a smartphone, this should be quite easy to access on-the-go (via the iPhone app for Dropbox or Evernote or the web interface for either). UPDATE: Carl Wonders on Twitter reminded me that Air Sharing is a fantastic iPhone app that can be used to transfer files to the iPhone so that there won’t be any reliance on network connectivity (a safe bet considering there won’t be wifi on the conference floor).  You can just transfer the pdf of your itinerary to your phone and not worry about spontaneous 3G outages or slow network traffic.  Thanks, Carl!

To create the pdf, first click on the “printable itinerary” button on the left, just underneath where it says “My Itinerary”

Click here to create your printable itinerary, then Print to PDF

Click here to create your printable itinerary, then Print to PDF

2)  You could view the meeting planner on your mobile device (on the web) – here’s how:

Navigate, on your mobile device’s web browser, to the meeting planner and log in.  Select “My Itinerary” to get to the screen shown below, then click on “Mobile Itinerary”

On your phone's browser, click on "Mobile Itinerary"

On your phone's browser, click on "Mobile Itinerary"

This will provide you with a decent, though hardly good, way to explore your planned events during the meeting.  That is, of course, if we have any data coverage whatsoever.  I was really hoping there would be some kind of OASIS iPhone app for this year (I’d pay $10 easy), but unfortunately we weren’t so lucky.

If I by any chance come up with a way to import the itinerary into Google Calendar, I’ll write up a walkthrough.  Of course, if you know of anything that makes planning the meeting any less stressful, please share in the comments.  Once I have things nailed down, I’ll post a preliminary version of my itinerary here as a pdf.  If there’s anything you think I should check out, please let me know – I’m always looking to meet interesting people doing interesting research.

UPDATE: According to a new story posted recently on the SFN Annual Meeting site, the abstract and daily books are available for download to your Kindle.  I don’t know how useful this will be to everyone (an interactive itinerary would be better…), but I’m sure some people will find this quite handy.  I’ll try downloading the Kindle versions later this week and see if there’s any additional utility there.  It would certainly be nice not to carry all 5 books around every day, but I can imagine pressing “next page” over and over again will be quite inconvenient.  If you’ve used these on your Kindle, feel free to post impressions in the comments.

NeuroTechnica at SFN 2009

I’ve just received word (along with dozens of others, it appears) that I’ve been selected as an SFN Neuroblogger for the 2009 conference next weekend (10/17-10/21)!  I’m extremely excited and honored to have this opportunity and look forward to sharing my thoughts on this year’s meeting with you all.  For those interested, I’ll also be tweeting, from @M_ostlyHarmless and hashtag #sfnthemef (and possibly #sfnthemeh, which is incidentally the worst hashtag ever).  If there’s anything in particular you’d like me to check out, especially for those not attending the meeting, feel free to let me know and I’ll do my best to cover it.

I look forward to seeing everyone (including the RIKEN 2009 Summer Program alums) in Chicago next weekend.  Until then, I’ll be locked away finishing my poster for the meeting (presentation 94.6, 1-5 pm on Sat at EE56).  If you’re around and interested in short duration perception, drop by.

PLoS releases article usage data

Yesterday afternoon, I received an exciting press release from PLoS (the text of which is largely similar to this blog post) – article usage data is now available for (nearly) all articles published in any of the open-access PLoS journals!  This is a big deal for, at least, two reasons:

1.  authors now have a great incentive to publish in PLoS journals, and

2. this could be a wonderful data set to mine for those interested in both the public and scientific reception of open access publishing

PLoS has published an xls file containing all the article-level metric data, which can be downloaded here.  I’ve played around with the data for a few minutes and a few things become clear rather quickly.

First, though I love the potential for interactivity which is a hallmark feature of the PLoS journals, it appears to be very infrequently used.  Of the 11059 research articles included in this data set, only 651 (~5.9%) have one or more ratings, while only 29 (< 0.3%) have 3 or more ratings.  I find this quite surprising – though I’m personally quite reluctant to comment on, leave notes on, or rate a peer-reviewed research article, that’s in large part due to my present academic standing (I don’t even have a Bachelor’s degree yet).  What authority do I have to say anything about the research of another lab?  This isn’t to say I never have something to say, but if so, I’d write a post here.  Conveniently, PLoS is also keeping track of blog trackbacks and mentions (though I’m sure there are mentions not counted in these metrics).  Examined this way, the situation appears a bit less bleak: 1196 of the 11059 included research articles (10.81%) were mentioned in at least one blog post (have a non-zero number of trackbacks).

The second obvious feature of the data set is that, as one would expect, a small number of articles appear to be viewed an enormous number of times (the 70 most-viewed articles, which amounts to .63% of all research articles, account for over 10% of all article views).  A notable example is one of this year’s media darlings published in PLoS One, “Complete Primate Skeleton…” with over 56000 views in just 2.5 months (the data go through 7/31/09).  Papers like this contrast starkly with the mean, which is closer to around 2100 views for a research article.  It’s likely that there are similar reasons for the large number of views for many of these other articles.  In the future, I’ll try comparing number of views to time since publication (a factor PLoS readily acknowledges skews these metrics) – perhaps this number simply reflects a trend towards publishing in open access journals in recent years.  PLoS is doing a great job of tracking blog references to papers, but perhaps there could be a similar metric for popular media mentions (such as Google News results/queries?).  This would be the interesting metric for understanding (and maybe factoring out or accounting for) the role of mass media in article popularity.  If researchers are working to gauge the influence of their article among their scientific community, pure page-views, especially when driven by media outlets, may not be the best metric.

Number of citations found in PubMed Central vs those found in CrossRef for each article (n = 11059)

Number of citations found in PubMed Central vs those found in CrossRef for each article (n = 11059)

Finally, it becomes clear that the various citation-tracking services (specifically, CrossRef, PubMed Central, and Scopus) have quite disparate results.  Even if we ignore Scopus for now (the folks at PLoS acknowledge an issue with their database in the ALM FAQ), we can see that there is not generally a 1:1 relationship between the number of citations ascribed to PubMed Central and number of citations ascribed to CrossRef.  I’m sure someone out there has a (or a number of) good reason(s) why this is the case – but it does seem a bit strange.

So what does this early data tell us about open-access and community-focused publishing?  Most importantly, despite all the encouragement on the part of PLoS and the blogging community, it appears that the enterprise of bringing an interactive discussion to an article (rather than having the discussion take place in the comments of blog posts) has been largely unsuccessful.  I find this at least a bit baffling – it’s not at all uncommon for readers (often researchers) to post comments on blog posts discussing peer-reviewed research using their real name.  If the trackback feature is working properly, anyone reading the original research article is just a click away from seeing this feedback.  Why the willingness to post a comment in one place, but not the other?  Or, take the 5-star rating system – this is a quick way to post a very general reaction to a paper.  The mean of the average ratings of the 651 rated papers is 4.16 – should this be taken as an indicator of very high average quality of research published in PLoS journals, or a signal that there is an inherent selection bias in those rating articles?  I know that personally I have a very tough time rating anything 1/5 (even my iTunes library reflects this – there are something like 1000/6000 songs rated 4+, and the remainder are unrated).   The problem here appears to be the lack of anonymity.  There’s, I think, a simple solution to this problem.  Now, when you look at a rated article (for example), you can see the user who rated it.  I think it makes complete sense to require a user to be registered to rate an article, but s/he should also be given the option of anonymity.  Requiring sign-in would still be useful for filtering out spam ratings (in ensuring only one rating per user, etc), but would allow users to post more honest reactions to articles.  Though it’s not unfeasible to institute a similar system for comments or text notes, I think those should be tracked to a particular user.

Though this data reveals some initial reluctance within the community to adopt this particular means of scientific dialogue, I’m optimistic that as the myspace and facebook generations grow to be competent graduate students and scientists we’ll have a more open and interactive culture of science.  It’s absolutely fantastic that PLoS released this data, and I hope in the near future they release increasingly-detailed metrics that can be further mined for interesting usage and publication patterns.  I really do think that the future of the scientific publishing “industry” will be in managing and profiting from usage data rather than scientific discourse.  The guys at Mendeley seem to understand this, and certainly are on their way to having a very impressive data set to work with.  Knowing what articles tend to cluster in researchers’ libraries (and references sections of articles) will allow for the creation of an iTunes Genius-like algorithm for suggesting papers – an absolutely killer feature many labs (and hopefully institutional libraries) would certainly be willing to pay for.

For further information about the PLoS Article-Level Metrics and the prospect of community-oriented science communication, check out the (non-exhaustive) set of links/articles below.  As always, I’d love any feedback you might have, so feel free to comment or email any thoughts/ideas/criticisms.

PLoS Journals – measuring impact where it matters – this post is especially interesting

Improving Science Through Online Commentary (Eagleman & Holcombe, 2003) [PDF]

PLoS Takes a Giant Leap Toward Science 2.0

EDIT: new links/posts/mentions

PLoS Article-Level Metrics Home

A Blog Around the Clock: Article-Level Metrics at PLoS

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005723

Now you see it, now you don’t

Being exposed to popular media and fiction about science, we’ve all heard the term ‘brain waves’, loosely related to the frequencies of electrical oscillations in the brain detected at the scalp using EEG.  These signals are extremely vague spatially (you may be able to differentiate left/right or front/back, but you won’t isolate the insula or cuneus), but carry a lot of temporal information (on the order of milliseconds).  Per the modern dogma of neuroscience, most every aspect of human behavior or conscious experience can be reduced to a discrete set of electrochemical processes in the brain.  This includes, obviously, visual perception.  There is an enormous body of research concerning what happens differently in your brain in response to different variations of a stimulus, but not quite as much work has looked at the opposite arrow of causality – that is, what’s going on in your brain that causes you to see the same stimulus in different ways?

For example, let’s say there is a single neuron responsible for perceiving a circular disc. When a disc is flashed, this neuron fires, and you have a vivid perception of a circle (well, as vivid as a circle can be).  Without this neuron, you would not perceive a circular disc, even if it were sitting blatantly in front of your eyes, which were accurately transmitting information to your visual brain.  This is a fairly straightforward, though grossly simplified account of how we often think about vision (but instead of single neurons, we usually consider enormous, brain-wide networks of neurons working in teams; but see Quiroga et al, 2005 for an observation which may suggest otherwise).  But what if we presented this circle in a way that made it difficult to see – say, it is flashed very dimly – so that you sometimes see the circle like normal and sometimes miss it completely.  What is that neuron up to in the time before we show the circle that causes it to be more or less likely to fire, thus leading to your perception of the circle?

A recent study published in the 3/4/09 issue of the Journal of Neuroscience by Matthewson and colleagues used EEG to test this idea – what is different about the global electrical activity in the brain when a hard-to-see flash is perceived compared to when it is not perceived?  To test this, the research group used a phenomenon called metacontrast masking, in which a short initial flash is rendered undetected by a surrounding flash that follows (here, the researchers used a circular disc, flashed for 12 ms, followed by a ring around the disc presented ~50 ms later for 24 ms).  Subjects (whose brain activity was being recorded with a spidery EEG cap) reported whether or not they detected the first ‘target’ circle (there were ‘catch’ trails in which no target was presented to make sure subjects were paying attention).  This type of stimulus allowed the researchers to gather EEG data over a roughly equal number of trials in which the target was detected and undetected.

The main finding was that a certain band of ‘brain waves’ (cortical oscillations) before the target was flashed were able to differentiate between trials in which the target was detected and undetected.  These oscillations, in the alpha band (a frequency range centered at 10 Hz, typically associated with decreased vigilance and alertness), when measured locked to onset of a fixation cross that came onscreen before the target, were found to have different phases for detected and undetected trials.  Since the alpha rhythm is rather slow, which often suggests a greater number of neurons firing in synchrony, the authors suggest that this phase difference reflects a different cortical susceptibility to visual stimulation.  When the target was presented at one peak of the oscillation, subjects were much more likely to report perceiving it – at different times of the rhythm, the visual cortex was more receptive of input.

Personally, I find this result quite fascinating.  I’ve been working to see if there’s a critical error in the methods used or analysis performed, but it seems like the authors were very careful in their work – this finding appears, by my best understanding, to be legit and important.  Though I’ve mentioned throughout this post the possibility of using brain state to predict perceptual state before the stimulus is shown, I want to be clear that this is not what the authors of this study did.  All this analysis and classification of alpha states was done after subjects were long-gone.

Now, what I’d really like to see is a group perform the predictive version of this experiment – keep a running monitor of alpha power and present hard-to-see stimuli at different phases of the alpha oscillations.  If this finding is robust, and computational power is plentiful enough, this experiment should be feasible and yield a positive result.  I’m really excited to see developments like this study, along with several others from the past year, concerning what’s happening neurally in the period before a stimulus is presented or a motor act is performed.  In our efforts to piece together an explanation of human behavior (both subjective experience and objective action) in terms of neural events, this kind of work is just as important as understanding the effects of these behaviors (perception and action) on the brain.

What do you think?  If you’re experienced with EEG experiments/analysis, I’d love to hear a more in-depth evaluation of the methods used in this paper.  Leave a comment, or email me at neurotechnica on gmail.

Cracked tackles neuroscience

I was browsing Digg today when I happened upon this Cracked article which talks about different illusions in neuroscience and does a pretty decent job explaining them in a humorous, mostly-accurate way.  I found their description of change blindness to be particularly funny.

I only had one bone to pick with their post (and it’s only a technical note): they discuss (what must be) Changizi et al (2008)‘s predictive model of visual illusions as though it is the established understanding of how these illusions operate.  Additionally, the assertion that scientists, by dunking electrodes in your brain, “could tell you–with 100% accuracy–what decision you’ll make a few seconds from now” is obviously still too sci-fi for my liking.  But that’s just nit-picking – I think this is a great article, and that it has the potential to generate at least a tiny bit of interest in neuroscience to some of the people who will read it.  Any time a scientific topic can be cast in a way so as to garner attention it wouldn’t otherwise receive is a great opportunity to capture the interest of a new population.  Bill Nye is fantastic in this regard – much of my current interest in science goes back to when I used to watch is show every day after school at my grandparents’ house.  Before him, Carl Sagan was a hero to hundreds, if not thousands, of young soon-to-be scientists.  As I’ve mentioned before, Robert Krulwich and Jad Abumrad also do a great job with their work on Radio Lab in reaching to a more mainstream (well, public radio) audience.

After looking around a little further, I found this other post they did a short while back about the psychology of advertising, providing lots of good, colorful examples throughout.

Do you have any other favorite science posts/articles/shows/podcasts that reach in creative ways?  Leave a comment, or email me at neurotechnica on gmail.

DRM, iPhone 2.2.1, & iTunes – Apple screwed up big time

I’ve recently been one of a large number of victims to a very unfortunate bug involving the iPhone 2.2.1 software update issued earlier this month.  Since I upgraded to 2.2.1, whenever I would attempt to sync anything with DRM to/from my phone (this includes ringtones, videos, movies, FairPlay music from the iTunes store and Apps(!)), iTunes would crash and the iPod app’s database would become slightly more corrupted (as in, some songs would not play, the current progress of my podcasts would be erased, etc).  Thus, I’m unable to sync my podcasts (99% of my use for my phone), can’t listen to music (the other 1%), and can’t fix this problem since, importantly, restoring the phone doesn’t do a single thing to solve the problem.

Plus, it looks like I’m not alone.  This thread on the Apple support forums details the struggles others have gone through in response to this bug.  Unfortunately, I didn’t find this until after I had restored my phone, so now I’m stuck with an App-less iPhone that only has a partial collection of my music.

And, as you can see from the support form, this is due entirely to some problem with protected music, movies, and applications.  This enfuriates me.  In general, I try and buy the music I like; same for TV shows and movies (which I usually rent, but nonetheless pay for).  Of course, there are exceptions, but for the most part I try and support the artists, etc, that I like.

If I had stolen all my music and videos, I wouldn’t have a single problem right now (except maybe with Apps) – but since I was honest for at least some of my library, I’m screwed.  Thanks, Apple.  Really.  Thanks.

Have you run into this problem as well?  Does anyone have other stories of DRM causing unnecessary problems?  Leave a comment, or email me at neurotechnica at gmail dot com.

Neurotechnica is on Nature Blogs

As of this morning, NeuroTechnica is now listed on Nature Blogs, a pretty incredible science blog aggregator, very similar to the one I proposed creating in a previous post.  The main difference between the current implementation and something I’d really like to see is automatic republishing (with author’s permission, of course) on a central portal.  I imagine it wouldn’t be terribly difficult for NPG to write a WordPress or Blogger plugin to take all posts (or a subset of author-selected posts) and republish them on the site.  I look forward to using this platform, though.  The content pointed to by Nature Blogs is top-notch, and I’m really excited to be a part of it.

The next week or two are really busy, but I plan on updating throughout my visit to the 2008 Society for Neuroscience Annual Meeting taking place Nov 15-19 in Washington DC.

Vitamin B12 – it does a nervous system good

This evening I came across an interesting article in the New York Times about the neurological risks of a vitamin B12 deficiency.  A number of recent studies seem to link a B12 deficiency with different neurological ailments, like Alzheimer’s disease and dementia.  The article mentions a recent study that found brain shrinkage in older adults with low levels of B12, an interesting finding given our rapidly-aging population.

Though I’m certainly interested in the health consequences of B12 shortages, I’ve for some time also been curious as to how B12 supplements may positively affect the body in individuals with normal B12 levels (like myself).  Since high school, I’ve used a B12-based energy drink called ZipFizz to give me an extra boost when I need to get up early or study late at night.  ZipFizz is rather similar to the infomercial-tastic Five Hour Energy, but contains more B12 and a number of other supplements.  To be clear, these kind of drinks still usually contain caffeine (100mg for ZipFizz).  But my experience of drinking ZipFizz is qualitatively rather different than guzzling down a pot of coffee.  When on B12, I don’t feel jittery or hyper, just calm, concentrated and alert.  Also, something I’ve found really useful about ZipFizz is that after the initial 100mg caffeine burst wears off (~1.5hrs, it seems like), you can easily go to sleep if you like.  Coffee-drinkers know that this would be impossible after several cups of coffee.  I’m sure at least some of the effects of these drinks can be attributed to the placebo effect, but after using ZipFizz for almost 3 years now, I really do think it works well as a vitamin-based energy supplement.

To my knowledge, not much work has been done on the possible health benefits of these B12 supplements, and I’d be curious to see if B12 can be found to act as a mild cognitive enhancer.  If anyone knows of any articles addressing this topic, leave them in the comments – I’d love to learn more about this.

Neurotechnica Review: Body Worlds 2 & The Brain, Our Three-Pound Gem

Body Worlds 2 & The Brain, Our Three-Pound Gem

Having been a huge fan of the first Houston exhibition, I was excited to learn that Body Worlds would be returning this year.  This time, it’s called “Body Worlds 2 & The Brain, Our Three-Pound Gem” (which naturally had me excited).

To start off with, this exhibit is extremely expensive for a museum showing.  My (student!) ticket came out to be $21, and standard adult admission is $25.  There’s definitely not enough to this exhibit to warrant that kind of ticket price (though I’d still suggest attending if you somehow missed the first Body Worlds showing).

Also, for those of you with a strong interest in neuroscience (like myself), Body Worlds 2 is definitely targeted towards a general audience.  There isn’t anything that isn’t taught in PSYC 101 or an intro neuroscience course, but it’s pretty cool that it’s presented in a very readable and exciting way.  The “three-pound gem” part seems to be an afterthought, though, as very little of the exhibit itself is geared towards the brain.  There are lots of wall hangings that briefly introduce different aspects of modern neuroscience (like development, personality, emotion, creativity, memory, consciousness, disease, etc).  These amount to little more than you’d find in a Time or New York Times article, and some even contradict each other.  One (I don’t remember which) attributed long term memory to  “the back of the brain”, and also defined “instantaneous memory” to be the type of memory used to remember a phone number (this is the classic example for working memory).  But, in general, these provide an interesting & broad overview of the more interesting parts of neuroscience.

So what brain-related plastination specimens are shown?  Like before, there are plastinated coronal, saggital, and axial slices of adult brains, as well as several specimens from stroke victims (slices & whole brains).  There are at least 2 examples of the entire nervous system (brain, spinal cord, and large peripheral nerves), which are very impressive and interesting to see, as well as one specimen from an Alzheimer’s disease victim.  The coolest brain-related specimen, I thought, was a cast of the cerebral blood vessels.  The structure is absolutely beautiful.  Also, several of the full-body plastinations placed a great deal of emphasis on the brain, like “The Ponderer“, which is a man seated comfortably in a contemplative pose w/ much of his brain exposed.

As far as the full-body plastinations go, there are some very creative examples on display.  It won’t do anyone much good for me to try and describe them, but there are at least 3 or 4 that I was very impressed with.  Gunther von Hagens is truly an artist.  The full-body specimens are much more artistic this time than they were in the previous exhibit, so perhaps those alone could be worth the price of admission.

It surprises me that they’re marketing this exhibit as focusing on the brain.  Aside from the wall hangings, there isn’t really any additional brain-related content this time around.  There is, however, a large and very interesting display of human development, from conception to birth.  This part of the exhibit should certainly be the main attraction, but for whatever reason (probably support from the Mischer Neuroscience Institute), the brain was this year’s focus.

Overall, I was a little disappointed in Body Worlds 2.  I guess I was expecting to be as impressed as I was the first time, which I unfortunatley wasn’t.  Don’t get me wrong, Body Worlds is a wonderful opportunity to see real human bodies and what happens to them as we age & suffer disease.  The full-body plastinations are as impressive as ever, if not moreso, and the neuroscience blurbs on the wall will hopefully further promote awareness of neuroscience as an important discipline.  But if you’re expecting something new and brain-centered, Body Worlds 2 isn’t quite there.

What: Body Worlds 2 & The Brain, Our Three-Pound Gem

Where: Houston Museum of Natural Science

When: until Feb 22

How (much): $21 for college students, $25 for adults, $17 for members (buy here)

Worth it? Depends on who you are.  Definitely check it out if you missed the first Houston showing, but otherwise, there’s not much new to see here.