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[0] Kipke DR, Vetter RJ, Williams JC, Hetke JF, Silicon-substrate intracortical microelectrode arrays for long-term recording of neuronal spike activity in cerebral cortex.IEEE Trans Neural Syst Rehabil Eng 11:2, 151-5 (2003 Jun)

[0] Narayanan NS, Kimchi EY, Laubach M, Redundancy and synergy of neuronal ensembles in motor cortex.J Neurosci 25:17, 4207-16 (2005 Apr 27)

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ref: -0 tags: diffusion models image generation OpenAI date: 12-24-2021 05:50 gmt revision:0 [head]

Some investigations into denoising models & their intellectual lineage:

Deep Unsupervised Learning using Nonequilibrium Thermodynamics 2015

  • Jascha Sohl-Dickstein, Eric A. Weiss, Niru Maheswaranathan, Surya Ganguli
  • Starting derivation of using diffusion models for training.
  • Verrry roughly, the idea is to destroy the structure in an image using diagonal Gaussian per-pixel, and train an inverse-diffusion model to remove the noise at each step. Then start with Gaussian noise and reverse-diffuse an image.
  • Diffusion can take 100s - 1000s of steps; steps are made small to preserve the assumption that the conditional probability, p(x t1|x t)N(0,I)p(x_{t-1}|x_t) \propto N(0, I)
    • The time variable here goes from 0 (uncorrupted data) to T (fully corrupted / Gaussian noise)

Generative Modeling by Estimating Gradients of the Data Distribution July 2019

  • Yang Song, Stefano Ermon

Denoising Diffusion Probabilistic Models June 2020

  • Jonathan Ho, Ajay Jain, Pieter Abbeel
  • A diffusion model that can output 'realistic' images (low FID / low log-likelihood )

Improved Denoising Diffusion Probabilistic Models Feb 2021

  • Alex Nichol, Prafulla Dhariwal
  • This is directly based on Ho 2020 and Shol-Dickstein 2015, but with tweaks
  • The objective is no longer the log-likelihood of the data given the parameters (per pixel); it's now mostly the MSE between the corrupting noise (which is known) and the estimated noise.
  • That is, the neural network model attempts, given x tx_t to estimate the noise which corrupted it, which then can be used to produce x t1x_{t-1}
    • Simpicity. Satisfying.
  • The also include a reweighted version of the log-likelihood loss, which puts more emphasis on the first few steps of noising. These steps are more important for NLL; reweighting also smooths the loss.
    • I think that, per Ho above, the simple MSE loss is sufficient to generate good images, but the reweighted LL improves the likelihood of the parameters.
  • There are some good crunchy mathematical details on how how exactly the the mean and variance of the estimated Gaussian distributions are handled -- at each noising step, you need to scale the mean down to prevent Brownian / random walk.
    • Taking these further, you can estimate an image at any point t in the forward diffusion chain. They use this fact to optimize the function approximator (a neural network; more later) using a (random but re-weighted/scheduled) t and the LL loss + simple loss.
  • Ho 2020 above treats the variance of the noising Gaussian as fixed -- that is, β \beta ; this paper improves the likelihood by adjusting the noise varaince mostly at the last steps by a ~β t~\beta_t , and then further allowing the function approximator to tune the variance (a multiplicative factor) per inverse-diffusion timestep.
    • TBH I'm still slightly foggy on how you go from estimating noise (this seems like samples, concrete) to then estimating variance (which is variational?). hmm.
  • Finally, they schedule the forward noising with a cosine^2, rather than a linear ramp. This makes the last phases of corruption more useful.
  • Because they have an explicit parameterization of the noise varaince, they can run the inverse diffusion (e.g. image generation) faster -- rather than 4000 steps, which can take afew minutes on a GPU, they can step up the variance and run it only for 50 steps and get nearly as good images.

Diffusion Models Beat GANs on Image Synthesis May 2021

  • Prafulla Dhariwal, Alex Nichol

In all of above, it seems that the inverse-diffusion function approximator is a minor player in the paper -- but of course, it's vitally important to making the system work. In some sense, this 'diffusion model' is as much a means of training the neural network as it is a (rather inefficient, compared to GANs) way of sampling from the data distribution. In Nichol & Dhariwal Feb 2021, they use a U-net convolutional network (e.g. start with few channels, downsample and double the channels until there are 128-256 channels, then upsample x2 and half the channels) including multi-headed attention. Ho 2020 used single-headed attention only at the 16x16 level. Ho 2020 in turn was based on PixelCNN++

PixelCNN++: Improving the PixelCNN with Discretized Logistic Mixture Likelihood and Other Modifications Jan 2017

  • Tim Salimans, Andrej Karpathy, Xi Chen, Diederik P. Kingma

which is an improvement to (e.g. add selt-attention layers)

Conditional Image Generation with PixelCNN Decoders

  • Aaron van den Oord, Nal Kalchbrenner, Oriol Vinyals, Lasse Espeholt, Alex Graves, Koray Kavukcuoglu

Most recently,

GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models

  • Alex Nichol, Prafulla Dhariwal, Aditya Ramesh, Pranav Shyam, Pamela Mishkin, Bob McGrew, Ilya Sutskever, Mark Chen

Added text-conditional generation + many more parameters + much more compute to yield very impressive image results + in-painting. This last effect is enabled by the fact that it's a full generative denoising probabilistic model -- you can condition on other parts of the image!

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ref: -2010 tags: neural signaling rate code patch clamp barrel cortex date: 03-18-2021 18:41 gmt revision:0 [head]

PMID-20596024 Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex

  • How did I not know of this paper before.
  • Solid study showing that, while a single spike can elicit 28 spikes in post-synaptic neurons, the associated level of noise is indistinguishable from intrinsic noise.
  • Hence the cortex should communicate / compute in rate codes or large synchronized burst firing.
    • They found large bursts to be infrequent, timing precision to be low, hence rate codes.
    • Of course other examples, e.g auditory cortex, exist.

Cortical reliability amid noise and chaos

  • Noise is primarily of synaptic origin. (Dropout)
  • Recurrent cortical connectivity supports sensitivity to precise timing of thalamocortical inputs.

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ref: -2019 tags: non degenerate two photon excitation fluorophores fluorescence OPO optical parametric oscillator date: 10-31-2019 20:53 gmt revision:0 [head]

Efficient non-degenerate two-photon excitation for fluorescence microscopy

  • Used an OPO + delay line to show that non-degenerate (e.g. photons of two different energies) can induce greater fluorescence, normalized to input energy, than normal same-energy excitation.

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ref: -2018 tags: Michael Levin youtube talk NIPS 2018 regeneration bioelectricity organism patterning flatworm date: 04-09-2019 18:50 gmt revision:1 [0] [head]

What Bodies Think About: Bioelectric Computation Outside the Nervous System - NeurIPS 2018

  • Short notes from watching the video, mostly interesting factoids: (This is a somewhat more coordinated narrative in the video. Am resisting ending each of these statements with and exclamation point).
  • Human children up to 7-11 years old can regenerate their fingertips.
  • Human embryos, when split in half early, develop into two normal humans; mouse embryos, when squished together, make one normal mouse.
  • Butterflies retain memories from their caterpillar stage, despite their brains liquefying during metamorphosis.
  • Flatworms are immortal, and can both grow and contract, as the environment requires.
    • They can also regenerate a whole body from segments, and know to make one head, tail, gut etc.
  • Single cell organisms, e.g. Lacrymaria, can have complex (and fast!) foraging / hunting plans -- without a brain or anything like it.
  • Axolotl can regenerate many parts of their body (appendages etc), including parts of the nervous system.
  • Frog embryos can self-organize an experimenter jumbled body plan, despite the initial organization having never been experienced in evolution.
  • Salamanders, when their tail is grafted into a foot/leg position, remodel the transplant into a leg and foot.
  • Neurotransmitters are ancient; fungi, who diverged from other forms of life about 1.5 billion years ago, still use the same set of inter-cell transmitters e.g. serotonin, which is why modulatory substances from them have high affinity & a strong effect on humans.
  • Levin, collaborators and other developmental biologists have been using voltage indicators in embryos ... this is not just for neurons.
  • Can make different species head shapes in flatworms by exposing them to ion-channel modulating drugs. This despite the fact that the respective head shapes are from species that have been evolving separately for 150 million years.
  • Indeed, you can reprogram (with light gated ion channels, drugs, etc) to body shapes not seen in nature or not explored by evolution.
    • That said, this was experimental, not by design; Levin himself remarks that the biology that generates these body plans is not known.
  • Flatworms can sore memory in bioelectric networks.
  • Frogs don't normally regenerate their limbs. But, with a drug cocktail targeting bioelectric signaling, they can regenerate semi-functional legs, complete with nerves, muscle, bones, and cartilage. The legs are functional (enough).
  • Manipulations of bioelectric signaling can reverse very serious genetic problems, e.g. deletion of Notch, to the point that tadpoles regain some ability for memory creation & recall.

  • I wonder how so much information can go through a the apparently scalar channel of membrane voltage. It seems you'd get symbol interference, and that many more signals would be required to pattern organs.
  • That said, calcium is used a great many places in the cell for all sorts of signaling tasks, over many different timescales as well, and it doesn't seem to be plagued by interference.
    • First question from the audience was how cells differentiate organismal patterning signals and behavioral signals, e.g. muscle contraction.

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ref: -2011 tags: ttianium micromachining chlorine argon plasma etch oxide nitride penetrating probes Kevin Otto date: 03-18-2019 22:57 gmt revision:1 [0] [head]

PMID-21360044 Robust penetrating microelectrodes for neural interfaces realized by titanium micromachining

  • Patrick T. McCarthyKevin J. OttoMasaru P. Rao
  • Used Cl / Ar plasma to deep etch titanium film, 0.001 / 25um thick. Fine Metals Corp Ashland VA.
  • Discuss various insulation (oxide /nitride) failure modes, lithography issues.

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ref: -2017 tags: calcium imaging seeded iterative demixing light field microscopy mouse cortex hippocampus date: 02-13-2019 22:44 gmt revision:1 [0] [head]

PMID-28650477 Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy

  • Tobias Nöbauer, Oliver Skocek, Alejandro J Pernía-Andrade, Lukas Weilguny, Francisca Martínez Traub, Maxim I Molodtsov & Alipasha Vaziri
  • Cell-scale imaging at video rates of hundreds of GCaMP6 labeled neurons with light-field imaging followed by computationally-efficient deconvolution and iterative demixing based on non-negative factorization in space and time.
  • Utilized a hybrid light-field and 2p microscope, but didn't use the latter to inform the SID algorithm.
  • Algorithm:
    • Remove motion artifacts
    • Time iteration:
      • Compute the standard deviation versus time (subtract mean over time, measure standard deviance)
      • Deconvolve standard deviation image using Richardson-Lucy algo, with non-negativity, sparsity constraints, and a simulated PSF.
      • Yields hotspots of activity, putative neurons.
      • These neuron lcoations are convolved with the PSF, thereby estimating its ballistic image on the LFM.
      • This is converted to a binary mask of pixels which contribute information to the activity of a given neuron, a 'footprint'
        • Form a matrix of these footprints, p * n, S 0S_0 (p pixels, n neurons)
      • Also get the corresponding image data YY , p * t, (t time)
      • Solve: minimize over T ||YST|| 2|| Y - ST||_2 subject to T0T \geq 0
        • That is, find a non-negative matrix of temporal components TT which predicts data YY from masks SS .
    • Space iteration:
      • Start with the masks again, SS , find all sets O kO^k of spatially overlapping components s is_i (e.g. where footprints overlap)
      • Extract the corresponding data columns t it_i of T (from temporal step above) from O kO^k to yield T kT^k . Each column corresponds to temporal data corresponding to the spatial overlap sets. (additively?)
      • Also get the data matrix Y kY^k that is image data in the overlapping regions in the same way.
      • Minimize over S kS^k ||Y kS kT k|| 2|| Y^k - S^k T^k||_2
      • Subject to S k>=0S^k >= 0
        • That is, solve over the footprints S kS^k to best predict the data from the corresponding temporal components T kT^k .
        • They also impose spatial constraints on this non-negative least squares problem (not explained).
    • This process repeats.
    • allegedly 1000x better than existing deconvolution / blind source segmentation algorithms, such as those used in CaImAn

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ref: -0 tags: curiosity exploration forward inverse models trevor darrell date: 02-01-2019 03:42 gmt revision:1 [0] [head]

Curiosity-driven exploration by Self-supervised prediction

  • Deepak Pathak, Pulkit Agrawal, Alexei A. Efros, Trevor Darrell
  • Key insight: “we only predict the changes in the environment that could possibly be due to actions of our agent or affect the agent, and ignore the rest”.
    • Instead of making predictions in the sensory space (e.g. pixels), we transform the sensory input into a feature space where only the information relevant to the agent is represented.
    • We learn this feature space using self-supervision -- training a neural network via a proxy inverse dynamics task -- predicting the agent’s action from the past and future sensory states.
  • We then use this inverse model to train a forward dynamics model to predict feature representation of the next state from present feature representation and action.
      • The difference between expected and actual representation serves as a reward signal for the agent.
  • Quasi actor-critic / adversarial agent design, again.
  • Used the asynchronous advantage actor critic policy gradient method (Mnih et al 2016 Asynchronous Methods for Deep Reinforcement Learning).
  • Compare with variational information maximization (VIME) trained with TRPO (Trust region policy optimization) which is “more sample efficient than A3C but takes more wall time”.
  • References / concurrent work: Several methods propose improving data efficiency of RL algorithms using self-supervised prediction based auxiliary tasks (Jaderberg et al., 2017; Shelhamer et al., 2017).
  • An interesting direction for future research is to use the learned exploration behavior / skill as a motor primitive / low level policy in a more complex, hierarchical system. For example, the skill of walking along corridors could be used as part of a navigation system.

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ref: -0 tags: rogers thermal oxide barrier neural implants ECoG coating accelerated lifetime test date: 12-28-2017 02:29 gmt revision:0 [head]

PMID-27791052 Ultrathin, transferred layers of thermally grown silicon dioxide as biofluid barriers for biointegrated flexible electronic systems

  • Thermal oxide proved the superior -- by far -- water barrier for encapsulation.
    • What about the edges?
  • Many of the polymer barrier layers look like inward-rectifiers:
  • Extensive simulations showing that the failure mode is from gradual dissolution of the SiO2 -> Si(OH)4.
    • Even then a 100nm layer is expected to last years.
    • Perhaps the same principle could be applied with barrier metals. Anodization or thermal oxidation to create a thick, nonporous passivation layer.
    • Should be possible with Al, Ta...

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ref: -0 tags: Courtine e-dura PDMS silicone gold platinum composite stretch locomotion restoration rats date: 12-22-2017 01:59 gmt revision:0 [head]

PMID-25574019 Biomaterials. Electronic dura mater for long-term multimodal neural interfaces.

  • Fabrication:
    • 120um total PDMS thickness, made through soft lithography, covalent (O2 plasma) bonding between layers
    • 35nm of Au (thin!) deposited through a stencil mask.
    • 300um Pt-PDMS composite for electrode sites, deposited via screenprinting
  • 100 x 200um cross section drug delivery channel.
  • Compared vs. stiff 25um thick PI film electrode.
    • stiff implants showed motor impairments 1-2 weeks after implantation.
  • Showed remarkable recovery of supported locomotion with stimulation and drug infusion (to be followed by monkeys).

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ref: -1977 tags: polyethylene surface treatment plasma electron irradiation mechanical testing saline seawater accelerated lifetime date: 04-15-2017 06:06 gmt revision:0 [head]

Enhancement of resistance of polyethylene to seawater-promoted degradation by surface modification

  • Polyethylene, when repeatedly stressed and exposed to seawater (e.g. ships' ropes), undergoes mechanical and chemical degradation.
  • Surface treatments of the polyethlyene can improve resistance to this degradation.
  • The author studied two methods of surface treatment:
    • Plasma (glow discharge, air) followed by diacid (adipic acid) or triisocyanate (DM100, = ?) co-polymerization
    • Electron irradiation with 500 kEV electrons.
  • Also mention CASING (crosslinking by activated species of inert gasses) as a popular method of surface treatment.
    • Diffuse-in crosslinkers is a third, popular these days ...
    • Others diffuse in at temperature e.g. a fatty acid - derived molecule, which is then bonded to e.g. heparin to reduce the thrombogenicity of a plastic.
  • Measured surface modifications via ATR IR (attenuated total reflectance, IR) and ESCA (aka XPS)
    • Expected results, carbonyl following the air glow discharge ...
  • Results:
    • Triisocyanate, ~ 6x improvement
    • diacid, ~ 50 x improvement.
    • electron irradiation, no apparent degradation!
      • Author's opinion that this is due to carbon-carbon crosslink leading to mechanical toughening (hmm, evidence?)
  • Quote: since the PE formulation studied here was low-weight, it was expected to lose crystallinity upon cyclic flexing; high density PE's have in fact been observed to become more crystalline with working.
    • Very interesting, kinda like copper. This could definitely be put to good use.
  • Low density polyethylene has greater chain branching and entanglement than high-density resins; when stressed the crystallites are diminished in total bulk, degrading tensile properties ... for high-density resins, mechanical working loosens up the structure enough to allow new crystallization to exceed stress-induced shrinkage of crystallites; hence, the crystallinity increases.

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ref: -0 tags: tungsten eletropolishing hydroxide cleaning bath tartarate date: 03-28-2017 16:34 gmt revision:0 [head]

Method of electropolishing tungsten wire US 3287238 A

  • The bath is formed of 15% by weight sodium hydroxide, 30% by weight sodium potassium tartrate, and 55% by weight distilled water, with the bath temperature being between 70 and 100 F.
    • If the concentration of either the hydroxide or the tartrate is below the indicated minimum, the wire is electrocleaned rather than electropolished, and a matte finish is obtained rather than a specular surface.
    • If the concentration of either the hydroxide or the tartrate is greater than the indicated maximum, the electropolishing process is quite slow.
  • The voltage which is applied between the two electrodes 18 and 20 is from 16 to 18.5 volts, the current through the bath is 20 to 24 amperes, and the current density is 3,000 to 4,000 amperes per square foot of surface of wire in the bath.

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ref: -0 tags: microstimulation rat cortex measurement ICMS spread date: 01-26-2017 02:52 gmt revision:0 [head]

PMID-12878710 Spatiotemporal effects of microstimulation in rat neocortex: a parametric study using multielectrode recordings.

  • Measure using extracellular ephys a spread of ~ 1.3mm from near-threshold microstimulation.
  • Study seems thorough despite limited techniques.

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ref: -0 tags: neural coding rats binary permutation retrosplenial basolateral amygdala tetrode date: 12-19-2016 07:39 gmt revision:1 [0] [head]

PMID-27895562 Brain Computation Is Organized via Power-of-Two-Based Permutation Logic.

  • Nice and interesting data, sort of kitchen sink of experiments but ...
  • At first blush it seems they have re-discovered Haar wavelets / the utility of binary decompositions.
  • Figures 9 and 10, however, suggest a discriminable difference in representation in layers 2/3 and 5/6, supporting their binary hypothesis.
    • The former targeted the mouse's large retrosplenial cortex; the latter, the hamster's prelimbic cortex.

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ref: -0 tags: PEDOT electropolymerization electroplating gold TFB borate counterion acetonitrile date: 10-18-2016 07:49 gmt revision:3 [2] [1] [0] [head]

Electrochemical and Optical Properties of the Poly(3,4-ethylenedioxythiophene) Film Electropolymerized in an Aqueous Sodium Dodecyl Sulfate and Lithium Tetrafluoroborate Medium

  • EDOT has a higher oxidation potential than water, which makes polymers electropolymerized from water "poorly defined".
  • Addition of SDS lowers the oxidation potential to 0.76V, below that of EDOT in acetonitrile at 1.1V.
  • " The potential was first switched from open circuit potential to 0.5 V for 100 s before polarizing the electrode to the desired potential. This initial step was to allow double-layer charging of the Au electrode|solution interface, which minimizes the distortion of the polymerization current transient by double-layer capacitance charging.17,18 "
    • Huh, interesting.
  • Plated at 0.82 - 0.84V, 0.03M EDOT conc.
  • 0.1M LiBF4 anion / electrolyte; 0.07M SDS sufactant.
    • This SDS is incorporated into the film, and affects redox reactions as shown in the cyclic voltammagram (fig 4)
      • Doping level 0.36
    • BF4-, in comparison, can be driven out of the film.

Improvement of the Electrosynthesis and Physicochemical Properties of Poly(3,4-ethylenedioxythiophene) Using a Sodium Dodecyl Sulfate Micellar Aqueous Medium

  • "The oxidation potential of thiopene = 1.8V; water = 1.23V.
  • Claim: "The polymer films prepared in micellar medium [SDS] are more stable than those obtained in organic solution as demonstrated by the fact that, when submitted to a great number of redox cycles (n ≈ 50), there is no significant loss of their electroactivity (<10%). These electrochemical properties are accompanied by color changes of the film which turns from blue-black to red-purple upon reduction."
  • Estimate that there is about 21% DS- anions in the PEDOT - SDS films.
    • Cl - was at ~ 7%.
  • I'm still not sure about incorporating soap into the electroplating solution.. !

Electrochemical Synthesis of Poly(3,4-ethylenedioxythiophene) on Steel Electrodes: Properties and Characterization

  • 0.01M EDOT and 0.1M LiClO4 in acetonitrile.
  • Claim excellent adhesion & film properties to 316 SS.
  • Oxidation / electrodeposition at 1.20V; voltages higher than 1.7V resulted in flaky films.

PMID-20715789 Investigation of near ohmic behavior for poly(3,4-ethylenedioxythiophene): a model consistent with systematic variations in polymerization conditions.

  • Again use acetonitrile.
  • 1.3V vs Ag/AgCl electrode.
  • Perchlorate and tetraflouroborate both seemed the best counterions (figure 4).
  • Figure 5: Film was difficult to remove from surface.
    • They did use a polycrystaline Au layer:
    • "The plating process was allowed to run for 1 min (until approximately 100 mC had passed) at a constant potential of 0.3 V versus Ag/AgCl in 50 mM HAuCl4 prepared in 0.1 M NaCl."
  • Claim that the counterions are trapped; not in agreement with the SDS study above.
  • "Conditions for the consistent production of conducting polymer films employing potentiostatic deposition at 1.3 V for 60-90 s have been determined. The optimal concentration of the monomer is 0.0125 M, and that of the counterion is 0.05 M. "

PMID-24576579 '''Improving the performance of poly(3,4-ethylenedioxythiophene) for brain–machine interface applications"

  • Show that TFB (BF4-) is a suitable counterion for EDOT electropolymerization.
  • Comparison is between PEDOT:TFB deposited in an anhydrous acetronitrile solution, and PEDOT:PSS deposited in an aqueous solution.
    • Presumably the PSS brings the EDOT into solution (??).
  • figure 3 is compelling, but long-term, electrodes are not that much better than Au!
    • Maybe we should just palate with that.

PEDOT-modified integrated microelectrodes for the detection of ascorbic acid, dopamine and uric acid

  • Direct comparison of acetonitrile and water solvents for electropolymerization of EDOT.
  • "PEDOT adhesion is best on gold surface due to the strong interactions between gold and sulphur atoms.
  • images/1353_2.pdf
    • Au plating is essential!

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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: image registration optimization camera calibration sewing machine date: 07-15-2016 05:04 gmt revision:20 [19] [18] [17] [16] [15] [14] [head]

Recently I was tasked with converting from image coordinates to real world coordinates from stereoscopic cameras mounted to the end-effector of a robot. The end goal was to let the user (me!) click on points in the image, and have the robot record that position & ultimately move to it.

The overall strategy is to get a set of points in both image and RW coordinates, then fit some sort of model to the measured data. I began by printing out a grid of (hopefully evenly-spaced and perpendicular) lines via a laserprinter; spacing was ~1.1 mm. This grid was manually aligned to the axes of robot motion by moving the robot along one axis & checking that the lines did not jog.

The images were modeled as a grating with quadratic phase in u,vu,v texture coordinates:

p h(u,v)=sin((a hu/1000+b hv/1000+c h)v+d hu+e hv+f h)+0.97 p_h(u,v) = sin((a_h u/1000 + b_h v/1000 + c_h)v + d_h u + e_h v + f_h) + 0.97 (1)

p v(u,v)=sin((a vu/1000+b vv/1000+c v)u+d vu+e vv+f v)+0.97 p_v(u,v) = sin((a_v u/1000 + b_v v/1000 + c_v)u + d_v u + e_v v + f_v) + 0.97 (2)

I(u,v)=16p hp v/(2+16p h 2+16p v 2) I(u,v) = 16 p_h p_v / ( \sqrt{ 2 + 16 p_h^2 + 16 p_v^2}) (3)

The 1000 was used to make the parameter search distribution more spherical; c h,c vc_h,c_v were bias terms to seed the solver; 0.97 was a duty-cycle term fit by inspection to the image data; (3) is a modified sigmoid.

I I was then optimized over the parameters using a GPU-accelerated (CUDA) nonlinear stochastic optimization:

(a h,b h,d h,e h,f h|a v,b v,d v,e v,f v)=Argmin u v(I(u,v)Img(u,v)) 2 (a_h,b_h,d_h,e_h,f_h | a_v,b_v,d_v,e_v,f_v) = Argmin \sum_u \sum_v (I(u,v) - Img(u,v))^2 (4)

Optimization was carried out by drawing parameters from a normal distribution with a diagonal covariance matrix, set by inspection, and mean iteratively set to the best solution; horizontal and vertical optimization steps were separable and carried out independently. The equation (4) was sampled 18k times, and equation (3) 34 billion times per frame. Hence the need for GPU acceleration.

This yielded a set of 10 parameters (again, c hc_h and c vc_v were bias terms and kept constant) which modeled the data (e.g. grid lines) for each of the two cameras. This process was repeated every 0.1 mm from 0 - 20 mm height (z) from the target grid, resulting in a sampled function for each of the parameters, e.g. a h(z)a_h(z) . This required 13 trillion evaluations of equation (3).

Now, the task was to use this model to generate the forward and reverse transform from image to world coordinates; I approached this by generating a data set of the grid intersections in both image and world coordinates. To start this process, the known image origin u origin| z=0,v origin| z=0u_{origin}|_{z=0},v_{origin}|_{z=0} was used to find the corresponding roots of the periodic axillary functions p h,p vp_h,p_v :

3π2+2πn h=a huv/1000+b hv 2/1000+(c h+e h)v+d hu+f h \frac{3 \pi}{ 2} + 2 \pi n_h = a_h u v/1000 + b_h v^2/1000 + (c_h + e_h)v + d_h u + f_h (5)

3π2+2πn h=a vu 2/1000+b vuv/1000+(c v+d v)u+e vv+f v \frac{3 \pi}{ 2} + 2 \pi n_h = a_v u^2/1000 + b_v u v/1000 + (c_v + d_v)u + e_v v + f_v (6)

Or ..

n h=round((a huv/1000+b hv 2/1000+(c h+e h)v+d hu+f h3π2)/(2π) n_h = round( (a_h u v/1000 + b_h v^2/1000 + (c_h + e_h)v + d_h u + f_h - \frac{3 \pi}{ 2} ) / (2 \pi ) (7)

n v=round((a vu 2/1000+b vuv/1000+(c v+d v)u+e vv+f v3π2)/(2π) n_v = round( (a_v u^2/1000 + b_v u v/1000 + (c_v + d_v)u + e_v v + f_v - \frac{3 \pi}{ 2} ) / (2 \pi) (8)

From this, we get variables n h,origin| z=0andn v,origin| z=0n_{h,origin}|_{z=0} and n_{v,origin}|_{z=0} which are the offsets to align the sine functions p h,p vp_h,p_v with the physical origin. Now, the reverse (world to image) transform was needed, for which a two-stage newton scheme was used to solve equations (7) and (8) for u,vu,v . Note that this is an equation of phase, not image intensity -- otherwise this direct method would not work!

First, the equations were linearized with three steps of (9-11) to get in the right ballpark:

u 0=640,v 0=360 u_0 = 640, v_0 = 360

n h=n h,origin| z+[30..30],n v=n v,origin| z+[20..20] n_h = n_{h,origin}|_{z} + [-30 .. 30] , n_v = n_{v,origin}|_{z} + [-20 .. 20] (9)

B i=[3π2+2πn ha hu iv i/1000b hv i 2f h 3π2+2πn va vu i 2/1000b vu iv if v] B_i = {\left[ \begin{matrix} \frac{3 \pi}{ 2} + 2 \pi n_h - a_h u_i v_i / 1000 - b_h v_i^2 - f_h \\ \frac{3 \pi}{ 2} + 2 \pi n_v - a_v u_i^2 / 1000 - b_v u_i v_i - f_v \end{matrix} \right]} (10)

A i=[d h c h+e h c v+d v e v] A_i = {\left[ \begin{matrix} d_h && c_h + e_h \\ c_v + d_v && e_v \end{matrix} \right]} and

[u i+1 v i+1]=mldivide(A i,B i) {\left[ \begin{matrix} u_{i+1} \\ v_{i+1} \end{matrix} \right]} = mldivide(A_i,B_i) (11) where mldivide is the Matlab operator.

Then three steps with the full Jacobian were made to attain accuracy:

J i=[a hv i/1000+d h a hu i/1000+2b hv i/1000+c h+e h 2a vu i/1000+b vv i/1000+c v+d v b vu i/1000+e v] J_i = {\left[ \begin{matrix} a_h v_i / 1000 + d_h && a_h u_i / 1000 + 2 b_h v_i / 1000 + c_h + e_h \\ 2 a_v u_i / 1000 + b_v v_i / 1000 + c_v + d_v && b_v u_i / 1000 + e_v \end{matrix} \right]} (12)

K i=[a hu iv i/1000+b hv i 2/1000+(c h+e h)v i+d hu i+f h3π22πn h a vu i 2/1000+b vu iv i/1000+(c v+d v)u i+e vv+f v3π22πn v] K_i = {\left[ \begin{matrix} a_h u_i v_i/1000 + b_h v_i^2/1000 + (c_h+e_h) v_i + d_h u_i + f_h - \frac{3 \pi}{ 2} - 2 \pi n_h \\ a_v u_i^2/1000 + b_v u_i v_i/1000 + (c_v+d_v) u_i + e_v v + f_v - \frac{3 \pi}{ 2} - 2 \pi n_v \end{matrix} \right]} (13)

[u i+1 v i+1]=[u i v i]J i 1K i {\left[ \begin{matrix} u_{i+1} \\ v_{i+1} \end{matrix} \right]} = {\left[ \begin{matrix} u_i \\ v_i \end{matrix} \right]} - J^{-1}_i K_i (14)

Solutions (u,v)(u,v) were verified by plugging back into equations (7) and (8) & verifying n h,n vn_h, n_v were the same. Inconsistent solutions were discarded; solutions outside the image space [0,1280),[0,720)[0, 1280),[0, 720) were also discarded. The process (10) - (14) was repeated to tile the image space with gird intersections, as indicated in (9), and this was repeated for all zz in (0..0.1..20)(0 .. 0.1 .. 20) , resulting in a large (74k points) dataset of (u,v,n h,n v,z)(u,v,n_h,n_v,z) , which was converted to full real-world coordinates based on the measured spacing of the grid lines, (u,v,x,y,z)(u,v,x,y,z) . Between individual z steps, n h,originn v,originn_{h,origin} n_{v,origin} was re-estimated to minimize (for a current zz' ):

(u origin| z+0.1u origin| z+0.1) 2+(v origin| z+0.1+v origin| z) 2 (u_{origin}|_{z' + 0.1} - u_{origin}|_{z' + 0.1})^2 + (v_{origin}|_{z' + 0.1} + v_{origin}|_{z'})^2 (15)

with grid-search, and the method of equations (9-14). This was required as the stochastic method used to find original image model parameters was agnostic to phase, and so phase (via parameter f f_{-} ) could jump between individual zz measurements (the origin did not move much between successive measurements, hence (15) fixed the jumps.)

To this dataset, a model was fit:

[u v]=A[1 x y z x 2 y 2 z 2 w 2 xy xz yz xw yw zw] {\left[ \begin{matrix} u \\ v \end{matrix} \right]} = A {\left[ \begin{matrix} 1 && x && y && z && x'^2 && y'^2 && \prime z'^2 && w^2 && x' y' && x' z' && y' z' && x' w && y' w && z' w \end{matrix} \right]} (16)

Where x=x10x' = \frac{x}{ 10} , y=y10y' = \frac{y}{ 10} , z=z10z' = \frac{z}{ 10} , and w=2020zw = \frac{ 20}{20 - z} . ww was introduced as an axillary variable to assist in perspective mapping, ala computer graphics. Likewise, x,y,zx,y,z were scaled so the quadratic nonlinearity better matched the data.

The model (16) was fit using regular linear regression over all rows of the validated dataset. This resulted in a second set of coefficients AA for a model of world coordinates to image coordinates; again, the model was inverted using Newton's method (Jacobian omitted here!). These coefficients, one set per camera, were then integrated into the C++ program for displaying video, and the inverse mapping (using closed-form matrix inversion) was used to convert mouse clicks to real-world coordinates for robot motor control. Even with the relatively poor wide-FOV cameras employed, the method is accurate to ±50μm\pm 50\mu m , and precise to ±120μm \pm 120\mu m .

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ref: -0 tags: reactive oxygen accelerated aging neural implants date: 10-07-2015 18:45 gmt revision:1 [0] [head]

PMID-25627426 Rapid evaluation of the durability of cortical neural implants using accelerated aging with reactive oxygen species.

  • Takmakov P1, Ruda K, Scott Phillips K, Isayeva IS, Krauthamer V, Welle CG.
  • TDT W / PI implants completely failed (W etched and PI completely flaked off) after 1 week in 87C H2O2 / PBS solution. Not surprising.
    • In the Au plated W, the Au remained, the PI flaked off, while thin fragile gold tubes were left. Interesting.
  • Pt/Ii + Parylene-C microprobes seemed to fare better; one was unaffected, others experienced a drop in impedance.
  • NeuralNexus (Si3N4 insulated, probably, plus Ir recording pads) showed no change in H2O2 RAA, strong impedance drop (thicker oxide layer?)
  • Same for blackrock / utah probe (Parylene-C), though there the parylene peeled from the Si substrate a bit.

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ref: -0 tags: third harmonic generation Nd:YAG pulsed laser date: 08-29-2015 06:44 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

Problem: have a Q-switched Nd:YAG laser, (flashlamp pumped, passively Q-switched) from ebay (see this album). Allegedly it outputs 1J pulses of 8ns duration; in practice, it may put several 100mJ pulses ~ 16ns long while the flashlamp is firing. It was sold as a tattoo removal machine. However, I'm employing it to drill micro-vias in fine polyimide films.

When focused through a 10x objective via the camera mount of an Leica microscope, 532nm (KTP doubled, second harmonic generation (SHG)) laser pulses both ablates the material, but does not leave a clean, sharp hole: it looks more like 'blasting': the hole is ragged, more like a crater. This may be from excessive 1064nm heating (partial KTP conversion), or plasma/flame heating & expansion due to absorption of the 532nm / 1064nm light. It may also be due to excessive pulse duration (should the laser not actually be q-switched... photodiode testing suggests otherwise, but I'd like to verify that), excessive pulse power, insufficient pulse intensity, or insufficient polyimide absorption at 532nm.

The solution to excessive plasma and insufficient polyimide absorption is to shift the wavelength to 355nm (NUV) via third harmonic generation, 1064 + 532 = 355nm. This requires sum frequency generation (SFG), for which LBO (lithium triborate) or BBO (beta-barium borate) seem the commonly accepted nonlinear optical materials.

To get SHG or THG, phase and polarization matching of the incoming light is critical. The output of the Nd:YAG laser is, I assume, non-polarized (or randomly polarized), as the KTP crystal simply screws on the front, and so should be rotationally agnostic (and there are no polarizing elements in the simple laser head -- unless the (presumed) Cr:YAG passive Q-switch induces some polarization.)

Output polarization of the KTP crystal will be perpendicular to the incoming beam; if the resulting THG / SFG crystal needs Type-1 phase matching (both in phase and parallel polarization), will need a half-wave plate for 1064nm; for Type-II phase matching, no plate is needed. For noncritical phase matching in LBO (which I just bought), an oven is required to heat the crystal to the correct temperature.

This suggests 73C for THG, while this suggests 150C (for SHG?).

Third harmonic frequency generation by type-I critically phase-matched LiB3O5 crystal by means of optically active quartz crystal Suggests most lasers operate in Type-1 SHG, and Type-II THG, but this is less efficient than dual Type-1; the quartz crystal is employed to rotate the polarizations to alignment. Both SHG and THG crystals are heated for optimum power output.

Finally, Short pulse duration of an extracavity sum-frequency mixing with an LiB3O5 (LBO) crystal suggests that no polarization change is required, nor oven control LBO temperature. Tight focus and high energy density is required, of course (at the expense of reduced crystal lifetime). Likely this is the Type-1,Type-II scheme alluded to in the paper above. I'll try this first before engaging further complexity (efficiency is not very important, as the holes are very small & material removal may be slow.)

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ref: -0 tags: berkeley airbears2 configuration linux debian 8.1 date: 08-13-2015 23:42 gmt revision:1 [0] [head]

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ref: -0 tags: polyimide adhesion aluminum integrated circuit date: 05-07-2014 19:29 gmt revision:0 [head]

Polyimide insulators for multilevel interconnections Arthur M. Wilson

  • Old article (1981), but has useful historical information on the development of various PI insulators and their adhesion to aluminum, SiOx, etc.
  • Suggests that a higher-temperature cure (400C) is needed to fully drive water from the PI & cause a glass-transition. Might want to do this for the second PI layer.

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ref: -0 tags: parylene microchannel micromolding glass transition temperature microfluidics date: 06-28-2013 17:34 gmt revision:3 [2] [1] [0] [head]

Parylene micromolding, a rapid low-cost fabrication method for parylene microchannel

  • doi:10.1016/j.snb.2003.09.038
  • Hong-Seok Noha∗ , Yong Huangb, Peter J. Hesketha Clemson
  • Parylene properties:
    • Glass transition temperature <90C; c.f. {1247}
    • Melting point 290C
    • Oxidation in air at 120C
    • Thermal bonding here at 200C in a vacuum oven @ 24MPa.

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ref: -0 tags: parylene interconnect monolithic integration silicon DRIE date: 02-26-2013 00:29 gmt revision:1 [0] [head]

A New Multi-Site Probe Array with Monolithically Integrated Parylene Flexible Cable for Neural Prostheses

    • Use DRIE to etch the back of the wafer after patterning the front. Clever!

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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: Sanders-2000.1 tags: polymer fiber immune reaction biocompatibility rats polycaprolactone recording electrodes histology MEA date: 01-28-2013 00:01 gmt revision:11 [10] [9] [8] [7] [6] [5] [head]

PMID-10906696[0] Tissue response to single-polymer fibers of varying diameters: evaluation of fibrous encapsulation and macrophage density.

  • Fibers smaller than 6μm6 \mu m show reduced immune response.
    • Fibers implanted in the subcutaneous dorsum (below the skin in the back of rats).
    • Polypropylene. (like rope).
    • Wish the result extended to small beads & small electrodes. 7μm7 \mu m is tiny, but possible with insulated Au wires.
      • Beads: try PMID-1913150 -- shows that the 600um - 50um beads ('microspheres') are well tolerated.
      • Also {750}.
  • Macrophage density in tissue with fiber diameters 2.1-5.9um comparable to that of unoperated contralateral control.


fiber diametercapsule thickness


[0] Sanders JE, Stiles CE, Hayes CL, Tissue response to single-polymer fibers of varying diameters: evaluation of fibrous encapsulation and macrophage density.J Biomed Mater Res 52:1, 231-7 (2000 Oct)

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ref: Seymour-2009.1 tags: Parylene MEA biocompatibility pin hole water saturation PPX date: 01-25-2013 01:19 gmt revision:2 [1] [0] [head]

PMID-19703712[0] The insulation performance of reactive parylene films in implantable electronic devices.

  • Describe the development and testing of a superior form of parylene: poly(p-xylylene) functionalized with reactive group X (PPX-X)
  • Heat-treated PPX-X device impedance was 800% greater at 10kHz and 70% greater at 1Hz relative to heated parylene-C controls after 60 days (in saline).
  • Better wet attachment to the metal.


[0] Seymour JP, Elkasabi YM, Chen HY, Lahann J, Kipke DR, The insulation performance of reactive parylene films in implantable electronic devices.Biomaterials 30:31, 6158-67 (2009 Oct)

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ref: Stice-2007.06 tags: electrodes recording small rats S1 PGA histology GFAP date: 01-24-2013 21:07 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-17409479[0] Thin microelectrodes reduce GFAP expression in the implant site in rodent somatosensory cortex.

  • Implanted 12 um and 25 um polymide coated stainless steel
    • Wires coated with poly-glycolic acid (PGA) to facilitate implantation.
  • Only looked to 4 weeks.
  • 12 um implants significantly less GFAP (astrocyte) reactivity at 4 weeks, no difference at 2 weeks (figure 9 & 10).
    • B = bare, P = PGA coated.
  • Can use to bolster the idea that smaller implants are less irritating.


[0] Stice P, Gilletti A, Panitch A, Muthuswamy J, Thin microelectrodes reduce GFAP expression in the implant site in rodent somatosensory cortex.J Neural Eng 4:2, 42-53 (2007 Jun)

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ref: -0 tags: neural recording topologies circuits operational transconductance amplifiers date: 01-02-2013 20:00 gmt revision:0 [head]

PMID-22163863 Recent advances in neural recording microsystems.

  • Decent review. Has some depth on the critical first step of amplification.

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ref: Freire-2011.01 tags: Nicolelis BMI electrodes immune respones immunohistochemistry chronic arrays rats 2011 MEA histology date: 06-29-2012 01:20 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-22096594[0] Comprehensive analysis of tissue preservation and recording quality from chronic multielectrode implants.

  • Says what might be expected: tungsten microelectrode arrays work, though the quality gradually declines over 6 months.
  • Histological markers correlated well with recording performance.
  • Shows persistent glial activation around electrode sites + cell body hypertropy.
    • Suggest that loss in recording quality may be due to glial encapsulation.
  • References
    • Szarowski et al 2003 {1028}
    • Ward et al 2009
  • Histology:
    • NADPH-d: nicotinamide adenine dinucleotide phosphate-diaphorase, via beta-NADP
    • CO: cytochrome oxidase, via diamnibenzidine DAB, cytochrome c and catalase.
      • both good for staining cortical layers; applied in a standard buffered solution and monitored to prevent overstaining.
  • Immunohistochemistry:
    • Activated microglia with ED-1 antibody.
    • Astrocytes labeled with glial fibrillary acid protein.
    • IEG with an antibody against EGR-1, 'a well-known marker of calcium dependent neuronal activity'
    • Neurofilament revealed using a monoclonal NF-M antibody.
    • Caspace-3 with the associated antibody
    • Details the steps for immunostaining -- wash, blocknig buffer, addition of the antibody in diluted blocking solution (skim milk) overnight, wash again, incubate in biotinylated secondary antibody, wash again, incubate in avidin-biotin-peroxidase solution.
    • Flourescent immunohistochemistry had biotynlation replaced with alexa Fluor 488-conjugated horse anti-mouse and Alexa Fluor 594-conjugated goat anti-rabbit overnight.


[0] Freire MA, Morya E, Faber J, Santos JR, Guimaraes JS, Lemos NA, Sameshima K, Pereira A, Ribeiro S, Nicolelis MA, Comprehensive analysis of tissue preservation and recording quality from chronic multielectrode implants.PLoS One 6:11, e27554 (2011)

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ref: -0 tags: locomotion decerebrated monkeys spinal cord section STN stimulation date: 03-01-2012 23:53 gmt revision:0 [head]

PMID-7326562 Locomotor control in macaque monkeys

  • Were not able to induce walking with in monkeys with a sectioned spinal cord
  • Were able to induce walking motion by pulsed stimulation of the STN, with varying walking speed with varying currents!
  • Detailed, informative report, more than I have time to record here today.

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ref: -0 tags: bilateral STN lesion rats perseverence nose poke impulsivity DBS basal ganglia date: 02-29-2012 17:44 gmt revision:1 [0] [head]

PMID-9421169 Bilateral lesions of the subthalamic nucleus induce multiple deficits in an attentional task in rats.

  • Excitotoxic lesion of STN alleviate motor impairment found in PD dopamine depletion model.
  • What about normal rats?
  • investigated the behavioural effects of bilateral excitotoxic lesions of the STN in rats performing a five-choice test of divided and sustained visual attention, modelled on the human continuous performance task.
  • This task required the animals to detect a brief visual stimulus presented in one of five possible locations and respond by a nose-poke in this illuminated hole within a fixed delay, for food reinforcement
  • STN lesion:
    • decreased discriminatory activity
    • increase premature responses & preservative panel pushes and nose-poke responses.
  • Subsequent D1/D2 anatagonist administration reduced premature responses but not preservative nose-pokes.
  • Consistent with action selection and inhibition.
  • Suggest that these cognitive-type effects should be examined in humand that have STN DBS.

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ref: Mallet-2008.04 tags: DBS oscillations STN beta 6-OHDA rats ECoG acute date: 02-29-2012 01:11 gmt revision:4 [3] [2] [1] [0] [head]

PMID-18448656[0] Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex.

  • STN has pronounced beta band oscillations in PD patients.
  • 6-OHDA rodent model (here) shows the same, depending on state.
    • Synchronization in both local cellular assemblies and broadly across the STN + ECoG.
    • ECoG looks causal in their studies.
    • Frequencies > 15 Hz, not lower (theta), as in other studies.
  • Excessively synchronized beta oscillations reduce the information coding capacity of STN neuronal ensembles, which may contribute to parkinsonian motor impairment.
  • Acute disruption of dopamine transmission in control animals with antagonists of D(1)/D(2) receptors did not exaggerate STN or cortical beta oscillations.
    • This despite the potent agonist induced catalepsy in the rats!
    • Must be neural plasticity & structural.
    • Takes > 4 days.
    • Actual striatal DA levels decrease within 1 h of midbrain 6-OHDA
  • Under normal conditions, beta synchronization may be useful for sensory-motor processing (Uhlhaas and Singer 2006).
  • Synchronized activity is preferentially transmitted due to temporal summation.


[0] Mallet N, Pogosyan A, Sharott A, Csicsvari J, Bolam JP, Brown P, Magill PJ, Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex.J Neurosci 28:18, 4795-806 (2008 Apr 30)

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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: Teagarden-2007.03 tags: STN striatum operant conditioning behavior rats 2006 DBS date: 02-15-2012 03:36 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-17182916[0] Subthalamic and Striatal Neurons Concurrently Process Motor, Limbic, and Associative Information in Rats Performing an Operant Task

  • STN encodes behavioral events (reinforcement, nose poke, correct / incorrect trials). So does the striatum.
  • This study is rather nonspecific, but it makes sense that a conserved and well connected region is active during learning & general behavior.
    • That is, while the subthalamic nucleus is considered an output relay of the basal ganglia, more likely it operates in parallel to facilitate forms of learning; as such, responses are shown to rewards, cues, etc.


[0] Teagarden MA, Rebec GV, Subthalamic and striatal neurons concurrently process motor, limbic, and associative information in rats performing an operant task.J Neurophysiol 97:3, 2042-58 (2007 Mar)

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ref: Wiener-2008.08 tags: STN operant conditioning timing rats lesion DBS impulsivity date: 01-26-2012 17:29 gmt revision:3 [2] [1] [0] [head]

PMID-18562098[0] Accurate timing but increased impulsivity following excitotoxic lesions of the subthalamic nucleus.

  • Synopsis: Animals whose STNs were lesioned were able to maintain temporal control and response on a peak interval timing task, but they were unable to inhibit operant responses late into the trial. This suggests that STN may be used in impulse control / behavioral inhibition.


[0] Wiener M, Magaro CM, Matell MS, Accurate timing but increased impulsivity following excitotoxic lesions of the subthalamic nucleus.Neurosci Lett 440:2, 176-80 (2008 Aug 1)

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ref: Foffani-2004.07 tags: STN motor preparation human 2003 basal_ganglia DBS SMA date: 01-26-2012 17:23 gmt revision:3 [2] [1] [0] [head]

PMID-15249649 Involvement of the human subthalamic nucleus in movement preparation

  • STN receives large afferent from SMA, so it should be involved in movement planning.
  • the STN and nearby structures are active before self-paced movements in humans.
  • normal patients show a negative EEG movement-related potential (MRP) starting 1-2 seconds before the onset of self-paced movements.
  • STN also shows premovement negative MRP.
    • REquire very sensitive methods to record this MRP -- it's on the order of 1 uv.
  • the amplitude of the scalp MRP is reduced in parkinson's patients.
    • impairment of movement preparation in PD may be related to deficits in the SMA and M1, e.g. underactivity.
    • the MRP is normalized with the administration of levodopa.
  • MPTP monkeys have increased activity in the STN
  • examined the role of the STN in movement preparation and inhibition via MRP recorded from DBS electrodes in the STN + simultaneously recorded scalp electrodes.
  • their procedure has the leads externalized during the first week after surgery.

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ref: Florio-2001.11 tags: STN PPN lesions preparatory rats DBS date: 01-26-2012 17:22 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-11704255[0] Unilateral lesions of the pedunculopontine nucleus do not alleviate subthalamic nucleus-mediated anticipatory responding in a delayed sensorimotor task in the rat.

  • the title says it all ;)
  • they describe hemiballismus as "stereotyped repetitive involuntary movements of the cotralateral limbs" (might have to see this to understand it)
  • what the rat had to do:
    1. press lever 1 upon trigger 1 stimuli
    2. wait 3-4 seconds for the trigger 2 stimuli
    3. then press lever 2, upon which a pellet of food was given to the rat.
  • lesions of the STN in the rat do not induce hyperkinetic movements in overt behaviors, but cause anticipatory motor responses in delayed-reaction tasks, like a nose-poke.
    • see figure 7 for the bar-graph of this.
    • rats tended to release the lever before the reward or CS for reward was triggered
    • still - this might be a cognitive problem, not a lack of anticipation.
  • the PPN has remarkable reciprocating connections with the STN, and other basal ganglia nuclei
    • PPN lesion increases reaction time during conditioned movements, making the animals bradykinetic or akinetic
      • "the animals bearing the combined lesion were severely impaired in conditioned responding to salient stimuli involved in the paradigm and showed side-specific lengthening of reaction and movement times without global motor impairments."
      • has anybody looked at activity in the PPN of parkinsonian monkeys? hum.
    • compare to [1] - PPN lesions can restore normal activity in SNr & STN. but, if you don't have the STN to restore, then PPN doesn't matter.


[0] Florio T, Capozzo A, Cellini R, Pizzuti G, Staderini EM, Scarnati E, Unilateral lesions of the pedunculopontine nucleus do not alleviate subthalamic nucleus-mediated anticipatory responding in a delayed sensorimotor task in the rat.Behav Brain Res 126:1-2, 93-103 (2001 Nov 29)
[1] Breit S, Lessmann L, Unterbrink D, Popa RC, Gasser T, Schulz JB, Lesion of the pedunculopontine nucleus reverses hyperactivity of the subthalamic nucleus and substantia nigra pars reticulata in a 6-hydroxydopamine rat model.Eur J Neurosci 24:8, 2275-82 (2006 Oct)

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ref: Obeid-2003.02 tags: Obeid integrated circuits recording Morizio Nicolelis date: 01-15-2012 04:35 gmt revision:2 [1] [0] [head]

IEEE-1185151 (pdf) Two multichannel integrated circuits for neural recording and signal processing

  • pretty basic, nothing tricky. Actually, they are rather scarce with the details -- Morizio?
  • all 16 capacitors are placed off chip; on chip capacitors are only 950e-18 F/um^2 or 0.001pF/um^2 in the process they use.
  • designs with this circuit topology were rejected for noise concerns, as they would require resistors as large as 10G for to realize gain and filter cutoff.
    • and yet Reid's chips seem to be working fine without external capcitors ...
  • have variable gain (but not AGC).
  • 5uV RMS input noise; 3.5uV for the plexon headstage.


Obeid, I. and Morizio, J.C. and Moxon, K.A. and Nicolelis, M.A.L. and Wolf, P.D. Two multichannel integrated circuits for neural recording and signal processing Biomedical Engineering, IEEE Transactions on 50 2 255 -258 (2003)

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ref: Parikh-2009.04 tags: BMI rats cortex layer depth date: 01-10-2012 01:09 gmt revision:2 [1] [0] [head]

PMID-19255460[0] Lower layers in the motor cortex are more effective targets for penetrating microelectrodes in cortical prostheses.

  • Aggregate analysis (633 neurons) and best session analysis (75 neurons) indicated that units in the lower layers (layers 5, 6) are more likely to encode direction information when compared to units in the upper layers (layers 2, 3) (p< 0.05).
  • DUH. Have we forgotten all anatomy?


[0] Parikh H, Marzullo TC, Kipke DR, Lower layers in the motor cortex are more effective targets for penetrating microelectrodes in cortical prostheses.J Neural Eng 6:2, 026004 (2009 Apr)

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ref: Kipke-2003.06 tags: Michigan rat Kipke recording electrode MEA date: 01-08-2012 03:34 gmt revision:5 [4] [3] [2] [1] [0] [head]

IEEE-1214707 (pdf) Silicon-substrate intracortical microelectrode arrays for long-term recording of neuronal spike activity in cerebral cortex.

  • 4 of the 6 implants (66%) remaining functional for more than 28 weeks (7 mo)
  • Recording sites separated by 100um; at this site separation, adjacent sites may sometimes record the same unit.
  • It is notable that in each case in this series was terminated due to reasons other than the microelectrode not recording unit activity. (SC LIn agrees, pc).
  • around 80% of sites recorded neural activity.


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ref: Olds-1967.01 tags: Olds 1967 limbic system operant conditioning recording rats electrophysiology BMI date: 01-06-2012 03:59 gmt revision:2 [1] [0] [head]

PMID-6077726[0] The limbic system and behavioral reinforcement

  • Can't seem to find Olds 1965, as was a conference proceeding .. this will have to do, despite the lack of figures. images/966_1.pdf
  • First reference I can find of chronic (several weeks) (4-9 microelectrodes, single) recording from the rat.
  • Basically modern methods: commutator + solid state preamplifiers mounted to a counterbalanced slack-relieving arm.
    • If unit responses were observed in recordings from a given probe a week after surgery they were usually recordable indefinitely. 44 years later ...
  • Used a primitive but effective analog spike discriminator based on:
    • minimum amplitude
    • maximum amplitude
    • minimum fall time
    • maximum fall time.
  • Also had a head movement artifact detector, which blanked the recordings (stopped the paper roll) for 2 sec.
  • Reinforced on 'bursting', threshold sufficiently high that it only occurred once every 5-15 minutes.
  • Food reinforcement or 1/4 second train of brain stimulation (30ua, 60Hz, sine, in hypothalamus).
  • Reinforcement was conditioned on an 'acquisition' signal, which is visual (?) Bursting is rewarded for 2 minutes, ignored for 8 minutes.
  • Also recorded control neurons.
  • (they were looking at these things as though anew!) "The most striking aspect of the records so formed [on sheets of paper] was that all discriminators at one time or another exhibited rate changes that had the appearance of waves with a period of 10 to 20 minutes. Waves between units in the same animal were to some degree synchronized." Then describes a ramp ..
  • Longer term variations: FR would vary by a factor of 2-5 over a period of several hours.
    • This would make negatively correlated neurons (on a short time scale) appear positively correlated over long time scales (have to fix this in the BMI!)
  • As this was a conditional reinforcement task, they unexpectedly found that the acquisition periods were systematically different than extinction periods
    • More like pavlovian conditioning, esp in the hippocampus, where a conditioned response was also reflected on a control neuron.
    • Even when the light was lit throughout the acquisition period was replaced by a bell at the beginning of the acq. period, there was still a sustained change in FR.
      • Then during the extinction period: it appeared from the record of responses that a definite operant behavior was tried several times and then stopped altogether."
  • In the pontine nucleus (relay from M1 to cerebellum, v. roughly), judging from the control responses, all were conditioned.
    • Pontine responses seem to correspond with movement of the eyes or head that did not set off the movement detector/blanker.
  • Saw brief and very fast bursts during the extinction periods of the kind that Evarts found to characterize pyramical neurons during sleep.
  • When units shifted from food reward to ICS reward, units became undiffarentiated, and within a day they would be reconditioned.
  • Also tried paralyzing the animal to see if it could still generate operant responses; the animal died, results inconclusive.
  • Flood lights made it hard for the rats to produce the operant behavior.


[0] Olds J, The limbic system and behavioral reinforcement.Prog Brain Res 27no Issue 144-64 (1967)

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ref: BMI notes-0 tags: spike filtering rate_estimation BME 265 Henriquez date: 01-06-2012 03:06 gmt revision:1 [0] [head]


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ref: Nicolelis-1997 tags: nicolelis microwire array electrophysiology rats date: 01-05-2012 03:35 gmt revision:2 [1] [0] [head]

PMID-9136763[0] Reconstructing the engram: simultaneous, multisite, many single neuron recordings.

  • descibes Miguel's microwire arrays.
  • 100 units from 48 microwires in rats.
  • 2.3 units / microwire.
  • stable for weeks -- c.f. 2011. [1]


[0] Nicolelis MA, Ghazanfar AA, Faggin BM, Votaw S, Oliveira LM, Reconstructing the engram: simultaneous, multisite, many single neuron recordings.Neuron 18:4, 529-37 (1997 Apr)
[1] Freire MA, Morya E, Faber J, Santos JR, Guimaraes JS, Lemos NA, Sameshima K, Pereira A, Ribeiro S, Nicolelis MA, Comprehensive analysis of tissue preservation and recording quality from chronic multielectrode implants.PLoS One 6:11, e27554 (2011)

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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: Olson-2005 tags: Arizona rats BMI motor control training SVM single-unit left right closed-loop learning Olson Arizona date: 01-03-2012 23:06 gmt revision:1 [0] [head]

bibtex:Olson-2005 Evidence of a mechanism of neural adaptation in the closed loop control of directions

  • from abstract:
    • Trained rats to press left/right paddles to center a LED. e.g. paddles were arrow keys, LED was the cursor, which had to be centered. Smart rats.
      • Experiment & data from Olson 2005
    • Then trained a SVM to discriminate left/right from 2-10 motor units.
    • Once closed-loop BMI was established, monitored changes in the firing properties of the recorded neurons, specifically wrt the continually(?) re-adapted decoding SVM.
    • "but expect that the patients who use the devices will adapt to the devices using single neuron modulation changes. " --v. interesting!
  • First page of article has an excellent review back to Fetz and Schmidt. e.g. {303}
  • Excellent review of history altogether.
    • Notable is their interpretation of Sanchez 2004 {259}, who showed that most of the significant modulations are from a small group of neurons, not the large (up to 320 electrodes) populations that were actually recorded. Carmena 2003 showed that the population as a whole tended to group tuning, although this was imperfectly controlled.
  • Also reviewed: Zacksenhouse 2007 {901}
  • SVM is particularly interesting as a decoding algorithm as it weights the input vectors in projecting onto a decision boundary; these weights are experimentally informative.
  • Figure 7: The brain seems to modulate individual firing rate changes to move away from the decision boundary, or at least to minimize overlap.
  • For non-overt movements, the distance from decision function was greater than for overt movements.
  • Rho ( ρ\rho ) is the Mann-Whitney test statistic, which non-parametrically estimates the difference between two distributions.
  • δf(X t)\delta f(X_t) is the gradient wrt the p input dimensions o9f the NAV, as defined with their gaussian kernel SVM.
  • They show (i guess) that changes in ρ\rho are correlated with the gradient -- e.g. the brain focuses on neurons that increase fidelity of control?
    • But how does the brain figure this out??
  • Not sure if i fully understand their argument / support.
  • Conclusion comes early in the paper
    • figure 5 weakly supports the single-neuron modulation result.

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ref: Butovas-2007.04 tags: Butovas Schwarts ICMS stimulation rat barrel cortex date: 01-03-2012 06:55 gmt revision:2 [1] [0] [head]

PMID-17419757[0] Detection psychophysics of intracortical microstimulation in rat primary somatosensory cortex.

  • headposted rats, ICMS to barrel cortex
  • single pulse threshold = 2 nC, around the threshold for evocation of short-latency action potentials near an electrode.
  • one pulse saturated at 80% correct.
  • multiple pulses had a higher rate, though this saturated at 15 pulses.
  • double pulse optimal in terms of power / discrimination.


[0] Butovas S, Schwarz C, Detection psychophysics of intracortical microstimulation in rat primary somatosensory cortex.Eur J Neurosci 25:7, 2161-9 (2007 Apr)

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ref: Blum-2004.01 tags: microstimulator MEA Georgia Blum integrated circuit date: 01-03-2012 06:53 gmt revision:3 [2] [1] [0] [head]

PMID-17271195[0] Models of stimulation artifacts applied to integrated circuit design.

  • for MEAs.
  • Idea: develop a model of the stimulation artifact so they can optimize removal in SPICE.
  • reference documents that say that biphasic stimulation + active artifact suppression (by discharging the electrodes after stimulation, [1]) are acknowledged means of reducing stimulus artifact.
  • artifact appears to be 1ms saturating, 6ms non-saturating pulse.
  • a little light on details.


[0] Blum R, Ross J, Das S, Brown E, Deweerth S, Models of stimulation artifacts applied to integrated circuit design.Conf Proc IEEE Eng Med Biol Soc 6no Issue 4075-8 (2004)
[1] Jimbo Y, Kasai N, Torimitsu K, Tateno T, Robinson HP, A system for MEA-based multisite stimulation.IEEE Trans Biomed Eng 50:2, 241-8 (2003 Feb)

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ref: Donoghue-1990.01 tags: Donoghue Suner Sanes rat motor cortex reorganization M1 tuning surprising date: 01-03-2012 03:30 gmt revision:4 [3] [2] [1] [0] [head]

PMID-2340869[0] Dynamic organization of primary motor cortex output to target muscles in adult rats. II. Rapid reorganization following motor nerve lesions.

  1. Map out the motor cortex into vibrissa and forelimb areas using ICMS.
  2. Implant a simulating electrode in the vibrissa motor cortex.
  3. Implant EMG electrodes in the forearm.
  4. Sever the buccal and mandibular branches of the facial nerve.
  5. stimulate, and wait for forearm EMG to be elicited by ICMS. Usually occurs! Why? Large horizontal axons in motor cortex? Uncovering of silent synapses, and homeostatic modulation of firing rates?


[0] Donoghue JP, Suner S, Sanes JN, Dynamic organization of primary motor cortex output to target muscles in adult rats. II. Rapid reorganization following motor nerve lesions.Exp Brain Res 79:3, 492-503 (1990)

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ref: Blum-2007.12 tags: stimulation recording Blum integrated circuit ASIC date: 01-03-2012 03:26 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

IEEE-4358608 (pdf) An Integrated System for Simultaneous, Multichannel Neuronal Stimulation and Recording

  • Use capacitor-feedback amplifier with a seperate feedback amp to provide a DC path.
  • Input amplifier is disabled during stimulation (hopefully without blowing out gate oxide..)
  • Charge stored in the feedback caps acts as a S/H. clever!
  • Due to topology, noise increases with bias current of feedback amp.
  • Stimluation was a measly 9ua.
  • Use a feedback amplifier to actively discharge the electrode after stimulation.
  • Generally a well-though-out, informative paper, with insight as to the design compromises.

Blum RA, Ross JD Brown EA and DeWeerth SP (2007) An Integrated System for Simultaneous, Multichannel Neuronal Stimulation and Recording IEEE Trans. Circuits Syst. I. Regular Pap 54, 2608-2618

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ref: -0 tags: Chapin Hawley roborat Talwar date: 12-31-2011 19:55 gmt revision:0 [head]

PMID-11986657 Rat navigation guided by remote control.

  • "Here we show that by removing the physical contraints associated with the delivery of cues and rewards, learning paradigms based on brain microstimulation enable conditioning approaches to be used that help to transcend traditional boundaries in animal learning."

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ref: Nicolelis-1998.11 tags: spatiotemporal spiking nicolelis somatosensory tactile S1 3b microwire array rate temporal coding code date: 12-28-2011 20:42 gmt revision:3 [2] [1] [0] [head]

PMID-10196571[0] Simultaneous encoding of tactile information by three primate cortical areas

  • owl monkeys.
  • used microwires arrays to decode the location of tactile stimuli; location was encoded through te population, not within single units.
  • areas 3b, S1 & S2.
  • used LVQ (learning vector quantization) backprop, LDA to predict/ classify touch trials; all yielded about the same ~60% accuracy. Chance level 33%.
  • Interesting: "the spatiotemporal character of neuronal responses in the SII cortex was shown to contain the requisite information for the encoding of stimulus location using temporally patterned spike sequences, whereas the simultaneously recorded neuronal responses in areas 3b and 2 contained the requisite information for rate coding."
    • They support this result by varying bin widths and looking at the % of correctly classivied trials. in SII, increasing bin width decreases (slightly but significantly) the prediction accuracy.


[0] Nicolelis MA, Ghazanfar AA, Stambaugh CR, Oliveira LM, Laubach M, Chapin JK, Nelson RJ, Kaas JH, Simultaneous encoding of tactile information by three primate cortical areas.Nat Neurosci 1:7, 621-30 (1998 Nov)

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ref: delgado-0 tags: Delgado roborat ICMS stimulation control date: 12-16-2011 06:41 gmt revision:2 [1] [0] [head]


All the loose speculation provoked by roborats is ironic considering that the experiment is just a small-scale replay of a major media event that is 40 years old. In 1964, José Delgado, a neuroscientist from Yale University, stood in a Spanish bullring as a bull with a radio-equipped array of electrodes, or "stimoceiver," implanted in its brain charged toward him. When Delgado pushed a button on a radio transmitter he was holding, the bull stopped in its tracks. Delgado pushed another button, and the bull obediently turned to the right and trotted away. The New York Times hailed the event as "probably the most spectacular demonstration ever performed of the deliberate modification of animal behavior through external control of the brain."

from: http://discovermagazine.com/2004/oct/cover

from: http://www.angelfire.com/or/mctrl/chap16.htm

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ref: bookmark-0 tags: typing keyboard bitrate probability reaching bandwidth date: 12-07-2011 02:35 gmt revision:3 [2] [1] [0] [head]

From Scott MacKenzie:

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ref: Friston-2002.1 tags: neuroscience philosophy feedback top-down sensory integration inference date: 10-25-2011 23:24 gmt revision:0 [head]

PMID-12450490 Functional integration and inference in the brain

  • Extra-classical tuning: tuning is dependent on behavioral context (motor) or stimulus context (sensory). Author proposes that neuroimaging can be used to investigate it in humans.
  • "Information theory can, in principle, proceed using only forward connections. However, it turns out that this is only possible when processes generating sensory inputs are invertible and independent. Invertibility is precluded when the cause of a percept and the context in which it is engendered interact." -- proof? citations? Makes sense though.
  • Argues for the rather simplistic proof of backward connections via neuroimaging..

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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: sciences artificial Simon organizations economic rationality date: 12-01-2010 07:33 gmt revision:2 [1] [0] [head]

These are notes from reading Herbert A. Simon’s The Sciences of the Artificial, third edition, 1996 (though most of the material seems from the 70s). They are half quoted / half paraphrased (as needed when the original phrasing was clunky). I’ve added a few of my own observations, and reordered the ideas from the book.

“A large body of evidence shows that human choices are not consistent and transitive, as they would be if a utility function existed ... In general a large gain along one axis is required to compensate for a small loss along another.” HA Simon.

Companies within a capitalist economy make almost negligible use of markets in their internal functioning” - HA Simon. Eg. they are internally command economies. (later, p 40...) We take the frequent movability and indefiniteness of organizational boundaries as evidence that there is often a near balance between the advantages of markets and organizations”

  • Retail sales of automobiles are handled by dealerships
  • Many other commodities are sold directly to the consumer
  • In fast food there are direct outlets and franchises.
  • There are sole source suppliers that produce parts for much larger manufacturers.
I’m realizing / imagining a very flexible system of organizations, tied together and communicating via a liquid ‘blood’ of the market economy.

That said: organizations are not highly centralized structures in which all the important decisions are made at the center; this would exceed the limits of procedural rationality and lose many of the advantages attainable from the use of hierarchical authority. Business organizations, like markets, are vast distributed computers whose decision processes are substantially decentralized. In fact, the work of the head of a corporation is a market-like activity: allocating capital to promising or desirable projects.

In organizations, uncertainty is often a good reason to shift from markets to hierarchies in making decisions. If two different arms of a corporation - production and marketing - make different decisions on the uncertain number of units to be sold next year, there will be a problem. It is better for the management to share assumptions. “Left to the market, this kind of uncertainty leads directly to the dilemmas of rationality that we described earlier in terms of game theory and rational expectations”

I retain vivid memories of the astonishment and disbelief expressed by the architecture students to whom I taught urban land economics many years ago when I pointed to medieval cities as marveluosly patterned systems that had mostly just ‘grown’ in response to myriads of individual human decisions. To my students a pattern implied a planner in whose mind it had been conceived and whose hand it had been implemented. The idea that a city could acquire its patter as naturally as a snowflake was foreign to them ... they reacted to it as many christian fundamentalists responded to Darwin: no design without a Designer!

Markets appear to conserve information and calculation by assigning decisions to actors who can make them on the basis of information that is available to them locally. von Hayek: “The most significant fact about this system is the economy of knowledge with which it operates, o how little the individual participants need to know in order to make the right action”. To maintain actual Pareto optimality in the markets would require information and computational requirements that are exceedingly burdensome and unrealistic (from The New Palgrave: A dictionary of Economics)

Nelson and winter observe that in economic evolution, in contract to biological evolution, sucessful algorithms (business practices) may be borrowed from one firm to the other. The hypothesized system is Lamarkian, because any new idea can be incorporated in opearting procedures as soon as its success is observed" . Also, it's good as corporations don't have secual reproduction / crossover.

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ref: work-0 tags: metacognition AI bootstrap machine learning Pitrat self-debugging date: 08-07-2010 04:36 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

Jacques Pitrat seems to have many of the same ideas that I've had (only better, and he's implemented them!)--

A Step toward and Artificial Scientist

  • The overall structure seems good - difficult problems are attacked by 4 different levels. First level tries to solve the problem semi-directly, by writing a program to solve combinatorial problems (all problems here are constraint based; constraints are used to pare the tree of possible solutions; these trees are tested combinatorially); second level monitors lower level performance and decides which hypotheses to test (which branch to pursue on the tree) and/or which rules to apply to the tree; third level directs the second level and restarts the whole process if a snag or inconsistency is found, forth level gauges the interest of a given problem and looks for new problems to solve within a family so as to improve the skill of the 3 lower levels.
    • This makes sense, but why 4? Seems like in humans we only need 2 - the actor and the critic, bootstrapping forever.
    • Also includes a "Zeus" module that periodically checks for infinite loops of the other programs, and recompiles with trace instructions if an infinite loop is found within a subroutine.
  • Author claims that the system is highly efficient - it codes constraints and expert knowledge using a higher level language/syntax that is then converted to hundreds of thousands of lines of C code. The active search program runs runtime-generated C programs to evaluate and find solutions, wow!
  • This must have taken a decade or more to create! Very impressive. (seems it took 2 decades, at least according to http://tunes.org/wiki/jacques_20pitrat.html)
    • Despite all this work, he is not nearly done - it has not "learning" module.
    • Quote: In this paper, I do not describe some parts of the system which still need to be developed. For instance, the system performs experiments, analyzes them and finds surprising results; from these results, it is possible to learn some improvements, but the learning module, which would be able to find them, is not yet written. In that case, only a part of the system has been implemented: on how to find interesting data, but still not on how to use them.
  • Only seems to deal with symbolic problems - e.g. magic squares, magic cubes, self-referential integer series. Alas, no statistical problems.
  • The whole CAIA system can effectively be used as a tool for finding problems of arbitrary difficulty with arbitrary number of solutions from a set of problem families or meta-families.
  • Has hypothesis based testing and backtracking; does not have problem reformulation or re-projection.
  • There is mention of ALICE, but not the chatbot A.L.I.C.E - some constraint-satisfaction AI program from the 70's.
  • Has a C source version of MALICE (his version of ALICE) available on the website. Amazingly, there is no Makefile - just gcc *.c -rdynamic -ldl -o malice.
  • See also his 1995 Paper: AI Systems Are Dumb Because AI Researchers Are Too Clever images/815_1.pdf

Artificial beings - his book.

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ref: work-0 tags: sine wave synthesis integrator date: 02-03-2010 05:52 gmt revision:1 [0] [head]

I learned this in college, but have forgotten all the details - Microcontroller provides an alternative to DDS

freq=|F|2πτ freq = \frac{\sqrt{|F|}}{2 \pi \tau} where τ\tau is the sampling frequency. F ranges from -0.2 to 0.

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ref: work-0 tags: Cohen Singer SLIPPER machine learning hypothesis generation date: 10-25-2009 18:42 gmt revision:2 [1] [0] [head]


  • "One disadvantage of boosting is that improvements in accuracy are often obtained at the expense of comprehensibility.
  • SLIPPER = simple learner with iterative pruning to produce error reduction.
  • Inner loop: the weak lerner splits the training data, grows a single rule using one subset of the data, and then prunes the rule using the other subset.
  • They use a confidence-rated prediction based boosting algorithm, which allows the algorithm to abstain from examples not covered by the rule.
    • the sign of h(x) - the weak learner's hyposthesis - is interpreted as the predited label and the magnitude |h(x)| is the confidence in the prediction.
  • SLIPPER only handles two-class problems now, but can be extended..
  • Is better than, though not dramatically so, than c5rules (a commercial version of Quinlan's decision tree algorithms).
  • see also the excellent overview at http://www.cs.princeton.edu/~schapire/uncompress-papers.cgi/msri.ps

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ref: Chapin-1999.07 tags: chapin Nicolelis BMI neural net original SUNY rat date: 09-02-2009 23:11 gmt revision:2 [1] [0] [head]

PMID-10404201 Real-time control of a robot arm using simultaneously recorded neurons in the motor cortex.

  • Abstract: To determine whether simultaneously recorded motor cortex neurons can be used for real-time device control, rats were trained to position a robot arm to obtain water by pressing a lever. Mathematical transformations, including neural networks, converted multineuron signals into 'neuronal population functions' that accurately predicted lever trajectory. Next, these functions were electronically converted into real-time signals for robot arm control. After switching to this 'neurorobotic' mode, 4 of 6 animals (those with > 25 task-related neurons) routinely used these brain-derived signals to position the robot arm and obtain water. With continued training in neurorobotic mode, the animals' lever movement diminished or stopped. These results suggest a possible means for movement restoration in paralysis patients.
The basic idea of the experiment. Rat controlled the water lever with a forelimb lever, then later learned to control the water lever directly. They used an artificial neural network to decode the intended movement.

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ref: Ribeiro-2004.12 tags: Sidarta Ribeiro reverberation sleep consolidation integration replay REM SWS date: 03-26-2009 03:19 gmt revision:2 [1] [0] [head]

PMID-15576886[0] Reverberation, storage, and postsynaptic propagation of memories during sleep

  • Many references in the first paragraph! They should switch to the [n] notation; the names are disruptive.
  • Show reverberation (is this measured in a scale-invariant way?) increases after novel object is placed in cage. Recorded from a single rat for up to 96 hours.
  • also looked at Zif-268 activation in the cortex (autoradiogram);
    • Previous results showed that Zif-268 levels are up-regulated in REM but not SWS in the hippocampus and cerebral cortex of exposed animals. (Ribeiro 1999)
    • hippocampal inactivation during REM sleep blocked zif-268 upregulation.
    • quote: "Increased activity is necessary but not sufficient to induce zif-268 expression, which also requires calcium inflow via NMDA channels and phosphorilation of the cAMP response element-binding protein (CREB)"
  • Sleep deprivation is much more detrimental to implicit than to explicit memory consolidation (Fowler et al. 1973; Karni et al. 1994; Smith 1995, 2001; Stickgold et al. 2000a; Laureys et al. 2002; Walker et al. 2002; Maquet et al. 2003; Mednick et al. 2003)


[0] Ribeiro S, Nicolelis MA, Reverberation, storage, and postsynaptic propagation of memories during sleep.Learn Mem 11:6, 686-96 (2004 Nov-Dec)

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ref: Wagner-2004.01 tags: sleep insight mental restructure integration synthesis consolidation date: 03-20-2009 21:31 gmt revision:1 [0] [head]

PMID-14737168[0] Sleep Inspires Insight.

  • Subjects performed a cognitive task requiring the learning of stimulus–response sequences, in which they improved gradually by increasing response speed across task blocks. However, they could also improve abruptly after gaining insight into a hidden abstract rule underlying all sequences.
    • number reduction task - three numbers 1, 4, 9, in short sequence, with a simple comparison rule to generate a derivative number sequence; task was to determine the last number in sequence; this number was always the same as the second number.
  • This abstract rule was more likely to be learned after 8 hours of sleep as compared to 8 hours of wakefulness.
  • My thoughts: replay during sleep allows synchronous replay of cortical activity seen during the day (presumably from the hippocampus to the neocortex), replay which is critical for linking the second number with the last (response) number. This is a process of integration: merging present memories with existing memories / structure. The difference in time here is not as long as it could be .. presumably it goes back to anything in your cortex that is activated buy the hippocampal memories. In this way we build up semi-consistent integrated maps of the world. Possibly these things occur during dreams, and the weird events/thoughts/sensations are your brain trying to smooth and merge/infer things about the world.


[0] Wagner U, Gais S, Haider H, Verleger R, Born J, Sleep inspires insight.Nature 427:6972, 352-5 (2004 Jan 22)

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ref: Eschenko-2006.12 tags: sleep spindle learning rats date: 03-20-2009 00:40 gmt revision:1 [0] [head]

PMID-17167082[0] Elevated sleep spindle density after learning or after retrieval in rats.

  • sleep spindles = 12–15 Hz oscillations superimposed on slow waves (<1 Hz)
    • they say these 'promote' but infact they may just be effects of some lower-level synchronization / ensemble depolarization.
  • used an odor-response-reward task.
  • spindles reliably appear 1 hour after sleep begins.
  • hippocampal ripples are temporally related to cortical spindles and both are grouped by slow oscillations.
  • showed that pure exploration of novel environments (without the odorant pairing) does not change sleep spindle occurence frequency.


[0] Eschenko O, Mölle M, Born J, Sara SJ, Elevated sleep spindle density after learning or after retrieval in rats.J Neurosci 26:50, 12914-20 (2006 Dec 13)

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ref: Narayanan-2005.04 tags: Laubach M1 motor rats statistics BMI prediction methods date: 09-07-2008 19:51 gmt revision:4 [3] [2] [1] [0] [head]

PMID-15858046[] Redundancy and Synergy of Neuronal Ensembles in Motor Cortex

  • timing task.
  • rats.
  • 50um teflon microwires in motor cortex
  • ohno : neurons that were the best predictors of task performance were not necessarily the neurons that contributed the most predictive information to an ensemble of neurons.
  • most all contribute redundant predictive information to the ensemble.
    • this redundancy kept the predictions high, even if neurons were dropped.
  • small groups of neurons were more synergistic
  • large groups were more redundant.
  • used wavelet based discriminant pursuit.
    • validated with draws from a random data set.
  • used R and Weka
  • data looks hella noisy ?


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ref: -0 tags: laser power concentration GFP mCherry calibration date: 02-01-2008 19:22 gmt revision:0 [head]

above, a set of curves for determining fluorescent protein concentration (GFP & mCherry) from received photon count in a two-photon microscope. Unfortunately, these depend on efficiency & power of the entire setup, so the curve is non-transferable to other microscopes.

one pass of mCherry @ 5x dilution did not seem the same as the others -- perhaps the reading light was left on?

% given a series of files, 
% calculate a quadratic to convert intensity to concentration. 
% assumed formula: 
% green intensity = background + const*[GFP]*laserpower^2
% red intensity = background + const*[RFP]*laserpower^2 +
%               const2[GFP]*laserpower^2
close all
basename = 'T002-gfp-100xdil-'; 
int_gfp100 = IntensReadfile('T002-gfp-100xdil-', 11, 2); 
int_gfp10 = IntensReadfile('T002-gfp-10xdil-', 8, 2);
int_mcherry10 = IntensReadfile('T002-mcherry-10xdil-', 7, 2);
int_mcherry5 = IntensReadfile('T002-mcherry-5xdil-', 7, 2);
int_mcherry5_2 = IntensReadfile('T002-mcherry-5xdil2-', 7, 2);
int_mcherry5_4 = IntensReadfile('T002-mcherry-5xdil4-', 6, 2);

bg_green = (int_gfp100(1) + int_gfp10(1))/2;
bg_red = (int_mcherry10(1) + int_mcherry5(1)...
    + int_mcherry5_2(1) + int_mcherry5_4(1))/4; 
powers = (0:0.1:1).^2;
int_gfp_all = [int_gfp100-bg_green, (int_gfp10-bg_green)/10]; 
pow_gfp_all = [powers(1:11), powers(1:8)]; 
green_intensity_perpower = pow_gfp_all'\int_gfp_all'
green_lab = ['green intensity = ' num2str(green_intensity_perpower) ' * power^2 + ' ...
    num2str(bg_green) ' (photons/10us) @ 8.7 ug/ml conc. gfp']; 

plot(sqrt(powers(1:11)), int_gfp100, 'o'); 
hold on
plot(sqrt(powers(1:8)), (int_gfp10-bg_green)/10+bg_green, 'or'); 
plot(sqrt(pow_gfp_all), pow_gfp_all * green_intensity_perpower + bg_green, 'gx'); 
legend('100x dilution','10x dilution','parabolic fit'); 
title('intensity of gfp vs. laser power normalized to 100x dilution')

int_mch_all = [(int_mcherry10-bg_red)/10, (int_mcherry5-bg_red)/20, ...
    (int_mcherry5_2-bg_red)/20, (int_mcherry5_4-bg_red)/20]; 
pow_mch_all = [powers(1:7), powers(1:7), powers(1:6), powers(1:7)]; 
red_intensity_perpower = pow_mch_all'\int_mch_all'
red_lab = ['red intensity = ' num2str(red_intensity_perpower) ' * power^2 + ' ...
    num2str(bg_red) ' (photons/10us) @ 8.7 ug/ml conc. mcherry']; 

plot(sqrt(powers(1:7)), (int_mcherry10-bg_red)/10+bg_red, 'o'); 
hold on
plot(sqrt(powers(1:7)), (int_mcherry5-bg_red)/20+bg_red, 'or'); 
plot(sqrt(powers(1:7)), (int_mcherry5_2-bg_red)/20+bg_red, 'ok'); 
plot(sqrt(powers(1:6)), (int_mcherry5_4-bg_red)/20+bg_red, 'om');
plot(sqrt(pow_mch_all), pow_mch_all * red_intensity_perpower + bg_red, 'gx'); 
legend('10x dilution','5x dilution','5x dilution(2)','5x dilution(4)','parabolic fit'); 
title('intensity of mcherry vs. laser power normalized to 100x dilution')

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ref: bookmark-0 tags: Ruby gmail imap migration date: 12-20-2007 18:03 gmt revision:0 [head]

http://wonko.com/article/554 -- niice :)

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ref: notes-0 tags: flock OSS opensource Mozilla LGPL money corporations browser comment embedded mobile opera date: 12-20-2007 16:23 gmt revision:0 [head]

I'm posting my comments about http://flock.com/ here just in case they are removed from the actual site

This is all very interesting. I just downloaded it, and flock seems to work well. I'm probably not going to use it unless there is some demonstrable technical superiority (e.g. leaks less memory than firefox), as the social sites just distract me from getting work done.

Anyway, I have a question: how are you going to make money? How are you paying the developers? If you are not and it is all OSS, where is the source? It seems like the VC's are just throwing money away for the (hypothetical) good of the social-network crowd. Or, rather, you are indirectly funding the popularity of sites that flock makes it easy to get at. Are these sites (e.g. facebook) paying you? Wait -- flock allows you to look at content and not the ads. They are not paying you.

Perhaps you are moving along the lines of Opera, and intending to get people addicted to flock to a degree that they demand it on their mobile devices. Mobile devices are closed (for now .. check google), hence you can make money licensing software to phone manufacturers. I imagine that you'll have to rewrite the Mozilla core to do this (unless phones become significantly more powerful - not likely, they are battery devices. ) Mozilla is (L)GPL - you'll have to release the source. To the best of my knowledge, with non-physical goods money can only be made from gradients in knowledge (pun.. intended), therefore you will have to keep the source closed. If this is the case, you'll be able to make money (on this, i don't know what else you have planned) for a while, and when you can no longer, I hope you open the source like netscape.

Technically, though, excellent job! your website is also very pretty!

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ref: notes-0 tags: multirate downsample DSP filter date: 08-09-2007 19:14 gmt revision:0 [head]

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ref: bookmark-0 tags: RF penetration tissue 1978 date: 07-24-2007 04:15 gmt revision:2 [1] [0] [head]


  • from the perspective of NMR imaging.
  • gives the penetration depths & phase-shifts for RF waves from 1 - 100Mhz. I can obly assume that it is much worse for 400Mhz and 2.4Ghz.
    • that said, Zarlink's MICS transceiver works from the GI tract at 400mhz with low power, suggesting that the attenuation can't be too too great.
  • includes equations used to derive these figures.
  • document describing how various antenna types are effected by biological tissue, e.g. a human head.

even more interesting: wireless brain machine interface

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ref: notes-0 tags: kicad footprint generator pcb design date: 05-22-2007 02:51 gmt revision:1 [0] [head]

oh yea!!! nice work mate!!


btw, kicad is the shit - and it is now in Debian!! I love debian! I love kicad!

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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: engineering notes-0 tags: homopolar generator motor superconducting magnet date: 03-09-2007 14:39 gmt revision:0 [head]


  • the magnets are energized in 'opposite directions - forcing the field lines to go normal to the rotar.
  • still need brushes - perhaps there is no way to avoid them in a homopolar generator.

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ref: notes-0 tags: leptin depression weight fat rats date: 0-0-2007 0:0 revision:0 [head]

  1. lepin is released by fat cells & gives the brain a reading of fat stores.
  2. obese people have high leptin levels, but their appetite still seems high; injecting obese people with leptin seldom causes them to loose weight.
  3. leptin injections encourage stressed or depressed rats to drink coke, i mean sugary liquid.
  4. leptin levels and appetite are low p>0.5 in depressed people.

items 2-4 are not in accord with the stated purpose of leptin (1).

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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]



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ref: bookmark-0 tags: information entropy bit rate matlab code date: 0-0-2006 0:0 revision:0 [head]


  • concise, well documented, useful.
  • number of bins = length of vector ^ (1/3).
  • information = sum(log (bincounts / prior) * bincounts) -- this is just the divergence, same as I do it.