NIH seminars available online

Today during the Tsien lab meeting, one of the post-docs mentioned an online repository of video/postcasts of NIH events and seminars. Intrigued, I harnessed the power of Google to find the NIH VideoCasting and Podcasting website, brought to us by the Center for Information Technology. The website contains a library of seminars, recorded in both video and audio forms, on subjects in Neuroscience, Bioethics, Career Development, and Evolution and Medicine.

Some examples from the list of available Neuroscience seminars:

• Molecular neurobiology of social bonding: implications for autism spectrum disorders, by Larry Young.
• Selectivity of local circuits in the neocortex by Stanford's own Shaul Hestrin.
• Receptors, Synapses and Memories by Richard "Not-to-be-confused-with-Huguenard" Huganir
• Common Mechanisms of Axon Guidance, Axon Regeneration and Vascular Patterning by Marc Tessier-Lavigne
• The Ins and Outs of Glutamate Receptor Synaptic Trafficking by Roger Nicoll
• Plasticity and Processing in the Whisker Map in Rat Somatosensory Cortex by Dan Feldman.
• Recurrent Inhibitory Circuits in the Cortex by Massimo Scanziani
• Synaptic Plasticity: Multiple Mechanisms and Functions by Rob Malenka

The list goes on. In short, a rich repository of fascinating talks given by experts in the field of neuroscience.

Again, these talks are available online at the NIH VideoCasting Website.

Mapping the Maturation of Neuroscience

An article in PLoS ONE presents a novel methodology for tracking change in large scale networks. Using the bootstrap statistical method, the authors analyze the citation patterns of 7000 scientific journals over the past decade, finding that  neuroscience has transformed into a mature and independent field. The authors point out that the analysis of large-scale network activity is integral to many scientific disciplines, from biological to economical. However, despite the great strides that have been made in tracking that activity, there are no significantly powerful tools for mapping changes to the structure of the network itself. Such a tool is critical if we are to continue to ask questions involving network activity; the authors seek to provide such a tool.

The basis of their method relies upon the bootstrap, "a statistic method for assessing the accuracy of an estimate by resampling from the empirical distribution." The power of the bootstrap method lies in its ability to handle data sets whose underlying distribution is not accessible. The authors developed a 4 set process for analyzing the change in a large scale network:

1. Cluster the original networks observed at each time point. 2. Generate and cluster the bootstrap replicate networks for each time point. 3. Determine significance of the clustering for at each time point. 4. Generate an alluvial diagram to illustrate changes between time points.

To demonstrate their method, they apply it to ~ 35 million citations from ~7000 scientific journals over the last 10 years. By using the citation patterns, they seek to track the flow of scientific ideas over time. The alluvial diagram they generate shows striking changes in citation behavior for distinct scientific disciplines, particularly for neuroscience.

In their citation behavior, neuroscientists have finally cleaved from their traditional disciplines and united to form what is now the fifth largest field in the sciences (after molecular and cell biology, physics, chemistry, and medicine). Although this interdisciplinary integration has been ongoing since the 1950s [17], only in the last decade has this change come to dominate the citation structure of the field and overwhelm the intellectual ties along traditional departmental lines.

The figure above shows an alluvial diagram for a set of biomedical fields for the years 2001, 2003, 2005, and 2007. As someone just starting her career, the obvious, rapid cohesion of citations into a Neuroscience field is thrilling.

The full paper makes for an interesting read, particularly if you are interested in methods of large data analysis, or if you enjoy admiring complex graphical depictions of large data sets.

Rosvall M, Bergstrom CT, 2010 Mapping Change in Large Networks. PLoS ONE 5(1): e8694. doi:10.1371/journal.pone.0008694

The Colors of the Dinosaurs

Research published today in Nature describes the discovery of melanosomes in fossils of several non-avian dinosaurs.

Melanosomes are melanin-containing organelles found in the feathers of birds, and responsible for the colors of those feathers. Researchers looked at the fossils of several non-avian dinosaur species possessing integumentary filaments which had previously (and controversially) been categorized as feathers. The controversy stemmed from the classification of these filamentous structures as feathers, with some researchers contending that the structures were degraded dermal collagen fibers, and not feathers at all.

Seeking to resolve this issue, Zhang et al examined the fossils using a scanning electron microscope, finding evidence of "sub-micrometre-sized bodies" that they interpret as fossilized melanosomes. Furthermore, the researchers identify the specific color associated with the fossilized melanosomes: a reddish-brown to yellow pigment.

Much of the letter is spent providing evidence to back up the claim that the identified structures are melanosomes, and it will be up to the experts to battle out a consensus. But based on their research, Zhang et al conclude the confirmation of the putative evolutionary precursors of true feathers, and the broach the possibility of decoding the external coloration of the dinosaurs. Indeed, the authors suggest some color schemes in the letter:

"Only phaeomelanosomes have been identified so far in filaments from the tail of Sinosauropteryx, and this suggests that the dark-coloured stripes along the tail in the fossil, and possibly also the filamentous crest along the back, exhibited chestnut to rufous (reddish-brown) tones."

For more details of their research, and more potential dinosaur color schemes, the article is available online:

Zhang et al. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature advance online publication 27 Jan 2010. doi:10.1038/nature08740

Image by Chuang Zhao and Lida Xing, courtesy of The Guardian, here.

Research Roundup: Grid cells, social value, migranes, fraud

Here's a collection of 3 recently published studies that caught my eye and one recently published case of massive scientific fraud. The Neurophilosophy Blog writes up a recent paper about the discovery of grid cell-like activity in humans. Spoilers: Researchers recorded activity very similar to that of mice grid cells. But with data collected only through population imaging, direct electrophysiological measurements are needed to show the existence of human grid cells.

Updated: Link to the original paper, published today in Nature.

Nature Neuroscience published a brief communication regarding activation of the dorsal amygdala in response to perceived inequality in subjects adverse to such inequality. See the paper for a better description of their methods and conclusions.

Another Nature Neuroscience article describes the neural mechanism behind exacerbation of migrane headaches by light. Spoiler: It's due to posterior thalamic neurons. These neurons receive nociceptive signals from cranial dura mater, but their activity is modulated by projections from retinal ganglion cells. So the light information modulates the nociceptive signal being passed through the thalamus to layers I-V of somatosensory, visual, and associative cortices.

Meanwhile, over at the journal Acta Crystallographica Section E, an editorial published last month reveals some extensive scientific frauds involving papers published during 2007. The editorial states that at least 70 structures were falsified, and that the number of structures will most likely rise. Credit for the discovery goes to Ton Spek. The basis of the fraud involves using a real set of data from a correctly determined structure to produce multiple papers wherein authors changed one or more atoms in the structure to produce a new, wholly imaginary compound. At most, more than 18 fraudulent structures were composed from a common data set.

The editorial states:

"The correspondence authors are Dr H. Zhong and Professor T. Liu, both from Jinggangshan University, Jian, China. The co-authors on these papers included other workers from Jinggangshan University together with authors from different institutions in China. Both these correspondence authors and all co-authors have signed forms agreeing to the retraction of 41 papers published by Dr Zhong and 29 by Professor Liu. Details of these retractions appear elsewhere in this issue of the journal. Having found these problems with articles from Jinggangshan University, all submissions from this University to Acta Crystallographica Sections E or C have now been identified and are being checked for authenticity. Preliminary results indicate that further retractions will result from this exercise."

Editorial by Willian T.A. Harrison, Jim Simpson, Matthias Weil. Acta Crystallographica Section E Structure Reports. Vol 66, pages e1-e2. Jan. 2010. via @bengoldacre

John Cleese Explains Neuroanatomy

I've spent quite a lot of time over the past couple of weeks listening to neuroanatomy lectures. Now, thanks to Vaughan over at Mind Hacks, and @brainshow, I'll probably spend the next couple of weeks wishing that my neuroanatomy class was being taught by John Cleese. Another hopeless dream is born. The Brain as Explained by John Cleese.

Bat and Whales: echolocation siblings

Yesterday, my eye was caught by a post written by Ed Yong over at Not Exactly Rocket Science about two recent studies showing that the echolocational abilities of bats and whales are both based on the same 14 amino acid changes to a single gene, Prestin. It can be universally acknowledged that morphologically, phenotypically, and geographically, bats and whales are highly dissimilar species. Yet both bats and toothed whales use echolocation for navigation in environments hostile to more traditional photon-based sight. And although the exact mechanisms behind the ability of echolocate are different in bats and whales (as might be expected given the dissimilar physiologies and habitats), the two groups share a strong genetic similarity in Prestin. So strong, in fact, that a phylogeny drawn using the DNA sequences of Prestin places all echolocating mammals as close relatives, excluding established evolutionary relatives such as other bats and whales who do not echolocated.

This case of convergent evolution is made more interesting because of the extreme behavioral differences in the way whales and bats practice echolocation. Bats echolocate through the medium of air, creating their sonar pulses via their voicebox. Whales echolocate through water by passing air through their nasal bones. These mechanistic differences are too great to be encoded by a single similar genes. Indeed, Prestin does not per say confer the ability to generate echolocation signals upon bats and whales. Instead, Prestin confers the ability to detect the rebounding echos, altering outer hair cells to make them more sensitive to the ultrasonic frequencies used in echolocation. With their enhanced ability to detect high frequency sounds, bats and whales evolved distinct physiologies to generate those sounds, as mediated by the demands of their distinct environments.

As Ed Yong points out, the independent replication of such distinctive genetic changes, resulting in the generation of distinct mechanisms to take advantage of the shared ability, is frankly astounding. Yet again, convergent evolution reinforces the duality of beautiful complexity and mysterious simplicity in the natural world.

Echolocation in bats and whales based on same changes to same gene. By Ed Yong at Not Exactly Rocket Science.

The original papers:

Liu et al. Convergent sequence evolution between echolocating bats and dolphins. Current Biology: 20, R53-R54 (2010).

Li et al. The Hearing Gene Prestin Unites Echolocating Bats and Whales. Current Biology: 20, R55-R56 (2010).

Using brain imaging to diagnose PTSD

Last week, I came across a paper entitled "The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap". I've been mulling over whether to blog about this paper; on one hand, it presents some interesting conclusions, which I greet with some degree of skepticism. On the other hand, having training neither in human brain imaging, psychology, or post-traumatic stress disorder, I was loath to make any statements regarding the paper and it's conclusions.

However, after reading the paper, and discussing its existence with a number of people, I've decided to publish a post (this one) asking for the opinions of those readers who do know enough about the subject and the methodologies utilized to comment on the validity of the papers conclusions. Below I will describe the paper's methods, its conclusion, and a link to the article. Please, comment on the paper and its conclusions.

The paper, by Georgopoulous et al, published in the Journal of Neural Engineering, describes the use of magnetoencephalographic (MEG) recordings to diagnose PTSD. Recordings of synchronous neural interactions (SNI) were made while asking subjects to fixate on a spot of light for 60 seconds, allowing the researchers to "engage the brain in a stable condition". The recorded data were analyzed using "bootstrap-based analyses". The paper explains the choice to use a bootstrap-based analysis:

"This approach was motivated by the common practical situation where a ‘new’ subject S needs to be classified, given subjects of known condition, i.e. belonging to a control (i.e. non-PTSD) group C or to the PTSD group D."

Using their analysis, which is detailed in the paper, the authors claim they can successfully differentiate subjects suffering from PTSD from healthy control subjects with greater than 90% accuracy.

Conclude the authors:

"Altogether, these findings document robust differences in brain function between the PTSD and control groups that can be used for differential diagnosis and which possess the potential for assessing and monitoring disease progression and effects of therapy."

A note: although all PTSD subjects were veterans, not all were suffering from PTSD induced by military trauma. Some were affected due to childhood trauma or non-military trauma during adulthood. Given the differences in the causation, is it reasonable to expect that all suffers of the disorder would display distinguishable synchronous brain activity differences? Certainly, I do not find it impossible that the data could show differences in brain activity when comparing PTSD sufferers from healthy controls. But in my mind, a diagnostic tool is most useful if it can differentiate one psychological issue from another. Is it reasonable to expect that a patient will either have PTSD, or be completely psychologically normal? I wonder about the selectivity of  the SNI test. Can it differentiate between PTSD and any one of the myriad of psychological issues that can affect the human brain (especially following military service). The ability to distinguish between shades of grey, instead of black versus white, must be the final goal of any psychological diagnostic tool.

As previously mentioned, due to my inexperience with brain imaging and mathematical techniques of analyzing such data, I cannot comment of the use of the bootstrap analysis. Is there someone out there willing to read the paper and provide an analysis?

Georgopoulous et al. The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap. J. Neural Eng. 7 (2010). doi:10.1088/1741-2560/7/1/016011

Updated 1/25/2010: Have just seen that Vaughan Bell over at Mind Hacks wrote on the 24th about this article, brining up that same issue regarding the scan's ability to separate PTSD from normal, as opposed to PTSD from another disorder.

Annual Online Consciousness Conference

For those interested in discussing questions of consciousness: the Second Annual Online Consciousness Conference has been scheduled for February 19th-March 15h. The conference format is as follows: papers/commentary by invited commentators will become available two weeks before the conference (on February 5th). During the conference, the authors of the posted papers will discuss their papers with conference attendees in the online comments sections. Session topics include: Higher Order Consciousness, State of the Art in Brain Decoding, Inner Psychophysics: Correlates, Causes and the Neurobiology of Consciousness, Color Consciousness Conceptualism, Ghosts and Sparse Properties and many other.

Not being too familiar with researchers in the field of consciousness, I only recognize David Chalmers among the list of invited commentators. The full lists of the session topics and invited commentators is available online.

The host blog, Conciousness Online, was founded by Richard Brown. According to their website, the goal of the blog is:

" to bring consciousness researchers together in an online venue to promote widespread discussion and exchanging of views/data related to the scientific and philosophical study of consciousness, broadly construed."

NPR Interview: Darwin's Great-Great Grandson

Last evening, I happened to turn on NPR to hear Terry Gross of the program Fresh Air interviewing a man called Randal Keynes. Mr Keynes is a great-great grandson of Charles Darwin, who has written a book about Charles Darwin, the death of Darwin's first daughter, and the composing of the Darwin's theory of evolution. The book, entitled Darwin, His Daughter, and Human Evolution, is the book upon which the film Creation (recently mentioned on this blog) is based.

The NPR interview is available online in audio form (the transcript is also available).

Darwin, His Daughter, and Human Evolution. by Randal Keynes, at amazon.com