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[0] Hochberg LR, Serruya MD, Friehs GM, Mukand JA, Saleh M, Caplan AH, Branner A, Chen D, Penn RD, Donoghue JP, Neuronal ensemble control of prosthetic devices by a human with tetraplegia.Nature 442:7099, 164-71 (2006 Jul 13)

[0] Rousche PJ, Normann RA, Chronic recording capability of the Utah Intracortical Electrode Array in cat sensory cortex.J Neurosci Methods 82:1, 1-15 (1998 Jul 1)

[0] Mojarradi M, Binkley D, Blalock B, Andersen R, Ulshoefer N, Johnson T, Del Castillo L, A miniaturized neuroprosthesis suitable for implantation into the brain.IEEE Trans Neural Syst Rehabil Eng 11:1, 38-42 (2003 Mar)

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

[0] Santhanam G, Ryu SI, Yu BM, Afshar A, Shenoy KV, A high-performance brain-computer interface.Nature 442:7099, 195-8 (2006 Jul 13)[1] Shenoy KV, Meeker D, Cao S, Kureshi SA, Pesaran B, Buneo CA, Batista AP, Mitra PP, Burdick JW, Andersen RA, Neural prosthetic control signals from plan activity.Neuroreport 14:4, 591-6 (2003 Mar 24)

[0] Serruya M, Hatsopoulos N, Fellows M, Paninski L, Donoghue J, Robustness of neuroprosthetic decoding algorithms.Biol Cybern 88:3, 219-28 (2003 Mar)

[0] Aflalo TN, Graziano MS, Relationship between unconstrained arm movements and single-neuron firing in the macaque motor cortex.J Neurosci 27:11, 2760-80 (2007 Mar 14)

[0] Churchland MM, Afshar A, Shenoy KV, A central source of movement variability.Neuron 52:6, 1085-96 (2006 Dec 21)

[0] Serruya MD, Hatsopoulos NG, Paninski L, Fellows MR, Donoghue JP, Instant neural control of a movement signal.Nature 416:6877, 141-2 (2002 Mar 14)

[0] Ojakangas CL, Shaikhouni A, Friehs GM, Caplan AH, Serruya MD, Saleh M, Morris DS, Donoghue JP, Decoding movement intent from human premotor cortex neurons for neural prosthetic applications.J Clin Neurophysiol 23:6, 577-84 (2006 Dec)

[0] Bair W, Koch C, Temporal precision of spike trains in extrastriate cortex of the behaving macaque monkey.Neural Comput 8:6, 1185-202 (1996 Aug 15)[1] Shmiel T, Drori R, Shmiel O, Ben-Shaul Y, Nadasdy Z, Shemesh M, Teicher M, Abeles M, Neurons of the cerebral cortex exhibit precise interspike timing in correspondence to behavior.Proc Natl Acad Sci U S A 102:51, 18655-7 (2005 Dec 20)[2] Mainen ZF, Sejnowski TJ, Reliability of spike timing in neocortical neurons.Science 268:5216, 1503-6 (1995 Jun 9)

[0] Wood F, Fellows M, Donoghue J, Black M, Automatic spike sorting for neural decoding.Conf Proc IEEE Eng Med Biol Soc 6no Issue 4009-12 (2004)

[0] Teich MC, Heneghan C, Lowen SB, Ozaki T, Kaplan E, Fractal character of the neural spike train in the visual system of the cat.J Opt Soc Am A Opt Image Sci Vis 14:3, 529-46 (1997 Mar)

[0] Vyssotski AL, Serkov AN, Itskov PM, Dell'Omo G, Latanov AV, Wolfer DP, Lipp HP, Miniature neurologgers for flying pigeons: multichannel EEG and action and field potentials in combination with GPS recording.J Neurophysiol 95:2, 1263-73 (2006 Feb)[1] Otto KJ, Johnson MD, Kipke DR, Voltage pulses change neural interface properties and improve unit recordings with chronically implanted microelectrodes.IEEE Trans Biomed Eng 53:2, 333-40 (2006 Feb)

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ref: -0 tags: evolution simplicity symmetry kolmogorov complexity polyominoes protein interactions date: 04-21-2022 18:22 gmt revision:5 [4] [3] [2] [1] [0] [head]

Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution

  • Central hypothesis is that simplicity and symmetry arrive not through natural selection, but because these form are overwhelmingly represented in the genotype-phenotype map
  • Experimental example here was "polyominoes", where there are N=16 tiles, each with a 4 numbers (encoded with e.g. 6-bit binary numbers). The edge numbers determine how the tiles irreversibly bind, e.g. 1 <-> 2, 3 <-> 4 etc, with 4 and 2^6-1 binding to nothing.
  • These tiles are allowed to 'randomly' self-assemble. Some don't terminate (e.g. they form continuous polymers); these are discarded; others do terminate (no more available binding sites).
  • They assessed the complexity of both polyominoes selected for a particular size, eg 16 tiles, or those not selected at all, other than terminating.
  • In both complexity was assessed based on how many actual interactions were needed to make the observed structure. That is, they removed tile edge numbers and kept it if it affected the n-mer formation.
  • Result was this nice log-log plot:
  • Showed that this same trend holds for protein-protein complexes (weaker result, imho)
  • As well as RNA secondary structure
  • And metabolic time-series in a ODE modeled on yeast metabolism (even weaker result..)

The paper features a excellent set of references, including:
Letter to a friend following her article Machine learning in evolutionary studies comes of age

Read your PNAS article last night, super interesting that you can get statistical purchase on long-lost evolutionary 'sweeps' via GANs and other neural network models.  I feel like there is some sort of statistical power issue there?  DNNs are almost always over-parameterized... slightly suspicious.

This morning I was sleepily mulling things over & thought about a walking conversation that we had a long time ago in the woods of NC:  Why is evolution so effective?  Why does it seem to evolve to evolve?  Thinking more -- and having years more perspective -- it seems almost obvious in retrospect: it's a consequence of Bayes' rule.  Evolution finds solutions in spaces that have overwhelming prevalence of working solutions.  The prior has an extremely strong effect.  These representational / structural spaces by definition have many nearby & associated solutions, hence appear post-hoc 'evolvable'.  (You probably already know this.)

I think proteins very much fall into this category: AA were added to the translation machinery based on ones that happened to solve a particular problem... but because of the 'generalization prior' (to use NN parlance), they were useful for many other things.  This does not explain the human-engineering-like modularity of mature evolved systems, but maybe that is due to the strong simplicity prior [1]

Very very interesting to me is how the science of evolution and neural networks are drawing together, vis a vis the lottery ticket hypothesis.  Both evince a continuum of representational spaces, too, from high-dimensional vectoral (how all modern deep learning systems work) to low-dimensional modular, specific, and general (phenomenological human cognition).  I suspect that evolution uses a form of this continuum, as seen in the human high-dimensional long-range gene regulatory / enhancer network (= a structure designed to evolve).  Not sure how selection works here, though; it's hard to search a high-dimensional space.  The brain has an almost identical problem: it's hard to do 'credit assignment' in a billions-large, deep and recurrent network.  Finding which set of synapses caused a good / bad behaviior takes a lot of bits.

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ref: -0 tags: concept net NLP transformers graph representation knowledge date: 11-04-2021 17:48 gmt revision:0 [head]

Symbolic Knowledge Distillation: from General Language Models to Commonsense Models

  • From a team at University of Washington / Allen institute for artificial intelligence/
  • Courtesy of Yannic Kilcher's youtube channel.
  • General idea: use GPT-3 as a completion source given a set of prompts, like:
    • X starts running
      • So, X gets in shape
    • X and Y engage in an argument
      • So, X wants to avoid Y.
  • There are only 7 linkage atoms (edges, so to speak) in these queries, but of course many actions / direct objects.
    • These prompts are generated from the Atomic 20-20 human-authored dataset.
    • The prompts are fed into 175B parameter DaVinci model, resulting in 165k examples in the 7 linkages after cleaning.
    • In turn the 165k are fed into a smaller version of GPT-3, Curie, that generates 6.5M text examples, aka Atomic 10x.
  • Then filter the results via a second critic model, based on fine-tuned RoBERTa & human supervision to determine if a generated sentence is 'good' or not.
  • By throwing away 62% of Atomic 10x, they get a student accuracy of 96.4%, much better than the human-designed knowledge graph.
    • They suggest that one way thins works is by removing degenerate outputs from GPT-3.

Human-designed knowledge graphs are described here: ConceptNet 5.5: An Open Multilingual Graph of General Knowledge

And employed for profit here: https://www.luminoso.com/

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ref: -2014 tags: CNiFER Kleinfeld dopamine norepinephrine monoamine cell sensor date: 10-04-2021 14:50 gmt revision:2 [1] [0] [head]

Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex

  • CNiFERs are clonal cell lines engineered to express a specific GPCR that is coupled to the Gq pathway and triggers an increase in intracellular calcium concentration, [Ca2+], which in turn is rapidly detected by a genetically encoded fluorescence resonance energy transfer (FRET)-based Ca2+ sensor. This system transforms neurotransmitter receptor binding into a change in fluorescence and provides a direct and real-time optical readout of local neurotransmitter activity. Furthermore, by using the natural receptor for a given transmitter, CNiFERs gain the chemical specificity and temporal dynamics present in vivo.
    • Clonal cell line = HEK293.
      • Human cells implanted into mice!
    • Gq pathway = through the phospholipase C-initosol triphosphate (PLC-IP3) pathway.
  • Dopamine sensor required the engineering of a chimeric Gqi5 protein for coupling to PLC. This was a 5-AA substitution (only!)

Referenced -- and used by the recent paper Reinforcement learning links spontaneous cortical dopamine impulses to reward, which showed that dopamine signaling itself can come under volitional, operant-conditioning (or reinforcement type) modulation.

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ref: -0 tags: nonlinear hebbian synaptic learning rules projection pursuit date: 12-12-2019 00:21 gmt revision:4 [3] [2] [1] [0] [head]

PMID-27690349 Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation

  • Here we show that the principle of nonlinear Hebbian learning is sufficient for receptive field development under rather general conditions.
  • The nonlinearity is defined by the neuron’s f-I curve combined with the nonlinearity of the plasticity function. The outcome of such nonlinear learning is equivalent to projection pursuit [18, 19, 20], which focuses on features with non-trivial statistical structure, and therefore links receptive field development to optimality principles.
  • Δwxh(g(w Tx))\Delta w \propto x h(g(w^T x)) where h is the hebbian plasticity term, and g is the neurons f-I curve (input-output relation), and x is the (sensory) input.
  • The relevant property of natural image statistics is that the distribution of features derived from typical localized oriented patterns has high kurtosis [5,6, 39]
  • Model is a generalized leaky integrate and fire neuron, with triplet STDP

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ref: -0 tags: adaptive optics sensorless retina fluorescence imaging optimization zernicke polynomials date: 11-15-2019 02:51 gmt revision:0 [head]

PMID-26819812 Wavefront sensorless adaptive optics fluorescence biomicroscope for in vivo retinal imaging in mice

  • Idea: use backscattered and fluorescence light to optimize the confocal image through imperfect optics ... and the lens of the mouse eye.
    • Optimization was based on hill-climbing / line search of each Zernicke polynomial term for the deformable mirror. (The mirror had to be characterized beforehand, naturally).
    • No guidestar was needed!
  • Were able to resolve the dendritic processes of EGFP labeled Thy1 ganglion cells and Cx3 glia.

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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: -0 tags: Lucy Flavin mononucelotide FAD FMN fluorescent protein reporter date: 10-17-2019 19:54 gmt revision:1 [0] [head]

PMID-25906065 LucY: A Versatile New Fluorescent Reporter Protein

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ref: -2017 tags: neuromorphic optical computing nanophotonics date: 06-17-2019 14:46 gmt revision:5 [4] [3] [2] [1] [0] [head]

Progress in neuromorphic photonics

  • Similar idea as what I had -- use lasers as the optical nonlinearity.
    • They add to this the idea of WDM and 'MRR' (micro-ring resonator) weight bank -- they don't talk about the ability to change the weihts, just specify them with some precision.
  • Definitely makes the case that III-V semiconductor integrated photonic systems have the capability, in MMACs/mm^2/pj, to exceed silicon.

See also :

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ref: -0 tags: nanophotonics interferometry neural network mach zehnder interferometer optics date: 06-13-2019 21:55 gmt revision:3 [2] [1] [0] [head]

Deep Learning with Coherent Nanophotonic Circuits

  • Used a series of Mach-Zehnder interferometers with thermoelectric phase-shift elements to realize the unitary component of individual layer weight-matrix computation.
    • Weight matrix was decomposed via SVD into UV*, which formed the unitary matrix (4x4, Special unitary 4 group, SU(4)), as well as Σ\Sigma diagonal matrix via amplitude modulators. See figure above / original paper.
    • Note that interfereometric matrix multiplication can (theoretically) be zero energy with an optical system (modulo loss).
      • In practice, you need to run the phase-moduator heaters.
  • Nonlinearity was implemented electronically after the photodetector (e.g. they had only one photonic circuit; to get multiple layers, fed activations repeatedly through it. This was a demonstration!)
  • Fed network FFT'd / banded recordings of consonants through the network to get near-simulated vowel recognition.
    • Claim that noise was from imperfect phase setting in the MZI + lower resolution photodiode read-out.
  • They note that the network can more easily (??) be trained via the finite difference algorithm (e.g. test out an incremental change per weight / parameter) since running the network forward is so (relatively) low-energy and fast.
    • Well, that's not totally true -- you need to update multiple weights at once in a large / deep network to descend any high-dimensional valleys.

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ref: -2014 tags: gold nanowires intracellular recording korea date: 03-18-2019 23:02 gmt revision:1 [0] [head]

PMID-25112683 Subcellular Neural Probes from Single-Crystal Gold Nanowires

  • Korean authors... Mijeong Kang,† Seungmoon Jung,‡ Huanan Zhang,⊥ Taejoon Kang,∥ Hosuk Kang,† Youngdong Yoo,† Jin-Pyo Hong,# Jae-Pyoung Ahn,⊗ Juhyoun Kwak,† Daejong Jeon,‡* Nicholas A. Kotov,⊥* and Bongsoo Kim†*
  • 100nm single-crystal Au.
  • Able to get SUA despite size.
  • Springy, despite properties of bulk Au.
  • Nanowires fabricated on a sapphire substrae and picked up by a fine shapr W probe, then varnished with nail polish.

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ref: -2018 tags: cortex layer martinotti interneuron somatostatin S1 V1 morphology cell type morphological recovery patch seq date: 03-06-2019 02:51 gmt revision:3 [2] [1] [0] [head]

Neocortical layer 4 in adult mouse differs in major cell types and circuit organization between primary sensory areas

  • Using whole-cell recordings with morphological recovery, we identified one major excitatory and seven inhibitory types of neurons in L4 of adult mouse visual cortex (V1).
  • Nearly all excitatory neurons were pyramidal and almost all Somatostatin-positive (SOM+) neurons were Martinotti cells.
  • In contrast, in somatosensory cortex (S1), excitatory cells were mostly stellate and SOM+ cells were non-Martinotti.
  • These morphologically distinct SOM+ interneurons correspond to different transcriptomic cell types and are differentially integrated into the local circuit with only S1 cells receiving local excitatory input.
  • Our results challenge the classical view of a canonical microcircuit repeated through the neocortex.
  • Instead we propose that cell-type specific circuit motifs, such as the Martinotti/pyramidal pair, are optionally used across the cortex as building blocks to assemble cortical circuits.
  • Note preponderance of axons.
  • Classifications:
    • Pyr pyramidal cells
    • BC Basket cells
    • MC Martinotti cells
    • BPC bipolar cells
    • NFC neurogliaform cells
    • SC shrub cells
    • DBC double bouquet cells
    • HEC horizontally elongated cells.
  • Using Patch-seq

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ref: -2019 tags: three photon imaging visual cortex THG chirp NOPA mice GCaMP6 MIT date: 03-01-2019 18:46 gmt revision:2 [1] [0] [head]

PMID-30635577 Functional imaging of visual cortical layers and subplate in awake mice with optimized three photon microscopy

  • Murat Yildirim, Hiroki Sugihara, Peter T.C. So & Mriganka Sur'
  • Used a fs Ti:Saphirre 16W pump into a non-colinear optical parametric amplifier (both from Spectra-Physics) to generate the 1300nm light.
  • Used pulse compensation to get the pulse width at the output of the objective to 40 fS.
    • Three-photon cross section is inverse quadratic in pulse width:
    • NP 3δ(τR) 2(NA 22hcλ) 3 N \sim \frac{P^3 \delta}{(\tau R)^2} (\frac{NA^2}{2hc\lambda})^3
    • P is power, δ\delta is 3p cross-section, τ\tau is pulse width, R repetition rate, NA is the numerical aperture (sixth power of NA!!!), h c and λ\lambda Planks constant, speed of light, and wavelength respectively.
  • Optimized excitation per depth by monitoring damage levels. varied from 0.5nJ to 5 nJ.
  • Imaged up to 1.5mm deep! All the way to the white matter / subplate.
  • Allegedly used a custom scan and tube lens to minimize aberrations in the excitation path (hence improve 3p excitation)
  • Layer 5 neurons are more broadly tuned for orientation than other layers. But the data is not dramatic.
  • Used straightforward metrics for tuning, using a positive and negative bump gaussian fit, then vector averaging to get global orientation selectivity.
  • Interesting that the variance between layers seems higher than between mice.

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ref: -2019 tags: Arild Nokland local error signals backprop neural networks mnist cifar VGG date: 02-15-2019 03:15 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

Training neural networks with local error signals

  • Arild Nokland and Lars H Eidnes
  • Idea is to use one+ supplementary neural networks to measure within-batch matching loss between transformed hidden-layer output and one-hot label data to produce layer-local learning signals (gradients) for improving local representation.
  • Hence, no backprop. Error signals are all local, and inter-layer dependencies are not explicitly accounted for (! I think).
  • L simL_{sim} : given a mini-batch of hidden layer activations H=(h 1,...,h n)H = (h_1, ..., h_n) and a one-hot encoded label matrix Y=(y 1,...,y nY = (y_1, ..., y_n ,
    • L sim=||S(NeuralNet(H))S(Y)|| F 2 L_{sim} = || S(NeuralNet(H)) - S(Y)||^2_F (don't know what F is..)
    • NeuralNet()NeuralNet() is a convolutional neural net (trained how?) 3*3, stride 1, reduces output to 2.
    • S()S() is the cosine similarity matrix, or correlation matrix, of a mini-batch.
  • L pred=CrossEntropy(Y,W TH)L_{pred} = CrossEntropy(Y, W^T H) where W is a weight matrix, dim hidden_size * n_classes.
    • Cross-entropy is H(Y,W TH)=Σ i,jY i,jlog((W TH) i,j)+(1Y i,j)log(1(W TH) i,j) H(Y, W^T H) = \Sigma_{i,j} Y_{i,j} log((W^T H)_{i,j}) + (1-Y_{i,j}) log(1-(W^T H)_{i,j})
  • Sim-bio loss: replace NeuralNet()NeuralNet() with average-pooling and standard-deviation op. Plus one-hot target is replaced with a random transformation of the same target vector.
  • Overall loss 99% L simL_sim , 1% L predL_pred
    • Despite the unequal weighting, both seem to improve test prediction on all examples.
  • VGG like network, with dropout and cutout (blacking out square regions of input space), batch size 128.
  • Tested on all the relevant datasets: MNIST, Fashion-MNIST, Kuzushiji-MNIST, CIFAR-10, CIFAR-100, STL-10, SVHN.
  • Pretty decent review of similarity matching measures at the beginning of the paper; not extensive but puts everything in context.
    • See for example non-negative matrix factorization using Hebbian and anti-Hebbian learning in and Chklovskii 2014.
  • Emphasis put on biologically realistic learning, including the use of feedback alignment {1423}
    • Yet: this was entirely supervised learning, as the labels were propagated back to each layer.
    • More likely that biology is setup to maximize available labels (not a new concept).

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ref: -0 tags: feedback alignment Arild Nokland MNIST CIFAR date: 02-14-2019 02:15 gmt revision:0 [head]

Direct Feedback alignment provides learning in deep neural nets

  • from {1423}
  • Feedback alignment is able to provide zero training error even in convolutional networks and very deep networks, completely without error back-propagation.
  • Biologically plausible: error signal is entirely local, no symmetric or reciprocal weights required.
    • Still, it requires supervision.
  • Almost as good as backprop!
  • Clearly written, easy to follow math.
    • Though the proof that feedback-alignment direction is within 90 deg of backprop is a bit impenetrable, needs some reorganization or additional exposition / annotation.
  • 3x400 tanh network tested on MNIST; performs similarly to backprop, if faster.
  • Also able to train very deep networks, on MNIST - CIFAR-10, CIFAR-100, 100 layers (which actually hurts this task).

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ref: -0 tags: superresolution imaging scanning lens nanoscale date: 02-04-2019 20:34 gmt revision:1 [0] [head]

PMID-27934860 Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging

  • Recently, the diffraction barrier has been surpassed by simply introducing dielectrics with a micro-scale spherical configuration when using conventional optical microscopes by transforming evanescent waves into propagating waves. 18,19,20,21,22,23,24,25,26,27,28,29,30
  • The resolution of this superlens-based microscopy has been decreased to ∼50 nm (ref. 26) from an initial resolution of ∼200 nm (ref. 21).
  • This method can be further enhanced to ∼25 nm when coupled with a scanning laser confocal microscope 31.
  • It has achieved fast development in biological applications, as the sub-diffraction-limited resolution of high-index liquid-immersed microspheres has now been demonstrated23,32, enabling its application in the aqueous environment required to maintain biological activity.
  • Microlens is a 57 um diameter BaTiO3 microsphere, resolution of lambda / 6.3 under partial and inclined illumination
  • Microshpere is in contact with the surface during imaging, by gluing it to the cantilever tip of an AFM.
  • Get an image with the microsphere-lens, which improves imaging performance by ~ 200x. (with a loss in quality, naturally).

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ref: -0 tags: insertion speed needle neural electrodes force damage injury cassanova date: 06-01-2018 23:51 gmt revision:0 [head]

Effect of Needle Insertion Speed on Tissue Injury, Stress, and Backflow Distribution for Convection-Enhanced Delivery in the Rat Brain

  • Tissue damage, evaluated as the size of the hole left by the needle after retraction, bleeding, and tissue fracturing, was found to increase for increasing insertion speeds and was higher within white matter regions.
    • A statistically significant difference in hole areas with respect to insertion speed was found.
  • While there are no previous needle insertion speed studies with which to directly compare, previous electrode insertion studies have noted greater brain surface dimpling and insertion forces with increasing insertion speed [43–45]. These higher deformation and force measures may indicate greater brain tissue damage which is in agreement with the present study.
  • There are also studies which have found that fast insertion of sharp tip electrodes produced less blood vessel rupture and bleeding [28,29].
    • These differences in rate dependent damage may be due to differences in tip geometry (diameter and tip) or tissue region, since these electrode studies focus mainly on the cortex [28,29].
    • In the present study, hole measurements were small in the cortex, and no substantial bleeding was observed in the cortex except when it was produced during dura mater removal.
    • Any hemorrhage was observed primarily in white matter regions of the external capsule and the CPu.

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ref: -2015 tags: ice charles lieber silicon nanowire probes su-8 microwire extracellular date: 05-30-2018 23:40 gmt revision:3 [2] [1] [0] [head]

PMID-26436341 Three-dimensional macroporous nanoelectronic networks as minimally invasive brain probes.

  • Xie C1, Liu J1, Fu TM1, Dai X1, Zhou W1, Lieber CM1,2.
  • Again, use silicon nanowire transistors as sensing elements. These seem rather good; can increase the signal, and do not suffer from shunt resistance / capacitance like wires.
    • They're getting a lot of mileage out of the technology; initial pub back in 2006.
  • Su-8, Cr/Pd/Cr (stress elements) and Cr/Au/Cr (conductor) spontaneously rolled into a ball, then the froze in LN2. Devices seemed robust to freezing in LN2.
  • 300-500nm Su-8 passivation layers, as with the syringe injectable electrodes.
  • 3um trace / 7um insulation (better than us!)
  • Used 100nm Ni release layer; thin / stiff enough Su-8 with rigid Si support chip permitted wirebonding a connector (!!)
    • Might want to use this as well for our electrodes -- of course, then we'd have to use the dicing saw, and free-etch away a Ni (or Al?) polyimide adhesion layer -- or use Su-8 like them. See figure S-4
  • See also {1352}

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ref: Salcman-1973.07 tags: Salcman MEA microelectrodes chronic recording glass cyanocrylate date: 12-29-2017 04:33 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-4708761 Design, Fabrication, and In Vivo Behavior of Chronic Recording Intracortical Microelectrodes

  • Teflon-coated 25um Pt-Ir (90/10)
  • Heat fuse this with a glass micropipette & backfill with cyanoacrylate. {1011}
    • Isobutyl acrylate is hydrolysed more slowly and hence is less toxic to the surronding tissue
    • cyanoacrylate is apparently biodegradable.
  • Durable, stable: one electrode displayed a single cortical spike (though not necessarily the same one) for more than 90 consecutive days.
  • unacceptably low impedance = 100K or less
  • Unit activity was present only 10-24H after surgery.
  • formal review of even older microelectrode studies.
  • 10nA should be 100x too small to have any effect on a platinum tip [17]
  • A seperable cell with a SNR of 3:1 would become lost if the electrode tip moved 15um away from a 20um soma.
    • "It becomes clear that the problem of holding single units for prolonged periods in the unrestrained animal is not achieved without considerable difficulty". Yet they think they have solved it.


Salcman, Michael and Bak, Martin J. Design, Fabrication, and In Vivo Behavior of Chronic Recording Intracortical Microelectrodes Biomedical Engineering, IEEE Transactions on BME-20 4 253 -260 (1973)

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ref: -0 tags: robinson pasquali carbon nanotube fiber fluidic injection dextran neural electrode date: 12-28-2017 04:20 gmt revision:0 [head]

PMID-29220192 Fluidic Microactuation of Flexible Electrodes for Neural Recording.

  • Use viscous dextran solution + PDMS channel system
  • Durotomy (of course)
  • Parylene-C insulated carbon fiber electrodes, cut with FIB or razor blade
  • Used silver ink to electrically / mechanically attach for recordings.
  • Tested in hydra, rat brain slice (reticular formation of thalamus), and in-vivo rat.
  • Electrodes, at 12um diameter, E=120GPa, are approximately 127x stiffer than one 4x20um PI (E=9GPa) probe. Less damage though.

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ref: -0 tags: Lieber nanoFET review silicon neural recording intracellular date: 12-28-2017 04:04 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-23451719 Synthetic Nanoelectronic Probes for Biological Cells and Tissue

  • Review of nanowireFETS for biological sensing
  • Silicon nanowires can be grown via vapor-liquid-solid or vapor-solid-solid, 1D catalyzed growth, usually with a Au nanoparticle.
  • Interestingly, kinks can be introduced via "iterative control over nucleation and growth", 'allowing the synthesis of complex 2D and 3D structures akin to organic chemistry"
    • Doping can similarly be introduced in highly localized areas.
    • This bottom-up synthesis is adaptable to flexible and organic substrates.
  • Initial tests used polylysine patterning to encourage axonal and dendritic growth across a nanoFET.
    • Positively charged amino group interacts with negative surface charge phospholipid
    • Lieber's group coats their SU-8 electrodes in poly-d-lysine as well {1352}
  • Have tested multiple configurations of the nanowire FET, including kinked, one with a SiO2 nanopipette channel for integration with the cell membrane, and one where the cell-attached fluid membrane functions as the semiconductor; see figure 4.
    • Were able to show recordings as one of the electrodes was endovascularized.
  • It's not entirely clear how stable and scalable these are; Si and SiO2 gradually dissolve in physiological fluid, and no mention was made of longevity.

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ref: -0 tags: computational biology evolution metabolic networks andreas wagner genotype phenotype network date: 06-12-2017 19:35 gmt revision:1 [0] [head]

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

  • ‘’João F. Matias Rodrigues, Andreas Wagner ‘’
  • Our observations suggest that the robustness of the Escherichia coli metabolic network to mutations is typical of networks with the same phenotype.
  • We demonstrate that networks with the same phenotype form large sets that can be traversed through single mutations, and that single mutations of different genotypes with the same phenotype can yield very different novel phenotypes
  • Entirely computational study.
    • Examines what is possible given known metabolic building-blocks.
  • Methodology: collated a list of all metabolic reactions in E. Coli (726 reactions, excluding 205 transport reactions) out of 5870 possible reactions.
    • Then ran random-walk mutation experiments to see where the genotype + phenotype could move. Each point in the genotype had to be viable on either a rich (many carbon source) or minimal (glucose) growth medium.
    • Viability was determined by Flux-balance analysis (FBA).
      • In our work we use a set of biochemical precursors from E. coli 47-49 as the set of required compounds a network needs to synthesize, ‘’’by using linear programming to optimize the flux through a specific objective function’’’, in this case the reaction representing the production of biomass precursors we are able to know if a specific metabolic network is able to synthesize the precursors or not.
      • Used Coin-OR and Ilog to optimize the metabolic concentrations (I think?) per given network.
    • This included the ability to synthesize all required precursor biomolecules; see supplementary information.
    • ‘’’“Viable” is highly permissive -- non-zero biomolecule concentration using FBA and linear programming. ‘’’
    • Genomic distances = hamming distance between binary vectors, where 1 = enzyme / reaction possible; 0 = mutated off; 0 = identical genotype, 1 = completely different genotype.
  • Between pairs of viable genetic-metabolic networks, only a minority (30 - 40%) of reactions are essential,
    • Which naturally increases with increasing carbon source diversity:
    • When they go back an examine networks that can sustain life on any of (up to) 60 carbon sources, and again measure the distance from the original E. Coli genome, they find this added robustness does not significantly constrain network architecture.

Summary thoughts: This is a highly interesting study, insofar that the authors show substantial support for their hypotheses that phenotypes can be explored through random-walk non-lethal mutations of the genotype, and this is somewhat invariant to the source of carbon for known biochemical reactions. What gives me pause is the use of linear programming / optimization when setting the relative concentrations of biomolecules, and the permissive criteria for accepting these networks; real life (I would imagine) is far more constrained. Relative and absolute concentrations matter.

Still, the study does reflect some robustness. I suggest that a good control would be to ‘fuzz’ the list of available reactions based on statistical criteria, and see if the results still hold. Then, go back and make the reactions un-biological or less networked, and see if this destroys the measured degrees of robustness.

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ref: Schmidt-1993.11 tags: Normann utah array histology silicon electrode array cats date: 02-23-2017 22:03 gmt revision:4 [3] [2] [1] [0] [head]

PMID-8263001[0] Biocompatibility of silicon-based electrode arrays implanted in feline cortical tissue.

  • Tried two different times:
    • one day before euthanasia
    • 6 month implant.
  • Tried three different implants:
    • Uncoated silicon,
    • polymide coating
    • polymide coating with SiO2 adhesion layer / primer.
  • The last was the worst in terms of histopathological response.
  • Chronic implants showed relatively restrained immune response,
    • Gliosis was found around all tracks, 20-40um.
  • Encapsulation was less than 9um.
  • Edema and hemorrhage was minor but present on a subset of all implants.
  • Acute (24h) hemorrhage was more severe -- ~ 60%; edema ~ 20%.
  • Chronic histology revealed considerable macrophages w/ hemosiderin (a complex including ferritin)
  • See also [1]


[0] Schmidt S, Horch K, Normann R, Biocompatibility of silicon-based electrode arrays implanted in feline cortical tissue.J Biomed Mater Res 27:11, 1393-9 (1993 Nov)
[1] Jones KE, Campbell PK, Normann RA, A glass/silicon composite intracortical electrode array.Ann Biomed Eng 20:4, 423-37 (1992)

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ref: -0 tags: carbon nanotube densification conductivity strength date: 02-23-2017 02:52 gmt revision:2 [1] [0] [head]

Super-strong and highly conductive carbon nanotube ribbons from post-treatment methods

  • Conductivity of 1.2e6 S/m, about that of stainless steel.
    • 500 x 500nm wire, length 1cm will have a resistance of 40k.
  • Aerogel method: methane + ferrocene + thiophene + hydrogen.
    • Resulting in ~ 18% Fe, multi-walled carbon nanotubes, diameter 15nm, 15-20 walls.
  • Densified with a stainless-steel spatula on regular paper.
    • Resulting in ribbons 22um wide, 650nm thick.
  • Very high tensile strength, up to 5.2 GPa; moduls ~ 266 GPa.

High-strength carbon nanotube fibre-like ribbon with high ductility and high electrical conductivity

  • Slightly higher conductivity, 1.82 - 2.24e6 S/m.
  • Rolled until it was 500nm thick!
  • Spun from an aerogel (!!) using ethanol + ferrocent + thiophene.

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ref: -0 tags: iridium oxide nanotube intracellular recording electroplate MEA date: 02-22-2017 22:41 gmt revision:0 [head]

PMID-24487777 Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials.

  • Electrodeposition of IrOx "magically" forms 500nm tubes.
  • Holes in Si3N4 / SiO2 were formed via e-beam lithography; underlying Pt wires via liftoff.
  • Showed long (minutes) intracellular access, though it tended to dip with time.

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ref: -0 tags: carbon fiber thread spinning Pasquali Kemere nanotube stimulation date: 02-09-2017 01:09 gmt revision:0 [head]

PMID-25803728 Neural stimulation and recording with bidirectional, soft carbon nanotube fiber microelectrodes.

  • Poulin et al. demonstrated that microelectrodes made solely of CNT fibers22 show remarkable electrochemical activity, sensitivity, and resistance to biofouling compared to conventional carbon fibers when used for bioanalyte detection in vitro.23-25
  • Fibers were insulated with 3 um of block copolymer polystyrene-polybutadiene (PS-b-PBD) (polybutadiene is sythetic rubber)
    • Selected for good properties of biocompatibility, flexibility, resistance to flextural fatigue.
    • Available from Sigma-Aldrich.
    • Custom continuous dip-coating process.
  • 18um diameter, 15 - 20 x lower impedance than equivalently size PtIr.
    • 2.5 - 6x lower than W.
    • In practice, 43um dia, 1450um^2, impedance of 11.2 k; 12.6um, 151k.
  • Charge storage capacity 327 mC / cm^2; PtIr = 1.2 mC/cm^2
  • Wide water window of -1.5V - 1.5V, consistent with noble electrochemical properties of C.
  • Lasts for over 97e6 pulsing cycles beyond the water window, vs 43e6 for PEDOT.
  • Tested via 6-OHDA model of PD disease vs. standard PtIr stimulating electrodes, implanted via 100um PI shuttled attached with PEG.
  • Yes, debatable...
  • Tested out to 3 weeks durability. Appear to function as well or better than metal electrodes.

PMID-23307737 Strong, light, multifunctional fibers of carbon nanotubes with ultrahigh conductivity.

  • Full process:
    1. Dissolve high-quality, 5um long CNT in chlorosulfonic acid (the only known solvent for CNTs)
    2. Filter to remove particles
    3. Extrude liquid crystal dope through a spinneret, 65 or 130um orifice
    4. Into a coagulant, acetone or water
    5. Onto a rotating drum to put tension on the thread & align the CNTs.
    6. Wash in water and dry at 115C.
  • Properties:
    • Tensile strength 1 GPa +- 0.2 GPa.
    • Tensile modulus 120 GPa +- 50, best value 200 GPa
      • Pt: 168 GPa ; Au: 79 GPa.
    • Elongation to break 1.4 %
    • Conductivity: 0.3 MS/m, Iodine doped 5 +- 0.5 MS/m (22 +- 4 microhm cm)
      • Cu: 59.6 MS/m ; Pt: 9.4 MS/m ; Au: 41 MS/m
      • Electrical conductivity drops after annealing @ 600C
      • But does not drop after kinking and repeated mechanical cycling.
  • Theoretical modulus of MWCNT ~ 350 GPa.
  • Fibers well-aligned at ~ 90% the density (measure 1.3 g/cc) of close-packed CNT.

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ref: -0 tags: nanoprobe transmembrane intracellular thiol gold AFM juxtacellular date: 02-06-2017 23:45 gmt revision:3 [2] [1] [0] [head]

PMID-20212151 Fusion of biomimetic stealth probes into lipid bilayer cores

  • Used e-beam evaporation of Cr/Au/Cr 10/10/10 or 10/5/10 onto a Si AFM tip.
    • Approx 200nm diameter; 1800 lipid interaction at the circumference.
  • Exposed the Au in the sandwich via FIB
  • Functionalized the Au with butanethiol or dodecanthiol; former is mobile on the surface, latter is polycrystaline.
    • Butanethiol showed higher adhesion to the synthetic membranes
  • Measured the penetration force & displacement through synthetic multi-layer lipid bilayers.
    • These were made via a custom protocol with 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC) and cholesterol

PMID-21469728 '''Molecular Structure Influences the Stability of Membrane Penetrating Biointerfaces.

  • Surprisingly, hydrophobicity is found to be a secondary factor with monolayer crystallinity the major determinate of interface strength
  • Previous studies using ellipsometry and IR spectroscopy have shown that alkanethiol self-assembled monolayers display an abrupt transition from a fluid to a crystalline phase between hexanethiol and octanethiol.
    • This suggests the weakening of the membrane stealth probe interface is due to the crystallinity of the molecular surface with fluid, disordered monolayers promoting a high strength interface regime and rigid, crystalline SAMs forming weak interfaces.

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ref: -0 tags: nanopore membrane nanostraws melosh surface adhesion intracellular date: 02-06-2017 23:34 gmt revision:0 [head]

PMID-22166016 Nanostraws for Direct Fluidic Intracellular Access

  1. Used track-etched polycarbonate membranes, which have controlled pore density & ID.
  2. Deposited alumina on the pores & external surfaces using ALD
  3. Then etched away the top alumina
  4. and finally used O2 RIE to etch away the polycarbonate.
  • Show that these nanopores have cytosolic access (via Fluor 488 - hydrazide membrane impermeant dye
  • Also used nanostraws to deliver Co+2 to quench GFP fluorescence.

PMID-24710350, Quantification of nanowire penetration into living cells.

  • We discover that penetration is a rare event: 7.1±2.7% of the nanostraws penetrate the cell to provide cytosolic access for an extended period for an average of 10.7±5.8 penetrations per cell.
  • Using time-resolved delivery, the kinetics of the first penetration event are shown to be adhesion dependent and coincident with recruitment of focal adhesion-associated proteins.
    • Hours for unmodified, 5 minutes for adhesion-promoting surface.
  • Chinese hamster oviary cells expressing GFP, Co+2 quenching, EDTA chelation.
  • To modulate cell adhesion, nanostraw substrates were incubated in 10 μg ml−1 fibronectin, a well-characterized cell adhesion molecule, in addition to the standard polyornithine coating.

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ref: -0 tags: intracellular juxtacellular recording tungsten nanowire whole cell patch date: 02-06-2017 22:39 gmt revision:2 [1] [0] [head]

PMID-22905231 Neuronal recordings with solid-conductor intracellular nanoelectrodes (SCINEs).

  • <300 nm diameter W fibers, several um long, fabricated via FIB.
  • Functionalized with a hydrophobic silane on the oxide.
    • Quite complete & custom methods here.
  • Not quite whole cell recording, but excellent SNR; 4mv APs.
    • Slice, rat hippocampus organotypic.
    • Expected much larger recorded APs; suspect partial membrane penetration.
    • Only lasted a few seconds to minutes.
  • Needed custom recording setup for interfacing with 100Gohm electrodes; stray capacitance < 4 pf.
  • Intracellular electrodes must be designed to not shunt the membrane open upon insertion.
    • In a study where whole-cell recordings were established prior sharp microelectrode penetration, all neurons showed significant depolarization following impalement.
    • Here there was no change in membrane voltage in 10% of insertions of the silane-functionalized SCINEs. only in the functionalized electrodes).
    • Minor distortion of the AP was observed.
  • In whole-cell patch clamping, diffusion from the pipette to the cytosol interrupts biochemical processes necessary for normal cellular function (e.g. respiration!).
  • The hardness of the tungsten ensures that SCINEs can be repeatedly inserted millimeter-deep into brain tissue without noticeable damage to the tip.
    • E.g. 300 nm tungsten will not easily navigate vasculature...

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ref: -0 tags: nanotube tracking extracellular space fluorescent date: 02-02-2017 22:13 gmt revision:0 [head]

PMID-27870840 Single-nanotube tracking reveals the nanoscale organization of the extracellular space in the live brain

  • Extracellular space (ECS) takes up nearly a quarter the volume of the brain (!!!)
  • Used the intrinsic fluorescence of single-walled carbon nanotubes @ 1um, 845nm excitation, with super-resolution tracking of diffusion.
    • Were coated in phospholipid-polyethylene glycol (PL-PEG), which display low cytotoxicity compared to other encapsulants.
  • 5ul, 3ug/ml injected into the ventricles of young rats; allowed to diffuse for 30 minutes post-injection.
  • No apparent response of the microglia.
  • Diffusion tracking revealed substantial dead-space domains in the ECS.
    • As compared to patch-clamp loaded SWCNTs
  • Estimate from parallel and perpendicular diffusion rates that the characteristic scale of ECS dimension is 80 to 270nm, or 150 +- 40nm.
  • The ECS nanoscale dimensions as visualized by tracking similar in dimension and tortuosity to electron microscopy.
  • Viscosity of the extracellular matrix from 1 to 50 mPa S, up to two orders of magnitude higher than the CSF.
  • Positive control through hyalurinase + several hours to digest the hyaluronic acid.
    • But no observed changes in morphology of the neurons via confocal .. interesting.
    • Enzyme digestion normalized the spatial heterogenaity of diffusion.

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ref: -0 tags: vertical nanowire juxtacellular recording date: 02-01-2017 00:50 gmt revision:2 [1] [0] [head]

PMID-22231664 Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.

  • Note actual coupling is low, 0.002, compared to patch-clamp (400uV vs 200mV). Signal is rather noisy.
  • Dissociated cultures of rat cortical neurons
  • Stimulation current 200 pa enough to change membrane potential, but not initiate a spike.
    • This is 200e-12 / 20e-6 = 5 orders of magnitude lower current than typical ICMS.

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ref: -0 tags: ultrasonic BMI monkey LFP intan nordic Ozturk UCSD date: 09-30-2016 19:38 gmt revision:2 [1] [0] [head]

A Wireless 32-Channel Implantable Bidirectional Brain Machine Interface

  • Yi Su 1,2,*, Sudhamayee Routhu 2, Kee S. Moon 3, Sung Q. Lee 4, WooSub Youm 4 and Yusuf Ozturk 2,
  • Only LFP from a utah array, but solid work none-the-less.
  • 20V unipolar stimulation.
    • Through separate recording and stimulation electrodes.
  • 35mm x 10mm.
  • LFP due to limited bandwidth.
    • Less RF bw & compression that the wireless system I designed 6 years ago.
    • Reason: "Further, in order to analyze the integrative synaptic processes, LFP is the signal of interest instead of spikes, because synaptic processes cannot be captured by spike activity of a small number of neurons"
captured by spike activity of a small number of neurons.
  • Reference use of DuraGen followed by silicone elastomer.
  • Didn't cite us.

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ref: -0 tags: planned economy red plenty date: 08-08-2016 05:54 gmt revision:0 [head]


  • Quote: "That planning is not a viable alternative to capitalism (as opposed to a tool within it) should disturb even capitalism’s most ardent partisans. It means that their system faces no competition, nor even any plausible threat of competition."
    • And therefore not only cannot be improved, but must degrade with time. But see below.
  • Quote: What we can do is try to find the specific ways in which these powers we have conjured up are hurting us, and use them to check each other, or deflect them into better paths. Sometimes this will mean more use of market mechanisms, sometimes it will mean removing some goods and services from market allocation, either through public provision or through other institutional arrangements. Sometimes it will mean expanding the scope of democratic decision-making (for instance, into the insides of firms), and sometimes it will mean narrowing its scope (for instance, not allowing the demos to censor speech it finds objectionable). Sometimes it will mean leaving some tasks to experts, deferring to the internal norms of their professions, and sometimes it will mean recognizing claims of expertise to be mere assertions of authority, to be resisted or countered.
    • I like to think of this as a very unstable equilibrium: the only way to maintain function is to continuously expend energy to shore up and change the market, politics, and society in general; the specific regulatory solution has complexity commensurate with the complexity of the economy regulated, and it must adapt on the same scales that the market economy changes.
    • Perhaps to do this, it needs a self-reflective faculty, to know which parts of itself need changing; otherwise, you'd need to have a regulator regulating the regulator, and who is to prevent that from agglomerating power. Yet this too is an unstable equilibrium.

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ref: -0 tags: concentation of monoamine dopamine serotonin and norepinephrine in the brain date: 04-28-2016 19:38 gmt revision:3 [2] [1] [0] [head]

What are the concentrations of the monoamines in the brain? (Purpose: estimate the required electrochemical sensing area & efficiency)

  • Dopamine: 100 uM - 1 mM local, extracellular.
    • PMID-17709119 The Yin and Yang of dopamine release: a new perspective.
  • Serotonin (5-HT): 100 ng/g, 0.5 uM, whole brain (not extracellular!).
  • Norepinephrine / noradrenaline: 400 nm/g, 2.4 uM, again whole brain.
    • PMID-11744005 An enriched environment increases noradrenaline concentration in the mouse brain.
    • Also has whole-brain extracts for DA and 5HT, roughly:
      • 1200 ng/g DA
      • 400 ng/g NE
      • 350 ng/g 5-HT
  • So, one could imagine ~100 uM transient concentrations for all 3 monoamines.

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ref: -0 tags: adhesion polymer metal FTIR epoxy eponol paint date: 05-01-2015 19:20 gmt revision:0 [head]

Degradation of polymer/substrate interfaces – an attenuated total reflection Fourier transform infrared spectroscopy approach

  • Suggests why eponol is used as an additive to paint.
  • In this thesis, attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy has been used to detect changes at the interfaces between poly (vinyl butyral-co-vinyl alcohol-co-vinyl acetate) (PVB) and ZnSe upon exposure to ozone, humidity and UV-B light.
  • Also, the response of PVB-aluminum interfaces to liquid water has been studied and compared with the same for eponol (epoxy resin, diglycidyl ether of bisphenol A)-aluminum interfaces.
  • In the presence of ozone, humidity and UV-B radiation, an increase in carbonyl group intensity was observed at the PVB-ZnSe interface indicating structural degradation of the polymer near the interface. However, such changes were not observed when PVB coated ZnSe samples were exposed to moisture and UV-B light in the absence of ozone showing that ozone is responsible for the observed structural deterioration. Liquid water uptake kinetics for the degraded PVB monitored using ATR-FTIR indicated a degradation of the physical structural organization of the polymer film.
  • Exposure of PVB coated aluminum thin film to de-ionized water showed water incorporation at the interface. There were evidences for polymer swelling, delamination and corrosion of the aluminum film under the polymer layer.
    • On the contrary, delamination/swelling of the polymer was not observed at the eponol-aluminum interface, although water was still found to be incorporated at the interface. Al-O species were also observed to form beneath the polymer layer.
    • A decrease of the C-H intensities was detected at the PVB-aluminum interface during the water uptake of the polymer, whereas an increase of the C-H intensities was observed for the eponol polymer under these conditions.
    • This is assigned to rearrangement of the macromolecular polymer chains upon interaction with water.

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ref: -0 tags: Kewame carbon nanotube yarn wet spinning CNT date: 03-26-2015 18:29 gmt revision:0 [head]

Neural Stimulation and Recording with Bidirectional, Soft Carbon Nanotube Fiber Microelectrodes

  • 43um diameter CTN yarn
  • Shows superior charge injection / surface area.
  • polystyrene-polybutadiene co-polymer insulation (like ABS, without the acrylonitrile)
  • https://chemistry.beloit.edu/classes/nanotech/CNT/nanotoday3_5_24.pdf -- details on the process of spinning these CNT yarns.
    • Tensile strength still far below commercial carbon fibers or high-strength polymers.

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ref: -0 tags: gold carbon nanotube electroplating impedance PEG date: 10-24-2014 22:25 gmt revision:1 [0] [head]

PMID-21379404 Creating low-impedance tetrodes by electroplating with additives

  • Electroplated tetrodes to 30-70 kΩ by adding polyethylene glycol (PEG) or multi-walled carbon nanotube (MWCNT) solutions to a commercial gold-plating solution.
  • Cui and Martin [12] showed that altering the concentration of gold-plating solution and electroplating current can change the morphology of a gold-plated microelectrode coating.
  • Additionally, Keefer et al. [13] found that adding multi-walled carbon nanotubes (MWCNTs) to a gold-plating solution created microelectrode coatings with a “rice-like” texture and very low impedances.
  • Au electroplating solution made of non-cyanide, gold-plating solution (5355, SIFCO Selective Plating, Cleveland, OH).
  • A one-second, reversed-polarity pulse helped to clean the surface of the tetrode tip and lowered the impedances to 2MΩ to 3 MΩ before electroplating.
  • Electroplating pulses were one to five seconds long and were repeated until the tetrodes reached the desired impedances. After electroplating, the tetrodes were soaked in DI, air dried, and checked for shorts.

Conclusion: 75% PEG, commercial electropating solution, 0.1ua current pluses to 250K or less.

  • Though the Caswell Au plating solution will likely behave differently ..

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ref: -0 tags: intracortical utah array fabrication MEMS Normann date: 08-14-2014 01:35 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-1937509 A silicon-based, three-dimensional neural interface: manufacturing processes for an intracortical electrode array.

  • Campbell PK1, Jones KE, Huber RJ, Horch KW, Normann RA. (1991)
  • One of (but not the) first papers describing their methods / idea (I think).
  • First conf paper: {1294} (1988)
  • later adopted glass frit insulator --

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ref: -0 tags: utah array development failure mode donoghue date: 08-14-2014 01:30 gmt revision:0 [head]

PMID-24216311 Failure mode analysis of silicon-based intracortical microelectrode arrays in non-human primates

  • Barrese JC, Rao N, Paroo K, Triebwasser C, Vargas-Irwin C, Franquemont L, Donoghue JP. (2013)
  • Most failures (56%) occurred within a year of implantation, with acute mechanical failures the most common class (48%), largely because of connector issues (83%).
  • Among grossly observable biological failures (24%), a progressive meningeal reaction that separated the array from the parenchyma was most prevalent (14.5%).

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ref: -0 tags: polyimide anodic release 2005 date: 06-16-2014 23:58 gmt revision:1 [0] [head]

IEEE-1416914 (pdf) Partial release and detachment of microfabricated metal and polymer structures by anodic metal dissolution

  • recommend 100nm Cr/Al release layer.
  • finished devices just 'float to the surface' of saline solution.

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ref: -0 tags: noise triboelectric implant BMI date: 05-16-2014 17:28 gmt revision:1 [0] [head]

source -- Durand

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ref: -0 tags: stretchable nanoparticle conductors gold polyurethane flocculation date: 12-13-2013 02:12 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-23863931 Stretchable nanoparticle conductors with self-organized conductive pathways.

  • 13nm gold nanoparticles, citrate-stabilized colloidal solution
    • Details of fabrication procedure in methods & supp. materials.
  • Films are prepared in water and dried (like paint)
  • LBL = layer by layer. layer of polyurethane + layer of gold nanoparticles.
    • Order of magnitude higher conductivity than the
  • VAF = vacuum assisted floculation.
    • Mix Au-citrate nanoparticles + polyurethane and pass through filter paper.
    • Peel the flocculant from the filter paper & dry.
  • Conductivity of the LBL films ~ 1e4 S/cm -> 1e-6 Ohm*m (pure gold = 2 x 10-8, 50 x better)
  • VAF = 1e3 S/cm -> 1e-5 Ohm*m. Still pretty good.
    • This equates to a resistance of 1k / mm in a 10um^2 cross-sectional area wire (2um x 5 um, e.g.)
  • The material can sustain > 100% strain when thermo-laminated.
    • Laminated: 120C at 20 MPa for 1 hour.
  • See also: Preparation of highly conductive gold patterns on polyimide via shaking-assisted layer-by-layer deposition of gold nanoparticles
    • Patterned via MCP -- microcontact printing(aka rubber-stamping)
    • Bulk conductivity of annealed (150C) films near that of pure gold (?)
    • No mechanical properties, though; unlcear if these films are more flexible / ductile than evaporated film.

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ref: -0 tags: Kozai carbon nanotube electrode rcording histology date: 08-02-2013 05:42 gmt revision:1 [0] [head]

PMID-23142839 Ultrasmall implantable composite microelectrodes with bioactive surfaces for chronic neural interfaces.

  • Here, we report the development of an integrated composite electrode consisting of a carbon-fibre core, a poly(p-xylylene)-based thin-film coating that acts as a dielectric barrier and that is functionalized to control intrinsic biological processes, and a poly(thiophene)-based recording pad.
  • 7um diameter carbon nanotubes slide easily into cortex & yield good recording.
  • only 0.8um of parlyene-N coating.
    • Does it stick well? Does it crack?
  • Functionalized the parylene with 50nm of bromine / oxygen complex, bromoisobutyrate.
  • PEDOT recording surface drastically lowered impedance.
  • Difficult to assemble these little buggers!

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ref: -0 tags: polyimide platinum nanowire recording electrode plating date: 06-28-2013 00:46 gmt revision:2 [1] [0] [head]

IEEE-5734597 (pdf) A novel platinum nanowire-coated neural electrode and its electrochemical and biological characterization

  • Young-Hyun Jin ; IMTEK, Univ. of Freiburg, Freiburg, Germany ; Daubinger, P. ; Fiebich, B.L. ; Stieglitz, T.
  • 10um thick RIE etched polyimide and platinum electrodes.
  • polyimide was spin coated onto wafers.
  • Used relatively simple wet chemistry to plate platinum onto electrodes:
    • 0.14 M-% chloroplatin acid hexahydrate (H2PtCl6·6H2O, Sigma-Aldrich) and 7.4 M-% formic acid (HCOOH, Sigma-Aldrich) were mixed in de-ionized (DI) water. The fabricated device was floated upside down on the solution.
  • Let this plate for 7 days & effective site was enlarged by 617 times!

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

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

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

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

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

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

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

PMID-23514423 Nanotools for Neuroscience and Brain Activity Mapping

  • human brain has roughly 85e9 neurons, 1e14 synapses, 100 neurotransmitters.
  • focus on novel nanoprobes.
  • Assuming a uniform connaction probability, the lielihood of finding synaptically coupled cells increases quadratically with N.
  • pretty high-level article.
  • Multiferroic antennas (?) -- must look this up!
  • Look up ref 146 -- microendoscope. Did they design the camera module?

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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: Leung-2008.08 tags: biocompatibility alginate tissue response immunochemistry microglia insulation spin coating Tresco recording histology MEA date: 01-28-2013 21:19 gmt revision:4 [3] [2] [1] [0] [head]

PMID-18485471[0] Characterization of microglial attachment and cytokine release on biomaterials of differing surface chemistry

  • The important result is that materials with low protein-binding (e.g. alginate) have fewer bound microglia, hence better biocompatibility. It also seems to help if the material is highly hydrophilic.
    • Yes alginate is made from algae.
  • Used Michigan probes for implantation.
  • ED1 = pan-macrophage marker.
    • (quote:) Quantification of cells on the surface indicated that the number of adherent microglia appeared higher on the smooth side of the electrode compared to the grooved, recording site side (Fig. 2B), and declined with time. However, at no point were electrodes completely free of attached and activated microglial cells nor did these cells disappear from the interfacial zone along the electrode tract.
    • but these were not coated with anything new .. ???


[0] Leung BK, Biran R, Underwood CJ, Tresco PA, Characterization of microglial attachment and cytokine release on biomaterials of differing surface chemistry.Biomaterials 29:23, 3289-97 (2008 Aug)

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ref: Chestek-2011.08 tags: shenoy Utah array reliability recording BMI date: 01-28-2013 20:54 gmt revision:2 [1] [0] [head]

PMID-21775782[0] Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex (Shenoy)

  • Overall, this study suggests that action potential amplitude declines more slowly than previously supposed, and performance can be maintained over the course of multiple years when decoding from threshold-crossing events rather than isolated action potentials.
  • During most time periods, decoder performance was not well correlated with action potential amplitude (p > 0.05 for three of four arrays)
    • Perhaps we are chasing the wrong dragon?
    • Still, minimal invasiveness / more channels is useful.


[0] Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV, Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex.J Neural Eng 8:4, 045005 (2011 Aug)

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ref: Stevenson-2011.02 tags: Kording neural recording doubling northwestern chicago date: 01-28-2013 00:12 gmt revision:1 [0] [head]

PMID-21270781[0] How advances in neural recording affect data analysis.

  • Number of recorded channels doubles about every 7 years (slowish).
  • "Emerging data analysis techniques should consider both the computational costs and the potential for more accurate models associated with this exponential growth of the number of recorded neurons."


[0] Stevenson IH, Kording KP, How advances in neural recording affect data analysis.Nat Neurosci 14:2, 139-42 (2011 Feb)

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ref: Harris-1998.08 tags: noise wolpert harris motor planning Fitt velocity variance control theory date: 01-27-2013 22:33 gmt revision:1 [0] [head]

PMID-9723616[0] Signal-dependent noise determines motor planning.

  • We present a unifying theory of eye and arm movements based on the single physiological assumption that the neural control signals are corrupted by noise whose variance increases with the size of the control signal
    • Poisson noise? (I have not read the article -- storing here for future reference.)
  • This minimum-variance theory accurately predicts the trajectories of both saccades and arm movements and the speed-accuracy trade-off described by Fitt's law.


[0] Harris CM, Wolpert DM, Signal-dependent noise determines motor planning.Nature 394:6695, 780-4 (1998 Aug 20)

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ref: Harris-2011.08 tags: microelectrodes nanocomposite immune response glia recording MEA date: 01-27-2013 22:19 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-21654037[0] In vivo deployment of mechanically adaptive nanocomposites for intracortical microelectrodes

  • J P Harris, A E Hess, S J Rowan, C Weder, C A Zorman, D J Tyler and J R Capadona Case Western University.
  • Simple idea: electrodes should be rigid enough to penetrate the brain, yet soft enough to not damage it once implanted.
  • Many studies have shown that shear stress around a microelectrode shaft causes neural die-off and glial response.
  • You can only record from neurons if they are < 100um from the electrode tip.
  • Nanocomposite material is inspired by sea cucumber skin.
    • Our materials exhibit this behaviour by mimicking the architecture and proposed switching mechanism at play in the sea cucumber dermis by utilizing a polymer NC consisting of a controllable structural scaffold of rigid cellulose nanofibres embedded within a soft polymeric matrix. When the nanofibres percolate, they interact with each other through hydrogen bonding and form a nanofibre network that becomes the load-bearing element, leading to a high overall stiffness of the NC. When combined with a polymer system which additionally undergoes a phase transition at physiologically relevant temperatures, a contrast of over two orders of magnitude for the tensile elastic modulus is exhibited.
  • Probes were 200um wide, 100um thick, and had a point sharpened to 45deg.
  • Buckle force testing was done on 53um thick, 125um wide probes sharpened to a 30deg point.
  • Penetration stress through the rat pia is 1.2e7 dynes/cm^2 for a Si probe 40um thick and 80um wide.
  • See also {1198}


[0] Harris JP, Hess AE, Rowan SJ, Weder C, Zorman CA, Tyler DJ, Capadona JR, In vivo deployment of mechanically adaptive nanocomposites for intracortical microelectrodes.J Neural Eng 8:4, 046010 (2011 Aug)

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ref: -0 tags: Shenoy eye position BMI performance monitoring date: 01-25-2013 00:41 gmt revision:1 [0] [head]

PMID-18303802 Cortical neural prosthesis performance improves when eye position is monitored.

  • This proposal stems from recent discoveries that the direction of gaze influences neural activity in several areas that are commonly targeted for electrode implantation in neural prosthetics.
  • Can estimate eye position directly from neural activity & subtract it when performing BMI predictions.

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ref: Narayanan-2005.04 tags: BMI reliability noise Laubach Yale synergy date: 01-23-2013 20:50 gmt revision:1 [0] [head]

PMID-15858046[0] Redundancy and synergy of neuronal ensembles in motor cortex.

  • Reaction time task.
  • Neurons that were the best individual predictors of task performance were not necessarily the neurons that contributed the most predictive information to an ensemble of neurons.
  • Small ensembles [of neurons] could exhibit synergistic interactions (e.g., 23 +/- 9% of ensembles with two neurons were synergistic).
  • In contrast, larger ensembles exhibited mostly redundant interactions (e.g., 99 +/- 0.1% of ensembles with eight neurons were redundant).
  • Possible interpretation: redundancy enables robustness.


[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: Hochberg-2006.07 tags: BMI Donoghue Utah probe Nature tetraplegia Hochberg 2006 date: 01-23-2013 18:49 gmt revision:4 [3] [2] [1] [0] [head]

PMID-16838014[] Neuronal ensemble control of prosthetic devices by a human with tetraplegia

  • patient was able to talk?
  • 96-channel microelectrode array implanted in arm/hand knob or right precentral gyrus.
  • around 30 units / day observed.
  • 90% of units showed significantly varied firing rates (K-S test) during imagined movements.
  • 2D control. Good pursuit tracking and center-out performance.
  • Used Wiener filter.
  • also see the technology review


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ref: Chestek-2009.09 tags: BMI problems address critique spike sorting Shenoy date: 01-23-2013 02:23 gmt revision:3 [2] [1] [0] [head]

IEEE-5332822 (pdf) Neural prosthetic systems: Current problems and future directions

  • Where there is unlikely to be improvements: spike sorting and spiking models.
  • Where there are likely to be dramatic improvements: non-stationarity of recorded waveforms, limitations of a linear mappings between neural activity and movement kinematics, and the low signal to noise ratio of the neural data.
  • Compare different sorting methods: threshold, single unit, multiunit, relative to decoding.
  • Plot waveform changes over an hour -- this contrasts with earlier work (?) {1032}
  • Figure 5: there is no obvious linear transform between neural activity and the kinematic parameters.
  • Suggest that linear models need to be replaced by the literature of how primates actually make reaches.
  • Discuss that offline performance is not at all the same as online; in the latter the user can learn and adapt on the fly!


Chestek, C.A. and Cunningham, J.P. and Gilja, V. and Nuyujukian, P. and Ryu, S.I. and Shenoy, K.V. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE 3369 -3375 (2009)

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ref: -0 tags: neural imaging recording shot noise redshirt date: 01-02-2013 02:20 gmt revision:0 [head]


  • Shot Noise: The limit of accuracy with which light can be measured is set by the shot noise arising from the statistical nature of photon emission and detection.
    • If an ideal light source emits an average of N photons/ms, the RMS deviation in the number emitted is N\sqrt N .
    • At high intensities this ratio NN\frac{N}{\sqrt N} is large and thus small changes in intensity can be detected. For example, at 10^10 photons/ms a fractional intensity change of 0.1% can be measured with a signal-to-noise ratio of 100.
    • On the other hand, at low intensities this ratio of intensity divided by noise is small and only large signals can be detected. For example, at 10^4 photons/msec the same fractional change of 0.1% can be measured with a signal-to-noise ratio of 1 only after averaging 100 trials.

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ref: -0 tags: git notes date: 08-22-2012 22:28 gmt revision:3 [2] [1] [0] [head]

This from: http://www.youtube.com/watch?v=ZDR433b0HJY also: http://gitref.org/

Useful commands.

git config --global user.name "Tim Hanson"
git config --global user.email "err@gmail.com"
git config --global color.ui true
git clone https://github.com/tlh24/sabes-exp-ctrl.git
	Clone our experimental control repository. 
	Piggbacks on ssh. 
git status
	Review changed files. 
git commit -am "message" 
	Add all changed files to the local database 
	basically the same as svn ci
git checkout -b 'label1' 'label2'
	Creates a new branch called 'label1' from the branch 'label2'
git push origin 'label'
	Push local commits to origin (in htis case github) for the master branch. 
	Does *not* do merging. 
git merge 'label'
	merge the present branch with branch 'label'
	You can merge multiple times, efficiently -- perfect for different lab setups. 

Full list:

git init
git clone https://github.com/tlh24/sabes-exp-ctrl.git
	Clone our experimental control repository. 
	Piggbacks on ssh. 
git add .
	Stages changes for all files in the current directory.
git add -p
	Add files in sections -- in case you don't want to add all changes in a file.
git add <resolved file>
	Commit changes / conflict resolved file (after a merge)
git status
	Review changed files. 
git commit -m "message"
	(commits changes to local database)
git commit -am "message" 
	Add all changed files to the local database 
	basically the same as svn ci
git log
	Examine the current branch's log
git log --oneline 'label'
	Simplified log for branch 'label'. 
git log master ^origin/master
	Show the changes that are in local master branch, but not in origin master.
	This is equivalent to outgoing changes not yet pushed.
git log origin/master ^master
	Show the changes in origin/master, but not in the local master. 
	This is equivalent to 'incoming'. 
git branch
	List the available branches
git branch 'label'
	Make a new branch!
	Since branches are nothing but pointers to commits, this is a cheap operation. 
	Branching is a good way of saving state; it's easy to revert to one once labeled.
git checkout -b 'label'
	switches to branch 'label'
git checkout -b 'label1' 'label2'
	Creates a new branch called 'label1' from the branch 'label2'
git merge 'label'
	merge the present branch with branch 'label'
	You can merge multiple times, efficiently -- perfect for different lab setups. 
git merge --ff-only master
	Particuarly, can use to merge from master into particular setups!
		Much better than subversion.
git mergetool 
	Open a visual merging tool (kdiff3, etc -- same format as subversion)

git diff
	Shows changed files relative to local DB. 
	All comparisons are on local data, so are fast!

git push origin master
	Push local commits to origin (in htis case github) for the master branch. 
	Does *not* do merging. 
	If you do need to merge changes:
git fetch 
	Pull down *all* changes from the origin. 
git merge origin/master
	Merge current branch with that from the server.
git pull
	Pull the current branch from the origin, and automatically try to locally merge.
	ujst a shortcut for git fetch and merge; better not to use unless you're allways on master.
	"If you do a pull in a branch that is not tracked you're totally screwed."
git remote add <label> <url>
	Add a remote repository, which you can hten fetch (and merge) from. 
	Opposite direction from subversion -- the mantainers pull from trusted sources, 
	rather than developers pushing to a central repository. 
	This is sort-of how the linux kernel does it. 

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ref: -0 tags: SUA LFP BMI decoding Donoghue date: 07-24-2012 15:54 gmt revision:0 [head]

PMID-22157115 Decoding 3D reach and grasp from hybrid signals in motor and premotor cortices: spikes, multiunit activity, and local field potentials.

  • Idea: you get more information from SUA (what they call SA) activity than broadband LFPS for predicting reach direction / position for a freely moving monkey.
  • C.F. {253}

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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: Rousche-1998.07 tags: BMI Utah cat Normann recording electrode MEA histology date: 06-29-2012 01:12 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-10223510 Chronic recording capability of the Utah Intracortical Electrode Array in cat sensory cortex.

  • Focus on (surprisingly) chronic recording from the utah array: they want to demonstrate that it works.
  • Platinum coating.
  • insulated with 2-3um polymide.
  • 10 cats, 12 arrays: 2 in S1, 8 in auditory ctx, 2 V1.
  • 11 electrodes connected in each array.
  • After a 6-month implant period, 60% of implanted arrays could still record 'some type of activity'.
  • They were completely targeting neuroprostheses.
    • But acknowledge that 'the presence of fibrous encapsulation and chronic astrogliosis suggests that more research is necessary before the UIEA can be uses as a cornerstone of a neuroprosthetic device for human use.
      • And yet they went through with the human trials?
  • Electrode impedance gave no hint as to the ability of a given electrode to record neural units: many electrodes with average impedance could not record neural activity.
  • Impedances generally decreased , which is not unusual (Schmidt and Bak, 1976).
    • Likely that the polymide had become permeated with water vapor to and equilibrium point. (rather than pinhole leaks or water permeation).
  • Quiet amplifiers: 2uv pk-pk.
  • No significant trend in background activity was noted over the implant durations.
  • In nearly every cat, the dura above the electrode array adhered to the bone flap, and the electrode array adhered to the dura. Therefore, when the bone flap was removed, the UIEA was concurrently explanted from the cortex.
    • Similar to Hoogerwerf and Wise 1994 {1025}
    • The explanted UIEAs typically had become encapsulated, the encapsulation was the cause of the cortical depression.
    • Only 1 did not become encapsulated in dura.
    • This encapsulation explains the gradually varying recording properties -- the electrodes were moving out of the brain.
    • "The capsule which formed around the substrate of the UIEA was usually continuous with the dura, which was enmeshed directly to the overlying skull. The encapsulated array therefore had no freedom of movement with respect to the skull, and this may have caused local trauma which reduced the possibility of recording neural activity. This relative micromovement between the fixed array and the ‘floating’ cortical tissue may also be responsible for sustaining continued growth of the encapsulation as described above."
    • Have tried putting teflon on the top of the Utah array -- did this work?
  • Two UIEAs were not found near the cortical surface -- these two arrays were totally removed from the leptomeningeal space. although originally implanted into the cortex beneath the dura, at the time of sacrafice these arrays were found above the repaired dura, and the implanted cortex showed no evicence of cortical implant.
  • Some electrodes healthy; other showed chronic inflammation.
  • General and intense inflamation in the upper layers of cortex even on their best-performing array; no guarantee that this ctx was working properly, as it is heavily compressed with fibroblasts.
  • Regarding vascluature, see {1024}.
  • Say that the largest impediment is the formation of a capsule around the implant. (Do not mention issue of infection; I guess cats have strong immune systems as well?)
  • Rather good biological discussion and conclusion. worth a re-read. "We currently recommend that the UIEA be used for acute and short-term applications."
    • Not too many follow-ups re teflon or fixing the encapsulation problem: See {1026}
      • Indeed, {1027} doesn't even cite this! Too disastrous?


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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: Wichmann-1994.08 tags: STN normal physiology delong wichmann date: 02-27-2012 22:05 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-7983514[0] The Primate Subthalamic Nucleus. 1. Functional Properties in Intact Animals.

  • Lots of cells -- 301 cells in the STN, 1589 microstimulation sites, 72 cross-correlation pairs.
  • 55% modulated to passive contralateral movement, 86% of these to muscle palpitation, 25% to light touch.
  • Caudalventral STN devoid of calls responding to touch or movement.
  • Somatotopic organization: lateral arm, medial leg.
    • Representation of proximal muscles / portions much larger than distal portions, consistent with Carpenter 1950.
  • Mostly rate increases in response to step tracking tasks, usually uniphasic.
  • 40ua, 200-500 ms train duration, 400 Hz did not produce movement. Stimulation of the lateral borders often led to eye movements.
  • 11% of pairs were seen to be synchronized, separated by 100-200um.
    • Much smaller than in the cortex.
    • This strongly supports the concept of functional segregation in the basal ganglia-thalamocortical pathways.
  • Mean firing rate 23 Hz old studies, 19 Hz present study.
  • "Most hypotheses concerning the role of the basal ganglia in movement were derived from experience with diseases originating in the basal ganglia or from experiments involving the activation or inactivation of large parts of BG nuclei. These results are notoriously hard to interpret, because gross changes in motor circuit activity likely results in rather nonspecific activity changes in multiple parts of the neuraxis, unlike minute alterations in the firing patterns of individual neurons in the basal ganglia may have under physiological conditions".
  • Basal ganglia may have a role in the late phases of movement, perhaps even their termination.
  • "More is known about the role of the indirect pathway in the pathophysiology of movement disorders such as Parkinson's disease and ballism than in the control of normal movement." word, yes.


[0] Wichmann T, Bergman H, DeLong MR, The primate subthalamic nucleus. I. Functional properties in intact animals.J Neurophysiol 72:2, 494-506 (1994 Aug)

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

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

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

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ref: Hershey-2010.12 tags: DBS impulsivity STN feedback stability gonogo date: 02-22-2012 22:04 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

PMID-20855421[0] Mapping Go-No-Go performance within the subthalamic nucleus region.

  • Support the dorsal-ventral motor-cognitive model.
  • Only ventral subthalamic stimulation effected Go-No-Go accuracy.
    • Both ventral and dorsal stimulation showed positive motor effects.
  • On inhibition in the STN: (Aron and Poldrack 2006; Frank et al 2007).
    • Thought: if methamphetamine and L-Dopa have similar impulsivity / punding / hobbyism effects, why do they think that the function is localized exclusively in the STN? These behaviors seem a more general problem of dopamine disregulation. Meth heads presumably have intact STN. The pausing hypothesis (e.g. STN controls pausing in conflict situations) seems better to me (maybe); have to check rat results.
    • Such is the problem with taking one thing out of a feedback loop and assuming the resultant deficit corresponds with the original 'function' insofar as one can be assigned. Think if you adjust the coefficients on a filter -- it gets all F'ed, with minor projection onto the frequency response.
    • Low-order systems are less sensitive to drastic parameter adjustment, but still purpose is obscured in feedback systems.
    • See {1082}
  • STN DBS can lead to impaired withholding strong prepotent responses with strong response conflict
    • Such as the Stroop task (Jahanshahi et al 2000; Schroeder et al 2002; Witt et al 2004)
    • Stop signal task (Ray et al 2009)
    • Go-nogo tasks (Hershey et al 2004; Ballanger et al 2009).
    • Rats show the same deficit in inhibiting responses in strong conflict cases (Baunex et al 1995, 2001; Baunez and Robbins 1997).
  • Suggest that significant variability in treatment responses could be from the exact location of stimulation.
    • Ventral STN closer to SNr, and dorsal is closer to the ZI and thalamus.


[0] Hershey T, Campbell MC, Videen TO, Lugar HM, Weaver PM, Hartlein J, Karimi M, Tabbal SD, Perlmutter JS, Mapping Go-No-Go performance within the subthalamic nucleus region.Brain 133:Pt 12, 3625-34 (2010 Dec)

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ref: Mirabella-2011.08 tags: DBS STN inhibition nogo Italy date: 02-22-2012 18:26 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-21810782[0] Deep Brain Stimulation of Subthalamic Nuclei Affects Arm Response Inhibition In Parkinson’s Patients

  • Inhibitory control is improved only when both DBS are active, that is, the reaction time to the stop signal is significantly shorter in the DBS-ON condition than in all the others (left, right, or neither).
    • Inhibition is probably not lateralized.
  • CF [1]
  • The STN plays a critical role in the control of movements by integrating cortical inputs from several motor areas (Mink 1996, Romanelli et al 2005) (but how -- in what role?)
    • Alteration of STN functioning leads to loss of the ability to control movements as in the case of Parkinson's disease (Obeso et al 2008).
    • This control can be partially restored by DBS (Perlmutter and Mink 2006).
    • I don't agree with this. Things are far more nuanced, and the STN likely has a different role.
  • Theri metric is the SSRT:the stop signal reaction time.
    • One study found that SSRT was longer when DBS was on.
    • Two others bilateral DBS decreased length of the SSRT.
  • This task creates conflict on all trials, as they are instructed to both move as fast as possible, but also avoid hitting the target on stop trials.
    • In healthy subjects this leads to a delay strategy.
  • SSRT is not measured, but rather estimated from a 'race condition' between Go and Stop cues.
  • They propose that DBS affects the procrastination strategy, and that this strategy was less often adopted by PD patients than normal controls.
    • Or that STN / BG affects the ability to stop currently proceeding active movements.


[0] Mirabella G, Iaconelli S, Romanelli P, Modugno N, Lena F, Manfredi M, Cantore G, Deep Brain Stimulation of Subthalamic Nuclei Affects Arm Response Inhibition In Parkinson's Patients.Cereb Cortex no Volume no Issue no Pages (2011 Aug 1)
[1] Frank MJ, Samanta J, Moustafa AA, Sherman SJ, Hold your horses: impulsivity, deep brain stimulation, and medication in parkinsonism.Science 318:5854, 1309-12 (2007 Nov 23)

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ref: notes-3000 tags: darpa 2007 misha report oscillations old notes date: 02-16-2012 17:50 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

We have found the following types of neurons during acute intraoperative recrodings from the subthalamic nucleus (STN) of awake parkinson's patients. During the surgeries the patients opened and closed their hand, instrumented through a virtual-reality data glove, in order to move a cursor to randomly presented targets in a 1-dimensional field.

It is thought that the STN controls the gating and timing of movements, and this gate/relay is implicated in the pathological oscillatory loop seen in Parkinson's disease. Therefore, it is not surprising that we have found cells that are tuned to both movement initiation and simultaneously tuned to oscillatory features of the behavior.

Below the probability of firing, (red = high, blue = low) is plotted vs time (x-axis) and y (target gating signal). The target gating signal is 1 400 ms around the appearance of a new target to the right of the cursor, -1 when the target appears to the left of the cursor, and 0 everywhere else; 1 corresponds to the top of the graph, and -1 to the bottom. This probability was caluclated in sliding 50ms lags across the x axis to illuminate any fixed temporal relationships; that is, if a neuron had a high probability of firing 500 ms before target appearance, the image would be red @ a lag of 0.5 (on the x axis) and 1 on the y axis. This method is a nonparametric, minimal-assumption way of looking at the correlations between behavior and neural firing. It is only assumed that the relationship between neural firing times and behavior is stationary, e.g. it does not evolve with time; this is a relatively safe assumption given the recording are generally short.

This plot shows a neuron which fires preferentially when a target appears and the patient moves to the left (again, in this graph: y = -1 indicates target appears to the left, + 1 target to the right, and 0 otherwise). Note that there is noticable oscillations, due to the fact that the patient's behavior was very periodic, with a period of around 2 seconds. The neuron was inhibited around the instant of target apperance, independent of direction, as indicated by the blue regions at y = -1 and 1 around lag 0.

This plot shows a neuron which is inhibited just before target apperance (in this plot, y = 1 400ms around target appearance, independent of direction). That is, the neuron stops firing upon sucessful completion of a movement. This neuron shows no pathological oscillatory tuning; therefore, it might be assumed that not all of the STN is incapacitated by Parkinson's disease.

Here is another example of a neuron that does not show oscillatory firing behavior. In this graph, y = 1 when the patient is opening or closing his hand (equivalently the cursor velocity exceeds a threshold); y = 0 otherwise. This neuron is therefore inhibited during periods of movement. Note that around a lag of 2.5 seconds, the neuron has a higher probability of firing (the red region), possibly indicating positive firing upon successful completion of a movement.

Another example of a neuron that is tuned to thresholded cursor velocity, though this time, the firing rate becomes positive just around the instant of movement. Note here there is evidence of highly periodic behavior, as seen in the green/yellow regions spaced about 1.6 seconds apart along y=1. The region at lag = 1.6 secons corresponds to the movement following target acquisition, hence exhibits a higher firing rate.

This neuron, like the one above, fires strongly whenever the hand moves. Interestingly, there appeared to be no directional information in either of these cells.

Finally, we discovered that there appears to be error-correlated firing within the STN. The neuron shown above is selectively inhibited around periods where the cursor and target positions differ. In the plot above y=1 indicates the absolute value of the target position - the cursor position exceeds a threshold of 20% of the total range (this is subtly different from the target apperance signal, as the patient can over shoot or under shoot the target position with the cursur, upon which this signal will be 1.

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ref: notes-3000 tags: old notes date: 02-16-2012 17:50 gmt revision:13 [12] [11] [10] [9] [8] [7] [head]

what do we need to do to finish up with the human data??

  1. segment data? need to eliminate noise!!
    1. tim = manual (dan has a manual segmenting program too).
    2. dan = automatic, 2sec windows are located based on correlation to analog variables. idea: BLAST DNA search.
      1. assume stationarity?
    3. what about excluding sections or windows of data based on ISI distribution?
      1. neurons are not around long enough to make broad assumptions about stationarity.
  2. decide what to look for; or: what type of neurons are we looking for?
    1. gating neurons. req:
      1. should fire before, 400-600ms prior; min 100ms before movement.
    2. error feedback neurons.
    3. oscillatory neurons / two broad classes of neurons.
  3. can also look at intrinsic properties of the neurons themselves, e.g. oscillatory activity. However, we do not really have a control?
    1. might need a video of the patient to show that they were not moving (some other) part of their body?
  4. What about VIM?
  5. Can we predict target hit & target change?
    1. what algorithms can be used to predict things like:
      1. initiation of movement
      2. target hit
      3. target change
    2. which analog variable is best predicted by our dataset?
    3. how about resorting then predict? need some way of eliminating the crappy, noisy on-line sorting that I did.
  6. With what time lag are these cells correlated to kinesthetic movements? e.g. what are the dynamics of response?
  7. or rather, can some part of the behavior be reconstructed? we'd need at least:
      1. start
      2. stop
      3. direction
      4. force or magnitude.
    1. i might guess that the simpler (binary) analog variables will be better predicted, eg. start/stop.
  8. might want to look at the delay between STN activity and target appearance .. unfortunately, we do not have a control.

for future cases:

  1. EMG recording to see if STN/VIM are tuned to active or passive movements.
    1. problem: artifact from surface EMG may excessively contaminate the signal.
  2. larger movements, perhaps the whole arm.
  3. we looked for 'effort' cells (as in the monkeys) - should we try this again? (the one time we tried this, the patient became rather frustrated)
    1. a more fundamental question: are the cells in the STN/ VIM under voluntary control? most likely.
  4. if subcortical cells cannot do it all (e.g. motor prothesis), what can they do? It is a rather invasive procedure.
  5. should look for changes in cortical LFP and or firing properties in response to DBS.
  6. fix the ECoG recording there must be a reason why people are doing differential EEG.. though perhaps most new machines are referential.
  7. try a BIS monitor. (already in the OR, but need to determine how to get the data out)
    1. some of the neurons only fire when the patient is awake (and vice-vercia) (sleep-wake states.. that might be an interesting study.)

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ref: Nordhausen-1996.07 tags: Normann Utah array recording date: 02-06-2012 21:37 gmt revision:3 [2] [1] [0] [head]

PMID-8836553[0] Single unit recording capabilities of a 100 microelectrode array. Nordhausen CT, Maynard EM, Normann RA.

  • Used the Utah array in visual stimulus-evoked response in cats.
  • 58.6% of electrodes in the array recorded neural activity.
  • The density of the electrodes in the UIEA makes it impossible to simply push the needles into the cortex with forceps. This only results in surface dimpling, incomplete insertion, and possible cortical damage.
    • We have instead designed a high speed pneumatic insertion tool which takes advantage of viscoelectric properties of the cortical tissue by advancing the electrodes into the tissue at very high velocity.


[0] Nordhausen CT, Maynard EM, Normann RA, Single unit recording capabilities of a 100 microelectrode array.Brain Res 726:1-2, 129-40 (1996 Jul 8)

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

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


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

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ref: -0 tags: microstim ICMS axons soma Nowak NMDA date: 01-27-2012 23:30 gmt revision:1 [0] [head]

PMID-9504843 Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. I. Evidence from chronaxie measurements.

  • Slice experiments / in vitro.
  • The chronaxie for orthodromic activation was similar to that for axonal activation, but was 40 times smaller than the chronaxie for direct cell body activation. This suggests that, whenever a postsynaptic response is elicited after electrical stimulation of the cortical gray matter, axons (either axonal branches or axon initial segments), but not cell bodies, are the neuronal elements activated.

PMID-9504844 Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. II. Evidence from selective inactivation of cell bodies and axon initial segments.

  • Blocked soma and proximal axons / dendrites from firing AP through iontophoresis of NMDA.
  • When the NMDA-induced depolarization block was performed at the site of electrical stimulation, an unexpected increase in the amplitude of the orthodromic (backwards, into the white matter) responses was observed.
    • Possibly due to an increase in axonal excitability (?)
    • Superexitability eventually washed out, leading to responses that was 15-20% lower than before NMDA soma / proximal axon block.
  • "Since the neocortex is organised as a network of local and long-range reciprocal connections, great attention must be paid to the interpretation of data obtained with electrical stimulation."

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ref: BAdi-2009.09 tags: dopamine L-Dopa levodopa agonist young reward novelty punisment learning date: 01-24-2012 04:05 gmt revision:1 [0] [head]

PMID-19416950[0] Reward-learning and the novelty-seeking personality: a between- and within-subjects study of the effects of dopamine agonists on young Parkinson's patients

  • dopamine agonist administration in young patients with Parkinson's disease resulted in increased novelty seeking, enhanced reward processing, and decreased punishment processing may shed light on the cognitive and personality bases of the impulse control disorders, which arise as side-effects of dopamine agonist therapy in some Parkinson's disease patients.


[0] Bódi N, Kéri S, Nagy H, Moustafa A, Myers CE, Daw N, Dibó G, Takáts A, Bereczki D, Gluck MA, Reward-learning and the novelty-seeking personality: a between- and within-subjects study of the effects of dopamine agonists on young Parkinson's patients.Brain 132:Pt 9, 2385-95 (2009 Sep)

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ref: Zhang-2009.02 tags: localized surface plasmon resonance nanoparticle neural recording innovative date: 01-15-2012 23:00 gmt revision:4 [3] [2] [1] [0] [head]

PMID-19199762[0] Optical Detection of Brain Cell Activity Using Plasmonic Gold Nanoparticles

  • Used 140 nm diameter, 40 nm thick gold disc nanoparticles set in a 400nm array, illuminated by 850nm diode laser light.
    • From my reading, it seems that the diameter of these nanoparticles is important, but the grid spacing is not.
  • These nanoparticles strongly scatter light, and the degree of scattering is dependent on the local index of refraction + electric field.
  • The change in scattering due to applied electric field is very small, though - ~ 3e-6 1/V in the air-capacitor setup, ~1e-3 in solution when stimluated by cultured hippocampal neurons.
  • Noteably, nanoparticles are not diffraction limited - their measurement resolution is proportional to their size. Compare with voltage-sensitive dyes, which have a similar measurement signal-to-noise ratio, are diffraction limited, may be toxic, and may photobleach.


[0] Zhang J, Atay T, Nurmikko AV, Optical detection of brain cell activity using plasmonic gold nanoparticles.Nano Lett 9:2, 519-24 (2009 Feb)

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ref: Holleman-2007.08 tags: amplifier recording NEF low noise original date: 01-15-2012 22:08 gmt revision:1 [0] [head]

IEEE-4353193 (pdf) A Sub-Microwatt Low-Noise Amplifier for Neural Recording

  • 0.805 uA from a 1V supply, gain of 36dB and 44db.
  • open loop amplfier, pass band between 0.3 and 4.7 kHz.
  • 3.5 uV rms input referred noise.
  • NEF 1.8


Holleman, J. and Otis, B. Engineering in Medicine and Biology Society, 2007. EMBS 2007. 29th Annual International Conference of the IEEE 3930 -3933 (2007)

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ref: Mojarradi-2003.03 tags: MEMS recording telemetry Normann Andersen wireless date: 01-15-2012 04:29 gmt revision:2 [1] [0] [head]

PMID-12797724[0] A miniaturized neuroprosthesis suitable for implantation into the brain.

  • Standard tricks: cascode configuration, deep-ohmic PMOS Devices for resistive feedback, wide PMOS weak-inversion input stage for good transconductance and low noise.
  • Varaible power for variable noise levels & bandwidths.
  • Wireless transceiver and power stage are in early concept stages.


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ref: Song-2009.08 tags: wireless neural recording RF Brown laser optical Donoghue date: 01-15-2012 00:58 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

IEEE-5067358 (pdf) Wireless, Ultra Low Power, Broadband Neural Recording Microsystem

  • 16 channels.
  • Use a VCSEL (vertical cavity surface emission laser) to transmit data through the skin.
  • Nice design, and they claim to have made recordings for 1 month already.
  • One PCB, kapton substrate reinforced with alumina where needed.
  • Custom 12mW neural amplifier.


Song, Y.-K. and Borton, D.A. and Park, S. and Patterson, W.R. and Bull, C.W. and Laiwalla, F. and Mislow, J. and Simeral, J.D. and Donoghue, J.P. and Nurmikko, A.V. Active Microelectronic Neurosensor Arrays for Implantable Brain Communication Interfaces Neural Systems and Rehabilitation Engineering, IEEE Transactions on 17 4 339 -345 (2009)

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

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

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


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ref: Santhanam-2006.07 tags: Shenoy BMI BCI trials date: 01-08-2012 23:37 gmt revision:4 [3] [2] [1] [0] [head]

PMID-16838020[0] A high-performance brain-computer interface

  • the speed and accuracy with which keys can be selected using BCIs is still far lower than for systems relying on eye movements.
    • What is the eye-movement rate?
  • implanted in PMD. 96 electrodes (utah array).
  • used an instructed-delay task. figure 1
    • monkey had to move to target when center target disappeared. peripheral target appeared several seconds prior.
  • actually had the monkey reach to targets; if correct, monkey was immediately rewarded.
    • real movement trials were interspersed to keep the monkey engaged.
  • decoding model: assume that the spike counts come from a poisson or gaussian distribution. Apply ML decoding.
    • poisson better than gaussian.
  • up to 6.5 bits per second, or approximately 15 words per minute, with 96 electrodes.
    • Peak of continuous control = 1.6 bits per second.
  • ITRC = information transfer rate capacity. this metric is proportional to the single trial accuracy / trial length (sorta, see ref 23 - Blahut-Arimoto algorithm)
  • most of their neurons seem to be responsive to actual movements (que supressa!)
  • maximum bandwidth with a trial length of 250ms.
    • lots of other good information-theoretic analysis.
  • PMID-12657892[1] Neural prosthetic control signals from plan activity. -- the preceding Neuroreport simulation study.
    • performance to exceed 90% with as few as 40 neurons.
    • maximum likelihood decoders controlling a FSM.


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ref: Song-2005.06 tags: recording wireless silicon utah probe Donoghue 2005 date: 01-08-2012 23:24 gmt revision:3 [2] [1] [0] [head]

PMID-16003903[0] Development of a chipscale integrated microelectrode/microelectronic device for brain implantable neuroengineering applications.

-- second from this

  • They have mated a 16-channel silicon microprobe to a low-power (50uW/channel) VLSI chip, including a CMOS amplifier.
    • Epoxy ball-bond.
    • 7mW total power.
  • Suggest photovoltaic power using GaAs/AlGaAs photodiodes. 3 in series yielding 3V at about 20% efficiency. Not bad! Then they can use the fiber to get data out, too.


[0] Song YK, Patterson WR, Bull CW, Beals J, Hwang N, Deangelis AP, Lay C, McKay JL, Nurmikko AV, Fellows MR, Simeral JD, Donoghue JP, Connors BW, Development of a chipscale integrated microelectrode/microelectronic device for brain implantable neuroengineering applications.IEEE Trans Neural Syst Rehabil Eng 13:2, 220-6 (2005 Jun)

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ref: Serruya-2003.03 tags: BMI Serruya Donoghue date: 01-08-2012 03:31 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-12647229[0] Robustness of neuroprosthetic decoding algorithms

  • chronic intracortical arrays
  • step tracking and slow continuous tracking tasks
  • compared two models:
    • ML model to predict reaching directions
    • linear model to predict hand trajectory
  • Less than 1 min of data for the discrete task (8 to 13 neurons) and less than 3 min (8 to 18 neurons) for the continuous task were required to build optimal models
    • however, their definition of 'optimal' is discounted for the cost of training the model.
    • increasing the time between training and applying the model did not significantly impact the efficacy of the predictor.
      • linear predictors trained on one day & tested on another were not differentn in error characteristics from linear filters trained on the same day (!!!)
  • point out that more neurons most likely means a longer model training time
  • interesting facts: 600,000 patients in the US suffer each year from motor impairment de to spinal-cord and brainstem trauma (that's a lot; I kinda don't trust that number!)


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ref: bookmark-2007.08 tags: donoghue cyberkinetics BMI braingate date: 01-06-2012 03:09 gmt revision:3 [2] [1] [0] [head]

images/425_1.pdf August 2007

  • provides more extensive details on the braingate system.
  • including, their automatic impedance tester (5mv, 10pa)
  • and the automatic spike sorter.
  • the different tests that were required, such as accelerated aging in 50-70 deg C saline baths
  • the long path to market - $30 - $40 million more (of course, they have since abandoned the product).

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ref: notes-2000.09 tags: BMI recording technology Chapin Nicolelis battery Wolf date: 01-06-2012 03:09 gmt revision:4 [3] [2] [1] [0] [head]

from the book "Neural Prostheses for Restoration of Sensory and Motor Function" edited by John Chapin and Karen Moxon.

Phillip Kennedy's one-channel neurotrophic glass electrode BMI (axons apparently grew into the electrode, and he recorded from them)

Pat Wolf on neural amplification / telemetry technology

battery technology for powering the neural telemetry

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ref: Brown-2007 tags: Kalman filter BMI Black spike_sorting Donoghue date: 01-06-2012 00:07 gmt revision:1 [0] [head]

From Uncertain Spikes to Prosthetic Control a powerpoint presentation w/ good overview of all that the Brown group has done

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ref: Hatsopoulos-2005.01 tags: BMI Hatsopoulos Donoghue cortex date: 01-03-2012 22:49 gmt revision:4 [3] [2] [1] [0] [head]

PMID-17282055[0][] Cortically controlled brain-machine interface

  • conference proceedings. describe the 6month teraplegic trial.
  • (above, monkey)
    • lets them record from 40% of electrodes.
    • 100-200uv units, 20uv noise.
    • one year to three years post implantation.
  • advocate hybrid multimodal control.
    • M1 = continuous control
    • PMd = discrete control
      • used a probabilistic model for this (poisson firing rate, individual neurons are independent)


[0] Hatsopoulos N, Mukand J, Polykoff G, Friehs G, Donoghue J, Cortically controlled brain-machine interface.Conf Proc IEEE Eng Med Biol Soc 7:1, 7660-7663 (2005)

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ref: Tian-2010.08 tags: nanowire nanoprobe silicon FET doping cis trans extracellular intracellular recording neuro MEA date: 01-03-2012 16:35 gmt revision:4 [3] [2] [1] [0] [head]

PMID-20705858[0] Three-Dimensional, Flexible Nanoscale Field-Effect Transistors as Localized Bioprobes

  • Made a silicon nanowire with 60 deg. kinks via trans/cis manipulation.
  • Doped one part of the N nanowire P to make a 200nm long FET whose gate is simply the surface of the nanowire (I think, have to check the refs)
  • Attached the nanoprobe / nanowire to flexible PMMA / SM-8 support which, due to interfacial stress, rose off the substrate (clever!)
  • Coated tip with phospholipid layers -> better cell attachment / penetration.
    • Possible to have the cell pull the nanoprobe in via endocytic pathways.
  • Were able to record intracellular and extracellular AP from rabbit cardiocytes. (!!!)


[0] Tian B, Cohen-Karni T, Qing Q, Duan X, Xie P, Lieber CM, Three-dimensional, flexible nanoscale field-effect transistors as localized bioprobes.Science 329:5993, 830-4 (2010 Aug 13)

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ref: life-notes-2007 tags: electrode assay technology electrophysiology hack ad-hoc date: 01-03-2012 07:10 gmt revision:3 [2] [1] [0] [head]

properties of electrodes that are to penetrate the pia mater of a rhesus macaque:

  1. must easily go into a canned peach (in heavy or light sauce, it does not matter)
  2. does not go into pineapple cross-grain
  3. does go into the end-grain of pineapple
  4. penetrates the skin of a red grape (somewhat fresh) ~= pia
    1. The pia is a bit more tough than this, but is much less firm - if you are implanting electrodes that are any less than extremely sharp - e.g. etched - it will dimple the surface and not penetrate. Very sharp electrodes are key for getting through this tough membrane - which is even tougher in humans!
      • dimpling seems to silence cortical activity (observational evidence for this only)
      • however, once implanted lower-impedance electrodes work better. Low current microstimulation may be able to round the sharp tips of tungsten electrodes - we may want to test this.
    1. microdissection of the pia often damages the surface vasulature of the cortex, leading to localized infarctions, and hence should be avoided (unless you are really good)
    2. Bunching multiple elctrodes into one shaft - that is, making the shaft thicker and duller (albiet staggered) is not a good strategy for entering the brain (need to test the present monkeys).
  1. Cortical layer V (location of large pyramidal cells + betz cells in M1) in humans is 3-3.5mm below the surface, and ~1.6mm deep in rhesus. microwire/microwire arrays should have at least 2mm free wire length if intended for monkeys, and 4mm free wire if intended for humans.
    1. M1/S1 / central sulcus region is mostly inactive under isoflouro anesthesia, somewhat mangled/depressed with light ketamine, and silent with fentanyl. So, be careful with intraoperative recordings - the monkey/rat may be too deep, hence no cells to listen to!

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ref: Aflalo-2007.03 tags: Graziano motor cortex M1 SUA macaque monkey electrophysiology tuning date: 01-03-2012 03:37 gmt revision:1 [0] [head]

PMID-17360898[] Relationship between Unconstrained Arm Movements and Single-Neuron Firing in the Macaque Motor Cortex

  • the best explanation of neuronal firing was the final mulijoint configuration of the arm - it accounted for 36% of the SUA variance.
  • the search for the 'correct' motor parameter (that neurons are tuned to) is an ill-posed experimental question because motor parameters are very intercorrelated.
  • they knock experiments in which the animals are overtrained & the movements limited - and they are right!
  • single electrode recording with cronically implanted steel chamber - e.g. it took a damn long time!
    • imaged the central sulcus through the dura.
    • verified location with single unit responses to palpation of the contralateral hand/arm (in S1) & microstimulation-evoked movements in M1.
  • used optotrak to measure the position of the monkey.
  • occasionally, the monkey attemptted to scratch the experimenter with fast semi-ballistic arm movement. heh. :)
  • movements were seprarated based on speed analysis - that is, all the data were analyzed as discrete segments.
  • neurons were inactive during periods of hand stasis between movements.
  • tested the diversity of their training set in a clever way: they simulated neurons tuned to various parameters of the motion, and tested to see if their analysis could recover the tuning. it could.
    • however, they still used unvalidated regression analysis to test their hypothesis. regression analysis estimates how much variance is estimated by the cosine-tuning model - it returns an R^2.
  • either averaged the neuronal tuning over an entire movement or smoothed the firing rate using a 10hz upper cutoff.
  • Moran & Schwartz' old result seems to be as much a consequence of averaging across trials as it is a consequence of actual tuning...
    • whithout the averaging, only 3% of the variance could be attributed to speed tuning.
  • i think that they have a good point in all of this: when you eliminate sources of variance (e.g. starting position) from the behavior, either by mechanical restraint or simple omission of segments or even better averaging over trials, you will get a higher R^2. but it may be false, a compression of the space along an axis where they are not well correlated!
  • a model in which the final position matters little, but the velocity used to get there does, has been found to account for little of the neuronal variance.
    • instead, neurons are tuned to any of a number of movements that terminate near a preferred direction.
  • observational studies of of the normal psontaneous behavior of monkeys indicate that a high proportion of time is spent using the arm as a postural device.
    • therefore, they expect that neurons are tuned to endpoint posture.
    • modeled the neuronal firing as a gaussian surface in the 8-dimensional space of the arm posture.
  • in comparison to other studies, the offset between neural activity and behavior was not significantly different, over the entire population of recorded neurons, from zero. This may be due to the nature of the task, which was spontaneous and ongoing, not cue and reaction based, as in many other studies.
    • quote: This result suggests that the neuronal tuning to posture reflects reatively more and anticipation of the future state of the limb rather than a feedback signal about a recent state of the limb.


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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: Merletti-2009.02 tags: surface EMG multielectrode recording technology italy date: 01-03-2012 01:07 gmt revision:2 [1] [0] [head]

PMID-19042063[0] Technology and instrumentation for detection and conditioning of the surface electromyographic signal: state of the art

  • good background & review of surface EMG (sEMG) - noise levels, electrodes, electronics. eg. Instrumentation amplifiers with an input resistance < 100MOhm are not recommended, and the lower the input capacitance, the better: the impedance of a 10pf capacitor at 100hz is 160MOhm.
  • Low and balanced input impedances are required to reduce asymmetric filtering of common-mode power-line noise.


[0] Merletti R, Botter A, Troiano A, Merlo E, Minetto MA, Technology and instrumentation for detection and conditioning of the surface electromyographic signal: state of the art.Clin Biomech (Bristol, Avon) 24:2, 122-34 (2009 Feb)

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ref: Miranda-2010.06 tags: Meng Shenoy Hermes wireless neural recording digital COTS date: 01-03-2012 00:55 gmt revision:2 [1] [0] [head]

IEEE-5471737 (pdf) HermesD: A High-Rate Long-Range Wireless Transmission System for Simultaneous Multichannel Neural Recording Applications

  • 32 channels broadband 12 b/sample, FSK modulation of 3.7-4.1 carrier
  • 142mW lasts 33h using two 3.6V/1200maH LiSOCl2 batteries.
  • Circuarly polarized patch antenna + 13dBi circular horn antenna
  • -83dbM with a BER of 10^-9
  • Can easily be scaled up in terms of # of channels and bit rate to accomidate future systems.
  • they think that thresholding / compression / low bit-rate is dumb.
  • Cite Rizk and Obeid, and carefully review other work wrt saying that their present is the best (fair..)
  • [6][7] employ spike sorting -- have to check these.
    • "but the resources are usually too scarce to provide high-quality spike classification on a large number of channels simultaneously, with a reasonably low power-budged (false!)
  • My design is smaller.
  • Use utah array.
  • possible to have 6 receivers simultaneously.
  • 3.7-4.1Ghz good choice for transmission in terms of regulation / availability.
  • Transmission in cages below 1Ghz severly attenuated ; cages relatively transparent to anything above 4Ghz.
  • Used Intans RHA1016.
  • Input-referred noise 3.2uV; lsb value = 1.5uV, and spike amplitudes can be 6.3mV before clipping occurs.
  • CPLD packetizer.
  • FSK built around SMV3895A from Z-communications.
    • No PLL, as this consumes power, and both the room and the animal are temperature-controlled; temp drive 0.44Mhz/C
    • Only works for wideband systems: a 3.2Ghz signal with a b/w of only 10kHz is impractical without frequency stability mechanisms. finding a needle in a haystack..
  • Reciver and antenna use right-hand circular polarization (RHCP), which attenuates multipath.
    • The first and all odd ordered bounce reflections arrive at the reciever have their polarization reversed since their incidence angles are below the pseudo-brewster angle 60-70deg.
  • Receiver complicated to track variations in transmitter freq.
    • Use a transmission line to delay the FM signal @ IF for discrimination. (This is a noncoherent modulation technique).
    • Colpitts oscillator clock recovery. Clock storage time of about 30b!
    • Receiver sensitivity level -83 dBm.
  • set threshold at 3x RMS value of spike traces.
  • [11] Reid Harrison presents an 100 ch integrated amp with a total power consumption of only 3.5mW. {1006}


Miranda, H. and Gilja, V. and Chestek, C.A. and Shenoy, K.V. and Meng, T.H. HermesD: A High-Rate Long-Range Wireless Transmission System for Simultaneous Multichannel Neural Recording Applications Biomedical Circuits and Systems, IEEE Transactions on 4 3 181 -191 (2010)

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ref: Harrison-2009.08 tags: low power ASIC wireless neural recording Reid Harrison Shenoy date: 01-03-2012 00:55 gmt revision:2 [1] [0] [head]

IEEE-5061585 (pdf) Wireless Neural Recording With Single Low-Power Integrated Circuit

  • 100 channels, with threshold spike extraction.
  • 900Mhz FSK transmit coil.
  • Inductive power and data link.


Harrison, R.R. and Kier, R.J. and Chestek, C.A. and Gilja, V. and Nuyujukian, P. and Ryu, S. and Greger, B. and Solzbacher, F. and Shenoy, K.V. Wireless Neural Recording With Single Low-Power Integrated Circuit Neural Systems and Rehabilitation Engineering, IEEE Transactions on 17 4 322 -329 (2009)

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ref: Akin-1995.06 tags: Najafi neural recording technology micromachined digital TETS 1995 PNS schematics date: 01-01-2012 20:23 gmt revision:8 [7] [6] [5] [4] [3] [2] [head]

IEEE-717081 (pdf) An Implantable Multichannel Digital neural recording system for a micromachined sieve electrode

  • Later pub: IEEE-654942 (pdf) -- apparently putting on-chip isolated diodes is a difficult task.
  • 90mw of power @ 5V, 4x4mm of area (!!)
  • targeted for regenerated peripheral neurons grown through a micromachined silicon sieve electrode.
    • PNS nerves are deliberately severed and allowed to regrow through the sieve.
  • 8bit low-power current-mode ADC. seems like a clever design to me - though I can't really follow the operation from the description written there.
  • class e transmitter amplifier.
  • 3um BiCMOS process. (you get vertical BJTs and Zener diodes)
  • has excellent schematics. - including the voltage regulator, envelop detector & ADC.
  • most of the power is dissipated in the voltage regulator (!!) - 80mW of 90mW.
  • tiny!
  • rather than using pseudoresistors, they use diode-capacitor input filter which avoids the need for chopping or off-chip hybrid components.
  • can record from any two of 32 input channels. I think the multiplexer is after the preamp - right?


Akin, T. and Najafi, K. and Bradley, R.M. Solid-State Sensors and Actuators, 1995 and Eurosensors IX.. Transducers '95. The 8th International Conference on 1 51 -54 (1995)

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ref: Thorbergsson-2008.01 tags: recording nordic wireless neural date: 01-01-2012 19:05 gmt revision:2 [1] [0] [head]

PMID-19162894[0] Implementation of a telemetry system for neurophysiological signals.

  • used the Nordic chip with a 8051 on-board, along with an OPA348 and ADG804 multiplexer.
  • can only record one channel at at time, at only 3.7ksps.


[0] Thorbergsson PT, Garwicz M, Schouenborg J, Johansson AJ, Implementation of a telemetry system for neurophysiological signals.Conf Proc IEEE Eng Med Biol Soc 2008no Issue 1254-7 (2008)

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ref: notes-0 tags: data effectiveness Norvig google statistics machine learning date: 12-06-2011 07:15 gmt revision:1 [0] [head]

The unreasonable effectiveness of data.

  • counterpoint to Eugene Wigner's "The Unreasonable effectiveness of mathematics in the natural sciences"
    • that is, math is not effective with people.
    • we should not look for elegant theories, rather embrace complexity and make use of extensive data. (google's mantra!!)
  • in 2006 google released a trillion-word corpus with all words up to 5 words long.
  • document translation and voice transcription are successful mostly because people need the services - there is demand.
    • Traditional natural language processing does not have such demand as of yet. Furthermore, it has required human-annotated data, which is expensive to produce.
  • simple models and a lot of data triumph more elaborate models based on less data.
    • for translation and any other application of ML to web data, n-gram models or linear classifiers work better than elaborate models that try to discover general rules.
  • much web data consists of individually rare but collectively frequent events.
  • because of a huge shared cognitive and cultural context, linguistic expression can be highly ambiguous and still often be understood correctly.
  • mention project halo - $10,000 per page of a chemistry textbook. (funded by DARPA)
  • ultimately suggest that there is so so much to explore now - just use unlabeled data with an unsupervised learning algorithm.

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ref: Burnod-1982.11 tags: operant conditioning motor control learning Burnod Maton Calvet date: 11-26-2011 02:22 gmt revision:0 [head]

PMID-7140894 Short-term changes in cell activity of areas 4 and 5 during operant conditioning.

  • Seems that layers 4 and 5 act differently during operant conditioning of a simple task.
  • Layer 5 neurons become tuned to reward (?)
  • Can't get this article, have to go from the abstract.

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ref: -0 tags: entropy life proteonomics transcription factors date: 07-08-2011 22:42 gmt revision:0 [head]

Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes -- read the article. These are my disordered, mesothermophylic notes.

  • Low and high temperature prokaryotes seem to have less protein disorder (as estimated by amino acid content, mostly, not actual structure) called IDR/IDP (intrinsically disordered regions or proteins).
  • IDR / IDPs seem essential in certain protein functions, such as transcription factors and ribosomal proteins.
  • hyperthermophyles have low genomic complexity and low protein disorder, possibly to combat the high disorder of their environment.
  • "life appears to be incompatible with less than about 1.5% disorder ". I would say that this is a rather conservative threshold.
  • transcription factors: "disorder is correlated with the number of genes they regulate, which suggests that their disorder is directly linked with functional complexity of the organism"
  • Transcription factor disorder is higher in psychrophiles (low temp) than hyperthermophiles, even though both show decreased genome size. Furthermore, disordered regions may confer temperature robustness at 40-50C as well as at low temperatures.
  • "...there is many evidence in the literature that structural disorder and complexity are correlated, both at the level of individual proteins, where IDP functions correlate with signaling and regulation, and whole genomes, where the frequency of disorder increases with increasing complexity of the organism [24], [25], [41], [52]. Thus, evolutionary changes (point mutations, deletions of regions, silencing of genes, etc…) that reduce disorder will tend to strip the organism of functions that increase its complexity, and leave functions that are required for its basic, non-regulated existence. In this sense, reduction in disorder is not a side-effect of selection for reduced complexity, rather the mechanism of this evolutionary drive."

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ref: -0 tags: abortion religion human economics date: 03-14-2011 18:19 gmt revision:1 [0] [head]


This is a good sermon with a lot of good points (gasp! did an atheist just say that?), and is making me think hard -- or at least hard enough to write down how I feel on abortion.

I agree with the pastor that the community does seem at fault for not helping women whose 'unwanted' pregnancies might be wanted if there was more social support. I guess, atheist that I am, that religion has a strong and good role here by providing the impetus to make people be more cohesive and behave morally better. IMHO Thoreau-inspired mental integrity and thoughtful examination are another (better?) way to get there, but perhaps religion is a cultural shortcut to the same end, hence valuable. (As an aside, I'm irked by the repeated phrase that 'they need the church'. Seems like the church is the needy one here - if what it offers is valuable, it need not insist. A second irritation is that the church sometimes misappropriates credit/importance: things that a community of good people create (e.g. support for single mothers) the church assumes primary credit for. You preach humility, show some.)

I doubt women abort have children out of shame, as he suggests. More likely the mother understands the complex economies and timing of raising a child; presumably, in situations where an abortion is considered the mother could hope to have another child later, when she could support and raise he/she better - give he/she a happier life with more love to share to others. Are lives exchangeable in this way? You make these choices implicitly every time you choose not to have unprotected sex with someone - exchanging the possibility of creating a life presently with the possibility of creating an even better life later. This is normal and good, the point of decision has just been moved albeit utilitarian ... and of course utilitarianism is limited, because things aren't linear or monotonic. If we treat even unwanted pregnancy with 'mischievous joy' (i like that) as he suggests, perhaps the attitude of sacred life itself guarantees a happier existence than the attitude of exchangeable life. More basically: despite the logic above I intuitively and instinctively find the thought of killing anything remotely human horrific.

But, we kill things all the time. We kill (are killing..) solders in war. We kill a lot of pigs, which (this is a very iffy argument here) have as much if not more capability for suffering and pleasure than a very young fetus. And then we eat them. We, loosely and implicitly, kill people by not sending an section of our income to buy medicine, food - this to grown people with families, friends and standing importance. Is their death worse than the death of a fetus? My brain tells me that there is a continuum of existence and meaning, and in this messy realistic world, we have to admit ordering and make compromises; my soul still hates this fact.

Ultimately, human happiness and suffering, life and death, cannot be completely reduced to a utilitarian calculus. In such a calculus we should aim to optimize the total joy in the world, minus the pain and dread, integrated over lifetimes and people. To a rough and imperfect scale that is what we do, in our personal lives and more broadly. Treating all human lives as equal is an idea of both democracy and religion that makes the calculus balanced and fair, and allows us to derive usable laws and stable societies (integrated joy...), but it seems to break down in the case of abortion. This is why I think the oft myopic and special-interest swayed government should have no say in a woman's choice; if I can't come up with a solid reason either way, why should the government?

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ref: -0 tags: hike Culbreth North Carolina date: 02-07-2011 04:44 gmt revision:2 [1] [0] [head]

Excellent hike with So-- and Vi-- today. We somehow completely overshot the original southward path toward the car @ ~ 5:30-5:45 (marked with 'oops' on the map). In our race against the falling sun we continued too far west, ultimately all the way to Uzzle Rd; hence we had to return for a good number of miles on the road under the cooling night sky. Gorgeous country; the hill in that area is even 'large' (740') for Piedmont standards, and affords a view of the farms.

for S & V: the hill we saw from the top is right by Pyrophyllite Lake 3 miles south of the lookout point. Total hike distance was 9.5 miles.

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ref: ai-0 tags: automatic programming journal notes date: 12-31-2010 05:24 gmt revision:4 [3] [2] [1] [0] [head]

This evening, on the drive back from wacky (and difficult) Russian-style yoga, I got a chance to explain to my brother what I really want to be working on, the thing that really tickles my fancy. My brother and I, so much as genetic commonality and common upbringing seem to effect, have very similar styles of thinking, which made explaining things a bit easier. For you, dear readier, I'll expand a bit.

I'd like to write a program that writes other programs, iteratively, given some objective function / problem statement / environment in which to interact. The present concrete goal is to have a said program make a program that is able to lay out PCBs with quality similar to that of humans. The overarching framework that I'm planning on using is genetic/evolutionary algorithms (the latter does not have crossover, fyi), but no one has applied GA to the problem in this way: most people use GA to solve a particular instance of a problem. Rubbish, i say, this is energy wasteful!

Rubbish, you may return: the stated problem requires a degree of generalization and disconnect from the 'real world' (the PCB) that makes GAs extremely unlikely to come up with any solutions. Expressed another way: the space to be explored is too large (program begets program begets solution). This is a very sensible critique; there is no way in hell a GA can solve this problem. They are notably pathetic at exploring space in a energy-efficient way (to conclude a paragraph again with energy... ).

There are known solutions for this: memory -- cache the results, in terms of algorithm & behavior, of all 'hypotheses' or individuals tried out by a GA. This is what humans do -- they remember the results of their experiment, and substitute the result rather than running a test again. But humans do something far more sophisticated and interesting than just memory - they engineer systems; engineering is an iterative process that often goes down wrong design paths, yet it nonetheless delivers awesome things like Saabs and such.

As I described to K--, engineering is not magic and can be (has been?) described mechanistically. First of all, most engineering artifacts start off from established, well-characterized components, aggregated through the panoply of history. Some of these components describe how other components are put together, things that are either learned in school or by taking things apart. Every engineer, ala Newton, stands on the vast shoulders of the designers before; hence any program must also have these shoulders available. The components are assembled into a system in a seemingly ad-hoc and iterative procedure: sometimes you don't know what you want, so you play with the parts sorta randomly, and see what interesting stuff comes out. Other times you know damn well what you / your boss / the evil warlord who holds you captive wants. Both modes are interesting (and the dichotomy is artificial), but the latter is more computer-like, hence to be modeled.

Often the full details of the objective function or desired goal is very unclear in the hands of the boss / evil warlord (1), despite how reluctant they may be to admit this. Such an effect is well documented in Fred Brooks' book, __The Design of Design__. Likewise, how to get to a solution is unclear in the mind of an engineer, so he/she shuffles things around in the mind (2),

  1. looking for components that deliver particular desired features (e.g. in an electronic system, gain makes me think of an op-amp)
  2. looking for components that remove undesirable features (e.g. a recent noise problem on my wireless headstage made me think of a adaptive decorrelating filter I made once)
  3. looking for transforms that make the problem solvable in a linear space, something that Moshe Looks calls knob-twiddling.
    1. this is from both sides -- transforms that convert the problem or the nascent solution.
    2. An example would be the FFT. This makes it easy to see spectral features.
    3. Another example, used even more recently, is coordinate transforms - it makes thinks like line-line intersection much easier.
    4. When this doesn't work, you can do far more powerful automatic coordinate transform - math, calculus. This is ultimately what I needed when figuring out the shortest line segment between a line segment and a ellipse. Don't ask.

This search is applied iteratively, apparently a good bit of the time subconsciously. A component exists in our mind as a predictive model of how the thing behaves, so we simulate it on input, observe output, and check to see if anything there is correlated / decorrelated with target features. (One would imagine that our general purpose modeling ability grew from needing to model and predict the world and all the yummy food/dangerous animals/warlords in it). The bigger the number of internal models in the engineers mind, the bigger the engineers passion for the project, the more components can be simulated and selected for. Eventually progress is made, and a new subproblem is attacked in the same way, with a shorter path and different input/output to model/regress against.

This is very non-magical, which may appall the more intuitive designers among us. It is also a real issue, because it doesn't (or poorly) explains really interesting engineering: e.g. the creation of the Fourier transform, the creation of the expectation-maximization algorithm, all the statistical and mathematical hardware that lends beauty and power to our design lives. When humans create these things, they are at the height of their creative ability, and thus it's probably a bit ridiculous to propose having a computer program do the same. That does not prevent me from poking at the mystery here, though: perhaps it is something akin to random component assembly (and these must be well known components (highly accurate, fast internal models); most all innovations were done by people exceptionally familiar with their territory), with verification against similarly intimately known data (hence, all things in memory - fast 'iteration cycles'). This is not dissimilar to evolutionary approaches to deriving laws. A Cornell physicist / computer scientist was able to generate natural laws via a calculus-infused GA {842}, and other programs were able to derive Copernicus' laws from planetary data. Most interesting scientific formulae are short, which makes them accessible to GAs (and also aesthetically pleasurable, and/or memelike, but hey!). In contrast engineering has many important design patterns that are borrowed by analogy from real-world phenomena, such as the watermark algorithm, sorting, simulated annealing, the MVC framework, object-oriented programming, WIMP interface, verb/noun interface, programming language, even GAs themselves! Douglas Hofstadter has much more to say about analogies, so I defer to him here.

Irregardless, as K-- pointed out, without some model for creativity (even one as soulless as the one above), any proposed program-creating program will never come up with anything really new. To use a real-world analogy, at his work the boss is extremely crazy - namely, he mistook a circuit breaker for an elevator (in a one-story factory!). But, this boss also comes up with interminable and enthusiastic ideas, which he throws against the wall of his underlings a few dozen times a day. Usually these ideas are crap, but sometimes they are really good, and they stick. According to K--, the way his mind works is basically opaque and illogical (I've met a few of these myself), yet he performs an essential job in the company - he spontaneously creates new ideas. Without such a boss, he claimed, the creations of a program-creating-program will impoverished.

And perhaps hence this should be the first step. Tonight I also learned that at the company (a large medical devices firm) they try to start projects at the most difficult step. That way, projects that are unlikely to succeed are killed as soon as possible. The alternate strategy, which I have previously followed, is to start with the easiest things first, so you get some motivation to continue. Hmm...

The quandary to shuffle your internal models over tonight then, dear readers, is this: is creativity actually (or accurately modeled by) random component-combination creation (boss), followed by a selection/rejection (internal auditing, or colleague auditing)? (3)

  • (1) Are there any beneficent warlords?
  • (2) Yet: as I was educated in a good postmodernist tradition, this set of steps ('cultural software') is not the only way to design. I'm just using it since, well, best to start with something that already works.
  • (3) If anyone reads this and wants to comment, just edit this. Perhaps you want to draw a horizontal line and write comments below it? Anyway, writing is active thinking, so thanks for helping me think.

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ref: -0 tags: radiolab what does technology want Kevin Kelley teleology date: 12-19-2010 06:23 gmt revision:1 [0] [head]

What does technology want? An interview with Steven Johnson and Kevin Kelly at the New York Public Library, usefully condensed to a half-hour segment for the RadioLab podcast.

  • Many of the ideas are not new - its teleology: a means of understanding the world by interpreting everything in terms of 'wants' and 'desires'. As Douglas Hofstadter explains in his book, __I am a Strange Loop__, this is really just a cognitive shortcut - not much more, not much less - which allows us to interpret things which exhibit attractor-like dynamics. Hence, as the comments on the page note, the title is to some degree just a semantic trick.
  • That said, the idea behind the title is very interesting: technology, by virtue of being subject to recursive selection, iterative refinement, code reuse (aggressive copy-paste, idea promiscuity) just like biological organisms will open-system violate the second law of thermodynamics. (They don't actually say this, but that's my interpretation).
  • Here's my logic: Imagine a statistical distribution - a population of things, animals, ideas, products, whatever. Pass them through a statistical selection process, be it evolution, the marketplace, the predictive models of your mind & associated decision making processes, a political system (ok, maybe here), the immune system, the modern attention economy (maybe here, too). This gives you a new population of things, which the selective process has impinged a degree of information about itself (the real world, usually) upon. Duplicate, spawn some more, run it through the selective process recursively ad infinitum, and the (Shannon) information contained in the resulting populations will increase. Things do not tend toward disorder.
  • That carries some heavy caveats - the information content of the selection system (which may be interpreted as applying a 'fitness' or 'objective' function) must be, at every point, much higher than that of the population for the transfer to occur. In the real world, that's easy - the information content of even a minute of life is far greater than that of our DNA! Furthermore, due to {825 coevolution} -- other organisms are our world - the information content of the selective process continually increases.
    • This implies that in some stable evolutionary niches, e.g. algae, the Shannon information of the genome must be approximately the same as the expected (as in, integral) information content of the selectively-important events of it's life. (Yea, I don't know about that either..too wishy-washy and intuitive to be useful; also algorithmic complexity doesn't scale linearly).
  • Some selection systems don't seem to be evolving to increasing complexity, however.
    • The political system: lots of problems. (1) The population is small. (2) The population (candidates) has strong incentive to mislead the selective process (the voters) (3) The information passed from selective process to population is low (a few bits every 4 years, times however many senate seats there are, divided by partisanness/statistical dependence between the bits).
    • I am happy to say, the communication issue (3) seems to be getting better - we know more about what out leaders are doing, and they know more about us - but it is imperfect, filtered through a system (the media) who holds a different objective (garners interest) than the ultimate population (who wants, roughly, security and wealth).
    • The attention economy: very strong highpass characteristics (novelty rather than truthiness), strong limits on individual complexity in the population (the ideas must be conveyable). Yet! there is strong co-evolution. (Anyway, hell, it's supposed to keep us amused, doesn't it do that? It has never been proposed to be able to solve global problems..)
    • In both politics and media, our desire for novelty may be good - it directly forces the investigation of new ideas (new members of the population). New interpretations of events are continually sought; perhaps this is a worthy price to pay for losing a bit of objective reality?
      • This should be quantifiable using Bayes' rule, then tested in an experiment. That said, the loss-function for the reality weighting is dependent on estimates of environmental change.
  • Once again I have wandered away from the original subject. Oops. Yea, the other sections - about __Where Good Ideas Come From__ is basically common knowledge now / well covered by Thomas Kuhn. All good ideas are conceived by different people in different places at the same time; insight takes time and effort, and is seldom a eureka moment; often what is required is a perceptual shift, as per the discovery of air, again what Kuhn has covered.

This blog is probably failing in the attention economy. Again, oops ;-)

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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: no free lunch wolpert coevolution date: 07-19-2010 12:54 gmt revision:2 [1] [0] [head]


  • Just discovered this. It makes perfect sense - bias free learning is 'futile'. Learning need be characterized by its biases, which enable faster or better results in particular problem domains.
  • Equivalently: any two algorithms are equivalent when their performance is averaged across all possible problems. (This is not as strong as it sounds, as most problems will never be encountered).
  • Wolper 1996 provides an excellent geometric interpretation of this: the quality of the search/optimization algorithm within a particular domain iis proporational to the inner product of its expected search stream with the actual (expected?) probability distribution of the data.
  • However! with coevolutionary algorithms, there can be a free lunch - "in coevolution some algorithms have better performance than other algorithms, averaged across all possible problems." Wolpert 2005
    • claims that this does not (??) hold in biological evolution, where there is no champion. Yet biology seems all about co-evolution.
    • coevolution of a backgammon player details how it may be coevolution + the structure of the backgammon game, not reinforcement learning, which led Tesauro to his championship-level player. Specifically, coevolutionary algorithms tend to get stuck in local minima - where both contestants play mediocre and draw - but this is not possible in backgammon; there is only one winner, and the games must terminate eventually.
      • These authors introduce a very interesting twist to improve coevolutionary bootstrapping: Firstly, the games are played in pairs, with the order of play reversed and the same random seed used to generate the dice rolls for both games. This washes out some of the unfairness due to the dice rolls when the two networks are very close - in particular, if they were identical, the result would always be one win each.

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ref: -0 tags: reynolds number microorganisms engineering math fluid mechanics date: 01-25-2010 19:17 gmt revision:0 [head]

http://jilawww.colorado.edu/perkinsgroup/Purcell_life_at_low_reynolds_number.pdf - great! Never thought about this before.

  • On being a microorganism in water with an abundant food source: "It's like driving a datsun in Saudi Arabia"

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ref: life-0 tags: Little Pisgah mountain hiking Gerton North Carolina Florence nature preserve date: 10-21-2009 04:33 gmt revision:1 [0] [head]


awesome place! but watch out for the cows!

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ref: life-0 tags: attention economy papers authors GOSH date: 07-21-2009 22:45 gmt revision:18 [17] [16] [15] [14] [13] [12] [head]

to read!

  • Jonathan Crary __Suspensions of Perception: Attention, Spectacle, and Modern Culture___
  • Catherine Hales - ___How we became post-human___

to think!

  • DIWO - do it with others
  • openFrameworks - on the iphone! check the demos - so creative, so cool, so fun.
  • Art as research for the future of society and interfaces and life etc.
  • Ars Electronica - superdelux new building with LED facade.
  • POV tracking even with simple / low cost USB cameras. This allows video overlays.
  • Tempt graffiti artist - using eye tracking to enable a graffiti artist to draw again.
  • Inspiring the sense of wonder in children. 9
  • The west is planning ourselves into organized oblivion. Brazil has 600 ponto cultural(s) because "it is disorganized" - there are not really very many limitations; not very much bureaucracy; tthey are open to any and all new ideas for distribution; the policy response is organic but 'flaky'. Brazil may be pedagology more nimble than the west?
  • Open source as ultimately lowering the cost of entry / barrier of entry.
  • Art as a means of getting people interested in their world, interested in creating things, interested in taking things apart (deconstruction seems very relevant to western art)
  • TopoR - not really realated, but would be nice to have this in kicadocaml.
  • Open source needs not only coders, but also the support personnel - the equivalent of all the non-coders in a software corporation. These people's contributions can be as important as the coders'. (e.g. translators).
  • the mesh potato - Seems that many have the same idea at the same time.
  • Via Artigo - very small x86 motherboard / full computer solution. 1.0Ghz processor, video out, ethernet, usb, 2.5" hdd, all in a 5.25" (CD-ROM sized) case. Via Chris Csikszentmihalyi.
  • Goal-direction is best left to partially subconscious control (?) (at least according to some artists at the GOSH conference - but maybe that works best for artists?)
  • Programming languages need to be a good compromise between accurate / terse representation of algorithms & data structures (graphical programming languages are bad at representing complicated datastructures, which is why I don't like them), and understanding / exploiting information-processing strengths of the human brain (e.g. visual, linguistic). I actually find that some of the fold-left & fold-right reduce operators in Ocaml are rather non-obvious to use. But maybe I should just study harder :-)

to make!

to program!

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ref: life-0 tags: FORA longnow video lecture date: 07-07-2009 17:16 gmt revision:2 [1] [0] [head]

shows that I'd like to watch:

excellent lecture by Saul Griffith:

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


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

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ref: life-0 tags: education wikinomics internet age college university pedagogy date: 06-11-2009 12:52 gmt revision:0 [head]

Will universities stay relevant? and the rest of the wikinomics blog

  • Idea: for universities to remain relevant, they will have to change their teaching styles to match the impatient and interactive internet-raised generation.
  • Notable quotes:
    • [College students today] want to learn, but they want to learn only from what they have to learn, and they want to learn it in a style that is best for them.
    • In the old model, teachers taught and students were expected to absorb vast quantities of content. Education was about absorbing content and being able to recall it on exams. You graduated and you were set for life - just “keeping” up in your chosen field. Today when you graduate you’re set for say, 15 minutes. (heheh)
  • What matters now is a student's capacity for learning. Hence colleges should teach meta-learning: learning how to learn.
  • My opinion: Universities will not die, they are too useful given the collaborative nature of human learning: they bring many different people together for the purpose of learning (and perhaps doing research). This is essential, not just for professional learning, but for life-learning (learning from other's experience so you don't have to experience it). Sure, people can learn by consulting google or wikipedia, but it's not nearly as good as face-to-face lectures (where you can ask questions!) or office hours, because the teacher there has some idea what is going on in the student's mind as he/she learns, and can anticipate questions and give relevant guidance based on experience. Google and Wikipedia, for now, cannot do this as well as a good, thoughtful teacher or friend.

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ref: Darmanjian-2006.01 tags: wireless neural recording university Florida Principe telemetry msp430 dsp nordic date: 04-15-2009 20:56 gmt revision:1 [0] [head]

PMID-17946962[0] A reconfigurable neural signal processor (NSP) for brain machine interfaces.

  • use a Texas instruments TMS320VC33 200MFLOPS (yes floating point) DSP,
  • a nordic NRF24L01,
  • a MSP430F1611x as a co-processor / wireless protocol manager / bootloader,
  • an Altera EPM3128ATC100 CPLD for expansion / connection.
  • uses 450 - 600mW in use (running an LMS algorithm).


[0] Darmanjian S, Cieslewski G, Morrison S, Dang B, Gugel K, Principe J, A reconfigurable neural signal processor (NSP) for brain machine interfaces.Conf Proc IEEE Eng Med Biol Soc 1no Issue 2502-5 (2006)

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ref: Linderman-2006.01 tags: neural recording technology compact flash stanford Shenoy 2006 date: 04-15-2009 20:55 gmt revision:3 [2] [1] [0] [head]

PMID-17946450[0] An Autonomous, broadband, multi-channel neural recording system for freely behaving primates

  • goal: recording system for freely-behaving animals.
    • problems: battery life, size
    • cannot sample broadband.
    • non autonomous.
  • solution:
    • compact flash, ARM core
    • accelerometer?
    • mounted inside the monkey's skull in the dental cement.
  • specs


[0] Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV, An autonomous, broadband, multi-channel neural recording system for freely behaving primates.Conf Proc IEEE Eng Med Biol Soc 1no Issue 1212-5 (2006)

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ref: notes-0 tags: programming excellence norvig 10 years date: 04-07-2009 20:26 gmt revision:0 [head]

Teach yourself programming in 10 years

  • points out that, in order to be excellent at any difficult skill/art, you must practice 10 years or 10,000 hours, and this practice must be focused and deliberate.
    • quote: "have shown it takes about ten years to develop expertise in any of a wide variety of areas, including chess playing, music composition, telegraph operation, painting, piano playing, swimming, tennis, and research in neuropsychology and topology"
    • possibly this is partially due to competition - most other people drop out after 10 years!
    • Or this is due to the fact that, for general purpose behaviors, we are really no better than the present gradient descent & reinforcement learning algorithms which require repeated presentation of patterns and behaviors. Where humans achieve sub-gradient/RL performance is where evolution has supplied us with hardware or 'prior assumptions' to bias for a correct solution / correct solution space. These prior assumptions are (part of) that which the make study brain interesting!
  • "Life is short, [the] craft long, opportunity fleeting, experiment treacherous, judgment difficult." -- Hippocrates.

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ref: notes-0 tags: wireless nordic headstage bridge neurorecord pictures photo EMG myopen date: 03-12-2009 02:33 gmt revision:4 [3] [2] [1] [0] [head]

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ref: HilArio-2007.01 tags: Rui Costa endocannabinoid habit reward striatum basal ganglia date: 03-05-2009 19:04 gmt revision:0 [head]

PMID-18958234 Endocannabinoid Signaling is Critical for Habit Formation.

  • quick review (the intro is packed with grat information):
    • in goal-directed learning, behavior is highly sensitive to the incentive value of the outcome, and contingency between the action and the outcome.
    • with repetition actions become both more efficient and more automatic.
    • after extensive training, rats move from goal-directed behavior to more habitual response independent of outcome value.
      • random interval schedules favor this more than random ratio reward schedules.
        • in mice, random interval schedules promoted habit formation, whereas random ratio schedules promoted acquisition of goal-directed behaviors. does this also apply to humans? I would guess so. Might be an interesting tool to have in the toolbox.
        • interval schedules promoted the exploration of a random lever whereas ratio schedules promoted the exploitation of the reward lever.
    • the underlying circuitry supporting goal-directed behav and habit formation are different:
      • goal directed behavior seems to require the associative BG/cortex including:
        • dorsomedial or associative striatum (medial!)
          • COMT, a transporter, is more highly expressed here than DAT.
        • pre-limbic ctx
        • mediodorsal thalamus
      • habit formation requries:
        • dorsolateral or sensorimotor striatum (lateral!)
          • DAT, dopamine transporter, is highly expressed here.
        • infralimbic cortex
    • amphetamine sensitization can lead to increased spine density in medium spiny neurons in the dorsolateral striatum, while decreasing spine density in the dorsomedial striatum. (interesting!)
    • lesions of nigrostriatal input to dorsolateral striatum impairs habit formation;
    • infusion of dopamine into the ventral medial prefrontal cortex favors goal-directed behavior
      • that is a rather broad statement to make ...
  • endocannabinoid release in the striatum is required for LTD induction.
  • endocannabinoid signaling regulated bt DA.
  • CB1 (the receptor implicated in addiction) is highly expressed in the dorsolateral striatum (habit!) at both excitatory and inhibitory terminals.
  • used mice with CB1 mutations therefore!
  • CB1 mutant mice have impaired habit formation and enhanced exploration.
    • suggest that endocannabinoid signaling is critical for both habit formation and increased exploration in interval schedules.

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ref: -0 tags: puerto rico rincon photo panorama date: 01-06-2009 23:28 gmt revision:2 [1] [0] [head]

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ref: -0 tags: san_juan puerto rico panorama photo date: 01-06-2009 06:18 gmt revision:4 [3] [2] [1] [0] [head]

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ref: bookmark-0 tags: bell labs history DSP innovation invention date: 12-15-2008 04:12 gmt revision:0 [head]


  • again, to be annotated after break!

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ref: Churchland-2006.12 tags: motor_noise CNS Churchland execution variance motor_planning 2006 date: 12-08-2008 22:50 gmt revision:2 [1] [0] [head]

PMID-17178410[0] A central source of movement variability.

  • Small variations in preparatory neural activity were predictive of small variations in the upcoming reach
    • About half of the noise in reaching movements seems to be from variability during the preparatory phase, as estimated from regressions between preparatory neural activity and variability in performance.
  • even for a highly practiced task, the ability to repeatedly plan the same movement limits our ability to repeatedly execute the same movement.
  • when cocontraction increases, EMG variablility increases, but movement variability decreases. (This is consistent with poisson-based noise source?)
  • see the related articles!!


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ref: -0 tags: integer trigonometry sin cos fixed point date: 12-03-2008 21:23 gmt revision:5 [4] [3] [2] [1] [0] [head]

We approximated sine and cosine, needed to vector the stepper motor phase currents, in fixed-point arithmetic first in C on linux - where the results could be plotted in matlab - before converting to MSP430 code. Since the trigonometric functions are repeating, we only need a polynomial approximation of sine from 0 to pi/2. The taylor series for sine is

 sin(x) = x - x^3/3! + x^5/5! - x^7/7! ...
; a quick check in matlab showed that the first three terms are enough to get an accurate approximation in the domain of interest. The MSP430 does not have division, however, so we approximated 1/3! = 1/6 as (1/8 + 1/32 + 1/128) and 1/5! = 1/120 as 1/128; division by powers of two is possible with right bit-shift operations. We chose base 11 (5 bits whole, 11 bits fractional) representation to avoid overflow: if 2^11 -> 1, we need to represent (pi/2)^5 -> 9.5 ; ceil(log_2(9.5)) = 4 (plus one bit for safety). The C program below shows this test.

#include <stdio.h>

char qsin(short i){
       //i goes from  0 pi/2 base 11 or...
       // 0 to 3217
       unsigned int cube, fifth, result;
       cube = (i*i) >> 11;
       cube = (cube*i) >> 11; //max = 7937
       fifth = (cube*i) >> 11;
       fifth = (fifth*i) >> 11; // max = 19585
       //our approximation to sine based on taylor series:
       //original: sin(x) = x - x^3/3! + x^5/5!
       //sin(x) = x - x^3*(1/8+1/32+1/128) + x^5*(1/128)
       result = (unsigned int)i -
               ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7);
       //result is base 11.  need it to be base 7.
       result = result >> 4;
       if(result > 127) result = 127;
       return (char)result;
//this is tricky, as it involves shifts, x-inversions, and y-inversions. 
//but it all makes sense if you plot out the respective functions. 
char isin(short i){
       // i is base 2^11
       //but we accept 0 to 2*pi or 12867
       if(i >= 0 && i < 3217) return qsin(i);
       else if(i >= 3217 && i < 6434) return qsin(6434 - i);
       else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434);
       else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i);
       else return 0;
char icos(short i){
       // i is base 2^11
       //but we accept 0 to 2*pi or 12867
       if(i >= 0 && i < 3217) return qsin(3217 - i);
       else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217);
       else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i);
       else if(i >= 9651 && i < 12867) return qsin(i - 9651);
       else return 0;

int main(void){
	short i; 
	for(i=0; i<12867; i++){
		printf("%d\t%f\t%d\t%d\n", i, ((float)i)/2048.0, (int)(isin(i)), (int)(icos(i))); 
	return 0; 

We compiled and ran this program on the command line:

 gcc integer_trig.c 
 ./a.out > test.txt

Then we imported the data into matlab and plotted (Actual double floating-point sine and cosine are plotted on the same axis as thin black and magenta lines, respectively)

Later, we had to change the naive standard implementation of multiply to assembly to properly implement the fixed-point arithmetic - the MSP430's standard library did not implement the 16x16 multiply followed by shift correctly (it only keeps the bottom 16 bits). Note: this assembly function is for use with Code-Composer Studio, available from the Texas Instruments website. It seems that the IAR compiler uses different assembly syntax.

            .cdecls C,LIST,"msp430x54x.h"  ; Include device header file

            .text                           ; Progam Start
          ;;.sect "mply_11"
          ;;.asmfunc "mply_11"
                        .global mply_11 ;; this MUST BE PRECEDED BY TABS !!!!!

        PUSH	SR	; 
         DINT		; turn off interrupts here. 
         NOP			; required after DINT
         MOV.W	R12, &MPY ; load the first operand. 
         MOV.W	R13, &OP2 ; load the second operand & start multiplication. 
         MOV.W	&RESLO, R12 ; low to R12 (this is the return value)
         MOV.W	&RESHI, R13 ; high to R13
         RRA.W R12 ; 1
         RRA.W R12 ; 2
         RRA.W R12 ; 3
         RRA.W R12 ; 4 
         RRA.W R12 ; 5
         RRA.W R12 ; 6
         RRA.W R12 ; 7
         RRA.W R12 ; 8
         RRA.W R12 ; 9
         RRA.W R12 ; 10
         RRA.W R12 ; 11
         RLA.W R13 ; 1
         RLA.W R13 ; 2
         RLA.W R13 ; 3
         RLA.W R13 ; 4
         RLA.W R13 ; 5
        ;; r14 can be clobbered across a function call, according to the msp430 ABI
        MOV.W	#0x001f, R14
        AND.W	R14, R12 ; mask off all but the bottom 5 bits from RESLO
         ADD.W	R13, R12 ; add (logical OR) the results. R12 is the 11-bit fixed point result.
         POP.W 	SR	;
         RETA		; return from subroutine.


Note the MSP430 does not have an opcode for multiple arithmetic shifts, nor does it have code for logical shifts - hence the need for repeated shifts and bitmasks!

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ref: Serruya-2002.03 tags: BMI Donoghue 2002 Hatsopoulos Utah array Serruya date: 09-07-2008 19:08 gmt revision:1 [0] [head]

PMID-11894084[0] Instant neural control of a movement signal.

  • used only a few (7-30) motor cortex neurons
  • this let the monkey immediately manipulate a computer cursor, without extensive training (according to them).


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ref: notes-0 tags: robots Tokyo Institute of Technology date: 09-04-2008 17:30 gmt revision:5 [4] [3] [2] [1] [0] [head]

Robots & others designed & made at the Tokyo Institute of Technology (from the Hirose / Fukushima Robotics lab)

  • snake robots
  • gripper
      • with human-crushing, kid-grabbing power. frightening!
  • walking robots
      • -- 1994. can climb a 70 degree slope!
    • --window washing robot.
    • -- skating robot: walk ; skate. movie -- wow!
  • wheeled robots
  • other
    • -- prismatic, variable-speed eccentric linear drive. sorta like harmonic drive for linear motion? link

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ref: -0 tags: myopen EMG recordings NLMS noise date: 07-29-2008 18:32 gmt revision:2 [1] [0] [head]

Myopen amplifiers & analog/digital filters & NLMS are working properly! Below, a recording from my deltiod as I held my arm up: (only one EMG channel active, ground was my knee))

Yellow traces are raw inputs from ADC, blue are the output from the IIR / adaptive filters; hence, you only see 8 of the 16 channels. Read from bottom to top (need a -1 in some opengl matrix somewhere...) Below, the system with no input except for free wires attached to one channel (and picking up ambient noise). For this channel, NLMS could not remove the square wave - too many harmonics - but for all other channels the algorthim properly removes 60hz interference :)

Now, let me clean this EEG paste off my shoulder & leg ;)

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ref: notes-0 tags: nordic nrf24L01 state diagram flowchart SPI blackfin date: 06-25-2008 02:44 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]


The goal is to use a nRF24L01 to make an asymmetrical, bidirectional link. The outgoing bandwidth should be maximized, ~1.5mbps, and the incoming bandwidth can be much smaller, ~17kbps, though on both channels we want guaranteed latency, < 4ms for the outgoing data, and < 10ms for the incoming data. Furthermore, the processor that is being used to run this, a blackfin BF532, does not seem to play well when both SPI DMA is enabled and most CPU time is being spent in SPORT ISR reading samples & processing them. Fortunately, the SPI port and SPORT can be run synchronously (provided the SPI port is clocked fast enough), allowing the processor to run one 'thread' e.g. no interrupts. It seem that with high-priority interrupts, the DMA engine is not able to service the SPI perfectly, and without DMA, data comes out of the SPI in drips and drabs, and cannot keep the radio's fifo full. Hence, must program a synchronous radio controller, where states are stored in variables and not in the program counter (PC register, saved upon interrupt, etc).

As in other postings on the nRF24L01, the plan is to keep the transmit fifo full for most of the 4ms allowed by the free-running pll, then transition back into either standby-I mode, or send a status packet. The status packet is always acknowledged by the primary receiver with a command packet, and this allows both synchronization and incoming bandwidth. Therefore, there are 4 classes of transfers:

  1. just a status packet. After uploading, wait for TX_DS IRQ, transition to RX mode, wait for RX_DR irq, clear ce, read in the packet, and set back to TX mode.
  2. one data packet + status packet. There are timeouts on both the transmission of data packets and status packets; in this case, both have been exceeded. Here TX data state is entered, the packet is uploaded, CE is asserted, send the status packet, wait for IRQ from both packets. This requires a transition from tx data CE high state to tx status CSN low state.
  3. many data packets and one status packet. This is the same as above, only the data transmission was triggered by a full threshold in the outgoing packet queue (in processor ram). In this case, two packets are uploaded to the radio before waiting for a TX_DS IRQ, and, at the end of the process, we have to wait for two TX_DS IRQs after uploading the data packet.
  4. many data packets. This is straightforward - upload 2 packets, wait for 1 TX_DS IRQ, {upload another, wait for IRQ}(until packets are gone), wait for final IRQ, set CE low.

screenshot of the derived code working (yea, my USB logic analyzer only runs on windows..yeck):

old versions:

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

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

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

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ref: bookmark-0 tags: ECG wireless nordic quasar date: 12-07-2007 21:13 gmt revision:2 [1] [0] [head]

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ref: notes-0 tags: global warming bayes politics plik-l biofuel oil economics date: 11-21-2007 22:20 gmt revision:4 [3] [2] [1] [0] [head]

This was written for the plik-l mailing list, Nov 16 2007

I actually had a bit of an argument yesterday with my dentist, no less, about global warming:
  • Dentist: Hello, how are you today?
  • Tim: Ok.
  • D: Are you still in school?
  • T: <defers complicated explanation for the simplified>
  • D: Oh, so do you believe in global warming?
  • T: <cites scientific study, like http://www.ipcc.ch/ipccreports/assessments-reports.htm>
  • D: Well, i don't believe in it but even if it is happening, nobody is going to stop burning gas.
  • T: Yea, but if gas and electricity were more expensive, then people would make better economic decisions, smaller cars etc.
  • D: That would just prolong the supply. Oil is a great source of energy, and we are not going to stop using it until it become economically infeasible to do it. So, why worry? Oil will be depleted and the C02 will be stuck in the atmosphere, if not by us then by some other country that needs cheap energy to grow its economy, eventually. Economics.
  • T: You seem to be hinting of China, I guess. But, if our leaders decided to let the price of oil float to where it should be, and did not fight wars over it, then there would be greater economic impetus & possibly government funding to develop alternatives to oil. This would give us some energy-independence.
  • D: We are not in iraq for the oil. That's enough now, open up!
  • T: Wait wait! But don't you know what global warming will do to the envirnoment? More storms, droughts, floods, famines, etc - all very expensive, terrible.
  • D: I do not think there is sufficient organization in the world to impose the true costs of burning oil - e.g. the cost, accumulated over the future, of present greedy practices - upon present consumers.
  • T: True, i suppose if we integrated up, the cost would be almost boundless. Hence we should stop burning oil right now!
  • D: A responsibility to the future is not in the nature of man. They eventually die, and are selfish, greedy, and lack foresight during their lives. Besides, abstaining from oil imposes a severe economic disadvantage.
  • T: But what about their - your! children? and the climate then?
  • D: They are going to be rich dentists. See, I'm charging you $50 for 15 minutes of work. It's only going to get better.
  • T: Not if the economy collapses. It seems we have based it on unsustainable growth, fueled by unreasonably cheap energy. This could happen in your lifetime, or mine - and your kids. Present luxury and high wages are based on the efficiency / cheapness of transportation of goods into the US, and the developed world's exploitation of the developing world.
  • D: No. It is based on the labor/economic efficiency of manufacturing and agriculture. Anyway, take Europe for example - the price of oil there is high, and their economy is humming along.
  • T: Yet efficient manufacturing and agriculture is somewhat dependent on cheap transportation. As for Europe, that's because they tax oil to pay for public development, among other things. And Europeans consume half the oil of their American counterparts.
  • D: A gas tax that large would never happen here. People would go nuts, such a law would never pass!
  • T: True. The political system is irrational and irresponsible, but I can't think of an alternative structure. Humans were not designed for this, such responsibility!
  • D: If you keep talking I'm going to have to charge more.
  • T: <opens mouth>

Mostly I'd have to agree with the dentist - the oil is going to be burned eventually, because it is just such a cheap source of energy. We are going to have to deal with the consequences. However, for coal - of which we have a far greater supply, and is considerably more dangerous / expensive to obtain - there is good reason to search for alternatives, and putting a tax on oil/natural gas now fund development of alternatives is probably very future-responsible, and will shift the energy climate so we relinquish coal (and maybe some oil) earlier, resulting in less CO2 in the atmosphere.

There are infinitely many things more worthy/long-range responsible than the war, but our leaders have not touched on that. Correct me if I'm wrong, but there is little evidence that they even measured the worth of all alternatives, and decided rationally, based on integrating (over time and path probability) best-of-present knowledge of benefits and consequences. Or maybe they decided rationally, but with the worth of alternatives measured *personally*. It is this that truly angers me.

Bayes for president 2008!


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ref: notes-0 tags: Nordic RD nrf24l01 problem transceiver date: 11-02-2007 18:00 gmt revision:4 [3] [2] [1] [0] [head]

here is the final, concluding, email i sent to nordic semiconductor concerning my 'troubles' with their chip. I post it here in hopes that it may help somebody else out there via the magic of the internet. See {485} for the development of the mode-switch solution (2) and {484} for the dropped packet investigation.

Hi xxx,

Ok, i figured out both of my problems:

  1. The missing RX_DR IRQ was because I was clearing the RX fifo upon reading outone packet. Because a packet was being received while the SPI was reading it out (the PTX is continually transmitting), this caused the radio to drop the packet before it was completely received. Dumb! dumb!
  2. Concerning my old problem of lost packets during mode switches, I needed to do a number of things to get it to work:
    1. Add inline resistors to keep spi noise out of the radio
    2. Increase the SPI clock on both PTX and PRX, to avoid not being able to read out the packet after one IRQ and before another was received (as you suggested below).
    3. Added a 62us (of course, longer delays also work) delay between transitioning from RX mode to TX mode. During this time I do not assert CE. A delay in for the opposite transition is not needed. Not exactly sure why this is needed, but it works!
    4. On the PRX, when i send the 'acknowlegement' packet, it is necessary to only pulse CE after uploading the packet. Holding CE high until TX_DS IRQ is asserted somehow messes things up. I guess this is described on the state diagram on your spec sheet - it is best to go back into standby-I mode not standby-II, as there is no transition to RX mode from standby-II.

As a result, I'm getting 99.99 % reliability on bidirectional bandwidth of 1.39mbps PTX->PRX and 18.3kbps PRX->PTX. So, I'm a happy person :) :) Hence, I don't have to try another radio solution.

Just wanted to pass the information along in case it would help your other customers.

cheers, Tim Hanson

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ref: notes-0 tags: Nordic RF problem fifo transceiver date: 11-02-2007 17:59 gmt revision:14 [13] [12] [11] [10] [9] [8] [head]

Problem: switching modes on the nordic radios. see also {486}

  1. Standard scheme:
    1. headstage sends 16 data packets as per {484} by keeping the fifo continuously full, then send a status packet (as indicated by the first two bytes), then transitions to RX mode and waits for a reply.
    2. bridge listens & reads in each packet, again as {484}; when it notices that a status packet has been received, it immediately transitions to TX mode and sends out a packet. After waiting for the TX data sent IRQ, it then transitions back into RX mode.
      1. note: at present transitioning between modes flushes both RX and TX fifos.
    3. result: bridge gets 52% of all status packets sent by the headstage ;
    4. result: headstage, in return, receives replies to 47% of its status packets (that means the bridge transmission efficiency is 90.6%. This does not depend on the headstage matching the 2-byte code.
  2. If the headstage only sends one data packet prior the status packet, transmission reliability is not affected
  3. If the headstage sends no data packets hence only the status packet prior to waiting for a reply, the bridge hears exacly half of the status packets, while the headstage seems to hear every one of the bridge's replies.
    1. adding a small delay after setting TX mode marginally affects the reception ratios 51.2% headstage status packets are seen by the bridge, and ~ 90% of the bridge's replies are seen by the headstage.
  4. ok! new development: if a 62us (exactly) delay is inserted between reading out the status-ack packet on the headstage & transitioning to TX mode (e.g. BEFORE transitioning to TX mode), almost all the status packets are received (99.6%). however, if the delay is inserted AFTER transitioning to TX mode, half (exactly) of the status packets are lost. In both cases, the software on the bridge is the same. ''The delay should be essential, as it takes a bit longer for the bridge to switch back to RX mode after transmitting the packet than the headstage from RX to TX. Both transitions are synchronized by TX_DS IRQ on the bridge and RX_DR IRQ on the headstage.
    1. if, upon switching modes, we don't flush both fifos, reliability is decreased (with the 62us delay before switching modes) to 92% status packets received, 83% overall replies sseen on headstage.
    2. the same delay between RX and TX mode is not the same on the bridge -- adding it before decreases performance, adding it after transitioning & before DMA improves performance, provided the TX fifo is flushed upon transition. 100us too much.


  1. put a 62us (minimum) delay between reading in the status ACK packet on the headstage & transitioning to TX mode, to allow the bridge to be in RX mode before we send anything. Presently, i deassert CE during the delay.
  2. only pulse CE on the bridge when sending the packet, don't hold it high until the TX_DS IRQ is asserted. This leaves it in Standby-I mode, not standby-II.
  3. flush the appropriate TX or RX fifo whenever transitioning between modes (e.g. flush the TX fifo after going to TX mode). Not sure why - perhaps it is needed when starting or recovering from lost packets - but it works! Fifos are flushed after writing the configuration register.

present performance:

  txed packets = 118513 
  rxed packets = 118218 
 (note: computer has seen 118512 packets )
 (and 118414 status packets, ratio: 0.999165 )
 (note: 'stage ratio 0.997511 )
(this includes code validation)

now, if i boost the SPI clock on the bridge up to 5 mhz (headstage clock still running at 8.25mhz) to eliminate race-case (?) & add in 16 data packets before the status packets, perfection:

 txed packets = 44151 
 rxed packets = 44151 
 (note: computer has seen 750583 packets )
 (and 44152 status packets, ratio: 1.000023 )
 (note: 'stage ratio 1.000000 )
after adding separate counters for TXed status and TXed data packets:
  txed packets = 808640 
  rxed packets = 50538 
  txed status packets = 50540 
 (note: computer has seen 808639 packets, ratio : 0.999999 )
 (and 50540 status packets, ratio: 1.000000 )
 (note: 'stage ratio 0.999960 )
yay!! almost no dropped packets!!

This equates to :

  • a net incoming (to headstage) bandwidth of 32 * 8 / 3.48ms = 73.5 kbps. This seems like more than plenty - how much do we have to say to the bugger? 1/4 this bandwidth is probably sufficient = 18.375 kbps, or one 32 byte packet every ~ 11.2ms.
  • a net outgoing (from headstage) bandwidth of 32*16*8 bits / 3.48ms = 1.17 mbps
    • this can be tuned further by making the status packet transmission less frequent than once every 16 data packets.
    • 16 packets, with 3 byte address & 2 byte CRC, takes 2.72ms to transmit (CE enable to CE disable); hence, we should be able to transmit 23 packets within the 4ms time that the PLL is synched. ah, but 16 is such a nice number... and it is better not to get too close to device limits.
    • The maximum, excluding PLL resynchs, 1.6mbps (takes 160us to transmit a packet with 2 byte CRC, 5 byte address, and 32 data bytes).
    • The maximum, including pll resynchs every 4ms or less, is about 1.5mbps;
  • With status packet every 4th 16-packet block, we got an observed rate of 1.39mbps (empirical, based on computer's clock, including header, 5431.5 packets/sec) and an incoming bandwidth of about 18.3kbps (as above). This is enough to support 170 spikes/sec (28 sample waveform + header) on each of 32 channels!! :)
  • This is summarized in {487}

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ref: notes-0 tags: Nordic problem fifo transceiver email date: 11-02-2007 17:58 gmt revision:3 [2] [1] [0] [head]

here is an email I wrote to nordic semiconductor technical support concerning switching reception/transmission modes. see also {487} & {485}


I've been having problems with switching modes on the nRF24L01. I want to implement a asymmetric bidirectional link, where there is a periodic (every ~36ms) time when the primary transmitter sends a status packet, then listens for a 32-byte command packet from the primary receiver. The command packet is for conveying configuration information, etc. I am driving both radios with blackfin DSPs using the built-in SPI port @ 4mhz, and am very careful with the CSN signal. The shock-burst feature is not enabled.

Unidirectional transfer works great - I get nearly 0% dropped packets when the primary transmitter & receiver never change modes, up to a rate of about 1.5mbps. Of course, I am careful not to let the radio stay in TX mode for more than 4 ms - every 3ms i give it a 'break' by de-asserting CE.

But bidirectional does not work reliably. Here is my procedure, on the primary transmitter side, for sending a status packet then changing from TX to RX & back to TX, with the initial condition that CE is asserted:

  1. wait until the TX fifo is empty by polling the FIFO_STATUS register through spi
  2. clear TX_DS interrupt in status register
  3. send packet with code 0xa0
  4. wait for TX_DS interrupt on IRQ
  5. deassert CE
  6. flush the RX fifo code 0xe2 (not sure if this is needed, but somehow, it improves reliability).
  7. write the config register with the following bits set: MASK_TX_DS | MASK_MAX_RT | EN_CRC | CRC0 | PWR_UP | PRIM_RX
  8. clear interrupts by writing 0x70 to register 0x07
  9. assert CE
  10. wait for RX_DR iterrupt on IRQ (e.g. wait for a packet from the primary receiver - the reciever has to both read in the status packet and send out command packet through SPI, hence must wait for 544us )
  11. clear interrupts again
  12. read in packet w / 0x61 command
  13. deassert CE
  14. write the config register with the following bits set: MASK_TX_DS | MASK_MAX_RT | EN_CRC | CRC0 | PWR_UP
  15. clear interrupts by writing 0x70 to register 0x07
  16. assert CE

The process on the primary receiver is basically the same, but inverted. Upon receiving a packet of the correct type, it switches to transmit mode, sends off a packet, waits for the TX_DS interrupt, and switches back to RX mode.

Like I said, when the transmitter and receiver never switch modes, the packets always get through without any corruption. When they switch roles for one packet, only ~ 78% get through, making the status packet -> command packet reply about 62% reliable. This is when the radio is only sending status packets - hence mostly it is in what the datasheet calls 'standby-II mode'. When the radio is also transmitting data packets, the status packet -> command packet relay is about 79% reliable, suggesting that the first packet after a switch from RX to TX mode is somehow being lost. Indeed, when I look at the IRQ signals on an oscilloscope, it is apparent that a certain percentage of the time the TX_DS interrupt is not followed by a RX_DR interrupt.

so - what am I doing wrong??!! I'm desperate to make this work, and have tried almost every permutation!

thanks, Tim Hanson

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ref: notes-0 tags: nordic RF problem fifo date: 11-01-2007 18:03 gmt revision:16 [15] [14] [13] [12] [11] [10] [head]

experimential results with the Nordic nRF24l01 (recall, as per {477}, that all SPI signals have an in-line 100 ohm resistor on both the headstage and bridge)

  1. If the bridge is a transmitter & the headstage is a receiver, we let the DMA finish before asserting CE, we continuously pool the SPI bus on the headstage, and read the packet entirely in, then almost all packets get through (by my rough oscilloscope measuring). This requires 420us per packet, 290 to actually transmit the packet and 130 for SPI maneuvers.
    1. If this direction is reversed (normal: headstage is the transmitter & bridge is the receiver), the packet reliability is increased. The headstage takes 350us to transmit one packet -- 60us for SPI transation ( can run at a higher speed, as it the bus traces on that board are smaller). However, the reliability of the link in both regimes > 95%.
  2. If the fifo is filled (3 packets) on the headstage side, then CE is pulsed, only the first and third packet get through, with 320 us between each packet. again, SPI bus is polled on the bridge (receiver) side. Reception of the first packet is reliable, reception of the third is not so much. Clearing the RX fifo increases reliability of receiving the third packet.
    1. This is not affected by disabling 2-byte CRC.
    2. This is not affected by doing non-dma SPI transfers.
    3. If i press my finger on the crystal oscillator next to the nRF24l01 (presumably thereby affecting tuning, sometimes only the second packet is received , but still never all 3.
  3. Now, if we offer the same regime & listen for the IRQ pin to go low, then clear the status, the bridge receives all 3 packets, but not always - it only gets every other group of 3 packets.
    1. This is not affected by disabling CRC, nor does it seem to be affected by channel selection.
    2. This is dependent on clearing the RX fifo after reception -- of course, clearing the RX fifo while a packet is in the air will cause that packet to be rejected
  4. If the fifo is not filled (2 packets) on the headstage (= transmitter), then CE is pulsed, the first packet gets through, and the second one does, too (sometimes)
    1. This is not affected by disabling CRC nor by changing the radio channel.
  5. If the fifo is not filled (2 packets) on the bridge (= transmitter), then CE is pulsed, only the first packet gets through
  6. if we reverse the order - have the bridge send 3 packets over SPI then assert CE, and set the headstage to listen & immediately clear the IRQ on interception, the first packet is most always received, the third packet is usually received, but the second packet is never received.
    1. if we do the same as above, and read the entire packet over SPI & use polling to see when another packet is received, then once again both the first and second packets are received properly. The polling implies that noise from the SPI bus is not corrupting packet reception.
  7. Again, if we do pipelined transmission from headstage to bridge by keeping the fifo consistently full, then every other packet is dropped -- see {477}
I wish i had pictures for this.. wish i had a webcam!

finally, it is solved!

  1. don't clear the IRQ status multiple times
  2. don't poll the bus to see if there is a packet - wait for the IRQ pin, then read the packet in.
  3. don't clear the TX fifo or RX fifo, except in time of error or when starting up.
  4. keepin the fifo one-full works with a headstage (= transmitter) SPI clock of 8.25mhz. at this rate, can upload 2 packets before 1 is transmitted.

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ref: notes-0 tags: nordic fifo problem radio tranciever date: 11-01-2007 05:50 gmt revision:5 [4] [3] [2] [1] [0] [head]

I've been having problems transmitting packets in a pipelined fashion using the nordic nRF24L01 tranciever IC. Namely, I cannot send multiple packets at once by keeping the on-chip 3-packet fifo full (note packets are 32 bytes data, max; with header/CRC, they are close to 40 bytes). If this fifo is full, the radio should remain in transmit mode - see {470}, and also {484}

Above, what happens when I let the fifo go dry / empty, and force the PLL to resync for each transmitted packet, as per the following sequence:

  1. write a packet via SPI
  2. assert CE
  3. wait for the TX data sent IRQ to be asserted (0). This requires pll resync (130 us) and packet transmission (160us @ 2mbps)
  4. clear IRQ via SPI
  5. deassert CE
  6. if packet # < 16, go back to step 1.
The bottom trace is the receiver's IRQ line, which is 0 when data is received. I send them in groups of 16 so as to be as idential as possible to below, where it is necessary to get the radio out of TX mode to re-synch the pll. (however, it is possible to send indefinitely in this way..) On the receiver side, packets are either read in using DMA, or the RX fifo is cleared using the associated SPI command - either one works fine.

Note just about all packets are received properly and that the RX irq closely follows the TX irq.

Above, what happens when i try to pipeline transmission, e.g.

  1. upload a packet via SPI
  2. assert CE, force PLL to re-sync
  3. upload another packet
  4. wait for the data sent IRQ from the preceding packet & clear IRQ using SPI
  5. if packet number < 16, go back to step 3
  6. otherwise, wait for the final packet IRQ & clear using SPI
  7. de-assert CE
  8. wait 1ms or so.
The sequence should force the radio to stay in transmit mode for 16 sequential packets, and indeed the transmitter's IRQ line reflects this. However, only half of the (seemingly) transmitted packets are received, as indicated by the receiver's IRQ line, the bottom trace. What? I've been careful not to exceed the 4ms pll resync timeout. Also, the order of received packets sometimes changes - usually it gets the first packet in a group, but sometimes it does not (left segment of bottom trace).

One initial theory was that noise on the SPI bus was corrupting the packets. However:

  • If it was noise on the transmitter's bus, then every packet would be corrupted, as there is transmitter SPI activity (e.g. packet upload) during radio transmission of all but the last packet in a group.
  • If it was noise on the receiver, then continually polling the 'status' (0x07) and 'fifostatus' (0x17) registers would cause more packets to be dropped. However, i can poll using SPI with the transmission scheme in the first figure (wait for packet to be on the air before sending another), and will not get any more dropped packets than usual.
  • I tried adding 100 ohm resistors to all SPI signals on both the transmitter and receiver, but this did not affect the problem.
This is somewhat of a show-stopper for me...
  • If it takes 330us (130us pll sync, 160 to transnmit, 40us for SPI delays) to send 32 bytes, then the aggregate rate is only 775kbps, or 38% utilization of the 2mpbs radio, equivalent to a max 108 wf/sec/32 channels.
  • If i can use the fifos and pipeline the transmission, can get > 1.08 mbps, or 54% utilization, or 150wf/sec/32channels.
The latter is much more acceptable, as neurons can have firing rates > 100hz but not usually > 150hz.

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ref: picture-0 tags: nordic state control diagram radio date: 10-22-2007 18:58 gmt revision:2 [1] [0] [head]

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ref: notes-0 tags: nordic pinout nRF24L01 spark fun electronics date: 10-09-2007 19:59 gmt revision:5 [4] [3] [2] [1] [0] [head]

nordic semi links:

here is the connection list for the nRF24L01 module made by sparkfunelectronics
  1. VCC
  2. CE
  3. CSN
  4. SCK
  5. MOSI
  6. MISO
  7. IRQ
  8. GND
(1 is by the voltage regulator, obviously.) reversed:
  1. GND
  2. IRQ
  3. MISO
  4. MOSI
  5. SCK
  6. CSN
  7. CE
  8. VCC

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ref: bookmark-0 tags: quotes wisdom economist date: 10-08-2007 03:05 gmt revision:0 [head]


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ref: notes-0 tags: Phelps economist nobel date: 10-06-2007 22:55 gmt revision:2 [1] [0] [head]

  • nobel prize-winning economist
  • http://economistsview.typepad.com/economistsview/2006/10/phelps_dynamic_.html
    • one of my intense dislikes of capitalism is the vast duplication of information and effort; many corporations have to do, basically, the exact same thing, many times over. this is also why i like open-source software (besides the fact that i can use it to do things!)
    • Phelps says: "Not having to fear fluid market conditions, an entrenched company could afford to develop radical innovation. " yes, but will they want to ?
    • he also points out, correctly, that pluralism, means that there are many different ideas and many different ways to finance them, leading to greater 'dynamism'.
    • he also (seems to) misrepresents the efficiency of american and continental workers - French workers outproduce American workers on an hourly basis
    • the comments are really good on this page:

Its also very difficult to compare western euro productivty to US productivity due to healthcare costs. The US system employs a payroll deduction to lessen the input of the employer and reduce ECI while the european system does not. Further, this underweights those costs in CPI. Statisticians in europe catch that difference while the BLS does not.

One could point out, for example, that Europeans enjoy more leisure time, better health, less poverty, less inequality and thus more economic security, greater intergenerational economic mobility, better access to high-quality social services like health care and education, and manage to do it all in a far more environmentally sustainable way (Europe generates about half the CO2 emissions for the same level of GDP) compared to the US. I bet these facts don't show up in McKinsey's business productivity study.

Then there are the aspects of the American model that may be impossible and unwise for Europeans to copy, but boost US productivity statistics nonetheless: Much of the surprising acceleration of U. S. productivity growth since 1995 originates in the trade sector, particularly retail trade . . . perhaps the most important factor of production in making this format possible is a large plot of virgin land which is much more widely available in the sprawling American metropolitan areas . . . The American explosion of productivity growth in retailing calls attention to basic life-style choices that constitute yet another form of ʺAmerican Exceptionalism.ʺ While the American form of metropolitan organization may promote productivity growth, Europeans are rightly skeptical of unmeasured costs of low urban density in America as promoted by explicit government policies. Europeans decry side-effects of the American system that may promote productivity without creating consumer welfare, including excess energy use, pollution, and time spent in traffic congestion. Tom Geraghty.

  • we are financing some of our growth with the consumption of a huge national resource: our land, our environment.

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ref: bookmarks-0 tags: neurotechnology companies date: 08-30-2007 17:02 gmt revision:0 [head]

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ref: bookmark-0 tags: optimization function search matlab linear nonlinear programming date: 08-09-2007 02:21 gmt revision:0 [head]


very nice collection of links!!

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ref: bookmark-0 tags: federal reserve video printing money economics date: 06-01-2007 20:32 gmt revision:0 [head]


need to learn more about this infamous federal reserve!

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ref: notes-0 tags: entrepreneur MIT notes LLC tax law securities advice date: 05-22-2007 15:25 gmt revision:0 [head]


  • many good articles on setting up a subchapter S corporation (only taxed once, with limitations), LLC, obtaining good employees, dealing with securities and investment, etc!

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ref: Ojakangas-2006.12 tags: BMI Donoghue prosthetic DBS prefrontal cortex planning date: 04-09-2007 22:32 gmt revision:3 [2] [1] [0] [head]

PMID-17143147[0] Decoding movement intent from human premotor cortex neurons for neural prosthetic applications

  • they suggest using additional frontal areas beyond M1 to provide signal sources for human neuromotor prosthesis.
    • did recording in prefrontal cortex during DBS surgeries.
    • these neurons were able to provide information about movement planning production, and decision-making.
  • unusual for BMI studies, their significance levels are near 0.02 - they show distros of % correct based on a ML decoding scheme.


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ref: Bair-1996.08 tags: precise spike timing cortex behavior Sejnowski date: 04-09-2007 00:57 gmt revision:0 [head]

PMID-8768391[0] Temporal precision of spike trains in extrastriate cortex of the behaving macaque monkey

  • This temporal modulation is stimulus dependent, being present for highly dynamic random motion but absent when the stimulus translates rigidly -- that is, the response is markedly reproducable and precise to a few milliseconds.

PMID-16339894[1] Neurons of the cerebral cortex exhibit precise interspike timing in correspondence to behavior.

  • in the cortex, spikes can be very precise.
  • this was a slice investigation.

PMID-7770778[2] Reliability of spike timing in neocortical neurons.

  • neocortex of rats
  • suggest low intrinsic noise level in spike generation, allowing accurate transformation of synaptic input into spike generation


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ref: Wood-2004.01 tags: spikes sorting BMI Black Donoghue prediction kalman date: 04-06-2007 21:57 gmt revision:2 [1] [0] [head]

PMID-17271178[0] automatic spike sorting for neural decoding

  • idea: select the number of units (and, indeed, clustering) based on the ability to predict a given variable. makes sense!
  • results:
    • human sorting: 13,5 cm^2 MSE
    • automatic spike sorting: 11.4 cm^2 MSE
      • yes, I know, the increase is totally dramatic.
  • they do not say if this could be implemented in realtime or not. hence, probably not.


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ref: Teich-1997.03 tags: fractal LGN RGC electrophysiology SUA fano_factor date: 02-05-2007 19:00 gmt revision:0 [head]

PMID-9058948[0] Fractal character of the neural spike train in the visual system of the cat

  • excellent description of several analyses of point-process spike trains (here RGC and LGN cells): interevent-interval histogram, rescaled range analysis, the event-number histogram, the Fano factor, the Allan factor, and the periodogram.



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ref: Vyssotski-2006.02 tags: neurologger neural_recording recording_technology EEG SUA LFP electrical engineering date: 02-05-2007 06:21 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-16236777[0] Miniature neurologgers for flying pigeons: multichannel EEG and action and field potentials in combination with GPS recording.

Recording neuronal activity of animals moving through their natural habitat is difficult to achieve by means of conventional radiotelemetry. This illustration shows a new approach, exemplified by a homing pigeon carrying both a small GPS path recorder and a miniaturized action and field potential logger (“neurologger”), the entire assembly weighing maximally 35 g, a load carried easily by a pigeon over a distance of up to 50 km. Before release at a distant location, the devices are activated and store both positional and neuronal activity data during the entire flight. On return to the loft, all data are downloaded and can be analyzed using software for path analysis and electrical brain activity. Thus single unit activity or EEG patterns can be matched to the flight path superimposed on topographical maps. Such neurologgers may also be useful for a variety of studies using unrestrained laboratory animals in different environments or test apparatuses. The prototype on the hand-held pigeon records and stores EEG simultaneously from eight channels up to 47 h, or single unit activity from two channels during 9 h, but the number of channels can be increased without much gain in weight by sandwiching several of these devices. Further miniaturization can be expected. For details, see Vyssotski AL, Serkov AN, Itskov PM, Dell Omo G, Latanov AV, Wolfer DP, and Lipp H-P. Miniature neurologgers for flying pigeons: multichannel EEG and action and field potentials in combination with GPS recording. [1]


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ref: learning-0 tags: motor control primitives nonlinear feedback systems optimization date: 0-0-2007 0:0 revision:0 [head]

http://hardm.ath.cx:88/pdf/Schaal2003_LearningMotor.pdf not in pubmed.

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ref: Flash-2001.12 tags: Flash Sejnowski 2001 computational motor control learning PRR date: 0-0-2007 0:0 revision:0 [head]

PMID-11741014 Computational approaches to motor control. Tamar Flash and Terry Sejnowski.

  • PRR = parietal reach region
  • essential controviersies (to them):
    • the question of motor variables that are coded by neural populations.
    • equilibrium point control vs. inverse dynamics (the latter is obviously better/more correct)

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ref: notes-0 tags: spike patterns neural response LGN spike_timing Sejnowski vision date: 0-0-2006 0:0 revision:0 [head]


  • quote: " when a cortical neuron is repeatedly injected with the same fluctuating current stimulus, the timing of the spikes is highly precise from trial to trial and the spike pattern appears to be unique"
    • though: I'd imagine that somebody has characterized the actual transfer function of this.
  • mais: we conclude that the prestimulus history of a neuron may influence the precise timing of the spikes in repsonse to a stimulus over a wide range of time scales.
  • in vivo, it is hard to find patterns because neurons may jump between paterns & there is a large ammount of neuronal noise in there too. or there may be neural "attractors".
  • they observed long-term (seconds) firing patterns in cat LGN (interesting)

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


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ref: bookmark-0 tags: statistics logistic regression binomial logit BIC AIC SPSS date: 0-0-2006 0:0 revision:0 [head]


  • transform probabilities into logarithmic variables = logits

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ref: bookmark-0 tags: neural_recording recording_technology electrical engineering DSP date: 0-0-2006 0:0 revision:0 [head]

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ref: Dunn-2005.07 tags: immunology cancer edithing interferon date: 0-0-2006 0:0 revision:0 [head]

PMID-15951814 article --

  • sarcoma = cancer of the connective tissue.
  • RAG2 deficient mice lack mature thymocytes (T & B) PMID-1547487
  • MCA = carcinogen methylcholanthrene
  • review of immunoediting PMID-17063185
  • Regulation of MHC class II - MHC class II expression can be induced in any cell by interferon-gamma via CIITA.
  • Interferon-alpha: All type I IFNs bind to a specific cell surface receptor complex known as the IFN-α receptor (IFNAR) that consists of IFNAR1 and IFNAR2 chains.
    • there are a great many interferon type 1, many of them (so far characterized) are alpha

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ref: Wu-2004.06 tags: Switching Kalman Filter BMU Wei Wu Donoghue date: 0-0-2006 0:0 revision:0 [head]

PMID-15188861 Modeling and Decoding Motor Cortical Activity Using a Switching Kalman Filter