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[0] Shink E, Bevan MD, Bolam JP, Smith Y, The subthalamic nucleus and the external pallidum: two tightly interconnected structures that control the output of the basal ganglia in the monkey.Neuroscience 73:2, 335-57 (1996 Jul)

[0] Bevan MD, Magill PJ, Terman D, Bolam JP, Wilson CJ, Move to the rhythm: oscillations in the subthalamic nucleus-external globus pallidus network.Trends Neurosci 25:10, 525-31 (2002 Oct)[1] Bevan MD, Magill PJ, Hallworth NE, Bolam JP, Wilson CJ, Regulation of the timing and pattern of action potential generation in rat subthalamic neurons in vitro by GABA-A IPSPs.J Neurophysiol 87:3, 1348-62 (2002 Mar)[2] Magill PJ, Bolam JP, Bevan MD, Dopamine regulates the impact of the cerebral cortex on the subthalamic nucleus-globus pallidus network.Neuroscience 106:2, 313-30 (2001)[3] Magill PJ, Bolam JP, Bevan MD, Relationship of activity in the subthalamic nucleus-globus pallidus network to cortical electroencephalogram.J Neurosci 20:2, 820-33 (2000 Jan 15)

[0] Beurrier C, Bezard E, Bioulac B, Gross C, Subthalamic stimulation elicits hemiballismus in normal monkey.Neuroreport 8:7, 1625-9 (1997 May 6)

[0] Elble RJ, Central mechanisms of tremor.J Clin Neurophysiol 13:2, 133-44 (1996 Mar)

[0] Bar-Gad I, Morris G, Bergman H, Information processing, dimensionality reduction and reinforcement learning in the basal ganglia.Prog Neurobiol 71:6, 439-73 (2003 Dec)

[0] Santhanam G, Linderman MD, Gilja V, Afshar A, Ryu SI, Meng TH, Shenoy KV, HermesB: a continuous neural recording system for freely behaving primates.IEEE Trans Biomed Eng 54:11, 2037-50 (2007 Nov)

[0] Musallam S, Corneil BD, Greger B, Scherberger H, Andersen RA, Cognitive control signals for neural prosthetics.Science 305:5681, 258-62 (2004 Jul 9)

[0] Ferrari PF, Rozzi S, Fogassi L, Mirror neurons responding to observation of actions made with tools in monkey ventral premotor cortex.J Cogn Neurosci 17:2, 212-26 (2005 Feb)[1] Maravita A, Iriki A, Tools for the body (schema).Trends Cogn Sci 8:2, 79-86 (2004 Feb)[2] Sanchez J, Principe J, Carmena J, Lebedev M, Nicolelis MA, Simultaneus prediction of four kinematic variables for a brain-machine interface using a single recurrent neural network.Conf Proc IEEE Eng Med Biol Soc 7no Issue 5321-4 (2004)[3] Wood F, Fellows M, Donoghue J, Black M, Automatic spike sorting for neural decoding.Conf Proc IEEE Eng Med Biol Soc 6no Issue 4009-12 (2004)[4] Mehring C, Rickert J, Vaadia E, Cardosa de Oliveira S, Aertsen A, Rotter S, Inference of hand movements from local field potentials in monkey motor cortex.Nat Neurosci 6:12, 1253-4 (2003 Dec)[5] Won DS, Wolf PD, A simulation study of information transmission by multi-unit microelectrode recordings.Network 15:1, 29-44 (2004 Feb)[6] Schmidt EM, Single neuron recording from motor cortex as a possible source of signals for control of external devices.Ann Biomed Eng 8:4-6, 339-49 (1980)[7] Salcman M, Bak MJ, A new chronic recording intracortical microelectrode.Med Biol Eng 14:1, 42-50 (1976 Jan)[8] Patil PG, Carmena JM, Nicolelis MA, Turner DA, Ensemble recordings of human subcortical neurons as a source of motor control signals for a brain-machine interface.Neurosurgery 55:1, 27-35; discussion 35-8 (2004 Jul)[9] Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV, A high-performance brain-computer interface.Nature 442:7099, 195-8 (2006 Jul 13)[10] Brockwell AE, Rojas AL, Kass RE, Recursive bayesian decoding of motor cortical signals by particle filtering.J Neurophysiol 91:4, 1899-907 (2004 Apr)[11] Marzullo TC, Miller CR, Kipke DR, Suitability of the cingulate cortex for neural control.IEEE Trans Neural Syst Rehabil Eng 14:4, 401-9 (2006 Dec)[12] Jackson A, Mavoori J, Fetz EE, Long-term motor cortex plasticity induced by an electronic neural implant.Nature 444:7115, 56-60 (2006 Nov 2)

[0] Mehta MR, Cortico-hippocampal interaction during up-down states and memory consolidation.Nat Neurosci 10:1, 13-5 (2007 Jan)[1] Ji D, Wilson MA, Coordinated memory replay in the visual cortex and hippocampus during sleep.Nat Neurosci 10:1, 100-7 (2007 Jan)

[0] Ji D, Wilson MA, Coordinated memory replay in the visual cortex and hippocampus during sleep.Nat Neurosci 10:1, 100-7 (2007 Jan)

[0] Káli S, Dayan P, Off-line replay maintains declarative memories in a model of hippocampal-neocortical interactions.Nat Neurosci 7:3, 286-94 (2004 Mar)

[0] Foster DJ, Wilson MA, Reverse replay of behavioural sequences in hippocampal place cells during the awake state.Nature 440:7084, 680-3 (2006 Mar 30)

[0] Froemke RC, Merzenich MM, Schreiner CE, A synaptic memory trace for cortical receptive field plasticity.Nature 450:7168, 425-9 (2007 Nov 15)

[0] Rózsa B, Katona G, Kaszás A, Szipöcs R, Vizi ES, Dendritic nicotinic receptors modulate backpropagating action potentials and long-term plasticity of interneurons.Eur J Neurosci 27:2, 364-77 (2008 Jan)

[0] Graybiel AM, The basal ganglia: learning new tricks and loving it.Curr Opin Neurobiol 15:6, 638-44 (2005 Dec)

[0] Maravita A, Iriki A, Tools for the body (schema).Trends Cogn Sci 8:2, 79-86 (2004 Feb)[1] Iriki A, Tanaka M, Iwamura Y, Coding of modified body schema during tool use by macaque postcentral neurones.Neuroreport 7:14, 2325-30 (1996 Oct 2)

[0] Pastalkova E, Itskov V, Amarasingham A, Buzsáki G, Internally generated cell assembly sequences in the rat hippocampus.Science 321:5894, 1322-7 (2008 Sep 5)

[0] Chan SS, Moran DW, Computational model of a primate arm: from hand position to joint angles, joint torques and muscle forces.J Neural Eng 3:4, 327-37 (2006 Dec)

[0] Ashe J, Georgopoulos AP, Movement parameters and neural activity in motor cortex and area 5.Cereb Cortex 4:6, 590-600 (1994 Nov-Dec)

[0] Townsend BR, Paninski L, Lemon RN, Linear encoding of muscle activity in primary motor cortex and cerebellum.J Neurophysiol 96:5, 2578-92 (2006 Nov)

[0] Ferrari PF, Rozzi S, Fogassi L, Mirror neurons responding to observation of actions made with tools in monkey ventral premotor cortex.J Cogn Neurosci 17:2, 212-26 (2005 Feb)

[0] Shidara M, Aigner TG, Richmond BJ, Neuronal signals in the monkey ventral striatum related to progress through a predictable series of trials.J Neurosci 18:7, 2613-25 (1998 Apr 1)

[0] Pollak P, Benabid AL, Gross C, Gao DM, Laurent A, Benazzouz A, Hoffmann D, Gentil M, Perret J, [Effects of the stimulation of the subthalamic nucleus in Parkinson disease]Rev Neurol (Paris) 149:3, 175-6 (1993)

[0] Afanas'ev SV, Tolkunov BF, Rogatskaya NB, Orlov AA, Filatova EV, Sequential rearrangements of the ensemble activity of putamen neurons in the monkey brain as a correlate of continuous behavior.Neurosci Behav Physiol 34:3, 251-8 (2004 Mar)

[0] Kilgard MP, Merzenich MM, Cortical map reorganization enabled by nucleus basalis activity.Science 279:5357, 1714-8 (1998 Mar 13)

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ref: -0 tags: US employment top 100 bar chart date: 11-12-2018 00:02 gmt revision:1 [0] [head]

After briefly searching the web, I could not find a chart of the top 100 occupations in the US. After downloading the data from the US Bureau of Labor Statistics, made this chart:

Click for full-size.

Surprising how very service heavy our economy is.

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ref: -0 tags: kernel regression structure discovery fitting gaussian process date: 09-24-2018 22:09 gmt revision:1 [0] [head]

Structure discovery in Nonparametric Regression through Compositional Kernel Search

  • Use Gaussian process kernels (squared exponential, periodic, linear, and ratio-quadratic)
  • to model a kernel function, k(x,x) which specifies how similar or correlated outputs y and y are expected to be at two points $$x$ and x .
    • By defining the measure of similarity between inputs, the kernel determines the pattern of inductive generalization.
    • This is different than modeling the mapping y=f(x) .
    • It's something more like y=N(m(x)+k(x,x)) -- check the appendix.
    • See also: http://rsta.royalsocietypublishing.org/content/371/1984/20110550
  • Gaussian process models use a kernel to define the covariance between any two function values: Cov(y,y)=k(x,x) .
  • This kernel family is closed under addition and multiplication, and provides an interpretable structure.
  • Search for kernel structure greedily & compositionally,
    • then optimize parameters with conjugate gradients with restarts.
    • This seems straightforwardly intuitive...
  • Kernels are scored with the BIC.
  • C.f. {842} -- "Because we learn expressions describing the covariance structure rather than the functions themselves, we are able to capture structure which does not have a simple parametric form."
  • All their figure examples are 1-D time-series, which is kinda boring, but makes sense for creating figures.
    • Tested on multidimensional (d=4) synthetic data too.
    • Not sure how they back out modeling the covariance into actual predictions -- just draw (integrate) from the distribution?

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ref: -0 tags: platinum parylene electrodes brush dissolving stiffener gelatin date: 12-28-2017 02:44 gmt revision:0 [head]

PMID-27159159 Embedded Ultrathin Cluster Electrodes for Long-Term Recordings in Deep Brain Centers.

  • 12.5um pure Pt wires
  • Coated in 4um parylene-C
  • stiffened with gelatin
  • further protected with Kollicoat to retard dissolution.
  • Used a pulsed UV laser to ablate parylene, cut the platinum, and roughen the recording site.
  • See also {311}

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ref: -0 tags: photoacoustic tomography mouse imaging q-switched laser date: 05-11-2017 05:23 gmt revision:1 [0] [head]

Single-impulse panoramic photoacoustic computed tomography of small-animal whole-body dynamics at high spatiotemporal resolution

  • Used Q-switched Nd:YAG and Ti:Sapphire lasers to illuminate mice axially (from the top, through a diffuser and conical lens), exciting the photoacuostic effect, from which they were able to image at 125um resolution a full slice of the mouse.
    • I'm surprised at their mode of illumination -- how do they eliminate the out-of-plane photoacoustic effect?
  • Images look low contrast, but structures, e.g. cortical vasculature, are visible.
  • Can image at the rep rate of the laser (50 Hz), and thereby record cardiac and pulmonary rhythms.
  • Suggest that the photoacoustic effect can be used to image brain activity, but spatial and temporal resolution are limited.

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ref: -0 tags: photoacoustic tomography mouse imaging q-switched laser date: 05-11-2017 05:21 gmt revision:0 [head]

Single-impulse panoramic photoacoustic computed tomography of small-animal whole-body dynamics at high spatiotemporal resolution

  • Used Q-switched Nd:YAG and Ti:Sapphire lasers to illuminate mice axially, exciting the photoacuostic effect, from which they were able to image at 125um resolution a full slice of the mouse.
  • Images look low contrast, but structures, e.g. cortical vasculature, are visible.
  • Can image at the rep rate of the laser (50 Hz), and thereby record cardiac and pulmonary rhythms.
  • Suggest that the photoacoustic effect can be used to image brain activity, but spatial and temporal resolution are limited.

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ref: -0 tags: juxtacellular recording gold mushroom cultured hippocampal neurons Spira date: 02-01-2017 02:44 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

Large-Scale Juxtacellular Recordings from Cultured Hippocampal Neurons by an Array of Gold-Mushroom Shaped Microelectrodes

  • Micrometer sized Au mushroom MEA electrodes.
  • Functionalized by poly-ethylene-imine (PEI, positively charged)/laminin (extracellular matrix protein) undergo a process to form juxtacellular junctions between the neurons and the gMµEs.
  • No figures, but:
    • Whereas substrate integrated planar MEA record FPs dominated by negative-peak or biphasic-signals with amplitudes typically ranging between 40-100 µV and a signal to noise ratio of ≤ 5,
    • The gMµE-MEA recordings were dominated by positive monophasic action potentials.
    • It is important to note that monophasic high peak amplitudes ≥ 100 µV are rarely obtained using planar electrodes arrays, whereas when using the gMµE-MEA, 34.48 % of the gMµEs recorded potentials ≥ 200 µV and 10.64 % recorded potentials in the range of 300-5,085 µV.
  • So, there is a distribution of coupling, approximately 10% "good".

PMID-27256971 Multisite electrophysiological recordings by self-assembled loose-patch-like junctions between cultured hippocampal neurons and mushroom-shaped microelectrodes.

  • Note 300uV - 1mV extracellular 'juxtacellular' action potentials from these mushroom recordings. This is 2 - 5x better than microwire extacellular in-vivo ephys; coupling is imperfect.
    • Sharp glass-insulated W electrodes, ~ 10Mohm, might achieve better SNR if driven carefully.
  • 2um mushroom cap Au electrodes, 1um diameter 1um long shaft
    • No coating, other than the rough one left by electroplating process.
    • Impedance 10 - 25 Mohm.
  • APs decline within a burst of up to 35% -- electrostatic reasons?
  • Most electrodes record more than one neuron, similar to in-vivo ephys, with less LFP coupling.

PMID-23380931 Multi-electrode array technologies for neuroscience and cardiology

  • The key to the multi-electrode-array ‘in-cell recording’ approach developed by us is the outcome of three converging cell biological principals:
    • (a) the activation of endocytotic-like mechanisms in which cultured Aplysia neurons are induced to actively engulf gold mushroom-shaped microelectrodes (gMμE) that protrude from a flat substrate,
    • (b) the generation of high Rseal between the cell’s membrane and the engulfed gMμE, and
    • (c) the increased junctional membrane conductance.
  • Functionalized the Au mushrooms with an RGD-based peptide
    • RGD is an extracellular matrix binding site on fibronectin, which mediates it's interaction with integrin, a cell surface receptor; it is thought that other elements of fibronectin regulate specificity with its receptor. PMID-2418980

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ref: -0 tags: Kleinfeld vasculature cortex review ischemia perfusion date: 01-22-2017 19:40 gmt revision:3 [2] [1] [0] [head]

PMID-25705966 Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture.

  • "The penetrating arterioles that connect the pial network to the subsurface network are bottlenecks to flow; occlusion of even a single penetrating arteriole results in the death of a 500 μm diameter cylinder of cortical tissue despite the potential for collateral flow through microvessels."
  • The pioneering work of Fox and Raichle [7] suggest that there is simply not enough blood to go around if all areas of the cortex were activated at once.
  • There is strong if only partially understood coupling between neuronal and vascular dysfunction [15]. In particular, vascular disease leads to neurological decline and diminished cognition and memory [16].
  • A single microliter of cortex holds nearly one meter of total vasculature length wow! PMID-23749145
  • Subsurface micro vasculature (not arterioles or venules) is relatively robust to occlusion; figure 4.

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ref: -0 tags: polyimide aqueous degradation kapton date: 01-22-2017 05:51 gmt revision:0 [head]

Aqueous degradation of polyimides

  • Above ph 2, Kapton (PMDA-ODA) test specimens decreased both tensile strength and elongation to break with water, with a rate that increased with temperature.
  • No samples completely degraded, however; tensile strength decreased by about 2x, and elongation from 30% to 5%.
  • The authors suspect that ortho (off-molecular axis) amide bonding, at about 0.6% of the total number of imide bonds, is responsible for this (otherwise the film would completely fall apart.)
  • Imide bonds themselves are robust to all but strong bases and acids.
  • See also {1253}.

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ref: -0 tags: serial electron microscopy Lichtman reconstruction nervous tissue date: 01-17-2017 23:32 gmt revision:0 [head]

PMID-26232230 Saturated Reconstruction of a Volume of Neocortex.

  • Data presented at Cell "Big Questions in Neuroscience", perhaps the most impressive of the talks.

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ref: -0 tags: LCP polymer Zeus tensile modulus date: 11-11-2016 20:39 gmt revision:0 [head]


  • UTS 1.0 GPa; 80 MPa Youngs modulus.
  • No data on moisture uptake or molecular structure.

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ref: -0 tags: china trustwothiness social engineering communism date: 10-31-2016 05:42 gmt revision:1 [0] [head]

China 'social credit': Beijing sets up huge system

So long as it purports to measure just one social variable -- 'trustworthiness' -- it might be a good idea. Many commerce websites (.. ebay ..) have these sort of rating systems already, and they are useful. When humans live in smaller communities something like this is in the shared consciousness.

Peering into everyone's purchasing habits and hobbies, however, seems like it will be grossly myopic and, as the article says, Orwellian. Likely they will train a deep-belief network on past data of weakly and communist party defined success, with all purchasing and social media as the input data, and use that in the proprietary algorithm for giving people their scalars to optimize. This would be the ultimate party control tool -- a great new handle for controlling people's minds, even 'better' than capitalism.

Surprising that the article only hints at this, and that the Chinese themselves seem rather clueless that it's a power play. In this sense, it's a very clever play to link it to reproduction.

Other comments:

These sorts of systems may be necessary in highly populated countries, where freedom and individuality are less valued and social cohesion is requisite.

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ref: -0 tags: tungsten rhenium refactory metals book russia metalurgy date: 10-31-2016 05:14 gmt revision:1 [0] [head]

Physical Metallurgy of Refactory Metals and Alloys

Properties of tungsten-rhenium alloys

  • Luna metals suggests 3% Re improves the tensile strength of the alloy; Concept Alloys has 26% Re.
  • This paper mesured 20% Re, with a strength of 1.9 GPa; actual drawn tungsten wire has a strength of 3.3 GPa.
    • Drawing and cold working greatly affects metal, as always!

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ref: -0 tags: David Kleinfeld penetrating arterioles perfusion cortex vasculature date: 10-17-2016 23:24 gmt revision:1 [0] [head]

PMID-17190804 Penetrating arterioles are a bottleneck in the perfusion of neocortex.

  • Focal photothrombosis was used to occlude single penetrating arterioles in rat parietal cortex, and the resultant changes in flow of red blood cells were measured with two-photon laser-scanning microscopy in individual subsurface microvessels that surround the occlusion.
  • We observed that the average flow of red blood cells nearly stalls adjacent to the occlusion and remains within 30% of its baseline value in vessels as far as 10 branch points downstream from the occlusion.
  • Preservation of average flow emerges 350 mum away; this length scale is consistent with the spatial distribution of penetrating arterioles
  • Rose bengal photosensitizer.
  • 2p laser scanning microscopy.
  • Downstream and connected arterioles show a dramatic reduction in blood flow, even 1-4 branches in; there is little reduncancy (figure 2)
  • Measured a good number of vessels (and look at their density!); results are satisfactorily quantitative.
  • Vessel leakiness extends up to 1.1mm away (!) (figure 5).

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ref: -0 tags: David Kleinfeld cortical vasculature laser surgery network occlusion flow date: 09-23-2016 06:35 gmt revision:1 [0] [head]

Heller Lecture - Prof. David Kleinfeld

  • Also mentions the use of LIBS + q-switched laser for precisely drilling holes in the scull. Seems to work!
    • Use 20ns delay .. seems like there is still spectral broadening.
    • "Turn neuroscience into an industrial process, not an art form" After doing many surgeries, agreed!
  • Vasodiliation & vasoconstriction is very highly regulated; there is not enough blood to go around.
    • Vessels distant from a energetic / stimulated site will (net) constrict.
  • Vascular network is most entirely closed-loop, and not tree-like at all -- you can occlude one artery, or one capillary, and the network will route around the occlusion.
    • The density of the angio-architecture in the brain is unique in this.
  • Tested micro-occlusions by injecting rose bengal, which releases free radicals on light exposure (532nm, 0.5mw), causing coagulation.
  • "Blood flow on the surface arteriole network is insensitive to single occlusions"
  • Penetrating arterioles and venules are largely stubs -- single unbranching vessels, which again renders some immunity to blockage.
  • However! Occlusion of a penetrating arteriole retards flow within a 400 - 600um cylinder (larger than a cortical column!)
  • Occulsion of many penetrating vessels, unsurprisingly, leads to large swaths of dead cortex, "UBOS" in MRI parlance (unidentified bright objects).
  • Death and depolarizing depression can be effectively prevented by excitotoxicity inhibitors -- MK801 in the slides (NMDA blocker, systemically)

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ref: -0 tags: nucleus accumbens caudate stimulation learning enhancement MIT date: 09-20-2016 23:51 gmt revision:1 [0] [head]

Temporally Coordinated Deep Brain Stimulation in the Dorsal and Ventral Striatum Synergistically Enhances Associative Learning

  • Monkeys had to learn to associate an image with one of 4 reward targets.
    • Fixation period, movement period, reward period -- more or less standard task.
    • Blocked trial structure with randomized associations + control novel images + control familiar images.
  • Timed stimulation:
    • Nucleus Accumbens during fixation period
      • Shell not core; non-hedonic in separate test.
    • Caudate (which part -- targeting?) during feedback on correct trials.
  • Performance on stimulated images improved in reaction time, learning rate, and ultimate % correct.
  • Small non-significant improvement in non-stimulated novel image.
  • Wonder how many stim protocols they had to try to get this correct?

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ref: -0 tags: DBS dystonia globus pallidus witt date: 10-05-2013 23:42 gmt revision:2 [1] [0] [head]

PMID-23549056 Use of pallidal deep brain stimulation in postinfarct hemidystonia.

  • Witt J, Starr PA, Ostrem JL. 2013
  • Result: GPi DBS generates subjective improvements in movement after surgery;
  • However, one year after implantation, no effect could be measured.
  • See also: {1263}

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ref: -0 tags: DBS dystonia trial globus pallidus GPI witt date: 10-05-2013 23:41 gmt revision:1 [0] [head]

PMID-23787946 Predictive factors of outcome in primary cervical dystonia following pallidal deep brain stimulation.

  • Witt JL, Moro E, Ash RS, Hamani C, Starr PA, Lozano AM, Hodaie M, Poon YY, Markun LC, Ostrem JL. 2013
  • Some of the treatments do work, but the authors were unsuccessful in determining criteria to suggest proper candidates.

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ref: -0 tags: buszaki watson oscillations review gamma theta hippocampus cortex date: 09-30-2013 18:32 gmt revision:2 [1] [0] [head]

PMID-23393413 Brain rhythms and neural syntax: implications for efficient coding of cognitive content and neuropsychiatric disease.

  • His frequency band standards:
    • delta: 1.5 - 4Hz
    • theta: 4 - 10Hz
    • beta: 10 - 30 Hz
    • gamma: 30 - 80Hz
    • fast: 80 - 200 Hz
    • ultra fast: 200 - 600 Hz.
  • comodugram: power-power correlelogram
  • Reviews current understanding of important rhythms:
    • How gamma is preserved amongs mammals, owing to the same fundamental mechanisms (membrane time constant, GABA transmission, AMPA receptior latency) all around 25ms; suggests that this is a means of tieing neurons into meaningful groups. or symbols; (solves the binding problem?)
    • Theta rhythm, in comparison, varies between species, inversely based on the size of the hippocampus. Larger hippocampus -> greater axonal delay.
    • These and other the critical step is to break neurons into symbols (as part of a 'language' or sequenced computation), not arbitrarily long trains of spikes which are arbitrarily difficult to parse.
  • Reviews the potential role of oscillations in active sensing, though with a rather conjectorial voice: suggests that sensory systems
  • Suggests that neocortical slow-wave oscillations during sleep are critical for transferring information from the hippocampus to the cortex: the cortex become excitable at particular phases of SWS, which biases the fast ripples from the hippocampus. During wakefulness, the direction is reversed -- the hippocampus 'requests' information from the neocortex by gating gamma with theta rhythms.
  • "Typically, when oscillators of different freqencies are coupled, the network oscillation frequency is determined by the fastest one. (??)
  • I actually find figure 3 to be rather weak -- the couplings are not that obvious, espeically if this is the cherry-picked example.
  • Cross phasing-coupling, or n:m coupling: one observes m events associated with the “driven” cycle of one frequency occurring at n different times or phases in the “stimulus” cycle of the other.
    • The mechanism of cross-frequency coupling may for the backbone of neural syntax, which allows for both segmentation and linking of cell assemblies into assemblies (leters) and sequences (words). Hmm. this seems like a stretch, but I am ever cautious.
  • Brain oscillations for quantifiable phenotypes! e.g. you can mono-zygotic twins apart from di-zygotic twins.

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ref: -0 tags: asynchronous design Rajit Manohar Octasic date: 06-12-2013 00:19 gmt revision:5 [4] [3] [2] [1] [0] [head]

At Cornell I took a VLSI design class taught by Rajit Manohar (*), and even then - 2002/2003 - he was very excited about asynchronous circuit design. I was uncertain about the technology at the time, but generally I trusted his instinct. Seems that there is certainly some oil in those hills - Octasic has just released a new basestation IC based on asynchronous processor cores: http://www.octasic.com/en/products/oct2200/oct2224w.php

The associated product-brief/technology whitepaper gives some good motivations for why asynchronous design is superior to classical synchronous design: (I'll quote, since I find this fascinating, hope they don't mind!)

  • Elimination of clock trees - Synchronous high-speed processors require large clock trees to keep sequential blocks synchronized. These clock trees require high-power buffers to drive complex high-capacitance networks that cover most of the chip. Clocks change state twice per cycle, consuming power on both positive and negative edges. These clock trees do not perform any information processing, thus provide no useful computing work, yet they consume a significant portion of the total power. Eliminating the clock trees alone can reduce power consumption by as much as 40% in a high-performance processor.
  • Elimination of pipeline state elements - Modern synchronous high-performance processors rely heavily on pipeline design techniques. Those pipelines require the use of a very large number of inter-stage flip-flops and state elements to support a high clock frequency operation. However, these inter-stage flip-flops and state elements also dont contribute to the actual data processing and computing tasks performed by the processor. In an asynchronous design these storage elements are discarded, saving the silicon space they occupy and the large amount of power they consume.
  • Elimination of lost margin timing - These inter-stage flip-flops require set-up and hold times which force a significant portion of the time between clock edges to be unusable for computation in high-frequency synchronous designs. Moreover given that each sub-micron technology shrink tends to increase path timing uncertainty, this further shortens the active period that can be used to achieve useful work between clock edges. This also means that in a synchronous design, the inter-stage circuit logic needs to be designed to operate increasingly faster than a single clock period to perform the same work. This requires the increased use of larger, higher power buffers in the datapath. In an asynchronous processor design, the logic does not have to deal with such small time steps. They can be built using slower, smaller and lower power circuits, while still delivering the same level of overall performance. Because the gates can be slower, it allows more use of low-leakage high-threshold voltage (HVT) gates, which drastically reduces leakage and further reduces power consumption and die area.
  • Reducing wire interconnect length -The silicon area savings discussed above translate into even more power savings, because wires connecting two elements get shorter as the circuits between these elements shrink. Shorter wires have less capacitance, thus switching them requires less power by using smaller buffers

Cool! I expect to see these techniques in many processors in the future - from embedded, very power sensitive MCUs to GPUs!

(*) Rajit was a cool guy. Not only did he give us a good grade, but he even drove us 'downtown' (in the sense of down the hill, Ithaca doesn't really have a downtown) at one point to pick up some resistors and other electronic parts so we could test out MOSIS-fabricated ASIC.

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ref: -0 tags: brain mapping recording Yuste date: 04-10-2013 19:31 gmt revision:1 [0] [head]

PMID-22726828 The Brain Activity Map Project and the Challenge of Functional Connectomics

  • They are more interested in every neuron within a local circuit, e.g. cortical column.
  • Referenced papers, optical:
    • Yuste et al 2011 -- referenced several times.
    • Helmchen 2011
    • Yuste and Katz 1991 (calcium)
    • Grienberger and Konnerth 2012 (1000 recorded neurons)
    • Peterka 2011 -- voltage imaging
    • Mochalin 2012 -- nanodiamonds.
  • The optical techniques only gets you .. 400um? 2mm?
    • Suggest GRIn objectives for invasive recording of the e.g. hippocampus.
  • Interesting: DNA polymerases could be used as spike sensors since their error rates are dependent on cation concentration.
    • use synthetic cells, then sequence the molecular recording.
  • The Drosophila connectome is currently 20% complete at the mesoscale (Chiang et al 2011)
    • Drosophila has 135,000 neurons
  • Bock et al 2011 have reconstructed 1,500 cell bodies with 1e13 pixels.
  • In the human genome project, every dollar invested generated $141 in the economy. (Battelle 2011).

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ref: -0 tags: polymide flexible electrode Rousche incision needle assist date: 01-30-2013 06:38 gmt revision:3 [2] [1] [0] [head]

PMID-11327505 Flexible Polyimide-Based Intracortical Electrode Arrays with Bioactive Capability

  • Use gold / polymide fabrication; electrode is 20um thick, 160um wide.
  • Still quite flexible -- buckles at 0.003 N.
  • Successfully recorded by inserting it in an incision in rat barrel cortex -- needle assist.
    • Well, not too successfully.
  • Suggest that bioactive components can be applied to the permeable polymide surface.


' ''' ()

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ref: Kruger-2010.05 tags: microelectrode array nichrome 7 years rhesus electrophysiology MEA Kruger oblique inverted date: 01-29-2013 07:54 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-20577628[0] Seven years of recording from monkey cortex with a chronically implanted multiple electrode.

  • Seven years!! good recordings the whole time, too. As they say, this is a clinically realistic time period. Have they solved the problem?
  • Used 12.5um Ni-Cr-Al wire insulated with 3um of polymide.
    • Wires were then glued to an 8x8 connector block using conductive epoxy.
    • Glued the bundle together with a solution of plexiglas in dichloroethane.
    • Then introduced the 0.3mm bundle into a j-shaped cannula. This allowed them to approach the gray matter inverted, from below (the white matter).
    • implanted 64 ch array into ventral premotor cortex (arm representation?).
  • No apparent degradation of recording quality over that time.
  • Had some serious problems with the quality of their connector.
    • They recommend: "Rather, the contacts on the head should be made from noble metals and be flat or shallowly hollow, so that they can be easily cleaned, and no male contacts can break."
    • Really need to amplify and multiplex prior connector (imho).
  • Claim that them managed to record from two neurons on one channel for nearly 7 years (ch 54).
  • They cite us, but only to indicate that we recommend slow penetration of the brain. They agree with our results that lowering of individual electrodes is better than all at once.


[0] Kruger J, Caruana F, Volta RD, Rizzolatti G, Seven years of recording from monkey cortex with a chronically implanted multiple microelectrode.Front Neuroengineering 3 Issue 6 (2010 May 28)

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ref: Chhatbar-2010.05 tags: Lee von Kraus Francis SUNY downstate electrode floating headpost date: 01-28-2013 01:06 gmt revision:1 [0] [head]

PMID-20153370[0] A bio-friendly and economical technique for chronic implantation of multiple microelectrode arrays

  • Nesting design -- the headpost is the only transcutaneous object.


[0] Chhatbar PY, von Kraus LM, Semework M, Francis JT, A bio-friendly and economical technique for chronic implantation of multiple microelectrode arrays.J Neurosci Methods 188:2, 187-94 (2010 May 15)

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ref: Musallam-2007.02 tags: Musallam MEA floating rats electrodes date: 01-28-2013 00:42 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-17067683[0] A floating metal microelectrode array for chronic implantation

  • Cite Gualtierotti and Bailey (1968) for a neutral-boyancy electrode w/ rigid shaft.
  • Alumina ceramic base, laser drilled.
  • insulated with silane follwed by parylene-C, 3um.
  • Tips exposed by eximer laser. (Schmidt et al, 1995)
  • Electrophysiology, but not histology.
  • Earlier conference proceedings: PMID-17946982[1] Active floating micro electrode arrays (AFMA).


[0] Musallam S, Bak MJ, Troyk PR, Andersen RA, A floating metal microelectrode array for chronic implantation.J Neurosci Methods 160:1, 122-7 (2007 Feb 15)
[1] Kim T, Troyk PR, Bak M, Active floating micro electrode arrays (AFMA).Conf Proc IEEE Eng Med Biol Soc 1no Issue 2807-10 (2006)

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ref: -0 tags: neural recording McGill Musallam electrodes date: 07-12-2012 22:53 gmt revision:0 [head]

http://www.mdpi.com/1424-8220/8/10/6704/pdf NeuroMEMS: Neuro Probe Microtechnologies

  • Good review (as of 2008) of the many different approaches for nervous system recording.

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ref: Rosin-2011.1 tags: PD closed loop DBS globus pallidus oscillations STN Vaadia heterodyne beta date: 03-26-2012 16:23 gmt revision:16 [15] [14] [13] [12] [11] [10] [head]

PMID-22017994[0] Closed-loop deep brain stimulation is superior in ameliorating parkinsonism.

  • Also reviewed by Rui Costa: PMID-22017983[1]
    • Good, brief review -- with appropriate minimal references.
  • Partial goal of the work: parameter determination and optimization can take a long time, and are typically only done every 3-6 months initially. But the actually changes of activity / responsiveness occur on a faster timescale in the disease, even instantaneous; other studies have shown that updating the stimulation parameters more frequently helps patients. (of course, this is a different form of closed-loop).
  • Pathology: intermittent neuronal oscillations in the basal ganglia and motor cortex commonly observed.
    • In MPTP treated primates these oscillations occur in the tremor band (theta, 4-7Hz), and double-tremor band (9-15Hz, alpha) (Bergman et al 1994 {120}, Ras et al 2000 PMID-11069964 ).
    • Actual pathology still inconclusive; talk about disruption of pathological patterns and 'focal inhibition', but this is no thorough review by any estimate.
  • "In recent years, the role of pathological discharge patterns in the parkinsonian brain has emerged as pivotal in the disease pathology
    • Eusebio and Brown, 2007;
    • Hammond et al., 2007;
    • Kuhn et al., 2009;
    • Tass et al., 2010;
    • Vitek, 2008;
    • Weinberger et al., 2009;
    • Wichmann and DeLong, 2006;
    • Zaidel et al., 2009.
    • Automatic systems should disrupt this pattern of discharge (Feng 2006, Tass 2003).
      • However, the role of these oscillations as the neuronal correlate of PD motor symptoms is still debated (Hammond et al., 2007; Leblois et al., 2007; Lozano and Eltahawy, 2004; McIntyre et al., 2004; Tass et al., 2010; Vitek, 2002; Weinberger et al., 2009 {1089}).
  • 2 african green monkeys, MPTP treatment.
  • Recorded from GPi & M1 (127 and 210 neurons); stimulated GPi, 7 pulses at 130Hz, 80ms after spike from reference area (M1 or GPi).
    • 80ms delay coincided with the next double-tremor oscillatory burst (12.5Hz)
    • State of neuronal oscillatory discharge of cortico-BG loops often accompanied by synchronization btw cortex and BG (see also quote below)
    • GPi following M1 activity superior (GP|M1 in their notation).
    • single pulses did not work.
    • Stimulation: 80uA 200us bipolar biphasic (small and short!).
  • Stimiulus protocol (M1 trigger) abolishes oscillatory activity in recorded GPi neurons.
  • Also reduced akinesia as measured with an accelerometer & decreased firing rate in the GPi.
    • Both work better than constant 130Hz DBS.
    • Also much more irregular: fewer stimulation pulses at longer latency.
  • Open loop control (the control) did much less regarding FR oscillations & bursts and reduction in firing rate.
    • Dorval et al 2010: increasing the stimulus irregularity of open-loop DBS decreases its beneficial clinical effectcs. (also Baker et. al 2011).
  • GP train stimulation triggered on GP firing significantly worsened akinesia, despite the fact that the pallidial FR decreased.
    • Treatment increased spike oscillation at double-tremor frequency in M1.
  • Oscillations more important than firing rate changes (new vs. old hypothesis).
    • pallidal oscillatory activity was not correlated to the pallidal discharge rate either before or during the application of standard DBS or GP|M1.
  • In our data, may have double-frequency tremor effects. Heterodyne should detect this.
    • "Studies on the dynamics of the entire cortico-basal ganglia loops have frequently reported the emergence of intra-and interloop component synchrony and oscillatory activity."
    • "Nevertheless, the somewhat intuitive connection between neuronal oscillations and parkinsonian motor symptoms, which include rest and action tremors, has been challenged (Hammond et al., 2007 PMID-17532060 ; Leblois et al., 2007 {1146}; Lozano and Eltahawy, 2004; Tass et al., 2010 {1147}; Vitek, 2002; Weinberger et al., 2009). For instance, while the parkinsonian rest tremor occurs mainly at the 4–7 Hz frequency band, the oscillatory neuronal activity is observed in several characteristic frequency bands in both human PD patients (Hutchison et al., 2004) {1156} and animal models (Bergman et al 1994, Gubellini et al 2009) {1074}"
      • This also has import to our heterodyne results!
    • Synchrony between globus pallidus and M1 is dynamic and state-dependent (whatever that means -- have to check the refs, Levy et al 2002 {829}, Timmerman et al 2003 {1087})
  • Quote: "... it suggests that reduction of the abnormal parkinsonian oscillatory activity could in fact be the underlying mechanism by which DBS exerts its action and brings about the associated clinical improvement."
  • Neuronal oscillatory activity occurs as high as the beta-band, 15-35Hz, hence clinical app. would need a tuned antiphase lag.
  • Suggest that the closed-loop treatment may be applicable to other diseases with characteristic firing patterns, like schizophrenia.
  • Since synchonization and oscillations hend to coincide, .. we found this too.
    • Heimer et al 2006 {1076}: oscillations and synchrony can exist independently.
  • Figure suck. Text inconsistent and frequently too small.
    • Wavelet spectrograms are nice tho.

Other thoughts:

  • Somebody should measure the transfer function of the BG / cortical loop. H(z).
  • This seems like adding a comb-filter or zero at a particular frequency: GP|GP stimluation exacerbated the effect, GP|M1 minimized the effect as there is a negation in there. (e.g. GP actviity decreases firing of M1, and vice versa).


[0] Rosin B, Slovik M, Mitelman R, Rivlin-Etzion M, Haber SN, Israel Z, Vaadia E, Bergman H, Closed-loop deep brain stimulation is superior in ameliorating parkinsonism.Neuron 72:2, 370-84 (2011 Oct 20)
[1] Santos FJ, Costa RM, Tecuapetla F, Stimulation on demand: closing the loop on deep brain stimulation.Neuron 72:2, 197-8 (2011 Oct 20)

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ref: -0 tags: Hutchison oscillations basal ganglia beta gamma globus pallidus date: 03-26-2012 16:21 gmt revision:2 [1] [0] [head]

PMID-15496658 Neuronal oscillations in the basal ganglia and movement disorders: evidence from whole animal and human recordings.

  • This is a review / mini-symposium (only 3 pages)
    • Cites other Hutchison papers: 1997, 1998.
  • Critique classical hypothesis in that GPi firing does not increase that much, 10-22% in animal models. IT explains akinesia and bradykinesia, but not rigidity or tremor. (This was 8 years ago, remember!)
    • Plus, most neurons have intrinsic pacemaker-like properties that sets the rate of firing in the absence of synaptic input. (Bevan et al 2002).
  • Oscillations:
    • Alpha band enhanced after MPTP treatment in green monkeys and in the STN of some PD patients with tremor at rest.
    • Higher frequency oscillations (beta, 15-25Hz) can be observed in some patients without resting tremor.
    • Much slower oscillations discovered by Judith Walters, 6 OHDA rat (0.3 - 2Hz).
    • Also ultralow, multisecond oscillations, which appear in dopamine stimulated rats. (Ruskin et al 1999a,,b, 2003).
      • Lesion of the STN was not found to change these ultralow oscillations, but did modify the connectivity between GP and SNr.
    • Courtemanche et al 2003 studied the possible normal physiological function for oscillations in basal ganglia networks.
      • Beta band decreased during saccadic eye movements.
      • LFP syncronization showed task-related decrease, but only in sites engaged in the task, as evicenced by saccade-related activity.
  • Boraud tested gradual small-dose administration of MPTP toxin:
    • Minimal changes in the average firing rate of GPi neurons
    • Oscillatory activity between 4-9 and 11-14 Hz, with differences between monkeys.
      • Oscillations increased with symptom presentation.
  • Goldberg et al 2004: analyzed coherence between EEG and BG LFP; surmise that in the PD condition the basal ganglia and cortex become more closely entrained by global brain dynamics, which are reflected in the widespread local field potentials.
  • Peter Brown: oscillations in the beta band are enhanced to such an extent in Parkinson's disease that voluntary movements are not generated because motor command for initiation cannot override the enhanced oscillatory state.
    • That is, movement initiation corresponds to beta-band desynchronization, and movement command cannot 'break through'.

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ref: -0 tags: hippocampus theta oscillations memory date: 03-18-2012 18:09 gmt revision:0 [head]

PMID-21696996 The hippocampus: hub of brain network communication for memory

  • Their hypothesis: memory encoding is dominated by theta oscillations 6-10 Hz; during inactivity, hippocampal neurons burst synchronously, creating sharp waves, theoretically supporting memory consolidation.
  • (They claim): to date there is no generally accepted theoretical view on memory consolidation.
  • Generally it seems to shift from hippocampus to neocortex, but still, evidence is equivocal. (Other than HM & other human evidence?)
  • Posit a theory based on excitation ramps of reverse-replay, which seems a bit fishy to me (figure 3).
  • Didn't know this: replay in visual and PFC can be so precise that it preserves detailed features of the crosscorrelograms between neurons. [58, 65, 81].

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ref: -0 tags: hippocampus theta oscillations date: 03-18-2012 17:34 gmt revision:2 [1] [0] [head]

PMID-11832222 Theta Oscillations in the Hippocampus

  • Theta-alpha oscillations have been found in 'all mammals to-date, including humans. (Hence conserved, hence possibly essential).
    • Prevalent in REM sleep.
    • Present in slices bathed in carbachol, too.
    • As well as locomotor activities; but not usually when the animal is resting.
  • Other reviews: Bland 1986, VAnderwolf 1988, Lopes da Silva et al 1990, Buzaki et al 1994 Stewart and Fox 1990, Vinogradova 1995, Vertex and Kocsis 1997.
    • Modeling reviews used passive cable properties; actually, it seems neurons, and their dendrites are have active conductances & active oscillatory features.
  • Theta oscillations most strongly present in CA1
  • Along similar lamina, oscillations are similar.
  • Osc. visible in cortical structures ...
    • subicular complex, entorhinal cortex, perirhinal cortex, cingulate cortex, amygdala -- though none of these structures are capable of generating theta oscillations intrinsically.
  • Also apparent in subcortical structures,
    • Dorsal raphe nucleus, ventral tegmental nucleus, and anterior thalamic nuclei. None of these seem required for oscillation, however:
  • Oscillations may emanate from the medial-septum-diagonal band of Broca (MS-DBB); lesion inactivates theta oscillations in all cortical areas, but the relative role is uncertain, as MS-DBB oscillations may require hippocampal and entorhinal afferents.
    • EPSPs brought about by the MS-DBB cholinergic neurons on hippocampal pyramidal cells cannot be responsible for the atrophine-sensitive form of theta.
    • That said, even though atrophine treatment only modestrly affects theta, it is reduced several-fold after selective neurotoxin elminiation of MS-DBB cholinergic cells -- maybe it's nicotinic synapses?
  • Drugs:
    • Theta can be blocked by GABA antagonist (picrotoxin, induces epilepsy) or agonist (pentoparbital anesthesia).
    • Many other drugs affect oscillations.
    • Broken down into atrophine-sensitive and atrophine-resistant oscillations.
      • (Atrophine blocks muscarinic Ach receptors).
    • Amplitude and frequency of theta does not appreciably change even after large doses of systematic muscarinic blockers.
      • Same drugs abolish theta under anesthesia.
    • The neurotransmitter and receptor causative in theta have never been clearly determined.
  • Theta in CA3 is much smaller than in CA3:
    • Distal dendritic arbor of CA3 pyramidal cells is considerably smaller than that of CA1 pyramidal neurons.
    • CA3 pyramidal neurons receive perisomatic exitation near their somata from the large mossy terminals of granule cells.
      • Regarding this, size of mossy fiber projection correlates well with spatial ability in mice, possibly causative. link (note: used the dryland radial maze, more appropriate for non-swimming mice!)
    • Intrahippocampal oscillator (CA3?) can change its frequency and phase relatively independently from the extrahippocampal (entorhinal) theta inputs.
  • CA1 interneurons discharge on the descenting phase of theta in the pyramidal cell layer, and are assumed to be responsible for the increased gamma of this phase.
  • CA1 pyramidal cells discharge on the negative phase (makes sense) of theta as recorded from the CA1 pyramidal cell layer.
    • Phase fluctuation of spikesis not random and correlates with behavioral varaibles.
      • Stronger excitation = more spikes earlier in the theta negative phase.
    • Firing of place cells varies systematically with animal position and theta phase -- there is a phase precession.
      • Seems as though place is encoded in both which cell is firing as well as when in theta.
      • alternately, this may be an effect of the CA3 oscillator running slightly faster than the extrinsic oscillator.

Original model for theta oscillation creation (figure 2):

  • Note that all oscillations require a dipole which periodically inverts along it's axis, as is required in a conductive solution.
    • And yet there is no 'null' zone in theta oscillation, as dipole would imply. Rather, there is a gradual shift, more like a traveling wave.
  • Dendrites are passive cables, LFP generated by summed activity of IPSP and EPSP on soma and dendrites.
    • Excitation from perforant path,
    • Inhibition from septum to feed-forward inhibitory neuron inputs.
  • That said, the model is not completely consistent with experimental evidence:
    • The highest probability of discharge in the behaving rat occurs around the positive peak of theta recorded at the level of the distal dendrites, corresponding to the negative phase in the pyramidal level. (Remember, spiking corresponds to sodium influx, hence decreased extracellular +)
    • Cells may oscillate by themselves, without input.
    • The cell connections within the hippocampus matter a lot, too.


  • Induction is present / optimal when the spacing between pulses is 200ms.
    • Priming can be only one pulse!
    • Not clear how this works - endogenous cannabanoids?
  • Theta oscillation may provide a mechanism for bringing together time afferent inducing depolarization and dendritic invasion of fast spikes.


  • A theta cycle may be considered an information quantum, allowing the exchange of information among the linked members in a phase-locked manner. ...
  • This discontinuous mode of operation may be a unique solution to temporally segregate and link neuronal assemblies to perform various operations.
  • Notable support of this hypothesis:
    • Theta cycle phase resets upon sensory stimulation
    • Motor activity can become theta locked.


  • Ketamine blocks NMDA receptors.
  • Granule cells can be eliminated by neonatal X-ray exposure. (why?)

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ref: Hashimoto-2003.03 tags: DBS STN subthalamic nucleus globus pallidus electrophysiology date: 03-07-2012 21:57 gmt revision:3 [2] [1] [0] [head]

PMID-12629196[0] Stimulation of the Subthalamic Nucleus Changes the Firing Pattern of Pallidal Neurons

  • why does STN stim work? investigated the effects of STN HFS on neuronal activity of GPi and GPe.
  • monkeys were treated with MPTP
  • used a scaled-down version of human DBS stimulator (cool!)
  • high frequency stimulation resulted in stimulus-synchronized regular firing pattern, plus an overall increase in pallidal firing rate.
    • they think that this synchrony may underlie the beneficial effect of HFS in the STN
  • only behavior was, apparently, what amplitude and frequency were required to alleviate parkinsonian symptoms.
  • if i do DBS in normal monkeys, is there anything to say that the effect will be similar or comparable to treatment stimulation?
  • they remind us that HFS = lesion in terms of alleviating symptoms of parkinsons.


[0] Hashimoto T, Elder CM, Okun MS, Patrick SK, Vitek JL, Stimulation of the subthalamic nucleus changes the firing pattern of pallidal neurons.J Neurosci 23:5, 1916-23 (2003 Mar 1)

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ref: -0 tags: Albin basal ganglia dopamine 1989 parkinsons huntingtons hemiballismus date: 03-02-2012 00:28 gmt revision:1 [0] [head]

PMID-2479133 The functional anatomy of basal ganglia disorders.

  • Matrix neurons mainly containing substance P mainly project upon the GPi or SNr
    • while those containing enkephalins project on the GPe.
  • Striosome neurons projecting to the SNc contain mainly substance P.
  • Classical hypothesis:
  • Hyperkinetic disorders, which are characterized by an excess of abnormal movements, are postulated to result from the selective impairment of striatal neurons projecting to the lateral globus pallidus.
    • These are suppressed by D2 receptor antagonists & exacerbated by dopamine agonists.
    • Chorea is a primary example.
    • Despite Huntingtons, traumatic, ischemic, or ablative lesions of the striatum in man or animals rarely produces chorea or atheosis (writhing movements).
    • In HD, cholinergic agonists will alleviate choreoatheosis, while anti-cholinergic drugs exacerbate it.
  • Hypokinetic disorders, such as Parkinson's disease, are hypothesized to result from a complex series of changes in the activity of striatal projection neuron subpopulations resulting in an increase in basal ganglia output.
    • opposite of HD, exacerbated by D2 antagonists and ameliorated by DA agonists, as well as anti-cholinergics.
  • Dystonia = the spontaneous assumption of unusual fixed postures lasting from seconds to minutes.

  • Standard model suggests that striatal lesions should result in spontaneous movements, while this is not the case in man or other mammals. (less inhibition on GPi / SNr -> greater susceptibility of the thalamus to competing programs (?))
  • hyperkinetic movements can be produced by infusing bicululline, a GABA receptor antagonist, into GPe -- silencing it.
  • In early HD, when chorea is most prominent, there is a selective loss of striatal neurons projecting to the LGP (enkephalin staining).
    • Substance P containing neurons are lost later in the disease.
  • Administration of D2 antagonists increases the synthesis of enkephalins and pre-proenkephalin mRNA in the striatum.
    • This presumably represents increases in neuronal activity.
    • Inhibition of GPe neurons decreases hyperkinetic movements? But STN is excitatory? This does not add up.
  • Hemiballismus may be caused by disinhibition of SNr (?) and the VA/VL/MD/CM-Pf thalamocortical projections.


  • In both PD and HD, there are both increases in the latency of initiation of saccades, slowing of saccadic velocity, and interruption of saccades.
    • In HD, there is an early loss of substance-P containing striatal terminals in the SNr, possibly resulting in over-inhibition of tectal neurons.
    • HD patients cannot supress saccades to flashed stimulus.
    • No abnormalities in saccadic control in tourette's syndrome.
  • Hikosaka: suggest that caudate neurons involved in the initiation of saccades are part of a mechanism in which sensory data are evaluated in the context of learned behaviors and anticipated actions, and then used to initiate behavior.

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ref: Iansek-1980.04 tags: globus pallidus GPe GPi electrophysiology 1980 date: 02-29-2012 18:17 gmt revision:2 [1] [0] [head]

PMID-7411442 The monkey globus pallidus: neuronal discharge properties in relation to movement.

  • motor units are generally inactive during inactivity. the relationship to movement of the discharges of such neurons was found to be very specific
    • This is in comparison to other results, which report a sustained firing, esp in GPi.
  • the discharges (as analyzed through histograms) of many neurones were related to only a particular direction of movement about one joint in the right limb.
  • some discharges were related to multijoint movements -> probably due to control of contraction of particular muscles.
    • nonetheless, this relationship was a loose one; there is not a tight coupling between pallidal activity and muscle contraction.
  • some responded to ipsilateral as well as contralateral movements.
    • PMID-7925805 Unilateral leasions in the GP results in bilateral increase in reaction time. hence, GP is involved in initiation. RT speed eventually recovered.
  • only the posterior globus pallidus - well posterior to the maximum expansion - contained movement related cells.
    • the a-p stereotaxic coordinates were less useful than the location of the maximum mediolateral width of the structure.
    • cells occurred in clusters, separated by regoins of non-movement related.
  • cells in the internal segment had no such organization.
  • many of the non-movement related neurons were tonically active.
  • this was before there was A/D recording, apparently!

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ref: -0 tags: distrupted oscillations Mallet 2008 6-OHDA globus pallidus date: 02-29-2012 01:15 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-19109506 Parkinsonian beta oscillations in the external globus pallidus and their relationship with subthalamic nucleus activity.

  • Rat 6-OHDA.
  • On rate model: Although synchronization of GP unit activity increased by almost 100-fold during beta oscillations, the mean firing rate of GP neurons decreased compared with controls.
  • Synchronized firing persisted across different brain states, suggesting hardwiring.
  • GP and STN are frequency aligned but phase skewed.
    • Lateral inhibition in GP seems essential / see model.
  • Suggest that GPe / STN could generate oscillations that propagate to the rest of the BG.
    • But then why is the cortex required?

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ref: -0 tags: oscillations DBS globus pallidus parkinsons date: 02-28-2012 17:24 gmt revision:1 [0] [head]

PMID-17880401 Late emergence of synchronized oscillatory activity in the pallidum during progressive Parkinsonism.

  • In monkeys, progressive dopamine depetion process, recording changes during disease progression -- good!
  • No big change in firing rates, makes sense as this is likely controlled by other network or cellular homeostatic mechanisms.
  • Early in intoxication inhibitory responses to movement disappeared.
    • Yet synchrony did not appear at this time -- it is a sequelae?
    • Correlated activity appeared later, once the animals became severly akinetic.
  • Thus, a causality between the emergence of synchronous oscillations in the pallidum and main parkinsonian motor symptoms seems unlikely.
  • Probably it's movement related activity, not overall states. YES.

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ref: DeLong-1985.02 tags: globus pallidus subthalamic STN electrophysiology Georgopoulos DeLong DBS date: 02-24-2012 21:50 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-3981228[0] Primate globus pallidus and subthalamic nucleus: functional organization

  • cells respond to arm, leg, and orofacial movements (mostly in the arm tho)
  • ~25% of these responded to passive joint movement - the latency is in accord with proprioceptive driving.
  • arm-related neurons were found throughout the rostrocaudal extent of both globus pallidus segments
  • look @ the articles that cite this!


[0] DeLong MR, Crutcher MD, Georgopoulos AP, Primate globus pallidus and subthalamic nucleus: functional organization.J Neurophysiol 53:2, 530-43 (1985 Feb)

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ref: -0 tags: globus pallidus delong response tuning date: 02-24-2012 21:41 gmt revision:1 [0] [head]

PMID-4997823 Activity of Pallidal Neurons During Movement

  • GPe activity notably different from GPi.
    • "So characteristic were the discharge patterns of units in each segment that early in the course of the experiment ti be came apparent when the electrode entered and left each segment.
  • Two types of cells in GPe:
    • High frequency with periods of quiet (85%)
    • Low frequency with bursts.
  • Only one type in GPi: continuous HF discharge, 10-100 Hz, mean 63 Hz.
  • Mostly contralateral, ~ 15% ipsilateral related discharge.
  • Leg and arm responding units intermixed.
  • Conclusion: pallidus not involved in reflexes.
  • Substantia innominata = region posterior the pallidus, contains the nucleus basalis.
  • I'd really like to get recordings of this quality!

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ref: -0 tags: striatum microstimulation abnormal myclonus dyskinesia date: 02-24-2012 19:44 gmt revision:0 [head]

PMID-21508304 Discontinuous Long-Train Stimulation in the Anterior Striatum in Monkeys Induces Abnormal Behavioral States

  • Long-train microstimulation induces complex, abnormal behavior: finger licking and biting, dyskinesias, grooming; more anterior (associative) resulted in hyper, hypo manic or stereotyped behaviors.
  • Short-train stimulation induces myoclonic-like movements.

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ref: Carpenter-1981.11 tags: STN subthalamic nucleus anatomy tracing globus_pallidus PPN substantia_nigra DBS date: 02-22-2012 22:01 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-7284825[0] Connections of the subthalamic nucleus in the monkey.

  • STN projects to both segments of the globus pallidus in a laminar and organized fashion.
    • most fibers projected to the lateral pallidal segment (aka GPe).
  • also projected to specific thalamic nuclei (VAmc, VLm, DMpl).
  • the major projection of PPN is to SN.
  • striatum projects to the substantia nigra pars reticulata (SNr). interesting.
  • see also: PMID-1707079[1]
    • "Anterograde transport in fibers and terminal fields surrounded retrogradely labeled cells in the LPS (GPe), suggesting a reciprocal relationship [to the STN]"
  • These data suggest that the STN receives its major subcortical input from cell of the LPS (GPe) arranged in arrays which have a rostrocaudal organization.
  • No cells of the MPS (GPi) or SN project to the STN.
  • The output of the STN is to both segments of the GP and SNpr.
  • Major subcortical projections to PPN arise from the MPS (GPi) and SNpr (output of the BG) , but afferents also arise from other sources.
    • The major projection of PPN is to SN.
    • HRP injected into PPN produced profuse retrograde transport in cells of the MPS and SNpr and distinct label in a few cells of the zona incerta and STN.


[0] Carpenter MB, Carleton SC, Keller JT, Conte P, Connections of the subthalamic nucleus in the monkey.Brain Res 224:1, 1-29 (1981 Nov 9)
[1] Carpenter MB, Jayaraman A, Subthalamic nucleus of the monkey: connections and immunocytochemical features of afferents.J Hirnforsch 31:5, 653-68 (1990)

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ref: Boulet-2006.1 tags: hemiballismus PD parkinsons STN subtalamic DBS dyskinesia rats 2006 glutamate date: 02-22-2012 18:58 gmt revision:1 [0] [head]

PMID-17050715 Subthalamic Stimulation-Induced Forelimb Dyskinesias Are Linked to an Increase in Glutamate Levels in the Substantia Nigra Pars Reticulata

  • STN-HFS-induced forelimb dyskinesia was blocked by microinjection of the Glu receptor antagonist kynurenate into the SNr and facilitated by microinjection of a mixture of the Glu receptor agonists AMPA and NMDA into the SNr.
    • Well, that just makes sense. STN is excitatory, GPi is an output structure of the BG, and stimulation should activate the area.

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ref: Bergman-1998.01 tags: basal ganglia globus pallidus electrophysiology parkinsons 2001 DBS date: 02-22-2012 18:52 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-9464684[0] Physiological aspects of information processing in the basal ganglia of normal and parkinsonian primates.

  • The firing of neurons in the globus pallidus of normal monkeys is almost always uncorrelated.
  • after MPTP treatment, the firing patterns of GP became correlated and oscillatory (see the figures!!)
  • dopamine must support normal segregation of the informational channels in the basal ganglia, and breakdown of this causes the pathology of PD.
  • has a decent diagram of the basal ganglia-thalamo-cortical circuits.
  • two different hypotheses of BG function: segregated and convergent. data support the former.


[0] Bergman H, Feingold A, Nini A, Raz A, Slovin H, Abeles M, Vaadia E, Physiological aspects of information processing in the basal ganglia of normal and parkinsonian primates.Trends Neurosci 21:1, 32-8 (1998 Jan)

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ref: Holgado-2010.09 tags: DBS oscillations beta globus pallidus simulation computational model date: 02-22-2012 18:36 gmt revision:4 [3] [2] [1] [0] [head]

PMID-20844130[0] Conditions for the Generation of Beta Oscillations in the Subthalamic Nucleus–Globus Pallidus Network

  • Modeled the globus pallidus external & STN; arrived at criteria in which the system shows beta-band oscillations.
    • STN is primarily glutamergic and projects to GPe (along with many other areas..)
      • STN gets lots of cortical afferent, too.
    • GPe is GABAergic and projects profusely back to STN.
    • This inhibition leads to more accurate choices.
      • (Frank, 2006 PMID:,
        • The present [neural network] model incorporates the STN and shows that by modulating when a response is executed, the STN reduces premature responding and therefore has substantial effects on which response is ultimately selected, particularly when there are multiple competing responses.
        • Increased cortical response conflict leads to dynamic adjustments in response thresholds via cortico-subthalamic-pallidal pathways.
        • the model accounts for the beneficial effects of STN lesions on these oscillations, but suggests that this benefit may come at the expense of impaired decision making.
        • Not totally convinced -- impulsivity is due to larger network effects. Delay in conflict situations is an emergent property, not localized to STN.
      • Frank 2007 {1077}.
  • Beta band: cite Boraud et al 2005.
  • Huh parameters drawn from Misha's work, among others + Kita 2004, 2005.
    • Striatum has a low spike rate but high modulation? Schultz and Romo 1988.
  • In their model there are a wide range of parameters (bidirectional weights) which lead to oscillation
  • In PD the siatum is hyperactive in the indirect path (Obeso et al 2000); their model duplicates this.


[0] Holgado AJ, Terry JR, Bogacz R, Conditions for the generation of beta oscillations in the subthalamic nucleus-globus pallidus network.J Neurosci 30:37, 12340-52 (2010 Sep 15)

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ref: Shink-1996.07 tags: STN GPe GPi globus_pallidus anatomy retrograde tracing DBS date: 02-22-2012 15:34 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-8783253[0] The subthalamic nucleus and the external pallidum: two tightly interconnected structures that control the output of the basal ganglia in the monkey.

  • interconnected neurons in the subthalamic nucleus and the globus pallidus external innervate the same population of neurons in the internal segment of the globus pallidus.
    • e.g. there is a consistent functional organization between the three areas! (need to look up the organization of the striatum, too).
  • they did a similar study with injections of dextran amine into the GPi, and found that the labeled neurons in the STN and GPe were, as before, in register.
    • labeled GPe axons were not reactive to GABA & seemed to be from STN
    • labeled STN axons seemed to be from the GPe & were GABA reactive.
  • Has anyone traced out the connection in the brain of a Parkinson's patient? Does it change with the disease?


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ref: Magill-2001.01 tags: dopamine STN globus_pallidus cortex parkinsons DBS 6OHDA date: 02-22-2012 15:31 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-11566503[0] Dopamine regulates the impact of the cerebral cortex on the subthalamic nucleus-globus pallidus network

  • Compared unit activity STN / GP and EEG in rats under urethane anesthesia in control and 6OHDA rats.
  • DA depletion:
    • increased FR of STN neurons.
    • caused oscillations in GP neurons.
  • dopamine depletion causes the STN-GP circuit to become more reactive to the influence of the activity of cortical inputs. also see PMID-10632612[1]
  • oscillatory activity in the STN-GP network in anaesthetised rats is phase-locked to rhythmic cortical activity and is abolished by transient cortical activation as well as cortical ablation.
    • 15-20% of the network still oscillated following cortex removal, suggesting that intrinsic properties pattern activity when dopamine levels are reduced.
  • cool figures - nice recordings, high SNR, clear oscillations in the firing and ECoG signal


[0] Magill PJ, Bolam JP, Bevan MD, Dopamine regulates the impact of the cerebral cortex on the subthalamic nucleus-globus pallidus network.Neuroscience 106:2, 313-30 (2001)
[1] Magill PJ, Bolam JP, Bevan MD, Relationship of activity in the subthalamic nucleus-globus pallidus network to cortical electroencephalogram.J Neurosci 20:2, 820-33 (2000 Jan 15)

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ref: Guridi-2001.01 tags: STN DBS 2001 parkinsons hemiballismus Obeso date: 02-22-2012 15:14 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

PMID-11133783[0] The subthalamic nucleus, hemiballismus and Parkinson's disease: reappraisal of a neurosurgical dogma

  • Lesions of the globus pallidus, thalamus, as well as the STN can lead to hemiballismus
  • none-the-less, hemiballismus is a rather rare complication in STN DBS or lesion
  • GABA projection to the GPi is reduced in PD due to dopamine depletion
    • STN has projects glutamergic projections to GPi, so lesion would tend to worsten activity
    • STN also projects to the GPe, and lesioning it reduces hyper-activity there.
    • Therefore the balance of lesioning is to permit movements but not hemiballismus.
  • STN lesion in normal patients induces hemibalismus and chorea, but threshold for movements are raised with chronic dopamine depletion. cf {207}
  • Quality of life issues: perhaps everything has been learned already. {1124}


[0] Guridi J, Obeso JA, The subthalamic nucleus, hemiballismus and Parkinson's disease: reappraisal of a neurosurgical dogma.Brain 124:Pt 1, 5-19 (2001 Jan)

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ref: Bevan-2002.1 tags: STN GPe globus pallidus oscillations parkinsons DBS date: 02-22-2012 15:13 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

PMID-12220881[] Move to the rhythm: oscillations in the subthalamic nucleus-external globus pallidus network.

  • !!! autonomous oscillation of STN and GPe underlies tonic activity and is important for synaptic activity (e.g. normal??)
    • this is a review, of course.
  • during quiet wakefulness, neurons in STN and GPe fire differently without rhythm or strong correlation.
    • this is more pronounced when STN/GPe neurons are isolated from synaptic input (e.g. when prepared in a slice)-- they have inherent oscillatory characteristics. hum.
      • this may allow persistent activity or timed (gating) of planned activity (as opposed to timing of compensatory movement, which are mostly handled by the cerebellum).
      • the persistent activity must be more complicated than synchronized firing as in PD.
      • Random thought: I wonder if you 'clocked' the brain you would get discrete reaction times. Longshot; would need to review up and down states in the cortex?
  • during voluntary movement, GPe and STN neurons display a complex relationship to features of motor activity.
  • GPe and STN are reciprocally connected (STN with the Glu, GPe with the GABA)
    • as in other original papers, most of the axons from these regions have branched axons that mediate both reciprocal connections and innervation of output nuclei.
  • interesting thought: STN/GPe network could act as a 'generic' recursive pattern generator.
  • see figure 1 - single IPSP regulate the timing of spikes in the STN. large IPSP can synchronize and entrain the intrinsic high firing rate of STN neurons by prolonging the interspike interval.
    • bursts of IPSP can lead to rebound excitation, and hence a paradoxical increase in activity inn the STN. PMID-11877509[]
      • large IPSPs reset STN neurons oscillatory cycle & lead to synchronization
      • small IPSPs lead to phase-dependent delays and probably lead to desynchronization.
      • neuromodulators, like ACh, serotonin, and dopamine, can influence the polarization of STN neurons, and hence will have a profound effect on activity.
      • STN activity is more dependent one the pattern of afferent activity (of course!) than the gross magnitude of incoming spikes.
  • figure 2 - the network configuration between STN and GPe can markedly affect resulting activity. When there are possible reciprocal connections, the network produces tremor; when the network is more organized so that STN cannot recurrently activate GPe, multiple rhythms occur.
    • recall that both structures have extensive & sparsely connected dendritic fields, and are highly topographically organized.
  • figure 3 - [2,3]- oscillatory activity in the STN is a consequence of dopamine depletion and is also a feature of normal activity.
    • this is dependent on the presence of cortex. lack of cortex = regular firing.
    • GPe firing is tonic and constant in normal animals, and becomes oscillatory in 6-OHDA treated animals.
  • administration of dopamine agonists in PD patients causes higher frequency rhythms (30-70hz); without treatment, oscillations are in the 8-12 and lower range.

my notes:

  • IPSPs seem to have a very interesting and complex effect on the firing properties of tonically-active STN nenurons. who knows how this is being used, and in what representation the associated information is being processed?
  • still need to understand what dopamine is doing, and why absence leads to oscillations!
    • dopamine must modulate basal ganglia insensitivity to cortex.


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ref: Hamani-2004.01 tags: STN subthalamic nucleus movement disorders PD parkinsons basal_ganglia globus_pallidus anatomy DBS date: 02-22-2012 15:03 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

PMID-14607789[0] The subthalamic nucleus in the context of movement disorders

  • this is a good anatomy article, very descriptive -- almost too much information to grapple with.
  • STN = important structure for the modulation of activity of basal ganglia structures
  • STN is anterior-adjacent to the red nucleus
  • The average number of neurons in each STN nucleus varies from species to species and has been estimated to be ~25 000 in rats, 35 000 in marmosets, 155 000 in macaques, 230 000 in baboons and 560 000 in humans
  • The volume of the STN is ~0.8 mm3 in rats, 2.7 mm3 in marmosets, 34 mm3 in macaques, 50 mm3 in baboons and 240 mm3 in humans.
    • Number of neurons does not scale with volume, uncertain why not.
  • STN is divided into three functional units: motor, associative, and limbic cortical regions innervate, respectively motor, associative, and limbic regions of the striatum, pallidium SNr.
    • they give a complete list of these 3 in 'intrinsic organization of the STN'
    • STN is divided into 2 rostral thirds and one cauldal third.
      • medial rostral = limbic and associative
      • lateral rostral = associative
      • dorsal = motor circuits. (the largest part, see figure 2)
        • hence, the anterodorsal is thought to be the most effective target for DBS.
  • STN is populated primarily by projection neurons
  • the dendritic field of a single STN neurons can cover up to one-half of the nucleus of rodents
  • efferent projections (per neuron, branched axons)
    • GPe, GPi, SNr 21.3%
    • GPe and SNr 2.7%
      • in both segments of the pallidum, projections are uniformly arborized & affect an extensive number of cells.
    • GPe and GPi 48%
    • GPe only 10.7%
    • 17.3% remaining toward the striatum
  • most of the cortical afferents to the STN arise from the primary motor cortex, supplementary motor area, pre-SMA, and PMd and PMv; these target the dorsal aspects of the STN.
    • afferents consist of collaterals from the pyramidal tract (layer 5) & cortical fibers that also innervate the striatum (latter more prevalent). afferents are glutamergic.
  • ventromedial STN recieves afferents from the FEF (area 8) and suppl.FEF (9)
  • GPe projects extensively to STN with GABA. see figure 3 [1]
    • almost every cell in the STN resonds to pallidal GABAergic stimulation.
    • 13.2% of GPe neurons project to GPi, STN, and SNr
    • 18.4% to GPI and STN,
    • 52.6% to only the STN and SNr
    • 15.8% remaining to the striatum.
  • DA afferents from the SNc
  • ACh from the tegmentum
  • Glutamergic afferents from the centromedian thalamus (CM)
  • Serotonin from the raphe nucleus
  • fibers from the tegmentum, SNc, motor cortex, VM.pf of the thalamus, and dorsal raphe synapse on distal dendrites
    • pallidal inhibitory fibers innervate mostly proximal dendrites and soma.
firing properties:
  • about half of STN neurons fire irregularly, 15-25% regularly, 15-50% burst.
    • bursting is related to a hyperpolarization of the cell.
  • movement-related neurons are in the dorsal portion of STN and are activated by either/both active/passive movements of single contralateral joints
  • there is a somatotopic organizaton, but it is loose.
  • many units are responsive to eye fixation, saccadic movements, or visual stim. these are in the ventral portion.
    • activation of the STN drives SNr activity, which inhibits the superior colliculus, allowing maintainance of eye position on an object of interest.
  • ahh fuck: if high currents are delivered to STN or high concentrations of GABAergic antagonists are applied abnormal movements such as dyskinesias can be elicited
    • low concentrationns of GABA antagonists induces postural asymmetry and abnormal movements, but no excessive locomotion.
  • dyskinesias result from high-frequency or high-current stimulation to the STN! low frequency stimulation induces no behavioral effects. [2]
  • small (<4% !!) lesions cause focal dystonias
  • in parkinsonian patients, activity in the STN is characterized by increased synchrony and loss of specificity in receptive fields + mildly increased mean firing rate.
    • 55% of STN units in PD patients respond to passive movements, and 24% to ipsilateral movements (really?) - indicative of the increase in receptive field size caused by the disease.


[0] Hamani C, Saint-Cyr JA, Fraser J, Kaplitt M, Lozano AM, The subthalamic nucleus in the context of movement disorders.Brain 127:Pt 1, 4-20 (2004 Jan)
[1] Sato F, Lavallée P, Lévesque M, Parent A, Single-axon tracing study of neurons of the external segment of the globus pallidus in primate.J Comp Neurol 417:1, 17-31 (2000 Jan 31)
[2] Beurrier C, Bezard E, Bioulac B, Gross C, Subthalamic stimulation elicits hemiballismus in normal monkey.Neuroreport 8:7, 1625-9 (1997 May 6)

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ref: Fellows-2006.04 tags: parkinsons subthalamic nucleus thalamus DBS STN force velocity overshoot grasp date: 02-22-2012 14:51 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-16549385[0] The effect of subthalamic nucleus deep brain stimulation on precision grip abnormalities in Parkinson's disease

  • Deep Brain stimulation improves mobility/dexterity and dyskinesia of patients in general, via an increase in rate and decrease in reaction time, but it does not let the patient match force output to the object being manipulated (that is, the force is too large).
  • The excessive levels of grip force present in the stimulation 'off' state, and present from the early stages of the disease, however, were even more marked with STN stimulation on.
    • STN DBS may worsen the ability to match force characteristics to task requirements. (position control is improved?).
    • quite fascinating.

See also PMID-19266149[1] Distal and proximal prehension is differentially affected by Parkinson‘s disease The effect of conscious and subconscious load cues

  • asked PD and control patients to lift heavy and light objects.
  • While controls were able to normalize lift velocity with the help of both conscious and subconscious load cues, the PD patients could use neither form of cue, and retained a pathological overshoot in lift velocity.
  • Hence force control is remarkably affected in PD, which is consistent with the piper rhythm being absent / usually present for isometric contraction.


[0] Fellows SJ, Kronenbürger M, Allert N, Coenen VA, Fromm C, Noth J, Weiss PH, The effect of subthalamic nucleus deep brain stimulation on precision grip abnormalities in Parkinson's disease.Parkinsonism Relat Disord 12:3, 149-54 (2006 Apr)
[1] Weiss PH, Dafotakis M, Metten L, Noth J, Distal and proximal prehension is differentially affected by Parkinson's disease. The effect of conscious and subconscious load cues.J Neurol 256:3, 450-6 (2009 Mar)

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ref: Georgopoulos-1983.08 tags: STN monkeys primate Georgopoulos globus pallidus date: 02-10-2012 18:57 gmt revision:2 [1] [0] [head]

PMID-6875658[0] Relations between parameters of step-tracking movements and single cell discharge in the globus pallidus and subthalamic nucleus of the behaving monkey.

  • Step tracking task in monkeys; wrist flexion and extension.
    • first one in monkeys, apparently.
    • 87 neurons in GP, 36 in GPi, 29 in STN.
  • Linear tuning to direction and distance, same as in motor cortex by Georgopoulos.
    • More likely to see frequency increase.
  • Earlier firing rate change in STN than GPe than GPi.
  • Two patterns of firing in the globus pallidus external:
    • more frequent: high discharge rate interrupted with pauses of varying duration
    • less frequent: low average discharge rate with very high frequency bursts.
  • GPi: high frequency with frequent bursts.
  • GPi/e generally high firing rate - 80-100 Hz, with frequent bursts.
    • But not as deep movement tuning as M1.
  • Only primates have projections from the motor cortex to the STN.
    • This seems like an evolutionarily recent development -- apparently the cortex needs the extra level of control?

See also citing articles: http://scholar.google.com/scholar?cites=16339220378239936453&as_sdt=5,34&sciodt=0,34&hl=en


[0] Georgopoulos AP, DeLong MR, Crutcher MD, Relations between parameters of step-tracking movements and single cell discharge in the globus pallidus and subthalamic nucleus of the behaving monkey.J Neurosci 3:8, 1586-98 (1983 Aug)

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ref: Krack-2002.01 tags: DBS thalamus nomenclature Hassler date: 02-02-2012 03:04 gmt revision:2 [1] [0] [head]

PMID-11948749[0] Surgery of the motor thalamus: problems with the present nomenclatures.


[0] Krack P, Dostrovsky J, Ilinsky I, Kultas-Ilinsky K, Lenz F, Lozano A, Vitek J, Surgery of the motor thalamus: problems with the present nomenclatures.Mov Disord 17 Suppl 3no Issue S2-8 (2002)

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ref: Lenz-2002.04 tags: DBS VIM VOP thalamus essential tremor date: 02-02-2012 03:02 gmt revision:2 [1] [0] [head]

PMID-11929926[0] Single-neuron analysis of human thalamus in patients with intention tremor and other clinical signs of cerebellar disease.

  • VIM (ventral intermediate) is a cerebellar relay nucleus; VOP (ventralis oral posterior) is a pallidal relay.
  • Used pain controls. clever.
  • Observations:
    • VIM cells have a phase lag to EMG.
    • VIM firing rate decreased relative to pain controls.
    • ET patients show intention tremor -- usually under visual guidance.
      • This leads them to think that cells have been de-afferented by cerebellar injury, e.g. they get their input from basal ganglia / motor cortex / visual feedback, which has less forward phase margin (not a smith predictor), hence oscillations.


[0] Lenz FA, Jaeger CJ, Seike MS, Lin YC, Reich SG, Single-neuron analysis of human thalamus in patients with intention tremor and other clinical signs of cerebellar disease.J Neurophysiol 87:4, 2084-94 (2002 Apr)

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ref: LehAc)ricy-2001.09 tags: DBS thalamus lesions movement disorder VIM VOP date: 02-02-2012 03:02 gmt revision:2 [1] [0] [head]

PMID-11571334[0] Clinical characteristics and topography of lesions in movement disorders due to thalamic lesions

  • So hard to find a good sagittal diagram of the human thalamus!


[0] Lehéricy S, Grand S, Pollak P, Poupon F, Le Bas JF, Limousin P, Jedynak P, Marsault C, Agid Y, Vidailhet M, Clinical characteristics and topography of lesions in movement disorders due to thalamic lesions.Neurology 57:6, 1055-66 (2001 Sep 25)

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ref: Nishioka-2008.12 tags: STN hemiballismus lesion stroke MRI neurosurgery date: 01-26-2012 17:31 gmt revision:3 [2] [1] [0] [head]

PMID-18842415[0] Transient hemiballism caused by a small lesion of the subthalamic nucleus.

  • Hemiballism is most commonly caused by ischemic stroke and most cases have a favorable prognosis.
  • Lesions directly involving the subthalamic nucleus (STN) are the cause of a minority of cases but are usually associated with poor prognosis.
  • We report two patients with a small STN lesion who presented with transient hemiballism.
  • This may be a useful ref in the future.
  • This reports the same result: PMID-17702635


[0] Nishioka H, Taguchi T, Nanri K, Ikeda Y, Transient hemiballism caused by a small lesion of the subthalamic nucleus.J Clin Neurosci 15:12, 1416-8 (2008 Dec)

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ref: Lee-2005.07 tags: STN subthalamic nucleus hemiballismus DBS date: 01-26-2012 17:24 gmt revision:3 [2] [1] [0] [head]

PMID-16032642[0] Common causes of hemiballism.

  • stroke of the STN results in hemiballismus - wild movements of the limbs. recall the input to the STN is inhibitory from GPe, and the output is exitatory to the GPi. chemical treatment is via dopamine blockade (1976!)
  • hemiballism is rare, but usually associated with lesion to the contralateral STN.
    • however, half the cases of hemiballismus are associated with damage to the afferent or efferent pathways to the STN.
    • diabetes type 2 also commonly causes hemiballismus (hyperglycemia in asian women!)
  • hemiballismus is absent in sleep - the thalamocortical relay must be turned off.
  • hemiballismus is generally associated with high metabolic activity in the basal ganglia.
  • does this mean that stimulation to the STN in healthy monkeys will disinhibit large, possibly conflicting movements?
  • my thought: the subthalamic nucleus must be involved in the selection and regulation of appropriate movements.


[0] Lee HS, Kim SW, Yoo IS, Chung SP, Common causes of hemiballism.Am J Emerg Med 23:4, 576-8 (2005 Jul)

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ref: Beurrier-1997.05 tags: STN stimulation hemiballismus 2007 DBS date: 01-26-2012 17:20 gmt revision:4 [3] [2] [1] [0] [head]

PMID-9189903[] Subthalamic stimulation elicits hemiballismus in normal monkey.

  • the effects of stimulation on normal waking primates has never been evaluated (doh!)
  • In the normal monkey, HFS appears reversibly to incapacitate the STN and allow the emergence of involuntary proximal displacements, due to disinhibition of the thalamo-cortical pathway
  • in MPTP-treated monkey HFS buffers STN activity and alleviates akinesia and rigitity by reducing inputs to the internal segment of the globus pallidus. (STN output is excitatory) (or so the theory at the time goes)
  • perhaps i will need to buy this article ;(


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ref: Sato-2000.01 tags: globus_pallidus anatomy STN GPi GPe SNr substantia nigra tracing DBS date: 01-26-2012 17:20 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-10660885[0] Single-axon tracing study of neurons of the external segment of the globus pallidus in primate.

  • wow, check out the computerized tracing! the neurons tend to project to multiple areas, usually. I didn't realize this. I imagine that it is relatively common in the brain.
  • complicated, tree-like axon collateral projection from GPe to GPi.
    • They look like the from through some random-walk process; paths are not at all efficient.
    • I assume these axons are mylenated? unmylenated?
  • dendritic fields in the STN seem very dense.
  • study done in cyno. rhesus


[0] Sato F, Lavallée P, Lévesque M, Parent A, Single-axon tracing study of neurons of the external segment of the globus pallidus in primate.J Comp Neurol 417:1, 17-31 (2000 Jan 31)

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ref: Bergman-1994.08 tags: subthalamic nucleus STN basal ganglia globus pallidus electrophysiology 1994 MPTP DBS date: 01-26-2012 17:19 gmt revision:3 [2] [1] [0] [head]

PMID-7983515[0] The primate subthalamic nucleus. II. Neuronal activity in the MPTP model of parkinsonism

  • idea: record from STN and GPi before and after MPTP treatment in green monkeys.
  • recorded 4-8hz periodic activity (via autocorrelograms) in significantly more neurons from the MPTP treated animals in both the STN and GPi.
  • mean firing rate was increased in STN,
  • tremor-correlated cells found in both.
  • burst activity higher in both, too.
  • modulations in firing rate due to the application of flexion and extension torque pulses were higher in MPTP animals (duration and amplitude), in both areas.
  • spikes were longer in MPTP
  • no tyrosene hydroxylase activity in the PD mks.
  • PD tremor only frequently occurs in green mks following MPTP


[0] Bergman H, Wichmann T, Karmon B, DeLong MR, The primate subthalamic nucleus. II. Neuronal activity in the MPTP model of parkinsonism.J Neurophysiol 72:2, 507-20 (1994 Aug)

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ref: Monakow-1978.11 tags: motor_cortex STN subthalamic nucleus anatomy DBS date: 01-26-2012 17:17 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-83239[0] Projections of the precentral motor cortex and other cortical areas of the frontal lobe to the subthalamic nucleus in the monkey.

  • this paper is old and important!
  • The ipsilateral subthalamic nucleus receives a moderately strong and somatotopic organized projection from Woolsey's precentral motor cortex (PMd, M1 i guess)
    • No projections from the postcentral gyrus! (S1) (Is this still thought to be true?)
  • The remaining nucleus is occupied by less intensive projections from premotor and prefrontal areas
  • STN is a convergence site for pallidal and cortical motor/frontal projections.
  • autoradiography slices are damn hard for me to read.


[0] Monakow KH, Akert K, Künzle H, Projections of the precentral motor cortex and other cortical areas of the frontal lobe to the subthalamic nucleus in the monkey.Exp Brain Res 33:3-4, 395-403 (1978 Nov 15)

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ref: neuro notes-0 tags: STN globus_pallidus striatum diagram basal_ganglia date: 01-26-2012 17:16 gmt revision:1 [0] [head]

http://www.gpnotebook.co.uk/cache/-1248198589.htm (bitrotted)

  • note that the loop around both preserves sign, more or less, provided you take into account the D2 receptor along the 'indirect' pathway
  • this has some glaring flaws: the globus pallius external projects to the globus pallidus internal, cortex projects to STN, thalamus projects to striatum, etc.


  • has a good diagram of the neurotransmitters involved in the motor selection pathway. need to understand the kinetics of the dopamine receptor family

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ref: Benabid-2005.12 tags: Benabid famous DBS STN review date: 01-25-2012 00:22 gmt revision:2 [1] [0] [head]

PMID-16280671[0] Deep-brain stimulation in Parkinson's disease: long-term efficacy and safety - What happened this year?

  • 260 reports on DBS in 2004!
  • (from the abstract) There is an urgent need for the organization of research and reports, and no need to report small series replicating well-established conclusions. oopsie.
  • Clinical reports should concentrate on unobserved effects in relation to causative parameters, based on the precise location of electrodes,
  • and on clinical reports comparable between teams and on methods to optimize and facilitate the tuning of parameters and postoperative evaluations in order to make this treatment easier to provide for the neurologist


[0] Benabid AL, Chabardès S, Seigneuret E, Deep-brain stimulation in Parkinson's disease: long-term efficacy and safety - What happened this year?Curr Opin Neurol 18:6, 623-30 (2005 Dec)

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ref: Elble-1996.03 tags: tremor STN VIM thalamus basal_ganglia Elble Parkinson's ET dyskinesia thalamus VIM DBS date: 01-24-2012 21:19 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-8849968[] Central Mechanisms of Tremor -- available through Duke's Ovid system. also in email.

  • focuses at first on the nonlinear aspect of all control: the systems are hard to understand because of the complexities of their interactions.
    • nonlinear systems are capable of complex interactions that are not predicted by the sum of their individual behaviors.
  • in general, there are two different types of tremor:
    • mechanical reflex oscillations (depend on sensorimotor loops), permit damped oscillations in response to pulsate perturbations.
      • is effected by the stifness and inertia of the segment involved.
    • central oscillations
      • frequencies independent of limb mechanics/segment length.
      • still subject to modulation by sensorimotor feedback.
      • if the tremor is at the same frequency as the mechanical resonance, the tremor will be worse!
  • physiologic tremor has both components of mechanical oscillations (3-5Hz) and central oscillations (8-12hz), which are usually attenuated by the low-pass property of the musculoskeletal system.
    • associated spindle and tendon organ discharge are not sufficient to produce 8 - 12 Hz oscillation - hence, this is most likely from a central source, eg. the cortex, inferior olive, and thalamus.
  • Essential tremor is also centrally generated, though it appears to be affected by somatosensory driving.
    • essential tremor frequency is strongly correlated with patient age (where the frequency decreases with increasing age).
    • the origin of ET is unknown: postmortem examinations reveal no deficits in M1/S1, thalamus, inferior olive, raphe nucleus, and reticular nuclei, globus pallidus, and spinal cord...
    • but, the inferior olive seems to be the most likely culprit:
      • tremor induced by harmaline increased inhibition-rebound properties of neurons, and this induces intention-related tremor in monkeys
      • harmaline induced olivary oscillation is similar to ET in terms of frequency, EMG, and drug-response.
      • olivary hypothesis is supported by PET scans, which show increased glucose consumption there in ET patients.
      • the ventrolateral (VL) thalamus and Ventralis intermedius (VIM) receives input from the contralateral cerebellar nuclei.
        • this is why VIM is such a good target for treatment of ET.
  • parkinsons tremor:
    • VOP is a better target for treating bradykinesia and other symptoms of PD, while VIM is the best for treating tremor
    • neurons in the globus pallidus and STN become entrained to tremor. STN lesion / HFS is effective in treating dyskinesia and other PD symptoms.
    • in MPTP monkeys, STN/ GPi neurons are also entrained to the tremor frequency.
  • other tremor:
    • neuropathic/tumorogenic tremor usually takes weeks to appear, suggesting that CNS reorganization is a cause of tremor, not intrinsic sensorimotor deafferentation
      • local lesions in the striatum, thalamus, & globus pallidus often cause dystonias, not tremor.
  • Cerebellar tremor
    • seems to be caused by an inability to properly compensate/ brake with antagonist muscles during voluntary and postural movements. movement control becomes heavily dependent on sensory feedback, which is often too slow for adequate compensation.
  • neuroleptic drugs can often cause tremor (or tardive dyskinesia). Neurolepric - calming, tranquilizer, antipsychotic.
    • lithium can cause permanent tremor due to cerebellar gliosis!
  • VOP projects to the supplementary motor area (SMA) and dorsolateral prefrontal cortex (DLPFC) PMID-21629131 ; VIM projects to M1 & contralateral cerebellum, as mentioned above.


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ref: Krack-2001.09 tags: STN subthalamic nucleus stimulation PD parkinsons DBS date: 01-24-2012 05:48 gmt revision:1 [0] [head]

PMID-11746616[0] Mirthful laughter induced by subthalamic nucleus stimulation.

  • high stimulation parameters induces mirthful laughter
  • prescribed parameters induced hypomanic behavior with marked improvement in akinesia.
  • STN must be involved in psychomotor as well as motor regulation.


[0] Krack P, Kumar R, Ardouin C, Dowsey PL, McVicker JM, Benabid AL, Pollak P, Mirthful laughter induced by subthalamic nucleus stimulation.Mov Disord 16:5, 867-75 (2001 Sep)

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ref: BarGad-2003.12 tags: information dimensionality reduction reinforcement learning basal_ganglia RDDR SNR globus pallidus date: 01-16-2012 19:18 gmt revision:3 [2] [1] [0] [head]

PMID-15013228[] Information processing, dimensionality reduction, and reinforcement learning in the basal ganglia (2003)

  • long paper! looks like they used latex.
  • they focus on a 'new model' for the basal ganglia: reinforcement driven dimensionality reduction (RDDR)
  • in order to make sense of the system - according to them - any model must ingore huge ammounts of information about the studied areas.
  • ventral striatum = nucelus accumbens!
  • striatum is broken into two, rough, parts: ventral and dorsal
    • dorsal striatum: the caudate and putamen are a part of the
    • ventral striatum: the nucelus accumbens, medial and ventral portions of the caudate and putamen, and striatal cells of the olifactory tubercle (!) and anterior perforated substance.
  • ~90 of neurons in the striatum are medium spiny neurons
    • dendrites fill 0.5mm^3
    • cells have up and down states.
      • the states are controlled by intrinsic connections
      • project to GPe GPi & SNr (primarily), using GABA.
  • 1-2% of neurons in the striatum are tonically active neurons (TANs)
    • use acetylcholine (among others)
    • fewer spines
    • more sensitive to input
    • TANs encode information relevant to reinforcement or incentive behavior


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ref: -0 tags: electrode implantation spring modeling muscles sewing date: 01-16-2012 17:30 gmt revision:0 [head]

PMID-21719340 Modelization of a self-opening peripheral neural interface: a feasibility study.

  • Electrode is self-opening, and they outline the math behind it. This could be useful!

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ref: work-0 tags: gaussian random variables mutual information SNR date: 01-16-2012 03:54 gmt revision:26 [25] [24] [23] [22] [21] [20] [head]

I've recently tried to determine the bit-rate of conveyed by one gaussian random process about another in terms of the signal-to-noise ratio between the two. Assume x is the known signal to be predicted, and y is the prediction.

Let's define SNR(y)=Var(x)Var(err) where err=xy . Note this is a ratio of powers; for the conventional SNR, SNR dB=10*log 10Var(x)Var(err) . Var(err) is also known as the mean-squared-error (mse).

Now, Var(err)=(xyerr¯) 2=Var(x)+Var(y)2Cov(x,y) ; assume x and y have unit variance (or scale them so that they do), then

2SNR(y) 12=Cov(x,y)

We need the covariance because the mutual information between two jointly Gaussian zero-mean variables can be defined in terms of their covariance matrix: (see http://www.springerlink.com/content/v026617150753x6q/ ). Here Q is the covariance matrix,

Q=[Var(x) Cov(x,y) Cov(x,y) Var(y)]


Det(Q)=1Cov(x,y) 2

Then MI=12log 2[1Cov(x,y) 2]

or MI=12log 2[SNR(y) 114SNR(y) 2]

This agrees with intuition. If we have a SNR of 10db, or 10 (power ratio), then we would expect to be able to break a random variable into about 10 different categories or bins (recall stdev is the sqrt of the variance), with the probability of the variable being in the estimated bin to be 1/2. (This, at least in my mind, is where the 1/2 constant comes from - if there is gaussian noise, you won't be able to determine exactly which bin the random variable is in, hence log_2 is an overestimator.)

Here is a table with the respective values, including the amplitude (not power) ratio representations of SNR. "

SNRAmp. ratioMI (bits)
Note that at 90dB, you get about 15 bits of resolution. This makes sense, as 16-bit DACs and ADCs have (typically) 96dB SNR. good.

Now, to get the bitrate, you take the SNR, calculate the mutual information, and multiply it by the bandwidth (not the sampling rate in a discrete time system) of the signals. In our particular application, I think the bandwidth is between 1 and 2 Hz, hence we're getting 1.6-3.2 bits/second/axis, hence 3.2-6.4 bits/second for our normal 2D tasks. If you read this blog regularly, you'll notice that others have achieved 4bits/sec with one neuron and 6.5 bits/sec with dozens {271}.

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ref: Santhanam-2007.11 tags: HermesB Shenoy continuous neural recording Utah probe flash wireless date: 01-09-2012 00:00 gmt revision:4 [3] [2] [1] [0] [head]

PMID-18018699[0] HermesB: a continuous neural recording system for freely behaving primates.

  • saved the data to compact flash. could record up to 48 hours continuously.
  • recorded from an acceleromter, too - neuron changes were associated with high head accelerations (unsurprisingly).
  • also recorded LFP, and were able to tell with some accuracy what behavioral state the monkey was in.
  • interfaces to the Utah probe
  • not an incredibly small system, judging from the photos.
  • 1600maH battery, 19 hour life @ 2/3 recording duty cycle -> current draw is 120mA, or 450mW.
    • can only record from two channels at once!
    • amplifier gain 610.
    • used ARM microcontroller ADUC2106


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ref: Musallam-2004.07 tags: cognitive BMI Musallam Andersen PRR MIP date: 01-08-2012 23:13 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-15247483[0] Cognitive control signals for Neural Prosthetics

  • decode intended target from 200 to 1100ms of memory period (reward on correct, etc).
  • got good success rates with relatively few neurons (like 8 for 8 targets) -- yet decode rates were not that good, not at all as good as Fetz or Schmidt.
  • used pareital reach region (PRR), a subsection of posterior partietal cortex PPC, which represents the goals of the reach in visual coordinates. In the experiment, the implanted in media intrapareital (MIP)
    • in encodes the intended goal rather than the trajectory to achieve that goal.
    • PMd also seems to encode planning activity, though less is known about that.
  • used an adaptive database to map neuronal activity to targets; eventually, the database contained only (correct) brain-control trials.
  • neuronal responses were recorded from parietal reach region (PRR) with 64 microwire electrodes in 4 monkeys, plus 32 microwire electrodes in PMd
  • monkeys were tained to fixate on the center of the screen dring the task, though free fixation was also tested and seemed to work ok.
  • monkeys had to press cue, fixate, observe target location, wait ~2 sec, and move to the (remembered) target location when cue disappeared.
  • they use a static or continually updated 'database' for predicting which of four targets the monkey wants to go to during the instructed delay task.
  • able to predict with moderate accuracy the expected value of the target as well as its (discrete) position.
  • predictions were made during the delay period while there was no motor movement.
  • predictions worked equally well for updated and static databases.
  • monkeys were able to increase their performance on the BMI trials over the course of training.
  • reward type or size modulated the tuning of BMI neurons in the ecpected way, though aversive stimuli did not increase the tuning - suggesting that the tuning is not a function of attention (maybe).
  • the database consisted of 900ms of spike recordings starting 200ms after cue for 30 reach trials for each target. spike trains were projected onto Haar wavelets (sorta like a binary tree), and the filter coefficients were used to describe P(r), the probability of response, and P(r|s), probability of response given the target. then they used bayes rule (P(r) and P(r|s) were approximated with histograms, i think) to find P(s|r) - a discrete function - which it is easy to find the maximum of.
  • adding more trials offline improved the decode performance.
  • supporting online material.

PMID-15491902 Cognitive neural prosthetics

  • LFPs are easier to record and may last longer (but they are not as 'sexy').
  • suggest future electrodes will move automatically, peizo-drive perhaps.
  • PRR receives direct visual projections & codes for reaches in visual coordinates relative to the current direction of gaze.
  • PRR can hold the plan for a movement in short-term memory.
  • 16 neurons peak..?
  • In area LIP of PPC Platt and Glimcher PMID-10421364 found cells that code the expected value of rewards.
    • 20Hz beta-band oscillation indicated the behavioral state of the animal. While planning for a saccade it slowly increased, whereas at the time of movement in dramatically increased in amplitude.
    • LFP was better than spikes for a state decode.


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ref: Zacksenhouse-2007.07 tags: Zacksenhouse 2007 Odoherty Nicolelis cortical adaptation BMI date: 01-06-2012 03:10 gmt revision:3 [2] [1] [0] [head]

PMID-17637835[0] Cortical modulations increase in early sessions with brain-machine interface.

  • "we demonstrate that the modulations of the firing-rates of cortical neurons increased abruptly after the monkeys started operating the BMI"
    • My hypothesis: is this like LMAN? Injection of noise for the purpose of exploration?
    • Their hypothesis: we are listening to the noise or effect of increased processing / congnitive load.
    • Alternative: decreased feedback / scrabled feedback makes the individual control signals themselves less controlled.
  • Describes spikes as inhomogeneous poisson processes, and breaks things down thusly.
  • Also develop a parametric model of neuronal firing based on tuning to movement, including velocity and acceleration.
  • Fano factor of recorded neurons increased during BCWH & BCWOH.
  • Percent overall modulation (POM) higher in brain control. That is, the variance explained not by the inhomogeneous poisson process, but rather by firing rate variations.
    • "[T]he ensemble-POM increased mainly due to an increase in the variance of the spike-count, which was not matched by the change in the mean spike-count."
  • Figure 6 is pretty convincing, actually.
  • PVM (percent velocity modulation) correlates strongly with POM, but with a fractional slope, indicating that veolocity tuning accounts for only a fraction of the variance.
    • "Since the increase in POM was not matched by increasing PVM or PKM, the higher neuronal rate modulations observed during brain control cannot be explained only by increased modulations due to the kinematics of the movement."


[0] Zacksenhouse M, Lebedev MA, Carmena JM, O'Doherty JE, Henriquez C, Nicolelis MA, Cortical modulations increase in early sessions with brain-machine interface.PLoS One 2:7, e619 (2007 Jul 18)

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ref: Kim-2006.06 tags: Hyun Kim Carmena Nicolelis continuous shared control gripper BMI date: 01-06-2012 00:20 gmt revision:2 [1] [0] [head]

IEEE-1634510 (pdf) Continuous shared control for stabilizing reaching and grasping with brain-machine interfaces.

  • The pneumatic gripper for picking up objects.
  • 70% brain control, 30% sensor control optimal.
  • Talk about 20Hz nyquist frequency for fast human motor movements, versus the need to smooth and remove noise.
  • Method: proximity sensors
    • collision avoidance 'pain withdrawal'
    • 'infant palmar grasp reflex'
    • Potential field associated with these sensors to implement continuous shared control.
  • Not! online -- used Aurora's data.


Kim, H.K. and Biggs, J. and Schloerb, W. and Carmena, M. and Lebedev, M.A. and Nicolelis, M.A.L. and Srinivasan, M.A. Continuous shared control for stabilizing reaching and grasping with brain-machine interfaces Biomedical Engineering, IEEE Transactions on 53 6 1164 -1173 (2006)

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ref: Kim-2007.08 tags: Hyun Kim muscle activation method BMI model prediction kinarm impedance control date: 01-06-2012 00:19 gmt revision:1 [0] [head]

PMID-17694874[0] The muscle activation method: an approach to impedance control of brain-machine interfaces through a musculoskeletal model of the arm.

  • First BMI that successfully predicted interactions between the arm and a force field.
  • Previous BMIs are used to decode position, velocity, and acceleration, as each of these has been shown to be encoded in the motor cortex
  • Hyun talks about stiff tasks, like writing on paper vs . pliant tasks, like handling an egg; both require a mixture of force and position control.
  • Georgopoulous = velocity; Evarts = Force; Kalaska movement and force in an isometric task; [17-19] = joint dependence;
  • Todorov "On the role of primary motor cortex in arm movement control" [20] = muscle activation, which reproduces Georgouplous and Schwartz ("Direct cortical representation of drawing".
  • Kakei [19] "Muscle movement representations in the primary motor cortex" and Li [23] [1] show neurons correlate with both muscle activations and direction.
  • Argues that MAM is the best way to extract impedance information -- direct readout of impedance requires a supervised BMI to be trained on data where impedance is explicitly measured.
  • linear filter does not generalize to different force fields.
  • algorithm activity highly correlated with recorded EMG.
  • another interesting ref: [26] "Are complex control signals required for human arm movements?"


[0] Kim HK, Carmena JM, Biggs SJ, Hanson TL, Nicolelis MA, Srinivasan MA, The muscle activation method: an approach to impedance control of brain-machine interfaces through a musculoskeletal model of the arm.IEEE Trans Biomed Eng 54:8, 1520-9 (2007 Aug)
[1] Li CS, Padoa-Schioppa C, Bizzi E, Neuronal correlates of motor performance and motor learning in the primary motor cortex of monkeys adapting to an external force field.Neuron 30:2, 593-607 (2001 May)

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ref: Goldstein-1973.07 tags: Salcman microelectrodes bucking analysis stiffness youngs modulus mechanical MEA date: 01-04-2012 01:22 gmt revision:4 [3] [2] [1] [0] [head]

IEEE-4120642 (pdf) Mechanical Factors in the Design of Chronic Recording Intracortical Microelectrodes


Goldstein, Seth R. and Salcman, Michael Mechanical Factors in the Design of Chronic Recording Intracortical Microelectrodes Biomedical Engineering, IEEE Transactions on BME-20 4 260 -269 (1973)

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ref: Nicolelis-1993 tags: neurons somatosensory nicolelis rats thalamus date: 01-03-2012 23:30 gmt revision:2 [1] [0] [head]

from the Scientific American:

  • blocking (single?) neuron activity in S1 cortex affects the responses of VPM neurons in the thalamus - indicating that descending feedback signals in the cortex to the VPM could have a major role in modulating the ascending information.
  • if you implant a cuff electrode aroung the trigeminal nerve, the evoked responses in S1 and VPM are dependent on the behavioral state of the animal (of course!). this effect is so pronounced that, when the rats were not 'paying attention', only the first stimulus of a series evoked a response; when the rat was whisking, stimulation was faithfully reported.

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ref: neuro-2005 tags: NRSA background BMI tool use date: 01-03-2012 15:21 gmt revision:2 [1] [0] [head]

  • tool use:
    • [0]
    • [1] varying neural responses following tool acquisition
  • BMI
    • [2] simultaneous prediction of 4 variables
  • spike sorting
    • [3] donoghue
    • [4] LFP
    • [5] MUA
    • [6,7] - 1980!!
    • [8] STN bmi (nahh)
    • [9] Shenoy, eye movement better, 6.5 bits/sec
    • [10] PF
    • [11] in rats, in the cinglate, still they didn't get the point.
    • [12] Fetz stimulation


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ref: notes-2005.06 tags: Crick claustrum cortex telecephalon date: 01-03-2012 15:20 gmt revision:1 [0] [head]


  • small, sheetlike region, not very think 5mm in humans.
  • between the extreme capsule and the external capsule. in the sheep
  • there are remarkably few microelectrode investigations of claustral receptive fields in the claustrum & almost none in awake animals.
  • the claustrum is interconnected with the extrastriate visual areas (17 & 18), sensory cortex, and prefrontal cortex.
  • claustrum is highly vasularized and protected from stroke via multiple arteries.
    • hence, few selective lesions of the claustrum and so we don't know what effects its absence manifests.

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ref: Bures-1968 tags: inferior colliculus stimulation classical conditioning plasticity hebb Bures date: 01-03-2012 07:08 gmt revision:5 [4] [3] [2] [1] [0] [head]

bibtex:Bures-1968 Plastic changes of unit activity based on reinforcing properties of extracellular stimulation of single neurons

  • images/972_1.pdf
  • Trained neurons to respond to auditory stimuli throughout the brain (though mostly the IC) to a auditory tone.
    • Hebb's rule, verified.
  • Yoshii & Ogura (22): Reticular units, originally not responding to sciatic nerve US, started to respond to the CS after a few tens of trials, however the conditioned reactions disappeared with continued training.
    • This must be regarded as response to arousal at the initial stages of classical aversive (sciatic nerve pain?) conditioning.
  • Used capilary electrodes 1um in diameter, filled with KCl or sodium glutamate
  • Stimulation current 10-50nA DC, 0.3-1 sec.
  • Were able to record and stimulate at the same time using these glass microelectrodes.
  • The majority of units (cortex, reticular formation, thalamus) showed no response, though some did. These responses tended to fade with overtraining.
  • Quote: "The rather low incidence of positive results int he above experiment might be due to the fact that many examined neurons lack even an indirect acoustic input and cannot, therefore, be activated by acoustic stimuli."
  • Neurons in the IC show the strongest plastic change.
  • Their study is more specific than Loucks (15), Olds and Milner (17) Delgaso (6) Doty(7) which used less specific ICMS.
  • That said, there is no behavior .. so we don't know if the stimuli is being reacted to or attended to (might explain the low # of responses in areas).
  • They also think that the response can be credited to nonspecific phenomena like dominant focus, reflex sensitization, or heterosynaptic facilitation.
    • That said, the IC did show strong responses.

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ref: Delgado-1964 tags: Delgado wireless stimulation record stimoceiver rhesus monkey date: 01-03-2012 07:07 gmt revision:5 [4] [3] [2] [1] [0] [head]

bibtex: delgado-1964 Personality, education, and electrical stimulation of the brain

  • images/977_1.pdf
  • "Is it conceivable that behavior or the psyche can be related to electronics? Before answering these questions, we should ask one more: what is the main difference between primitive tribesmen still living in the jungle and the civilized human beings so well represented by this audience?" Education.
  • Kinda a ramble saying how education and understanding the brain is essential to our future.
  • Against atomic deterrence, unsurprisingly.
    • We are in the precarious race between the acquisition of many megatons of destructive power and the development of intelligent human beings who will make wise use of the forces at our disposal"
  • Radio receiver on a belt.
  • Elicited very complex movements from stimulating the thalamus, including walking from one side of the cage to the other, including avoiding the boss monkey!
    • He calls this 'electrical stimulation of the will'.
  • stimulate nucleus postero-ventralis induces targeted, well-directed attacks against other males of the group.
  • Stimulation of the caudate-septal lobes, just behind the frontal lobes, causes the boss monkey to become tame / tolerant / less aggressive.
  • When this function was enabled by pressing a button in the monkeys cage, the monkey most harrassed learned to press the button to halt the boss's aggressive behavior.
  • Regarding patients: "some of these patients have undergone testing for weeks or months, and lead a nearly normal life wthile 10, 20 or even more fine wires were present, in different cerebral areas and ready for stimulation from outside the scalp."
    • For example, in one patient, who spike a mean of 8.5 words per minute, by means of stimulation to the second temporal column increased his conversation to 44 words per minute." Menwhile, the number of friendly remarks increased by a factor of 9.
  • "Knowledge of the human mind may be decisive for our pursuit of happiness and for the very existence of mankind"

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ref: Lim-2009.09 tags: auditory midbrain implant deaf cochlea stimulation inferior colliculus date: 01-03-2012 06:55 gmt revision:2 [1] [0] [head]

PMID-19762428[0] Auditory midbrain implant: a review.

  • Inferior to a cochlear implant -- subjects, at the best, could understand speech only with lip-reading cues.
  • But! It's safe, and offers some degree of perception.
  • Also see: PMID-21157353[1]
    • Neurofibramatosis type 2 can also lead to cochlear deafness.
    • Implanted in the dorsal and ventral cochlear nuclei in the lateral recess of the IVth ventricle of the brain stem.
    • EABRs (evoked auditory brain stem responses); even though these were associated with electrodes in the right place, they could not be used for device fitting (?)


[0] Lim HH, Lenarz M, Lenarz T, Auditory midbrain implant: a review.Trends Amplif 13:3, 149-80 (2009 Sep)
[1] O'Driscoll M, El-Deredy W, Ramsden RT, Brain stem responses evoked by stimulation of the mature cochlear nucleus with an auditory brain stem implant.Ear Hear 32:3, 286-99 (2011 May-Jun)

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ref: notes-0 tags: k-means clustering neurophysiology sorting date: 01-03-2012 06:51 gmt revision:1 [0] [head]

k-means is easy!

% i want to do the k-means alg. 
v = [x y]; 
nc = 7;
dim = cols(v); 
n = rows(v); 
cent = rand(nc,dim); 
d = zeros(n, nc); 
for k = (1:500)
	for s = 1:nc
		d(:,s) = sqrt(sum((v - rvecrep(cent(s, :), n)).^2,2));
	% select the smallest
	[nada, g] = min(d'); 
	g = g';
	for s = 1:nc
		if(numel(find(g==s)) > 0)
			cent(s, :) = mean(v(g==s, :));

real data from clementine:

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ref: Wilson-1993.08 tags: Wilson McNaughton 1993 sleep hippocampus array recording date: 01-03-2012 00:57 gmt revision:2 [1] [0] [head]

PMID-8351520[0] Dynamics of the hippocampal ensemble code for space.

  • 73-148 neurons.
  • Could accurately decode the rat's movement through space.
  • "The parallel recording methods outlined here make possible the study of the dynamics of neuronal interactions during unique behavioral events."

PMID-8036517[1] Reactivation of hippocampal ensemble memories during sleep.

  • "Information acquired during active behavior is thus re-expressed in hippocampal circuits during sleep, as postulated by some theories of memory consolidation."


[0] Wilson MA, McNaughton BL, Dynamics of the hippocampal ensemble code for space.Science 261:5124, 1055-8 (1993 Aug 20)
[1] Wilson MA, McNaughton BL, Reactivation of hippocampal ensemble memories during sleep.Science 265:5172, 676-9 (1994 Jul 29)

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ref: Doty-1969.01 tags: Doty microstimulation brain behavior macaque conditioned stimulus attention motivation 1969 date: 12-29-2011 23:28 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

PMID-4888623[0] Electrical stimulation of the brain in behavioral context.

  • Excellent review.
  • Focal stimulation of macaques can induce insect-grabbing responses, after which they will carefully examine their hands to see what was caught!
    • Same thing has been observed in humans -- the patient reported that he wanted to catch 'that butterfly'.
  • Such complicated action must be the effect of downstream / upstream targets of the stimulated site, as the actual stimulation carries no information other than it's spatial locality within the brain.
  • Stimulation of the rostral thalamus in the language hemisphere can elicit phrases: "Now one goes home", "Thank you", "I see something".
    • These are muttered involuntarily and without recollection of having been spoken.
  • Doty stimulated macaques at 20ua for 500us as a CS in postcentral gyrus (S1?) for a lever press CR, which should (he says)only activate a few dozen neurons.
  • Can elicit mating behaviors in oposums with electrical stimulation of the hypothalamus, but only if another opossum or furry object is present.
  • Stimulation of the caudate nucleus in humans causes an arrest reaction: they may speak, smile, or laught inappropriately, but appropriate voluntary responses are brought to a halt.
  • Stimulation of the basolateral amygdala can cause:
    • Hungry cats to immediately stop eating
    • Stop stalking prey
    • Non-hunting animals to stalk prey, and indeed will solve problems to gain access to rats which can be attacked.
  • Prolonged stimulation of almost every place in the brain of a cat at 3-8Hz can put it to sleep, though since lab cats normally sleep 17/24hours, this result may not be significant.
  • Stimulation at most sites in the limbic system has the still mysterious ability to organize motor activity in any fashion required to produce more of the activity or to avoid it, as the case may be.
  • Rats that are stimulated in the periaqueductal gray will self-administer stimulation, but will squeal and otherwise indicate pain and fright during the stimulation. Increasing the duration of stimulation from 0.5 to 1 second makes self-administration of this apparently fearful stimulation stop in both rats and cats.
  • Certain patterns of activity within systems responsible for fearful or aggressive behavior, rather than being aversive are perversely gratifying. This is clearly recognized in the sociology of man...
  • Rats will self-stimulate with the same stimulus trains that will cause them to eat and drink, and under some conditions the self-stimulation occurs only if food or water is available.
  • On the other hand, rats will choose self-stimulation of the lateral hypothalamus instead of food, even when they are starving.
    • Electrically induced hunger is its own reward.
  • The work of Loucks (124, 125) forms the major point of origin for the concept that motivation is essential to learning. with careful and thorough training, Loucks was unable to form CRs to an auditory CS using stimulation of the motor cortex as the US. With this paradigm, the limb movements elicited by the US never appeared to the CS alone; but movements were readily established when each CS-US combination was immediately followed by the presentation of food.
    • However: Kupalov independently proved that stimulation of the motor cortex could be used as the US, at the same time using stimulation at other loci as the CS.
    • Why the difference? Attention -- failures are commonly obtained with animals that consistenly fidget or fight restraint, as most of them do.
    • Cortical stimulation itself is not rewarding or aversive; animals neither seek nor avoid stimulation of most neocortical areas.
  • On classical conditioning: [Bures and colleagues (20, 65) bibtex:Bures-1968 bibtex:Gerbrandt-1968] found that if an anticedent stimulus, which might or might not effect a neuron, were consistently followed by effective intracellular electrical stimulation of that individual neuron, in roughly 10 percent of the cells of the neocortex, hippocampus, thalamus, or mesencephalic reticular formation a change in the response of that cell to the antecedent stimulus could be observed.
  • With an apparent exception of the cerebellum it is possible to electrical excitation any place in the brain as a CS in chickens, rats, rabbits ...
  • Stimulation of group 1 proprioceptive muscle-afferent fibers in cats is ineffective as a CS.
    • Muscle spindles lack clear access to the systems subserving conditioned reflexes. (These instead go to the cerebellum)
  • Macaques can also discriminate between two stimulation sites 1-3 mm apart apparently over the entirety of the cortex, at frequencies between 2 and 100Hz, and over a 4-10fold range of currents.
  • In human cases where electrical stimulation or the cortex elicits specific memories, extirpation of the stimulated area does not effect recall of this memory (156) {973}.


[0] Doty RW, Electrical stimulation of the brain in behavioral context.Annu Rev Psychol 20no Issue 289-320 (1969)

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ref: PENFIELD-1963.12 tags: Penfield memory stimulation music epilepsy awesome date: 12-29-2011 22:21 gmt revision:4 [3] [2] [1] [0] [head]

PMID-14090522[0] The Brains record of auditory and visual experience -- A final summary and discussion

  • 102 pages. basically, this is a book.
  • Electrical stimulation causes 'hallucinations of things previously seen or heard or experienced.'
    • 'Both the experience and the interpretation are produced by discharge in the temporal cortex and not in other areas'
    • Experiential responses only followed stimulation in the temporal lobe.
  • These tests were done in an effort to locate the source of a seizure.
  • Damn, references the Caliph at Cordova as the first to document epileptic hallucinations (1519!)
    • And Hughlings Jackson (1888)!
  • Extirpation of memories elicited by ustim to an area persist after removal of that area.
  • Performed 1,288 surgeries, 520 of them for seizures in the temporal lobes, 40 of these with experiential responses, and 24 of those with experiential epileptic hallucinations.
    • Many of the patients' epilepsy was caused by ischemia, perhaps developmental; others by glioma..
  • Stimulation of the white matter has never produced an experiential response. Deep stimulation in the amygdala or hippocampus (??) also failed to elicit experiential responses.
  • Talks about 'difficult birth' -- was/is this the cause of some epilepsy? Or has that been discounted?
  • Buncha stuff on human cortical anatomy / topology, which is not so interesting to me.
  • Walker on the chimpanzee (1938) showed that the temporal cortex has no direct connections to the thalamus except posteriorly, where projections are received from nucleus lateralis posterior and pulvinar (visual attention), and within the transverse temporal gyri which receive auditory afferent projections from the medial geniculate body.
    • Also receives large fiber projections from the hippocampus.
  • This is absolutely fascinating. Memories, art, songs (music, so much music -- temporal lobe!), childbirth, counting, childhood molestation, a whole host of experiences were brought forth by electrical stimulation.
    • Case 9. E. Le. This 44-year old woman began to have seizures at age 22 during a pregnancy. The attack pattern was: (1) flushing of face and neck (2) automatism; (3) occasional generalized seizure. During and automatism she was apt to say, "I am alright". Then she would walk about the room and show marked affection toward anyone who happened to be present.
    • Repeated without warning: She said, "Yes, another experience, a different experience." Then she added, "A true experience. This man, Mr. Meerburger, he, oh well, he drinks. Twice his boy has run away. I went to the store once for an ice cream cone and I saw that he was back, and I said 'Hmm, he is back,' and the lady asked me 'What is the matter,' and I didn't know how to explain so I said, 'Well you know Mr. Meerburger drinks.' I thought that was the easiest way but later mother told me, no, and it made it a lot worse."
    • What surprises me is the relative lack of breadth in these --many of the responses to stimulation are quite similar, over a wide range of cortex, many of them very dream-like in features and recall.
      • Their impression: It is often evident that ''each stimulation leaves behind a facilitating influence so that the same response follows each stimulation and this facilitation may cause a given response to follow stimulation at one to three centimeters distance. Illustrated by the case 5, D.F
      • This deserves far more experimentation! E.g. ask the patient to think about something, and see if the same stimulation elicits different memories.
    • Another patient had a series of experiential hallucinations which all involved some aspect of 'grabbing' -- a man grabbing a rifle from a cadet during a parade, a man snatching his hat from the hat-check girl, grabbing a stick from a dog's mouth. In this epileptic, an instance of 'grabbing' was the ictal focus. Amazing.
  • Points out that stimulation must activate a great number of neural circuits, only one specific memory is recalled -- indicating that there is strong inhibition for mutual-exclusion.
  • Non-dominant, non-speech temporal cortex is almost always involved in interpretation: stimulation produces visual experiences, or visual interpretive illusions (change in distance or speed).
    • Stimluation also produces changes in the state-of-mind.
  • Certain sorts of experiences seem absent:
    • The times of making up ones mind
    • Times of carrying out skilled acts, writing messages or adding figures,
    • Eating food
    • Sexual excitement and experience (unless the patients may have self-censored this?)
    • Intense pain or suffering.
    • These things do not involve interpretation, and the focus of attention is not on the way that things are heard or seen.
  • They would remove quite large sections of the temporal lobe!
    • Still, the excision of these areas does not abolish memory: it does not contain a record of the past.
    • Yet stimulation in the temporal lobe recalls memories as nowhere else does.
  • There is a sharp frontier / boundary between auditory and visual temporal cortices and interpretive -- millimeters movement may change phosphenes into recall of a familiar person.
  • Note the comparison between speech cortex (dominant) and interpretive -- stimulation of speech cortex produces no speech, only aphasia, whereas stimulation of non-dominant termporal cortex forces recall.
  • "He who is faithfully analysing many cases of epilepsy is doing far more than studying epilepsy"



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ref: -0 tags: Georgoplous todorov M1 controversy square root bias PV date: 12-22-2011 22:52 gmt revision:2 [1] [0] [head]

PMID-11017158 One motor cortex, two different views

  • ref {950}, {952}, {953}
  • Georgopoulos re-analyzed their data without squareroot transformation and without smothing -- using only binned rates -- and found that it did not substantially change the porportions of tuned cells
  • In return, Todorov {955} responds that classifying cells based on maximal R^2 is stupid -- many cells lie on the decision boundaries in this manifold.

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ref: Laubach-2003.03 tags: cluster matlab linux neurophysiology recording on-line data_analysis microstimulation nicolelis laubach date: 12-17-2011 00:38 gmt revision:4 [3] [2] [1] [0] [head]

IEEE-1215970 (pdf)

  • 2003
  • M. Laubach
  • Random Forests - what are these?
  • was this ever used??

follow up paper: http://spikelab.jbpierce.org/Publications/LaubachEMBS2003.pdf

  • discriminant pusuit algorithm & local regression basis (again what are these? lead me to find the lazy learning package: http://iridia.ulb.ac.be/~lazy/


Laubach, M. and Arieh, Y. and Luczak, A. and Oh, J. and Xu, Y. Bioengineering Conference, 2003 IEEE 29th Annual, Proceedings of 17 - 18 (2003.03)

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ref: Hallworth-2005.07 tags: globus pallidus subthalamic nucelus parkinsons date: 12-07-2011 04:04 gmt revision:1 [0] [head]

PMID-16000620[0] Globus Pallidus Neurons Dynamically Regulate the Activity Pattern of Subthalamic Nucleus Neurons through the Frequency-Dependent Activation of Postsynaptic GABAA and GABAB Receptors

  • in normal animals, STN neurons are spontaneously active, with a resting rate between 10hz and 30hz.
  • during movement, STN neurons display somatotopic, spatiotemporally related changes in activity.
  • in parkinsonian animals, precise sonatotopy is lost, and there is an emergence of correlated, rhythmic activity. STN activity phase-related to tremor has been found in PD patients.
    • this study wants to try to explain why the rhythmic burst activity occurs.
  • one idea: synchronous barages of inhibitory activity results in hyperpolarization-induced high-frequency firing.
  • alternate: GABA_a receptors an mediate a tonic current that profoundly influences postsynaptic excitability. problem: GABA_a receptor antagonists have no effect on STN activity.
  • tonic GABA current was not observed, while there was plenty of GABA mediated IPSPs.
  • strong tetanic simulation of the internal capsule results in STN hyperpolarization followed by bursts of APs. (well then, why do we target the STN in DBS if the oscillations are not it's fault?)


[0] Hallworth NE, Bevan MD, Globus pallidus neurons dynamically regulate the activity pattern of subthalamic nucleus neurons through the frequency-dependent activation of postsynaptic GABAA and GABAB receptors.J Neurosci 25:27, 6304-15 (2005 Jul 6)

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ref: Kemp-1971.09 tags: globus pallidus striatum 1971 neuroanatomy date: 12-07-2011 04:03 gmt revision:1 [0] [head]

PMID-4399123[0] The connexions of the striatum and globus pallidus: synthesis and speculation. !! great figures, great synthesis !!

  • a striking feature of the striatum (caudate and putamen, functionally the same is the dense axonal plexus - this receives a major contribution from the contralateral branches the short axon terminals (interneurons) as well as afferent projections. perhaps the most important characteristic of the axonal plexus is that all the component fibers cross dendrites rather than lie parallel to them -- just like the cerebellum''.
  • the cerebellum also has excitatory input and inhibitory output. similar structure to do a similar thing? ++ plenty of interneurons ++plenty of dendritic spines.
  • all of the cerebral cortex projects to the cerebellum, even the visual cortex has projections to the pontine nuclei. however, there is an exceptionallly small projection from the visual cortex to both the cerebellum and striatum.


[0] Kemp JM, Powell TP, The connexions of the striatum and globus pallidus: synthesis and speculation.Philos Trans R Soc Lond B Biol Sci 262:845, 441-57 (1971 Sep 30)

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ref: Lin-2006.12 tags: nucleus_basalis GABA ACh attention basal_forebrain sleep date: 12-07-2011 03:51 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-16928796[0] Fast modulation of prefrontal cortex activity by basal forebrain noncholinergic neuronal ensembles

in the author's own words:

  • in the intro sections, you can find the summary background info you need, both anatomical and functional. Despite the fact that most people think of this as solely the cholinergic projection system, my data is pointing to a very important role for the non-ACh projection system (most likely GABAergic!) in fast cortical modulation and ATTENTION. The relevant thing for you here is that, when people stimulated nucleus basalis and claimed the effect to be cholinergic, I believe most stimulation protocols (short bursts) are in fact mimicking the natural activity pattern of non-ACh projection system, and therefore should be re-interpreted with caution.
  • the intro, as promised, is concise, relevant, and has a lot of references.
  • key hypothesis is that the BF has GABA projections onto GABAergic interneurons in the PFC
    • typically, people focus on ACh projections.. perhaps as a matter of tradition?
    • PFC is reciprocally connected to the BF
  • secondary thing to test was the difference in behavior of the basal-forebrain tonic neurons (BFTN) between sleep and wake states.


[0] Lin SC, Gervasoni D, Nicolelis MA, Fast modulation of prefrontal cortex activity by basal forebrain noncholinergic neuronal ensembles.J Neurophysiol 96:6, 3209-19 (2006 Dec)

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ref: BuzsAki-1996.04 tags: hippocampus neocortex theta gamma consolidation sleep Buzsaki review learning memory date: 12-07-2011 02:31 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-8670641[0] The hippocampo-neocortical dialogue.

  • the entorhinal ctx is bidirectionally conneted to nearly all areas of the neocortical mantle.
  • Buzsaki correctly predicts that information gathered during exploration is played back at a faster scale during synchronous population busts during (comnsummatory) behaviors.
  • looks like a good review of the hippocampus, but don't have time to read it now.
  • excellent explanation of the anatomy (with some omissions, click through to read the caption):
  • SPW = sharp waves, 40-120ms in duration. caused by synchronous firing in much of the cortex ; occur 0.02 - 3 times/sec in daily activity & during slow wave sleep.
    • BUzsaki thinks that this may be related to memory consolidation.
  • check the cited-by articles : http://cercor.oxfordjournals.org/cgi/content/abstract/6/2/8
[0] Buzsaiki G, The hippocampo-neocortical dialogue.Cereb Cortex 6:2, 81-92 (1996 Mar-Apr)

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ref: -0 tags: optical illusion date: 12-04-2011 16:54 gmt revision:1 [0] [head]

-- So cool! How do you come up with something like this?

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ref: -0 tags: hike bynum wandering bushwacking date: 01-17-2011 16:32 gmt revision:1 [0] [head]

Excellent hike in Bynum NC starting at the old homestead down there, crossed a number of random properties, entered and left Haw river state park, saw a good number of decomposing farmhouses, all on a gorgeous day. Route was taken clockwise; jog at the end away from main trail was to avoid a hunter in the main fields. This forced us to do a good bit of bushwacking and gave the opportunity to meet some local horses, goats, and runners. Total distance about 9 miles.

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ref: -0 tags: fragment of a dream san francisco frustration life date: 01-07-2011 05:33 gmt revision:1 [0] [head]

Remembered fragment of a dream, letter never sent.

Probably it was ill-fated to ---. Eh. That didn't distract me from having a batshit insane dream last night, feat three army goons, myself, and the vivacious ---. The goons and I were soldiers in charge of some truck-mounted machine gun in a logged and dried-mud hillcountry - probably Serbia - but whenever we tried to get it ready, the part in question would instantly transform into crochet. When the ammunition roll was finally in the yarn gun, all the bullets would fall on the ground; look away and it would resume metallic reality. On cue to amplify our disorganization a officer sped in to harass us in a Honda S2000. Annoyed, I threw gravel at him; it transformed into a lamborghini, then a porsche, a tesla, a toyota. (I've seen a lot of fancy cars this past week).

Given the frustrated Daliesque nature of the battlefield, we retreated, I as a restrained but irked soldier. Montage in, montage out, you enter to this scene as an bit-played angry estranged woman, pissed at my lack of caring / perceived neglect. Bitch complain threaten whine, I guilt but look outside and the vegetation is gorgeous, lush, the sky a mild hazy blue. I am a little thirsty.

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ref: -0 tags: perl music date: 12-22-2010 02:17 gmt revision:0 [head]

Short script for copying & tagging files from a playlist to a flat target.

sub rand_pass {
	my @chars = ('a'..'k','m','n','p'..'z','2'..'9');
	my $length = 8;
	my $password = '';
	for (0..$length) {
		$password .= $chars[int rand @chars];
	return $password;

open FH, "playedlst.txt"; 
my $targ = "/media/usb0"; 
while($k = <FH>){
	#print "$k\n";
	$k =~ s/^\.//; 
	$k =~ s/\n//; 
	my $dest = $k; 
	my $suffix = ".mp3"; 
	if($dest =~ /\.(\w+)$/){
		$suffix = $1; 
	#print("  suffix $suffix \n"); 
	if($dest =~ /\/([^\/]+)\.[^\.]+/){ #remove any suffix
		$dest = "/$1"; 
	if(-e "$targ/$dest.$suffix") { #test to see if the target exists
		$dest = rand_pass(); 
	my $src = "\"/mnt/crackle/hanson/music$k\""; 
	my $fdest = "\"$targ$dest.$suffix\""; 
	`cp $src $fdest`; 
	`id3v2 -r \"COMM\" $fdest`;
	`id3v2 -c \"$k\" $fdest`;
close FH; 

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ref: notes-0 tags: usbmon decode chart linux debug date: 07-12-2010 03:29 gmt revision:3 [2] [1] [0] [head]

From this and the USB 2.0 spec, I made this quick (totally incomprehensible?) key for understanding the output of commands like

# mount -t debugfs none_debugs /sys/kernel/debug
# modprobe usbmon
# cat /sys/kernel/debug/usbmon/2u

To be used with the tables from the (free) USB 2.0 spec:

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ref: notes-0 tags: Gladwell talent narcissism management structure business date: 11-19-2009 06:02 gmt revision:1 [0] [head]

http://www.gladwell.com/pdf/talent.pdf -- From 2002. Old but excellent. Structure is required to achieve broad, slow to ROI projects. (It's almost common sense when expressed this way!)

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ref: work-0 tags: machine learning manifold detection subspace segregation linearization spectral clustering date: 10-29-2009 05:16 gmt revision:5 [4] [3] [2] [1] [0] [head]

An interesting field in ML is nonlinear dimensionality reduction - data may appear to be in a high-dimensional space, but mostly lies along a nonlinear lower-dimensional subspace or manifold. (Linear subspaces are easily discovered with PCA or SVD(*)). Dimensionality reduction projects high-dimensional data into a low-dimensional space with minimum information loss -> maximal reconstruction accuracy; nonlinear dim reduction does this (surprise!) using nonlinear mappings. These techniques set out to find the manifold(s):

  • Spectral Clustering
  • Locally Linear Embedding
    • related: The manifold ways of perception
      • Would be interesting to run nonlinear dimensionality reduction algorithms on our data! What sort of space does the motor system inhabit? Would it help with prediction? Am quite sure people have looked at Kohonen maps for this purpose.
    • Random irrelevant thought: I haven't been watching TV lately, but when I do, I find it difficult to recognize otherwise recognizable actors. In real life, I find no difficulty recognizing people, even some whom I don't know personally - is this a data thing (little training data), or mapping thing (not enough time training my TV-not-eyes facial recognition).
  • A Global Geometric Framework for Nonlinear Dimensionality Reduction method:
    • map the points into a graph by connecting each point with a certain number of its neighbors or all neighbors within a certain radius.
    • estimate geodesic distances between all points in the graph by finding the shortest graph connection distance
    • use MDS (multidimensional scaling) to embed the original data into a smaller-dimensional euclidean space while preserving as much of the original geometry.
      • Doesn't look like a terribly fast algorithm!

(*) SVD maps into 'concept space', an interesting interpretation as per Leskovec's lecture presentation.

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ref: work-0 tags: covariance matrix adaptation learning evolution continuous function normal gaussian statistics date: 06-30-2009 15:07 gmt revision:0 [head]


  • Details a method of sampling + covariance matrix approximation to find the extrema of a continuous (but intractable) fitness function
  • HAs flavors of RLS / Kalman filtering. Indeed, i think that kalman filtering may be a more principled method for optimization?
  • Can be used in high-dimensional optimization problems like finding optimal weights for a neural network.
  • Optimum-seeking is provided by weighting the stochastic samples (generated ala a particle filter or unscented kalman filter) by their fitness.
  • Introductory material is quite good, actually...

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ref: life-0 tags: NYTimes genius talent skill learning date: 06-27-2009 18:36 gmt revision:1 [0] [head]

http://www.nytimes.com/2009/05/01/opinion/01brooks.html?_r=1 -- the 'modern view' of genius. Makes sense to me.

  • quote: "By practicing in this way, performers delay the automatizing process. The mind wants to turn deliberate, newly learned skills into unconscious, automatically performed skills. But the mind is sloppy and will settle for good enough. By practicing slowly, by breaking skills down into tiny parts and repeating, the strenuous student forces the brain to internalize a better pattern of performance." -- exactly!!
  • quote: The primary trait she possesses is not some mysterious genius. It’s the ability to develop a deliberate, strenuous and boring practice routine.
  • It's not who you are, it's what you do. (law of the cortex: you get good at what you do).
  • The subconcious / ability to push skills to the subconcious should not be neglected. Insight apparently is mostly subconcious, and rapid decisions are too - the rational/concious brain is simply too slow and deliberate to form realtime behavior & reactions, but as the above quote highlights, it is also too 'lazy' and accepting to carefully hone a true skill. This requires attention.
  • From the guardian -- "Sometimes an overload of facts is the mark of a dull and pedestrian mind, the antithesis of intelligence."
    • also: "Intelligence is a matter of output, not scores on a test." We know genius & talent by it's output.

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ref: work-0 tags: yushin robot data date: 06-25-2009 18:35 gmt revision:3 [2] [1] [0] [head]

U141 LMV1032 microSMD-4 -2.23315 -0.03575 180. 9394. 27366. 1675. 
L7 INDUCTOR 0603 -1.7784 -0.7561 0. 13171. 34955. 1727. 
C86 0.1uf 0402 1.0946 -0.0347 360. 37107. 27524. 1710. 
TP8 TP TP 0.222 -1.0285 0. 29815. 37809. 1767. 
TP9 TP TP 0.7021 -1.2484 0. 33805. 40090. 1787. 
C67 1uf 0603 0.8146 -0.7047 270. 34758. 34540. 1752. 
C68 1uf 0603 1.1946 -0.7247 270. 37920. 34730. 1758. 
C69 1uf 0603 1.2747 -0.7247 90. 38576. 34742. 1759. 
R4 33 0402 1.6937 -0.1982 180. 42071. 29215. 1728. 
R17 10k 0402 -1.685 -0.6615 270. 13941. 33981. 1723. 
U92 LMV1032 microSMD-4 -2.53285 -0.03585 180. 6912. 27381. 1671. 
U96 LMV1032 microSMD-4 -2.23315 -0.89075 180. 9364. 36340. 1732. 
TP10 TP TP 0.222 -1.1685 0. 29811. 39233. 1776. 
TP11 TP TP 0.222 -1.3084 0. 29807. 40698. 1786. 
R23 33 0402 0.2834 0.6142 180. 30371. 20682. 1659. 
U105 LMV1032 microSMD-4 -2.23315 -0.71965 180. 9368. 34557. 1720. 
U117 LMV1032 microSMD-4 -2.23315 -0.49165 180. 9366. 32055. 1705. 
U124 LMV1032 microSMD-4 -2.18025 -0.37765 180. 9820. 30853. 1698. 
U127 LMV1032 microSMD-4 -2.18025 -0.32065 180. 9826. 30273. 1695. 
U128 LMV1032 microSMD-4 -2.28685 -0.26365 180. 8940. 29697. 1690. 
R10 50k 0402 -0.9607 -0.3308 180. 19983. 30430. 1709. 

more data!

U136 LMV1032 microSMD-4 -2.18025 -0.14965 180. 9860. 28534. 1682. 
R47 20k 0402 1.1822 -1.3883 90. 37828. 41612. 1797. 
R48 20k 0402 0.942 -1.0284 270. 35838. 37757. 1771. 
U139 LMV1032 microSMD-4 -2.18025 -0.09265 180. 9863. 27964. 1678. 
C72 10nf 0603 1.3546 -0.6248 270. 39284. 33694. 1750. 
R45 12.5k 0402 1.1021 -1.3883 90. 37161. 41608. 1796. 
C37 33nF 0402 -1.0956 -0.7067 360. 18894. 34462. 1730. 
R46 12.5k 0402 1.0221 -1.0284 270. 36505. 37759. 1772. 
L7 INDUCTOR 0603 -1.7784 -0.7561 0. 13210. 34933. 1725. 
U142 LMV1032 microSMD-4 -2.18025 -0.03575 180. 9865. 27310. 1674. 
L8 INDUCTOR 0603 0.1745 -0.6447 270. 29446. 33849. 1738. 
C87 0.047uf 0402 -2.3611 -0.8811 360. 8363. 36186. 1729. 
R53 9.2k 0402 1.062 -1.3883 90. 36817. 41587. 1796. 
R36 3.3k 0402 1.9546 -0.8747 270. 44273. 36230. 1772. 
C88 0.047uf 0402 -2.361 -0.8241 360. 8356. 35593. 1725. 
R54 9.2k 0402 1.062 -1.0284 270. 36838. 37762. 1772. 
R38 3.3k 0603 0.8646 -0.8147 360. 35200. 35636. 1757. 
R37 3.3k 0402 1.9546 -1.1347 270. 44266. 38878. 1788. 
TP1 TP TP 1.302 -1.3882 0. 38828. 41596. 1797. 
C89 0.047uf 0402 -2.361 -0.7671 360. 8358. 35023. 1721. 
C83 0.1uf 0402 1.2246 -0.5147 0. 38206. 32492. 1741. 
C12 1uf 0402 0.8182 0.1876 270. 34842. 25228. 1692. 
R39 3.3k 0402 1.5146 -0.8747 90. 40609. 36213. 1767. 
TP3 TP TP 1.302 -1.2484 0. 38835. 40039. 1788. 
C85 0.1uf 0402 0.2946 -0.0348 180. 30497. 27541. 1701. 
C29 0.01uf 0402 -1.5749 -0.1575 270. 14907. 28634. 1690. 
TP4 TP TP 0.8219 -1.1684 0. 34852. 39172. 1778. 
C15 1uf 0402 1.6037 0.0518 270. 41377. 26681. 1709. 
TP5 TP TP 0.8219 -1.3084 0. 34835. 40731. 1787. 
C86 0.1uf 0402 1.0946 -0.0347 360. 37136. 27478. 1709. 
TP6 TP TP 1.3021 -1.1085 0. 38832. 38563. 1779. 
TP7 TP TP 0.7021 -1.3883 0. 33824. 41561. 1791. 
TP8 TP TP 0.222 -1.0285 0. 29855. 37751. 1763. 
C19 1uf 0402 -0.6901 -0.0599 90. 22286. 27662. 1693. 
TP9 TP TP 0.7021 -1.2484 0. 33830. 40042. 1782. 
C90 0.047uf 0402 -2.361 -0.7101 360. 8360. 34449. 1718. 
R40 3.3k 0402 1.5146 -1.1347 90. 40602. 38842. 1784. 
C28 7pf 0402 -1.0306 -0.562 270. 19447. 32944. 1722. 
C36 0.01uf 0402 -1.1968 0.0315 0. 18064. 26795. 1682. 
C67 1uf 0603 0.8146 -0.7047 270. 34787. 34503. 1750. 
R13 25 0402 -1.57 -0.34 0. 14940. 30478. 1701. 
C68 1uf 0603 1.1946 -0.7247 270. 37950. 34725. 1755. 
C38 0.01uf 0402 -0.9763 -0.1733 270. 19894. 28829. 1697. 
R14 25 0402 -1.5749 -0.4094 270. 14897. 31177. 1705. 
C69 1uf 0603 1.2747 -0.7247 90. 38616. 34707. 1755. 
R16 25 0402 -1.1956 -0.8867 180. 18053. 36282. 1739. 
R1 33 0402 1.4961 0.0314 90. 40482. 26822. 1709. 
R5 220k 0402 -0.5628 -0.1852 90. 23338. 28986. 1701. 
R3 33 0402 1.6937 -0.1282 180. 42120. 28451. 1721. 
R4 33 0402 1.6937 -0.1982 180. 42116. 29193. 1725. 
R28 2.2k 0402 1.9346 -1.4048 90. 44069. 41754. 1804. 
R29 2.2k 0402 1.8346 -1.4047 90. 43249. 41818. 1804. 
C70 1uf 0603 1.2747 -0.6246 270. 38619. 33709. 1749. 
R2 100k 0402 1.4173 0.0315 90. 39826. 26815. 1708. 
C42 0.01uf 0402 -1.1955 -0.7166 180. 18052. 34552. 1730. 
R43 3k 0402 1.242 -1.3085 270. 38319. 40701. 1792. 
C73 1uf 0603 1.8646 -0.7147 0. 43527. 34646. 1761. 
R44 3k 0402 0.882 -1.1085 90. 35337. 38556. 1776. 
R49 33k 0402 1.202 -1.2285 270. 37988. 39816. 1787. 
C77 1uf 0603 0.7446 -0.9347 0. 34197. 36870. 1764. 
C32 1uf 0402 -0.8976 -0.6615 180. 20551. 34005. 1729. 
C79 1uf 0603 0.8646 -0.8747 180. 35198. 36251. 1761. 
R30 2.2k 0402 1.7347 -1.4047 90. 42427. 41804. 1803. 
C35 1uf 0402 -1.2913 0.0315 180. 17298. 26781. 1681. 
R31 2.2k 0402 1.6346 -1.4047 90. 41584. 41800. 1802. 
R50 33k 0402 0.9345 -1.1548 90. 35772. 39028. 1779. 
R11 10k 0402 -0.0001 0.126 90. 28025. 25843. 1690. 
C46 1uf 0402 -1.1955 -0.6766 180. 18053. 34138. 1727. 
R12 10k 0402 0.0001 0.5196 90. 28038. 21612. 1662. 
R9 10k 0402 0.0001 0.2835 270. 28031. 24093. 1677. 
R17 10k 0402 -1.685 -0.6615 270. 13974. 33945. 1741. 
R18 10k 0402 -1.5998 -0.4875 90. 14688. 32018. 1710. 
C14 0.001uf 0402 -0.96 -0.26 0. 20044. 29712. 1703. 
U92 LMV1032 microSMD-4 -2.53285 -0.03585 180. 6926. 27289. 1670. 
R55 6.5k 0402 0.9821 -1.3883 90. 36150. 41583. 1795. 
R56 6.5k 0402 1.142 -1.0284 270. 37502. 37773. 1774. 
R19 22K 0402 -0.9958 -0.6867 90. 19712. 34257. 1729. 
C2 0.1uf 0402 1.6237 -0.2581 270. 41530. 29787. 1728. 
C30 5pf 0402 -1.1907 -0.562 90. 18114. 32929. 1720. 
C25 0.001uf 0402 0.2835 0.0787 180. 30398. 26352. 1694. 
C20 33pf 0402 -0.5628 -0.3352 90. 23328. 30458. 1712. 
C13 8pf 0402 1.6877 -0.4299 270. 42062. 31517. 1741. 
C27 0.001uf 0402 -0.9763 -0.5039 90. 19900. 32258. 1718. 
C17 8pf 0402 1.4476 -0.4299 90. 40063. 31519. 1738. 
C71 0.1uf 0603 1.3545 -0.7247 90. 39280. 34701. 1756. 
C49 2.2uf 0402 -2.2324 -0.9436 0. 9413. 36840. 1734. 
C50 2.2uf 0402 -2.4802 -0.9455 0. 7350. 36852. 1732. 
C51 2.2uf 0402 -2.4779 0.0152 0. 7399. 26905. 1670. 
C52 2.2uf 0402 -2.2347 0.0184 0. 9423. 26881. 1672. 
C40 0.001uf 0402 -1.1956 -0.7568 180. 18050. 34938. 1732. 
C53 2.2uf 0402 -1.9398 -0.7554 0. 11855. 34916. 1725. 
C54 2.2uf 0402 -1.6317 -0.315 270. 14433. 30225. 1700. 
C48 2.2nF 0402 -0.9154 -0.9464 90. 20377. 36919. 1747. 
C55 2.2uf 0402 -1.8616 -0.7549 180. 12506. 34903. 1726. 
C56 0.012uf 0402 -1.7107 -0.7353 270. 13762. 34716. 1726. 
C57 0.012uf 0402 -1.6956 -0.8478 90. 13875. 35886. 1733. 
R7 90k 0402 -0.8225 -0.266 90. 21176. 29782. 1704. 
C58 0.012uf 0402 -1.8891 -0.8466 90. 12274. 35834. 1731. 
R57 22k 0402 0.942 -1.3883 90. 35826. 41602. 1795. 
TP10 TP TP 0.222 -1.1685 0. 29847. 39154. 1772. 
C22 10uf 0603 -0.6428 -0.1653 360. 22687. 28750. 1700. 
TP11 TP TP 0.222 -1.3084 0. 29820. 40682. 1781. 
C23 10uf 0603 -0.7429 -0.1652 180. 21854. 28745. 1699. 
TP12 TP TP 0.7022 -1.1085 0. 33848. 38556. 1773. 
C61 2.2uf 0402 -1.8422 -0.8468 90. 12664. 35859. 1732. 
C62 2.2uf 0402 -2.0357 -0.8464 90. 11053. 35837. 1730. 
C63 2.2uf 0402 -2.0001 -0.0836 270. 11363. 27899. 1681. 
C64 2.2uf 0402 -2.0025 -0.1862 90. 11350. 28924. 1688. 
C44 1.5pF 0402 -0.8357 -0.8065 180. 21045. 35478. 1739. 
C65 0.012uf 0402 -1.8247 -0.9119 0. 12808. 36505. 1736. 
C66 0.012uf 0402 -2.0181 -0.913 0. 11198. 36540. 1734. 
C39 0.1uf 0402 -1.3229 -0.6772 180. 16993. 34136. 1726. 
R6 825k 0402 -0.5628 -0.2651 90. 23329. 29784. 1706. 
C41 0.1uf 0402 -1.1023 0.0314 180. 18851. 26789. 1683. 
C45 0.1uf 0402 -0.9763 -0.0787 90. 19897. 27845. 1691. 
R34 327k 0402 1.9046 -0.8747 270. 43856. 36228. 1771. 
R35 327k 0402 1.9046 -1.1347 90. 43849. 38858. 1788. 
R51 47k 0402 1.202 -1.3085 270. 37985. 40700. 1792. 
R52 47k 0402 0.9221 -1.1083 90. 35661. 38566. 1776. 
C74 4.7uf 0603 1.9346 -1.0047 360. 44101. 37581. 1780. 
C75 4.7uf 0603 1.9346 -0.9447 360. 44103. 36957. 1776. 
C76 4.7uf 0603 1.9346 -1.0648 180. 44099. 38174. 1784. 
R41 327k 0402 1.5646 -0.8747 90. 41026. 36215. 1768. 
C78 4.7uf 0603 1.7346 -0.7947 0. 42442. 35463. 1765. 
R42 327k 0402 1.5645 -1.1347 270. 41018. 38856. 1784. 
C59 0.1uf 0402 -1.8046 -0.2246 270. 12986. 29320. 1692. 
U124 LMV1032 microSMD-4 -2.18025 -0.37765 180. 9843. 30773. 1696. 
U127 LMV1032 microSMD-4 -2.18025 -0.32065 180. 9845. 30296. 1692. 
C80 4.7uf 0603 1.5346 -0.9447 360. 40773. 36984. 1772. 
C81 4.7uf 0603 1.5346 -1.0648 180. 40769. 38149. 1780. 
R10 50k 0402 -0.9607 -0.3308 180. 20034. 30408. 1706. 
C82 4.7uf 0603 1.5346 -1.0047 360. 40771. 37546. 1776. 
C84 4.7uf 0603 0.1746 -0.5347 270. 29464. 32629. 1732. 
C60 0.1uf 0402 -1.8032 -0.0862 270. 13012. 27892. 1683. 
R15 50k 0402 -1.1956 -0.7967 180. 18055. 35380. 1734. 
U130 LMV1032 microSMD-4 -2.18025 -0.26365 180. 9857. 29685. 1689. 
2.9mm_hole VAL** 2.9mm_hole -2.325 0.2 0. 8698. 24995. 1658. 
U133 LMV1032 microSMD-4 -2.18025 -0.20665 180. 9849. 29114. 1685. 
C47 1pF 0402 -0.8158 -0.7565 90. 21212. 34950. 1736. 

counts spaced at exactly 1mm:
0 -13206.000000
1 -12795.000000
2 -12349.000000
3 -11983.000000
4 -11545.000000
5 -11117.000000
6 -10710.000000
7 -10262.000000
8 -9813.000000
9 -9395.000000
10 -8957.000000
11 -8561.000000
12 -8154.000000
13 -7726.000000
14 -7298.000000
15 -6897.000000
16 -6477.000000
17 -6093.000000
18 -5700.000000
19 -5309.000000
20 -4871.000000
21 -4453.000000
22 -4046.000000
23 -3639.000000
24 -3232.000000
25 -2836.000000
26 -2429.000000
27 -2011.000000
28 -1594.000000
29 -1187.000000
30 -780.000000
31 -352.000000
32 65.000000
33 472.000000
34 900.000000
35 1318.000000
36 1708.000000
37 2104.000000
38 2490.000000
39 2908.000000
40 3325.000000

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ref: MAPlle-2009.03 tags: sleep spindles learning ripples LFP hippocampus neocortex synchrony SWS REM date: 03-25-2009 15:05 gmt revision:2 [1] [0] [head]

PMID-19245368[0] The influence of learning on sleep slow oscillations and associated spindles and ripples in humans and rats

  • Here we examined whether slow oscillations also group learning-induced increases in spindle and ripple activity, thereby providing time-frames of facilitated hippocampus-to-neocortical information transfer underlying the conversion of temporary into long-term memories.
  • No apparent grouping effect between slow oscillations and learning-induced spindles and ripples in rats.
  • Stronger effect of learning on spindles (neocortex) and ripples (hippocampus) ; less or little effect of learning on slow waves in the neocortex.
  • have a good plot showing their time-series analysis:


[0] Mölle M, Eschenko O, Gais S, Sara SJ, Born J, The influence of learning on sleep slow oscillations and associated spindles and ripples in humans and rats.Eur J Neurosci 29:5, 1071-81 (2009 Mar)

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ref: Mehta-2007.01 tags: hippocampus visual cortex wilson replay sleep learning states date: 03-09-2009 18:53 gmt revision:1 [0] [head]

PMID-17189946[0] Cortico-hippocampal interaction during up-down states and memory consolidation.

  • (from the associated review) Good pictorial description of how the hippocampus may impinge order upon the cortex:
    • During sleep the cortex is spontaneously and randomly active. Hippocampal activity is similarly disorganized.
    • During waking, the mouse/rat moves about in the environment, activating a sequence of place cells. The weights of the associated place cells are modified to reflect this sequence.
    • When the rat falls back to sleep, the hippocampus is still not random, and replays a compressed copy of the day's events to the cortex, which can then (and with other help, eg. ACh), learn/consolidate it.
  • see [1].


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ref: Ji-2007.01 tags: hippocampus visual cortex wilson replay sleep date: 03-09-2009 18:48 gmt revision:3 [2] [1] [0] [head]

PMID-17173043[0] Coordinated memory replay in the visual cortex and hippocampus during sleep.

  • EEG from Layer 5 of the visual cortex.
  • used tetrodes.
  • rats were trained to alternate loops in a figure-8 maze to get at food.
  • the walls of the maze were lined with high-contrast cues.
  • data for correlated activity between ctx and hippocampus weak - they just show that the frame ('up' period in cellular activity) start & end between the two regions are correlated. No surprise - they are in the same brain after all!
  • Found that cells in the deep visual cortex (V1 & V2) had localized firing fields. Rat vision is geared for navigation? (mostly?)
  • From this, they could show offline replay of the same sequence; these offline sequences were compressed by about 5-10.
    • shuffle tests on the replayed frames look pretty good - respectable degree of significance here.
    • Aside: possibly some of the noise of the recordings is reflective not of the noise of the system, but the noise / high dimensionality of the sensory input driving the visual ctx.
  • Also found some visual and some hippocampal cells that replayed sequences simultaneously; shuffle test here looks ok too.
  • picture from associated review, {692}


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ref: KAli-2004.03 tags: hippocampus memory model Dayan replay learning memory date: 03-06-2009 17:53 gmt revision:1 [0] [head]

PMID-14983183[0] Off-line replay maintains declarative memories in a model of hippocampal-neocortical interactions

  • (i'm skimming the article)
  • The neocortex acts as a probabilistic generative model. unsupervised learning extracts categories, tendencies and correlations from the statistics of the inputs into the [synaptic weights].
  • Their hypothesis is that hippocampal replay is required for maintenance of episodic memories; their model and simulations support this.
  • quote: "However, the computational goal of episodic learning is storing individual events rather than discovering statistical structure, seemingly rendering consolidation inappropriate. If initial hippocampal storage of the episode already ensures that it can later be recalled episodically, then, barring practical advantages such as storage capacity (or perhaps efficiency), there seems little point in duplicating this capacity in neocortex." makes sense!


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ref: Foster-2006.03 tags: hippocampus memory place cells reverse replay Wilson date: 03-06-2009 17:53 gmt revision:1 [0] [head]

PMID-16474382[0] Reverse replay of behavioral sequences in hippocampal place cells during the awake state.

  • wow: they show compressed reverse replay of firing sequences of hippocampal place cells during movement. While the rat is awake, too!
  • recorded up to 128 cells from the rat hippocampus; 4 animals.
  • the replay occurred while the rat was stopped, and lasted a few hundred milliseconds (~300).
  • phenomena appears to be very common, at least for the rats on the novel tracks.
  • replay events were coincident with ripples in the hippocampal EEG, which also occurs during sleep.
    • however, during slow-wave sleep, the replay was forward.
  • they offer a reasonable hypothesis for the reverse replay's function: it is used to propagate value information from the rewarded lcoation backwards along incoming (behavioral) trajectories.
    • quote "awake replay represents efficient use of hard-won experience."


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ref: bookmark-0 tags: goodbrush paintings favorite date: 11-24-2008 03:03 gmt revision:4 [3] [2] [1] [0] [head]

hopefully these links don't move..

I like these 'paints', too. Did you show them to me a long time ago? I remember someone showing them to me in the past and I am wondering if you were the one. -- Ana

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ref: Froemke-2007.11 tags: nucleus basalis basal forebrain acetylcholine auditory cortex potentiation voltage clamp date: 10-08-2008 22:44 gmt revision:2 [1] [0] [head]

PMID-18004384[0] A synaptic memory trace for cortical receptive field plasticity.

  • nucleus basalis = basal forebrain!
  • stimulation of the nucleus basalis caused a reorganization of the auditory cortex tuning curves hours after the few minutes of training.
  • used whole-cell current-clamp recording to reveal tone-evoked excitatory and inhibitory postsynaptyic currents.
  • pairing of nucleus basalis and auditory tone presentation (2-5 minutes) increased excitatory currents and decreased inhibitory currents as compared to other (control) frequencies.
  • tuning changes required simultaneous tone presentation and nucleus basalis stimulation. (Could they indiscriminately stimulate the NB? did they have to target a certain region of it? Seems like it.)
    • did not require postsynaptic spiking!
  • Pairing caused a dramatic (>7-fold) increase in the probability of firing bursts of 2+ spikes
  • Cortical application of atropine, an acetylcholine receptor antagonist, prevented the effects of nucleus basalis pairing.
  • the net effects of nucleus basalis pairing are suppression of inhibition (20 sec) followed by enhancement of excitation (60 sec)
  • also tested microstimulation of the thalamus and cortex; NB pairing increased EPSC response from intracortical microstim, but not from thalamic stimulation. Both cortical and thalamic stimulation elicited an effect in the voltage-clamped recorded neuron.
  • by recording from the same site (but different cells), they showed that while exitation persisted hours after pairing, inhibition gradually increased commensurate with the excitation.
  • Thus, NB stimulation leaves a tag of reduced inhibition (at the circuit level!), specifically for neurons that are active at the time of pairing.


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ref: RAzsa-2008.01 tags: nAChR nicotinic acetylchoine receptor interneurons backpropagating LTP hippocampus date: 10-08-2008 17:37 gmt revision:0 [head]

PMID-18215234[0] Dendritic nicotinic receptors modulate backpropagating action potentials and long-term plasticity of interneurons.

  • idea: nAChRs are highly permeable to Ca+2, LTP is dependent on Ca2+, so they tested nAChR -> LTP in interneurons of rat hippocampus using whole-cell electrophysiology and 2-photon imaging.
  • Here we show that precisely timed activation of dendritic α7-nAChRs boosts the induction of LTP by excitatory postsynaptic potentials (EPSPs) and synaptically triggered dendritic Ca2+ transients.
  • suggest that this rapid (ionotropic) method of memory encoding and retrieval via LTP/D facilitated by acetylcholine.
  • I haven't read much of the article, since it is much out of my field of experience.


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ref: -0 tags: thalamus sensory Ochoa date: 10-05-2008 16:41 gmt revision:2 [1] [0] [head]


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ref: Kimura-1996.12 tags: putamen globus pallidus learning basal ganglia electrophysiology projection date: 10-03-2008 17:05 gmt revision:1 [0] [head]

PMID-8985875 Neural information transferred from the putamen to the globus pallidus during learned movement in the monkey.

  • study of the physiology of the projection from the striatum to the external and internal segments of the globus pallidus.
  • Identified neurons which project from the striatum to pallidus via antridromic activation after stim to the GPe / GPi.
  • there were two classes of striatal neurons:
    • tonically active neurons (TANs, rate: 4-8hz)
      • TANs were never activated by antidromic stimulation. therefore, they probably do not project to the pallidus.
    • phasically active neurons (very low basal rate, high frequency discharge in relation to behavioral tasks
      • All PANs found projected to the globus pallidus.
      • PANs were responsive to movement or movement preparation. (or not responsive to the particular behaviors investigated)
        • the PANns that showed activity before movement initiation more frequently projected to GPi and not GPE (or both - need to look at the anatomy more).
      • PANs also show bursts of activity time-locked to the initiation of movement (e.g. time locked to a particular part of the movement).
      • no neurons with sensory response!
  • when they microstimulated in the putamen, a few pallidal neurons showed exitatory response; most showed inhibitory/supressive response.

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ref: Graybiel-2005.12 tags: graybiel motor_learning reinforcement_learning basal ganglia striatum thalamus cortex date: 10-03-2008 17:04 gmt revision:3 [2] [1] [0] [head]

PMID-16271465[] The basal ganglia: Learning new tricks and loving it

  • learning-related changes occur significantly earlier in the striatum than the cortex in a cue-reversal task. she says that this is because the basal ganglia instruct the cortex. I rather think that they select output dimensions from that variance-generator, the cortex.
  • dopamine agonist treatment improves learning with positive reinforcers but not learning with negative reinforcers.
  • there is a strong hyperkinetic pathway that projects directly to the subthalamic nucleus from the motor cortex. this controls output of the inhibitor pathway (GPi)
  • GABA input from the GPi to the thalamus can induce rebound spikes with precise timing. (the outputs are therefore not only inhibitory).
  • striatal neurons have up and down states. recommended action: simultaneous on-line recording of dopamine release and spike activity.
  • interesting generalization: cerebellum = supervised learning, striatum = reinforcement learning. yet yet! the cerebellum has a strong disynaptic projection to the putamen. of course, there is a continuous gradient between fully-supervised and fully-reinforcement models. the question is how to formulate both in a stable loop.
  • striosomal = striatum to the SNc
  • http://en.wikipedia.org/wiki/Substantia_nigra SNc is not an disorganized mass: the dopamergic neurons from the pars compacta project to the cortex in a topological map, dopaminergic neurons of the fringes (the lowest) go to the sensorimotor striatum and the highest to the associative striatum


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ref: Maravita-2004.02 tags: tool use monkey mirror neurons response learning date: 09-24-2008 17:02 gmt revision:2 [1] [0] [head]

PMID-15588812[0] Tools for the body schema

See also PMID-8951846[1] Coding of modified body schema during tool use by macaque postcentral neurones.


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ref: Corlett-2007.09 tags: delusions pFC substantia nigra date: 09-23-2008 06:15 gmt revision:0 [head]

PMID-17690132 Disrupted prediction-error signal in psychosis: evidence for an associative account of delusions.

  • Hypothesis: the creation and maintenance of psychotic or delusional beliefs is caused by (or causally related to) malfunction in the predictive error circuitry in the brain. (namely, the prefrontal cortex, substantia nigra, and striatum).
  • Previous studies have shown that administering Ketamine, a dissociative drug that can cause delusions, effects this same pathway.
  • The authors tested the hypothesis by training control and psychotic subjects in an associative task: subjects had to determine if a fictitious patient would be allergic to a meal given example meals and resulting allergic reaction.
  • Both sets had about the same behavioral performance; however, activation of the prefrontal cortex, substantia nigra, and left striatum was less in the psychotic (some drug treated) subjects. This comparison of activation was measured between control trials (no prediction error) and violation trials (prediction violated) as well as unovershadowing (a and b causes allergy, but a or b separately do not)

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ref: Pastalkova-2008.09 tags: hippocampus Buzsaki sequences date: 09-22-2008 21:25 gmt revision:1 [0] [head]

PMID-18772431[0] Internally generated cell assembly sequences in the rat hippocampus.

  • The task was unique: the rats had to run in a wheel for 10-20 seconds before choosing the left or right arms of a figure-8 maze. The rats were rewarded with water if they alternated arm choice.
  • Looked at the activity of pyramical cells - many of them place cells as well as episode-cells - in the hippocampus, and found that the pattern of firing per neuron was predictable and predictive or which choice the rat would take after running in the wheel.
  • The same pattern of hippocampal firing was not found in a control running task (one that did not require a choice).
  • The pattern of firing was phase locked to the theta oscillations in the hippocampus; this phase relationship gradually advanced during the course of trials.
  • During the wheel running, there seemed to be a series of delayed firing bursts by the hippocampal neurons.


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ref: bookmark-0 tags: murder cerebrum PET scan Adrian Raine violence prefrontal corpus callosum amygdala activation brain scan date: 08-29-2008 14:32 gmt revision:0 [head]

http://www.dana.org/news/cerebrum/detail.aspx?id=3066 -- great article, with a well thought out, delicate treatment of the ethical/moral/ legal issues created by the interaction between the biological roots of violence (or knowlege thereof) and legal / social systems. He posits that there must be a continuum between ratinoal free will and irrational, impulsive violent behavior, with people biased to both by genetics, development, traumatic head injury, and substance abuse (among others).

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ref: notes-0 tags: bjork music life date: 07-12-2008 15:46 gmt revision:0 [head]

Bjork has a special place in my heart - and not only because of stuff like this: http://www.youtube.com/watch?v=jX9y6AA5oOo ;) When I was in college - not so far back as Post, but before Selmasongs - we used to play a lot of pool. Not so much that we didn't get any work done, but enough that we started getting good. Near the end of that year we filmed a bunch of games & made a music video set to Underworld's remix of "Human Behavior". I don't know what happened to the actual end product, but I do clearly recall my mom complaining about the repetitive beats while I was cutting the shots so the ball collisions would align with snare/bass hits. Sometime later that year I was blown away by the real deal, the "All is full of love" music video, projected on the side of the art museum at ~ 2am when the mind is labile... Bjork & her music pervaded that period for me. I've found that music can 'tag' periods of life for me, such that when I remember the music first then the events. This winter it was Interpol, last fall was Metric, spring 2007 was Arca (you *have* to hear them!). When me and my brother went to Portugal for a few weeks we found two Pixies mix tapes in the tiny car that my friend generously let us use. Hence, Frank Black soaked our ears while the incredible Portuguese sun soaked our skin.

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ref: bookmark-0 tags: jocaml ocaml join calculus date: 06-17-2008 15:04 gmt revision:0 [head]

why do threads suck in ocaml? because join calculus is better! (well maybe) http://jocaml.inria.fr/

example of jocaml working well (indeed, faster than everything else): http://eigenclass.org/hiki/wide-finder-conclusions

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ref: notes-0 tags: expectation maximization EM clustering autosorting date: 06-16-2008 19:40 gmt revision:5 [4] [3] [2] [1] [0] [head]

so, I coded up the EM algorithm - it was not hard, though i did have to put the likelihood calculation in C++ because i couldn't figure out how to vectorize it properly. It fits the clusters pretty well, but it does not tell you how many clusters there are!

clustering with 5 underlying gaussians:

plot of the log-likelihood of fitted gaussian mixtures vs. number of gaussians:

the code is in subversion, of course.

James has code for gibbs-sampling to the correct number of components! Here is an example of the output - it quickly removes the unnecessary gaussian components:

images/227_4.pdf -- original CEM (classification expectation maximization) paper, 1992, by Celeux and Govaert. Note that CEM with no variance estimation and gaussian clusters is the same as k-means, see {224}. See also http://klustakwik.sourceforge.net/

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ref: bookmark-0 tags: memory supermemo leraning psychology Hermann Ebbinghaus date: 05-08-2008 15:25 gmt revision:0 [head]

http://www.wired.com/medtech/health/magazine/16-05/ff_wozniak -- wonderful article, well written. Leaves you with a sense of Piotr Wozniak (SuperMemo's inventor) crazy, slightly surreal, impassioned, purposeful, but self-regressive (and hence fundamentally stationary) life.

  • Quote: SuperMemo was like a genie that granted Wozniak a wish: unprecedented power to remember. But the value of what he remembered depended crucially on what he studied, and what he studied depended on his goals, and the selection of his goals rested upon the efficient acquisition of knowledge, in a regressive function that propelled him relentlessly along the path he had chosen.
  • http://www.wired.com/images/article/magazine/1605/ff_wozniak_graph_f.jpg
  • Quote: This should lead to radically improved intelligence and creativity. The only cost: turning your back on every convention of social life.

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ref: business-0 tags: North Carolina Business guide taxes date: 01-06-2008 17:39 gmt revision:2 [1] [0] [head]

http://www.nccommerce.com/NR/rdonlyres/CC5488D0-9B3E-4C32-BEF4-4B88630CE3F1/0/BusinessNotes.pdf ; linked from NC department of commerce business center

  • business owners are responsible for listing personal property with the county's assessor office in the county where the business is located.
  • must file income and franchise tax (obviously)
  • Security offers and sales in NC are subject to NC Securities act -- 919-733-3924, http://www.sosnc.com/

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ref: bookmark-0 tags: blackfin BF537 uClinux webserver USB2 vmware date: 11-21-2007 22:32 gmt revision:0 [head]

http://www.camsig.co.uk/ -- blackfin is hot like chernobyl. 1" sq 600mhz webserver etc.

  • uses NET2272 high-speed USB-2.0 peripheral from PLX technology.
  • has a 10/100 ethernet mac w/o magnetics
  • 99 GBP
  • specsheet - no power consumption figures
  • attaches with a rubberized compression connector - no solder required!
  • Develop programs with a VMware virtual appliance (openSuSE 10.2) - brilliant! (though the download is HUGE ... and hosted by amazon)

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ref: bookmark-0 tags: IEC fusion Bussard tokamak date: 10-31-2007 22:38 gmt revision:2 [1] [0] [head]

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ref: bookmark-0 tags: wideband oxygen sensor diffusion nernst lambda date: 10-22-2007 03:41 gmt revision:0 [head]


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ref: bookmark-0 tags: I2S bust serial protocol DAC date: 08-27-2007 16:54 gmt revision:0 [head]


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ref: notes-0 tags: activewire ez-usb an2131 cypress date: 08-16-2007 00:33 gmt revision:1 [0] [head]

to get the activewire board working under linux (debian):

  1. I had to install fxload (in the apt repository).
  2. install hex (1) , which is a simple LED blink routine from http://ezusb2131.sourceforge.net/ via:
    1. sudo fxload -I led2.hex -D /proc/bus/usb/006/118 where 118 is the address from dmesg | tail and led2.hex is hex(1)
  3. install hex (2), which is from http://activewire-osx.cvs.sourceforge.net/ -- it is the most recent i could find. translated via {427}
    1. sudo fxload -I awfirm2.hex -D /proc/bus/usb/006/118 awfirm2.hex is, of course, hex(2)
  4. check dmesg | tail - the EZ-USB chip should disconnect and reconnect with a new address. I don't know why the first ex is required - perhaps it resets the processor?
  5. run the awusb-linux program, for example, and do what you like.

I have no idea why this is required. perhaps my board is broken abit?

hex (1):




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ref: Chan-2006.12 tags: computational model primate arm musculoskeletal motor_control Moran date: 04-09-2007 22:35 gmt revision:1 [0] [head]

PMID-17124337[0] Computational Model of a Primate Arm: from hand position to joint angles, joint torques, and muscle forces ideas:

  • no study so far has been able to incorporate all of these variables (global hand position & velocity, joint angles, joint angular velocities, joint torques, muscle activations)
  • they have a 3D, 7DOF model that translate actual motion to optimized muscle activations.
  • knock the old center-out research (nice!)
  • 38 musculoskeletal-tendon units
  • past research: people have found correlations to both forces and higher-level parameters, like position and velocity. these must be transformed via inverse dynamics to generate a motor plan / actually move the arm.
  • used SIMM to optimize the joint locations to replicate actual movements...
  • assume that the torso is the inertial frame.
  • used infrared Optotrak 3020
  • their model is consistent - they can use the inverse model to calculate muscle activations, which when fed back into the forward model, results in realistic movements. still yet, they do not compare to actual EMG.
  • for working with the dynamic model of the arm, they used AUTOLEV
    • I wish i could figure out what the Kane method was, they seem to leverage it here.
  • their inverse model is pretty clever:
  1. take the present attitude/orientation & velocity of the arm, and using parts of the forward model, calculate the contributions from gravity & coriolis forces.
  2. subtract this from the torques estimated via M*A (moment of interia times angular acceleration) to yield the contributions of the muscles.
  3. perturb each of the joints / DOF & measure the resulting arm motion, integrated over the same period as measurement
  4. form a linear equation with the linearized torque-responses on the left, and the muscle torque contributions on the right. Invert this equation to get the actual joint torques. (presumably the matrix spans row space).
  5. to figure out the muscle contributions, do the same thing - apply activation, scaled by the PCSA, to each muscle & measure the resulting torque (this is effectively the moment arm).
  6. take the resulting 38x7 matrix & p-inverse, with the constraint that none of the muscle activations are negative, yielding a somewhat well-specified muscle activation. not all that complicated of a method


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ref: Ashe-1994.12 tags: Georgoplous motor control M1 S1 SUA electrophysiology 2D date: 04-09-2007 20:27 gmt revision:2 [1] [0] [head]

PMID-7703686[0] Movement parameters and neural activity in motor cortex and area 5

  • 290 cells in the motor cortex and 207 cells in area 5 (S1)
  • median R^2 = 0.581 & 0.530 in motor cortex
  • most prominent representation of target direction; least prominent representation of acceleration. (though statistically significant correlations were observed for all behavioral parameters)

Duke does not have online access to the article :(


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ref: Townsend-2006.11 tags: EMG muscle activity dentate M1 cerebellum date: 04-09-2007 00:52 gmt revision:0 [head]

PMID-16790591[0] Linear encoding of muscle activity in primary motor cortex and cerebellum

  • precision grip task.
  • we showed that cells in both M1 and dentate encode muscle activity in a linear fashion
  • Neural activity in M1 was significantly more correlated with both EMG and kinematic signals than was activity in dentate nucleus
  • spike history effects added no information (probably due to the limited bandwidth of the output)


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ref: Ferrari-2005.02 tags: tool use monkey neural response leaning mirror neurons F5 date: 04-03-2007 22:44 gmt revision:1 [0] [head]

PMID-15811234[] Mirror Neurons Responding to Observation of Actions Made with Tools in Monkey Ventral Premotor Cortex

  • respond when the monkey sees a human using a tool!


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ref: Shidara-1998.04 tags: ventral striatum nucleus accumbens monkey reward progress cue date: 03-27-2007 14:39 gmt revision:0 [head]

PMID-9502820[] Neuronal signals in the monkey ventral striatum related to progress through a predictable series of trials

  • neurons seem to cue/indicate/keep track of the state that a monkey is in during a sequence of reward-motivated behavior, e.g. there are neurons here which respond to the first trial, another group to anything other than 1st, others to first trial of schedules longer than one.
    • the recording site.


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ref: life-0 tags: spooky house ana adventure grave date: 03-19-2007 01:11 gmt revision:0 [head]


go there!! be frightened!!

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ref: Pollak-1993.01 tags: DBS STN subthalamic nucleus original 1993 Benabid date: 03-12-2007 04:58 gmt revision:2 [1] [0] [head]

PMID-8235208[] Effects of the stimulation of the subthalamic nucleus in Parkinson disease

  • the original study! (in french:)
  • even back then, they used a quadripolar medtronic stimulating electrode w/ stimulation frequency of 130Hz.
  • how far have we come? not too far.


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ref: Shapovalova-2006.1 tags: dopamine learning neocortex rats russians D2 date: 03-12-2007 01:58 gmt revision:0 [head]

PMID-17216714 Motor and cognitive functions of the neostriatum during bilateral blocking of its dopamine receptors

  • systemic application of D1 selective blockers reduced learning in rats
    • probably this effect is not neostriatal:
  • local application of the same blocker on the cortex did not markedly affect learning, though it did effect initiation errors
  • D2 antagonist (raclopride) locally applied to the striatum blocked learning.

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ref: SidibAc)-1997.06 tags: GPi anatomy retrograde tracing VL ventrolateral CM centromedian thalamus GPe striatum date: 03-11-2007 06:08 gmt revision:0 [head]

PMID-9183697 Efferent connections of the internal globus pallidus in the squirrel monkey: I. Topography and synaptic organization of the pallidothalamic projection.

  • ventrolateral (e.g. toward the bottom & side :) GPi projects to the postcommisural putamen & the VL thalamus & central CM.
  • dorsal GPi projects to the caudate and ventral striatum ("limbic striatum")
  • both areas also project to nuclei in the thalamus:
    • parvocellular ventral anterior nucleus (VApc)
    • dorsal VL
    • caudal CM/PF
  • the parafasicular nucleus (PF) was a site of a large number of associative/limbic projections.

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ref: Dum-2003.01 tags: cerebellum dentate_nucleus projections cerebrum prefrontal posterior_pareital M1 PM thalamus somatotopic date: 03-11-2007 04:42 gmt revision:2 [1] [0] [head]

PMID-12522208 An unfolded map of the cerebellar dentate nucleus and its projections to the cerebral cortex

  • the dentate nucleus of the cerebellum projects to (at least four sections of if not all) of the cerebral cortex in a spatially-organized way.
    • dentate nucleus projects via the ventral anterior (VA) nucleus of the thalamus
    • dentate nucleus receives projections from the lateral hemispheres of the cerebellum (neocerebellum), which receives extensive collaterals from the pyramidal tract.

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ref: Grabli-2004.09 tags: basal_ganglia gobus_pallidus pathology GPe date: 03-11-2007 04:22 gmt revision:0 [head]

PMID-15292053 Behavioural disorders induced by external globus pallidus dysfunction in primates: I. Behavioural study.

  • there is a functional map within the basal ganglia according to its cortical projections.
  • reversible and focal dysfunction induced by microinjections if bicuculline in the sensorimotor territory of the external globus pallidus can generate abnormal movements. They wanted to test this in the other parts.
  • We found that bicuculline microinjections induced stereotypy when performed in the limbic part of the GPe, and attention deficit and/or hyperactivity when performed in the associative part
  • the behavioural effects shared similar features with symptoms observed in Tourette's syndrome, attention deficit/hyperactivity and compulsive disorders

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ref: Kita-1999.05 tags: globus pallidus GPe caudate putamen anatomy projection date: 03-11-2007 04:09 gmt revision:0 [head]

PMID-10380964 Monkey globus pallidus external segment neurons projecting to the neostriatum.

  • horseradish-peroxidase study in rhesus monkeys.
  • 30% of GPe neurons project to the neostriatum (caudate and putamen)

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ref: physics notes-0 tags: plasma LDX dipole confinement fusion date: 02-24-2007 17:55 gmt revision:0 [head]

First Experiments to test plasma confinement by magnetic dipole

  • Beta is limited by the background pressure of lower-temperature gas - more gas = more stable & trapped electrons. presumably this is due to the presence of positive charges? I don't know, need to read more.
    • this is in the presence of 2-5Kw of microwave electron-cynchrotron radiation heating.
  • this is not levitated - it is the superconducting dipole held up with supports (steel cables? - looks pretty heavy!)
  • want to do catalyzed D-D fusion in the ultimate device
  • do say how they are going to get longer-term containment of the hot plasma.

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ref: notes-0 tags: patents USPTO date: 02-22-2007 04:28 gmt revision:0 [head]

http://0-www.uspto.gov.mill1.sjlibrary.org/web/offices/com/iip/transcriptsf_m.htm -- great FAQ

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ref: Afanasev-2004.03 tags: striatum learning reinforcement electrophysiology putamen russians date: 02-05-2007 17:33 gmt revision:3 [2] [1] [0] [head]

PMID-15151178[0] Sequential Rearrangements of the Ensemble Activity of Putamen Neurons in the Monkey Brain as a Correlate of Continuous Behavior

  • recorded 6-7 neurons in the putamen during alternative spatial selection
  • used discriminant analysis (whats that?) to analyze re-arrangements in spike activity
  • dynamics of re-arrangnement were dependent on reinforcement, and mostly contralateral striatum


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ref: Kilgard-1998.03 tags: dopamine basal_forebrain nucleus_basalis cortical_plasticity date: 0-0-2007 0:0 revision:0 [head]

PMID-9497289[0] Cortical map reorganization enabled by nucleus basalis activity

  • idea, very cool: that stimulation in the nucleus basalis (partially acetylcholine-releasing center in the brain) of the rat, when paired with audio tone presentation, causes the auditory cortex to to reorganize so as to better represent the presented stimulus(stimuli). Note the rats were not tasked with anything, and were placed in a soundproofed box.
  • stimulation protocol: 200ms of 70-150ua current delivered to the NB through bipolar platinum stimulation electrodes. current was set at the threshold needed to desynchronize cortical EEG during slow-wave sleep.
    • how ever did they come up with this metric? EEG desynchronizaton?
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ref: Gdowski-2001.02 tags: globus pallidus reward electrophysiology 2001 date: 0-0-2007 0:0 revision:0 [head]

PMID-11160530 Context Dependency in the Globus Pallidus Internal Segment During Targeted Arm Movements

  • most of the movement-responsive neurons had modulations in the cued segment of the task, not in the subsequent relaxed, self-paced phase.
  • this constitutes a reward or context-dependence.

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ref: Cooper-2000.09 tags: globus pallidus electrophysiology current clamp channel date: 0-0-2007 0:0 revision:0 [head]

PMID-10970430 Electrophysiological and morphological characteristics of three subtypes of rat globus pallidus neurone in vitro

  • there are 3 morphological types of neurons.
    • A: inward rectfier + low-threshold calcium current = anode break depolarizations.
    • B: no inward rectifier, just fast monophasic AHP. small.
    • C: big! (...)

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ref: bookmark-0 tags: thalamus basal ganglia neuroanatomy centromedian red nucleus images date: 0-0-2007 0:0 revision:0 [head]

http://www.neuroanatomy.wisc.edu/coro97/contents.htm --coronal sections through the thalamus, very nice!

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ref: bookmark-0 tags: neuroanatomy pulvinar thalamus superior colliculus image gray brainstem date: 0-0-2007 0:0 revision:0 [head]

http://en.wikipedia.org/wiki/Image:Gray719.png --great, very useful!

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ref: notes-0 tags: LSD rhesus monkeys date: 0-0-2007 0:0 revision:0 [head]


  • monkeys had a sucking behavior after large doses
  • human babies have synestesia
  • perhaps LSD has some endogenous equivalent found in babies?

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ref: Wannier-2002.01 tags: globus_pallidus electrophysiology caudate putamen basal_ganglia date: 0-0-2007 0:0 revision:0 [head]

PMID-11924876 Neuronal activity in primate striatum and pallidum related to bimanual motor actions

  • monkeys had to pull on a spring-loaded drawer and grab food with other hand.
  • half the recorded neurons were responsive to this task.
  • targeted: 20.1 to 14.v mm anterior to the interaural plane of the rhesus monkey brain.
    • 19.2 mm looks good for GPe
    • 17.4 for putamen and caudate (right below area 24 in the cortex - Ventral cingulate cortex)
    • 15.6 for putamen, GPe, and GPi.
  • can these be modulated by imagined movement? e.g. in a BMI?

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ref: GarciaRill-1991.01 tags: PPN pedunculopontine nucleus brainstem sleep locomotion consciousness 1991 date: 0-0-2007 0:0 revision:0 [head]

PMID-1887068 The Pedunculopontine nucleus

  • extensive review!

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ref: Di-1994.06 tags: dopamine NMDA striatum globus_pallidus ion_channels neurotransmitters date: 0-0-2007 0:0 revision:0 [head]

PMID-7521083 Modulatory functions of neurotransmitters in the striatum: ACh/dopamine/NMDA interactions.

  • in striatum, 2 basic classes of neural transmission:
    • fast neural transmission:
      • glutamate response in striatum to cortical/thalamic input via AMPA on medium spiny neurons
      • GABA output of the striatum
    • modulatory neural transmission:
      • NMDA
      • DA dopamine
      • substance P
      • ACh acetylecholine (large aspiny neurons, 30um soma! 1-2% of the population)
  • input to the cholinergic large aspiny neurons
    • GABA/substance P medium-spiny neurons which project to SNr + GPi
    • DA neurons from tegmentum, a8 a9 a10 groups
    • Glu neurons in the thalamus, and, to a lesser extent, from the cortex
  • DA D2 autoreceptors inhibit/regulate the release of DA, and it can also modulate the release of ACh + glu
    • specifically D2 has been demonstrated to inhibit ACh release, but not D1 (accourse)
  • figure 2 is kinda nice for the neurotransmitters in the basal ganglia
  • not really all that clear of an article

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ref: bookmark-0 tags: linear_algebra solution simultaneous_equations GPGPU GPU LUdecomposition clever date: 0-0-2006 0:0 revision:0 [head]


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ref: bookmark-0 tags: muscle artifial catalyst nanotubes shape-memory alloy date: 0-0-2006 0:0 revision:0 [head]


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ref: notes-0 tags: music hardm.ath.cx date: 0-0-2006 0:0 revision:0 [head]

  • Allee Der Kosmonauten Jazzanova Singles collection 1997-2000. gamelan-like, different though

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ref: Stapleton-2006.04 tags: Stapleton Lavine poisson prediction gustatory discrimination statistical_model rats bayes BUGS date: 0-0-2006 0:0 revision:0 [head]