SPF - Goodbye 2008!

I told you this would be the last one of the year :P It is a little incomplete, but I will post a supplemental section soon.

EndNote Library is located here.

Enjoy!

Bache, J. and Derwent, G. Access to computer-based leisure for individuals with profound disabilities. NeuroRehabilitation 23, 343-50, (2008).
Link.

Chakrabarty, S., Friel, K. M. and Martin, J. H. Activity-dependent plasticity improves M1 motor representation and corticospinal tract connectivity. J Neurophysiol, doi:91026.2008 [pii]
10.1152/jn.91026.2008 (2008).
Link.

Cheung, V. C., d'Avella, A. and Bizzi, E. Adjustments of motor pattern for load compensation via modulated activations of muscle synergies during natural behaviors. J Neurophysiol, doi:01387.2007 [pii]
10.1152/jn.01387.2007 (2008).
Link.

Guillery, R. W. Anatomical pathways that link perception and action. Prog Brain Res 149, 235-56, doi:S0079-6123(05)49017-2 [pii]
10.1016/S0079-6123(05)49017-2 (2005).
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Narayanan, R. and Johnston, D. The ascent of channels with memory. Neuron 60, 735-8, doi:S0896-6273(08)01007-6 [pii]
10.1016/j.neuron.2008.11.017 (2008).
Link.

Hampson, M., Tokoglu, F., King, R. A., Constable, R. T. and Leckman, J. F. Brain Areas Coactivating with Motor Cortex During Chronic Motor Tics and Intentional Movements. Biol Psychiatry, doi:S0006-3223(08)01435-2 [pii]
10.1016/j.biopsych.2008.11.012 (2008).
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Raichle, M. E. A brief history of human brain mapping. Trends Neurosci, doi:S0166-2236(08)00265-8 [pii]
10.1016/j.tins.2008.11.001 (2008).
Link.

Rauschecker, A. M., Pringle, A. and Watkins, K. E. Changes in neural activity associated with learning to articulate novel auditory pseudowords by covert repetition. Hum Brain Mapp 29, 1231-42, doi:10.1002/hbm.20460 (2008).
Link.

Nachev, P., Kennard, C. and Husain, M. Cognition and the supplementary motor complex. Nat Rev Neurosci 10, 78, doi:nrn2478-c2 [pii]
10.1038/nrn2478-c2 (2009).
Link.

Bode, S. and Haynes, J. D. Decoding sequential stages of task preparation in the human brain. Neuroimage, doi:S1053-8119(08)01222-6 [pii]
10.1016/j.neuroimage.2008.11.031 (2008).
Link.

Luu, S. and Chau, T. Decoding subjective preference from single-trial near-infrared spectroscopy signals. J Neural Eng 6, 16003, doi:S1741-2560(09)89426-3 [pii]
10.1088/1741-2560/6/1/016003 (2008).
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Zhou, X. and Merzenich, M. M. Developmentally degraded cortical temporal processing restored by training. Nat Neurosci 12, 26-8, doi:nn.2239 [pii]
10.1038/nn.2239 (2009).
Link.

Hattori, N., Shibasaki, H., Wheaton, L., Wu, T., Matsuhashi, M. and Hallett, M. Discrete parieto-frontal functional connectivity related to grasping. J Neurophysiol, doi:90249.2008 [pii]
10.1152/jn.90249.2008 (2008).
Link.

Ivanenko, Y. P., Poppele, R. E. and Lacquaniti, F. Distributed neural networks for controlling human locomotion: lessons from normal and SCI subjects. Brain Res Bull 78, 13-21, doi:S0361-9230(08)00155-X [pii]
10.1016/j.brainresbull.2008.03.018 (2009).
Link.

Lappin, J. M., Reeves, S. J., Mehta, M. A., Egerton, A., Coulson, M. and Grasby, P. M. Dopamine release in the human striatum: motor and cognitive tasks revisited. J Cereb Blood Flow Metab, doi:jcbfm2008146 [pii]
10.1038/jcbfm.2008.146 (2008).
Link.

Eisner-Janowicz, I., Barbay, S., Hoover, E., Stowe, A. M., Frost, S. B., Plautz, E. J. and Nudo, R. J. Early and late changes in the distal forelimb representation of the supplementary motor area after injury to frontal motor areas in the squirrel monkey. J Neurophysiol 100, 1498-512, doi:90447.2008 [pii]
10.1152/jn.90447.2008 (2008).
Link.

Holz, E. M., Doppelmayr, M., Klimesch, W. and Sauseng, P. EEG correlates of action observation in humans. Brain Topogr 21, 93-9, doi:10.1007/s10548-008-0066-1 (2008).
Link.

Ludwig, K. A., Miriani, R., Langhals, N. B., Joseph, M. D., Anderson, D. J. and Kipke, D. R. Employing a Common Average Reference to Improve Cortical Neuron Recordings from Microelectrode Arrays. J Neurophysiol, doi:90989.2008 [pii]
10.1152/jn.90989.2008 (2008).
Link.

Mazzoni, A., Panzeri, S., Logothetis, N. K. and Brunel, N. Encoding of naturalistic stimuli by local field potential spectra in networks of excitatory and inhibitory neurons. PLoS Comput Biol 4, e1000239, doi:10.1371/journal.pcbi.1000239 (2008).
Link.

Georgieva, S. S., Todd, J. T., Peeters, R. and Orban, G. A. The extraction of 3D shape from texture and shading in the human brain. Cereb Cortex 18, 2416-38, doi:bhn002 [pii]
10.1093/cercor/bhn002 (2008).
Link.

Leek, E. C. and Johnston, S. J. Functional specialization in the supplementary motor complex. Nat Rev Neurosci 10, 78; author reply 78, doi:nrn2478-c1 [pii]
10.1038/nrn2478-c1 (2009).
Link.

Bud Craig, A. D. How do you feel--now? The anterior insula and human awareness. Nat Rev Neurosci 10, 59-70, doi:nrn2555 [pii]
10.1038/nrn2555 (2009).
Link.

Dinstein, I. Human cortex: reflections of mirror neurons. Curr Biol 18, R956-9, doi:S0960-9822(08)01192-5 [pii]
10.1016/j.cub.2008.09.007 (2008).
Link.

Marzinzik, F., Wahl, M., Schneider, G. H., Kupsch, A., Curio, G. and Klostermann, F. The human thalamus is crucially involved in executive control operations. J Cogn Neurosci 20, 1903-14, doi:10.1162/jocn.2008.20124 (2008).
Link.

Deutschlander, A., Stephan, T., Hufner, K., Wagner, J., Wiesmann, M., Strupp, M., Brandt, T. and Jahn, K. Imagined locomotion in the blind: An fMRI study. Neuroimage, doi:S1053-8119(08)01235-4 [pii]
10.1016/j.neuroimage.2008.11.029 (2008).
Link.

Gomi, H. Implicit online corrections of reaching movements. Curr Opin Neurobiol, doi:S0959-4388(08)00154-2 [pii]
10.1016/j.conb.2008.11.002 (2008).
Link.

Albarracin, D., Handley, I. M., Noguchi, K., McCulloch, K. C., Li, H., Leeper, J., Brown, R. D., Earl, A. and Hart, W. P. Increasing and decreasing motor and cognitive output: a model of general action and inaction goals. J Pers Soc Psychol 95, 510-23, doi:2008-11108-002 [pii]
10.1037/a0012833 (2008).
Link.

Stevenson, I. H., Rebesco, J. M., Miller, L. E. and Kording, K. P. Inferring functional connections between neurons. Curr Opin Neurobiol, doi:S0959-4388(08)00159-1 [pii]
10.1016/j.conb.2008.11.005 (2008).
Link.

Kuhn, S., Haggard, P. and Brass, M. Intentional inhibition: How the "veto-area" exerts control. Hum Brain Mapp, doi:10.1002/hbm.20711 (2008).
Link.

Alaerts, K., Swinnen, S. P. and Wenderoth, N. Is the human primary motor cortex activated by muscular or direction-dependent features of observed movements? Cortex, doi:S0010-9452(08)00252-9 [pii]
10.1016/j.cortex.2008.10.005 (2008).
Link.

Tytell, E. D. Journal club: a neuroscientist marvels at our ability to learn unnatural tasks. Nature 456, 679, doi:456679e [pii]
10.1038/456679e (2008).
Link.

Radhakrishnan, S. M., Baker, S. N. and Jackson, A. Learning a novel myoelectric-controlled interface task. J Neurophysiol 100, 2397-408, doi:90614.2008 [pii]
10.1152/jn.90614.2008 (2008).
Link.

Xiong, J., Ma, L., Wang, B., Narayana, S., Duff, E. P., Egan, G. F. and Fox, P. T. Long-term motor training induced changes in regional cerebral blood flow in both task and resting states. Neuroimage, doi:S1053-8119(08)01218-4 [pii]
10.1016/j.neuroimage.2008.11.016 (2008).
Link.

Voss, M., Ingram, J. N., Wolpert, D. M. and Haggard, P. Mere expectation to move causes attenuation of sensory signals. PLoS ONE 3, e2866, doi:10.1371/journal.pone.0002866 (2008).
Link.

Minzenberg, M. J., Watrous, A. J., Yoon, J. H., Ursu, S. and Carter, C. S. Modafinil shifts human locus coeruleus to low-tonic, high-phasic activity during functional MRI. Science 322, 1700-2, doi:322/5908/1700 [pii]
10.1126/science.1164908 (2008).
Link.

Kemmerer, D., Castillo, J. G., Talavage, T., Patterson, S. and Wiley, C. Neuroanatomical distribution of five semantic components of verbs: evidence from fMRI. Brain Lang 107, 16-43, doi:S0093-934X(07)00261-1 [pii]
10.1016/j.bandl.2007.09.003 (2008).
Link.

Neurobiology: The motor-neuron driver. Nature 456, 843, doi:456843d [pii]
10.1038/456843d (2008).
Link.

Hall, C. N. and Attwell, D. Neuroscience: Brain power. Nature 456, 715-6, doi:456715a [pii]
10.1038/456715a (2008).
Link.

Biermann-Ruben, K., Jonas, M., Kessler, K., Siebner, H. R., Baumer, T., Schnitzler, A. and Munchau, A. Observing repetitive finger movements modulates response times of auditorily cued finger movements. Brain Cogn 68, 107-13, doi:S0278-2626(08)00167-X [pii]
10.1016/j.bandc.2008.03.005 (2008).
Link.

Hagni, K., Eng, K., Hepp-Reymond, M. C., Holper, L., Keisker, B., Siekierka, E. and Kiper, D. C. Observing virtual arms that you imagine are yours increases the galvanic skin response to an unexpected threat. PLoS ONE 3, e3082, doi:10.1371/journal.pone.0003082 (2008).
Link.

Casagrande, V. A., Sary, G., Royal, D. and Ruiz, O. On the impact of attention and motor planning on the lateral geniculate nucleus. Prog Brain Res 149, 11-29, doi:S0079-6123(05)49002-0 [pii]
10.1016/S0079-6123(05)49002-0 (2005).
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Burns, W. Online archives are revealing uncensored history of science. Nature 456, 870, doi:456870b [pii]
10.1038/456870b (2008).
Link.

Knutsen, P. M. and Ahissar, E. Orthogonal coding of object location. Trends Neurosci, doi:S0166-2236(08)00264-6 [pii]
10.1016/j.tins.2008.10.002 (2008).
Link.

Garza, J. P., Eslinger, P. J. and Barrett, A. M. Perceptual-attentional and motor-intentional bias in near and far space. Brain Cogn 68, 9-14, doi:S0278-2626(08)00035-3 [pii]
10.1016/j.bandc.2008.02.006 (2008).
Link.

Beck, J. M., Ma, W. J., Kiani, R., Hanks, T., Churchland, A. K., Roitman, J., Shadlen, M. N., Latham, P. E. and Pouget, A. Probabilistic population codes for bayesian decision making. Neuron 60, 1142-52, doi:S0896-6273(08)00803-9 [pii]
10.1016/j.neuron.2008.09.021 (2008).
Link.

Wadman, M. Rule change for human grants sparks spat at NIH. Nature 456, 682-3, doi:456682b [pii]
10.1038/456682b (2008).
Link.

Ascoli, G. A. and Samsonovich, A. V. Science of the conscious mind. Biol Bull 215, 204-15, doi:215/3/204 [pii] (2008).
Link.

Fishbach, A. and Mussa-Ivaldi, F. A. Seeing versus believing: conflicting immediate and predicted feedback lead to suboptimal motor performance. J Neurosci 28, 14140-6, doi:28/52/14140 [pii]
10.1523/JNEUROSCI.2612-08.2008 (2008).
Link.

Soechting, J. F. and Flanders, M. Sensorimotor control of contact force. Curr Opin Neurobiol, doi:S0959-4388(08)00158-X [pii]
10.1016/j.conb.2008.11.006 (2008).
Link.

Moisello, C., Crupi, D., Tunik, E., Quartarone, A., Bove, M., Tononi, G. and Ghilardi, M. F. The serial reaction time task revisited: a study on motor sequence learning with an arm-reaching task. Exp Brain Res, doi:10.1007/s00221-008-1681-5 (2008).
Link.

Nambu, A. Seven problems on the basal ganglia. Curr Opin Neurobiol, doi:S0959-4388(08)00155-4 [pii]
10.1016/j.conb.2008.11.001 (2008).
Link.

Furman, M. and Wang, X. J. Similarity effect and optimal control of multiple-choice decision making. Neuron 60, 1153-68, doi:S0896-6273(08)01049-0 [pii]
10.1016/j.neuron.2008.12.003 (2008).
Link.

Salinas, E. So Many Choices: What Computational Models Reveal about Decision-Making Mechanisms. Neuron 60, 946-9, doi:S0896-6273(08)01059-3 [pii]
10.1016/j.neuron.2008.12.011 (2008).
Link.

Gray, R. T. and Robinson, P. A. Stability and structural constraints of random brain networks with excitatory and inhibitory neural populations. J Comput Neurosci, doi:10.1007/s10827-008-0128-0 (2008).
Link.

Swayne, O. B., Rothwell, J. C., Ward, N. S. and Greenwood, R. J. Stages of motor output reorganization after hemispheric stroke suggested by longitudinal studies of cortical physiology. Cereb Cortex 18, 1909-22, doi:bhm218 [pii]
10.1093/cercor/bhm218 (2008).
Link.

Bauchet, L., Lonjon, N., Perrin, F. E., Gilbert, C., Privat, A. and Fattal, C. Strategies for spinal cord repair after injury: A review of the literature and information. Ann Readapt Med Phys, doi:S0168-6054(08)00223-7 [pii]
10.1016/j.annrmp.2008.10.004 (2008).
Link.

Morishima, Y., Akaishi, R., Yamada, Y., Okuda, J., Toma, K. and Sakai, K. Task-specific signal transmission from prefrontal cortex in visual selective attention. Nat Neurosci 12, 85-91, doi:nn.2237 [pii]
10.1038/nn.2237 (2009).
Link.

Gruzelier, J. A theory of alpha/theta neurofeedback, creative performance enhancement, long distance functional connectivity and psychological integration. Cogn Process, doi:10.1007/s10339-008-0248-5 (2008).
Link.

Brunelli, G. and Wild, K. Unsuspected plasticity of single neurons after connection of the corticospinal tract with peripheral nerves in spinal cord lesions. J Reconstr Microsurg 24, 301-4, doi:10.1055/s-2008-1078688 (2008).
Link.

Serences, J. T. Value-based modulations in human visual cortex. Neuron 60, 1169-81, doi:S0896-6273(08)00951-3 [pii]
10.1016/j.neuron.2008.10.051 (2008).
Link.

Miyawaki, Y., Uchida, H., Yamashita, O., Sato, M. A., Morito, Y., Tanabe, H. C., Sadato, N. and Kamitani, Y. Visual image reconstruction from human brain activity using a combination of multiscale local image decoders. Neuron 60, 915-29, doi:S0896-6273(08)00958-6 [pii]
10.1016/j.neuron.2008.11.004 (2008).
Link.

Haushofer, J. and Fehr, E. You shouldn't have: your brain on others' crimes. Neuron 60, 738-40, doi:S0896-6273(08)01009-X [pii]
10.1016/j.neuron.2008.11.019 (2008).
Link.

Myers, A. and Sowden, P. T. Your hand or mine? The extrastriate body area. Neuroimage 42, 1669-77, doi:S1053-8119(08)00691-5 [pii]
10.1016/j.neuroimage.2008.05.045 (2008).
Link.

Carbon nanotubes on and in the brain

Now that the embargo is lifted, I can talk about an interesting little ditty in Nature Nanotechnology on the use of carbon nanotubes as electrodes (kinda).

The miracle material that has been lauded as the solution to all the world's problems, from space elevators to unsightly scars, appears to integrate with neuronal membrane and conduct electricity with the greatest of ease. One interesting use being discussed is bridging between distal and proximal locations on a single neuron, which would effectively increase the response to inputs that would generally be more muffled by the distance from the soma.

Other possible uses include use as deep stimulating electrodes or electrode tips. Current DBS electrodes are huge compared to the areas they target, and damage is a very real possibility. On the topic of damage, carbon nanotubes are perhaps best known for their tensile strength and flexibility, making them perfect for navigating the densely packed, 3 pound lump of existence creating muck in the skull.

The paper is geared toward the interaction with the neuron's membrane. One thing that might shed some light on this interaction (my words, and I'm not a materials scientist, so i could be completely wrong on this) is a couple previous studies on nanotubes causing cancerous tumors. The effect was likened to asbestos, and injection caused significant inflammation. This could be due to these being shorter fragments or location of the injection, but the interaction with cellular membranes could also be key. To be fair, carbon nanotubes are also being touted as a means to precisely deliver anti-cancer treatments and drugs, so don't think I'm poo-pooing the research by bringing up the cancer link. I'm just pointing out the phenomenon because it might help explain or support the present paper.

It would be worth looking into the scale of the tubes, since a nanotube bridge would also be a cytoplasmic bridge (they are 'tubes'). How big that empty core is would be an important question, since other macromolecules and ions could be shuttled through the new proximal dendrite bypass. As a final thought, if the material itself is conductive, any passing active fiber could unintentionally influence the neuron. If carbon nanotubes are good conductors, then every segment becomes an en passant synapse without any neurotransmitter specificity. Maybe that matters, maybe not. I'm sure we'll see.

I did a quick once over of the paper, and might post a little more later, but I thought it was worth mentioning ASAP and in its own post. At this time of year, interesting papers can sneak by without much notice.

Obama on science

Just awesome.



Oh, and SPF is still coming. I thought I would wait for Nature and Science to get out the door before compiling the last one of the year.

Quick Notes

My desktop PC is borked right now, so updates may actually be more often in the short term. I tend to post from my laptop more for a couple reasons. Looks like I installed, uninstalled, reinstalled, upgraded, downgraded, and ratcheted things until Vista decided I should be punished by inexplicable freezes. In fairness, I have installed a couple hundred different programs, 2-3 dozen devices for product reviews (man, must have been about 8 keyboards alone!), AND the whole thing is an original, launch day install of Vista on an NVidia mobo 1st gen Intel SLI version with two different generation NVidia GPUs (NVidia's crappy-slow response to Vista's driver changes accounted for almost 1/3 of all crashes, according to the crash reports sent to MS). I'm amazed it lasted this long. There's one more thing I might try, but it is looking like a reinstall is needed, and that ain't happening.

So, second note, related to the first. The Intel Core i7 CPUs and chipset are out, and expensive. There is no upgrading from the previous generation - CPUs have different pins and some (I think all as of right now) motherboards support only DDR3. Important to note: If you are planning on buying/upgrading anytime soon, be aware that there is another major socket introduction in ~6 months. By socket, I mean the physical shape and number of pins that mount the CPU to the motherboard. These, too, will neither be compatible with the current (now 'old') crop, NOR the current i7 boards. The current i7 is Socket1366. The upcoming is something like Socket1066. The two i7 sockets will exist at the same time, with the 1366 marketed at enthusiasts and workstations (read: awesome pwnage machines), and the 1066 aimed at consumer and general use machines (read: nublet, whiney l00sorZ). Both will be major upgrades from the current architecture (Socket775). The 1366 has an on dye memory controller, similar to AMD's Hypertransport, meaning massively fast communication between CPU and memory, and no dealing with the rest of the device bus. I believe the 1066 has the memory controller on the mobo, but still dedicated to CPU-RAM communication only. Basically, on dye means faster performance, more upgradable, more transistors on the CPU wafers, and more complexity to manufacture, hence the two lines. So, if you want a blazing fast computer but heard that there is a new upgrade coming out in 6 months, unless you want to wait for the price drops (and that is a legit concern, since mobos are running AT LEAST $200, and the top of the line CPU is $1500 alone), the current 1366 i7 is the way to go. The mainstream 1066 will still be very fast, still outpacing the current architecture (775 that is), so don't think of this as a "Pentium versus Celeron" situation at all. It is more along the lines of the Xeon versus Pentium (not really, but you get the idea). I'll be upgrading to it within the next month, and no, I'm not aiming at the $1500 CPU, thank you very much, but I will post my experience. Maybe a few build pics to go along with it?

Next, as I said, Mendeley is on top of things, and they snuck out an update - 0.6.1 - which resolves the file renaming issue and a couple other bugs. I'd bet that the syncing has been addressed as well, but haven't tried that feature. The site doesn't list it prominently, so just download the installer that is listed in the usual download section. Oh, and the metadata extraction is at least 100x's faster than the 0.5.X versions. Nearly instantaneous. And I didn't notice before, but now you can query the DOI identifiers for metadata that is incorrectly identified. Again, haven't tried it yet, but there seems to be some type of new online check that runs after the metadata extraction that cleans up a ton of minor errors and inconsistencies. I dropped 40 papers in and it failed to extract data from 2, and had slightly messy recognition for 2. The others were perfect. Also, more accurate metadata means less chance of renaming files to ridiculous lengths, though it doesn't look like there is a check in there yet (still gives the fill title name).

Aaaaand... today's SPF will be the last for the year, probably.


Aaaaand... I will be in Iceland for the New Year's celebration, and giving a talk. Details will be posted as I get them. Probably at a nice bar, with drinks to follow. General audience. Come help the Icelandic krona rebound!

Aaaaaaaaand... oh! Almost forgot. Another computer bit. If you want to try a really spiffy music program with all the slickness of iTunes, plus the add-on capabilities of Firefox, and the responsiveness and limited resource use of Notepad (okay, lil more memory, but still great), definitely check our Songbird. This open source, Firefox code based, cross platform, iPod supporting, iTunes library syncing bundle of awesome is, um, awesome! After using iTunes for so long, I forgot what it was like to open my music program in 2 seconds and have buttons click as I click the mouse, rather than 5-10 seconds afterwards (Apple software on Windows machines sucks goat nads). And, it doesn't need 3 different background processes loaded into memory when not in use, oh, AND you don't have to download a crappy video player *coughQuicktimecough*, oh, and it integrates with a bunch of major music services, like Last.fm. No, there is no iTunes store, so iPhone users are stuck there. When my desktop gets working again, I will try syncing my iPhone's music to see if the only issues are app installing and Outlook syncing. I'd expect Outlook syncing to come in the form of an add on sometime within the next 4 months, or so. Anyhow, very excited about this app, as you can tell. I tried it in early beta and was less than impressed, but it has really matured.

SPF

Yup, another big one! EndNote file is here. There are three groups - one for the last SPF, one or this one, and one for all SPFs. Ignore the 'all' group - that's just used to get rid of the extra citations due to searching.

No top 10 list this time, but here are a couple worth noting ;)

Donoghue, J. P. Bridging the brain to the world: a perspective on neural interface systems. Neuron 60, 511-21, doi:S0896-6273(08)00897-0 [pii]
10.1016/j.neuron.2008.10.037 (2008).
Link.

Bedard, P. and Sanes, J. N. Gaze and hand position effects on finger-movement related human brain activation. J Neurophysiol, doi:90683.2008
10.1152/jn.90683.2008 (2008).
Link.

Kim, S. P., Simeral, J. D., Hochberg, L. R., Donoghue, J. P. and Black, M. J. Neural control of computer cursor velocity by decoding motor cortical spiking activity in humans with tetraplegia. J Neural Eng 5, 455-76, doi:S1741-2560(08)86260-X [pii]
10.1088/1741-2560/5/4/010 (2008).
Link.

I may start posting the actual papers to a limited access-type site, so readers of the blog can download them more easily. I have to look into it more, but it should be legal as long as they aren't publicly available. The idea would be that if you want access, you email me with a specific subject, which will automatically spit back the login info or file password.

And now the list...

Abbott, L. F. Theoretical neuroscience rising. Neuron 60, 489-95, doi:S0896-6273(08)00892-1 [pii]
10.1016/j.neuron.2008.10.019 (2008).
Link.

Abernethy, B., Zawi, K. and Jackson, R. C. Expertise and attunement to kinematic constraints. Perception 37, 931-48, (2008).
Link.

Altevogt, B. M., Hanson, S. L. and Leshner, A. I. Molecules to minds: grand challenges for the 21st century. Neuron 60, 406-8, doi:S0896-6273(08)00910-0 [pii]
10.1016/j.neuron.2008.10.036 (2008).
Link.

Ascari, L., Bertocchi, U., Corradi, P., Laschi, C. and Dario, P. Bio-inspired grasp control in a robotic hand with massive sensorial input. Biol Cybern, doi:10.1007/s00422-008-0279-0 (2008).
Link.

Bachev, S. and Petkova, E. A national computer-based epidemiological information system. Methods Inf Med 15, 83-7, (1976).
Link.

Badets, A. and Pesenti, M. The effects of intention and practice on a non-motor duration estimation task. Acta Psychol (Amst) 129, 243-8, doi:S0001-6918(08)00088-7 [pii]
10.1016/j.actpsy.2008.06.006 (2008).
Link.

Ball, T., Demandt, E., Mutschler, I., Neitzel, E., Mehring, C., Vogt, K., Aertsen, A. and Schulze-Bonhage, A. Movement related activity in the high gamma range of the human EEG. Neuroimage 41, 302-10, doi:S1053-8119(08)00171-7 [pii]
10.1016/j.neuroimage.2008.02.032 (2008).
Link.

Balleine, B. W., Liljeholm, M. and Ostlund, S. B. The integrative function of the basal ganglia in instrumental conditioning. Behav Brain Res, doi:S0166-4328(08)00599-8 [pii]
10.1016/j.bbr.2008.10.034 (2008).
Link.

Barriere, G., Leblond, H., Provencher, J. and Rossignol, S. Prominent role of the spinal central pattern generator in the recovery of locomotion after partial spinal cord injuries. J Neurosci 28, 3976-87, doi:28/15/3976 [pii]
10.1523/JNEUROSCI.5692-07.2008 (2008).
Link.

Bedard, P. and Sanes, J. N. Gaze and hand position effects on finger-movement related human brain activation. J Neurophysiol, doi:90683.2008 [pii]
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Link.

Publishing beyond the scientific paper realm

I talked with John D yesterday for a bit about publishing, online resources, and the general structure of the scientific literature world, which was interesting since we come from different backgrounds and generations. He emphasized the importance of the different 'levels' of journals, for instance, that Nature Neuroscience papers are generally better than EBR, etc. I think that can be something that gets wrapped in or emerges from an online community (ala Digg, Reddit, etc.).

Well, fresh off my rss of doom (you should have seen the librarians faces when I said, "Yeah, 900 unread items right now. I'll get through that in about 30-45 minutes." Google Brain FTW), is this bit from The Urban Elitist (via Polymeme) on good ole book publishing, which I often forget about. In the wake of the Kindle's success and Google's agreements with universities and now magazines, the author asks how they will remain a viable business.

Books are significantly different from papers in many, many ways, but they share some similar problems. We still have another 30-50 years before a truly paperless society is possible, and current media have a much shorter lifespan that good ole paper and clay tablets (a topic for another day, but I would not be surprised to see a major project get funded for looking into storage devices that last 10's of thousands of years). Books are unidirectional and stylized, while research papers are really made to be discussed. But, books aren't the TV to primary lit's video games because they, too require active participation, and focused attention.

Anyhow, something worth a few minutes of meditating on.

Oh, and SPF is still coming today...

Online and software options

I met with the university e-resources people yesterday for a couple hours to go over some of the lesser known, start-up type services and programs out there. Below is an excerpt from a follow up email.

For software products, W=Windows, M=Mac, L=Linux.

http://www.mendeley.com/ (WML) (My favorite :) )
http://www.labmeeting.com/signin (Also has a Firefox plugin.)
http://laboratree.org/pages/home
http://ologeez.stanford.edu/
http://jabref.sourceforge.net/index.php (Used by engineering students)
http://www.pubmedreader.com/
http://pubget.com/search (Nice for browsing a journal at a time, but duplicates much of what PubMed does already - email alerts, saved searches, etc. Does allow tagging individual articles and filtering by tags.)
http://www.connotea.org/ (Also has a Firefox plugin, requires disabling Firefox plug in security checks)
http://www.easybib.com/ Bibliography maker
http://www.scribd.com/ Didn't mention, but worth noting. Online, unlimited storage of documents (doc, pdf, txt, ppt, xls + a few more). Can be public or faux-private (the url to the doc can be shared, it just doesn't show up in searches by site visitors or Google).
http://www.nextbio.com/b/home/home.nb Another option I forgot to mention. Has a nice iPhone app that pulls down full text of articles. More about searching through databases and raw results from published datamines.

Few of the old standards:
http://www.citeulike.org
https://www.refworks.com

General web services to note:
http://www.getdropbox.com/ (WML)
Public and private documents. Desktop client syncs indicated folders automatically. Direct link for each file, which can also be accessed from the desktop app side without internet connectivity.
http://www.mediafire.com/about.php?type=1
Unlimited media-only storage. Links to website, where the file link resides (forces other people to visit their site to download, but they don't have to sign up. Can be removed by purchasing a pro account). Provides embedding code for websites.
https://www.mesh.com (WM)
I didn't mention this specifically, but it is part of the Microsoft online universe, and they have done a great job with it. Integrates with the other Live services, which is MS's big push towards cloud computing. Mesh allows the creation of a 'webtop' (web based desktop in the browser) where files can reside. Files can be synced to any computer with the Mesh client installed. The Mesh client also allows the user to log on remotely to any PC in their 'Mesh' that is online and use it as if they were sitting in front of it. Supports Mac, works in Firefox, allows sharing and syncing between any computer (so Mac -> PC and PC -> Mac). Comes with 25GB of remote storage. Mesh is the center around which MS is building their web based applications, so expect it to be everywhere eventually. It is also from their new research division, which actually makes good, interesting, and creative software, and not at all similar to the 'old Microsoft'.
https://www.foldershare.com/ (WM)
Part of the MS Live universe. Automatically syncs folders between computers directly (no Mesh desktop syncing) More online storage options broken down here:
http://lifehacker.com/5064688/online-storage-feature+by+feature-comparison-chart

http://www.evernote.com (WM +iPhone +WinMobile +FF Plugin)
Simple but powerful note taking app. Built in OCR, tagging, syncing between all PCs, free for 40MB, premium account allows 500MB. Allows txt, voice, and picture notes, along with web clippings and files.
http://www.zoho.com/
Before Google Docs, there was Zoho. They are considered neck-and-neck with Google Docs, but Google Docs has the luxury of being integrated with Gmail and all the other widely adopted Google services.
http://feedrinse.com/
I didn't get to talk about this one, but this service filters RSS feeds, repackages them, and then sends them off as a new feed.

RSS in general
Plenty of clients people can download, plenty of web based clients (Google Reader is still ranked as one of the best, and what I use). Open standard, and far more ubiquitous than thought by almost anyone I've talked to in the sciences. Implementing RSS for university services would not be enough - there would have to be a serious push to make faculty and students aware of it.

Software only products:
Bookends: http://www.sonnysoftware.com/ (M)
Papers: http://mekentosj.com/papers/ (M)
IdeaMason: http://www.ideamason.com/default.htm (W) (More of a brainstorming, organization program.)

Mendeley news items

First, I've been messing with the latest Mendeley release, and the performance/speed issues are much improved. Unfortunately, there are several new nasty bugs, which the company is aware of and working on. These problems stem from the complete rewrite of the code that finished just prior to public release (more on this later), so I'd expect them to be in working order very soon (I assume version 0.6.1 will be at the bug-free level of v 0.5.9). The most significant issue is the inability to sync libraries to the server, which will be addressed first. Auto-renaming on Windows (at least) is broken as well, which isn't really a bad thing, since a previous bug could cause trouble for less savvy Windows users - see my post about the file name length issue.

Now, the good/big news is that I got to meet with Victor Henning, one of the two co-founders of Mendeley. Awesome guy, and we ended up talking for about 4 hours about various topics, from research to Mendeley business.

On the topic of the bugs in 0.6.0, Victor mentioned that there were several setbacks in the schedule due to all the non-coding workings which took time from the bug squashing. They promised the new version by the end of November and wanted to deliver on it, which they did, but needed about 2 weeks to work out the new code's kinks. There were some other things, but overall they needed this version out when it was released and getting everything up to the functionality of 0.5.9 is priority #1, and should be a matter of weeks. What's reassuring is that it isn't a case of not knowing what is wrong, or the problems being unexpected. They're on top of it all. Figuring out how to optimize the code and make things run smoother is MUCH more difficult from a coding perspective, so the fact they they addressed that so impressively means the smaller bugs should be cake.

The vision of the program and service, and some of the collaborations (sorry, all hush hush, but the details are very sweet), make me truly excited about the future of the project. The next post will cover some of the similar, but either more unstable or less usable options, and none of them hold a candle to where Mendeley will be in a year, or so. Victor and company are very interested in keeping the system features responsive to users' needs, and the push is far more towards openness and adoption than hoarding and proprietary knowledge. So, I had high expectations and they were all met or exceeded by what I heard.

Oh, and Victor was toting a few interesting books, which I need to look into: Quantum Enigma, Physics Encouters Consciousness by Rosenblum and Kuttner and The Quest for Consciousness by Koch

As a slightly random aside...

One question, of course, is why not go open source? From my perspective (my thoughts only), this is a big project that requires full time resources. Firefox, Linux, and a few other projects are always pointed to as if they are the norm, but there are 10's of thousands of projects that are crap, dead, or updated at a glacial pace, and those are the real norm. We did talk about how a project this size requires investment from outside sources to get off the ground, and those sources are rarely OSS friendly (not unreasonable, especially in the current economic climate). This flies in the face of the official OSSI standing, so you end up in a situation where you are controlled entirely by outside interests. IMO, the OSSI is remarkably close minded for being about 'openness', and abiding by their requirements seems unreasonable.

Updates

Hey all. This time of year always gets crazy, but it seems doubly so this year. I have a half finished SPF, that I'm going to post Friday (I promise!), meetings out the wazoo, grant work, project work, prelim/project layout work, university 'volunteer' work, computer reconfiguring, cat health, condo repairs, oh and hear there's some holiday type things coming up that I need to shop for. Anyhow, enough bitching. Here are some tidbits...

Get it while it's hot!

New version of Mendeley is out (0.6.0) - a big rewrite for the folks there - so go grab it. MUCH snappier, much more refined, nicer looking, easier to use, etc. Overall, a very nice improvement. Word of caution - I haven't had a chance to confirm that my database corrupting bug has been squashed, and the file renaming can still cause the issue I posted about earlier (easy enough to remedy). I'll probably try for a full migration later this week.

Speaking of Mendeley, I'll be meeting with one of the creators this weekend, which should be fun. I'm also meeting next Monday with the university task force for enhancing Brown's electronic resources, so hopefully I will learn about some bits and pieces that slipped by my radar. I'll be preparing a rundown of all the various options out there, so once that is compiled, I will post it here.

Sorry about the lack of updates - duty calls...

Monday break for the weird

Monday afternoon. Meh. Everyone needs a distraction, he here you go...
(btw-I will post some SfN wrapup when I get a chance later this week)

UFO sighting or prophecy of the XBox 360? You decide.

Cortex has a whole issue devoted to the paranormal. Not the totally crazy paranormal, but the more legit stuff, like taking MRIs while 'abductees' recount their abduction experience. Even better, when you read these in the lab, it will look like you are being responsible and checking out literature. Thanks, Heida, for the link.

Alright. Back to work!

SfN Wifi WTF?

Dear SfN,

Your wireless sucks.

Signed,
Everyone

(Posted from my laptop tethered to my iPhone, which is infinitely faster. That's sad.)

Sf'nN

Should be fun! (And educational. And fun!)

SPF format follow-up

I've heard back from a few people, and I think the new format works much better than the previous ones. I am posting the EndNote libraries (ENL files, not papers) to my DropBox account, which seems to work well - just a quick right click for me and no accounts needed for everyone else. If you don't have a drop box account, no need to get one, but it does rock. Personally, I like Microsoft's Live Mesh more, but there's no option to share with people outside the service (now with Mac and Linux Clients).

One person posted that fewer items with a brief rundown would be helpful. The only reason for the long list this tome was that it was the first SPF in over a month, so wading through the papers should be easier when I am good about posting weekly. As for abstracts, there are two options:

1) The links are to the PubMed entry, usually, which means that you can find the papers that look interesting from the titles and stack up a bunch of tabs in the background (hold down control in FF or IE when clicking the link, and if it opens as the active tab, check your preferences). So, the easiest thing to do is just control-click down the list when something piques your interest and load up a bunch of tabs. Do a quick perusal of the abstracts and close the tabs for those that don't interest you.
2) Alternatively, use the EndNote file, which has the abstract included (usually).

I'll try to single out a top 5 or 10 and post them at the top with a brief 1-3 sentences, but they are going to be the ones that I like, meaning they might not mesh with your interests (particularly, there will probably be few EEG/ECoG papers). I do read all the abstracts for these, and they all hit on something worthwhile or of personal interest, so it isn't like I just dump my feeds into the list. The 30 or so weekly papers are chosen out of around 500-1000 that make it to my aggregator, so a great deal of filtering is already in place. I have expanded the criteria a little since beginning in the interest of the site, but that means I no longer read all the papers posted. (I also have a few each week that I don't post for person interest and to keep everyone's idea of my exact project purposely murky.)

So, things will keep evolving, but this is a good start, IMO.