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[0] Gage GJ, Ludwig KA, Otto KJ, Ionides EL, Kipke DR, Naive coadaptive cortical control.J Neural Eng 2:2, 52-63 (2005 Jun)

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

[0] Lin SC, Nicolelis MA, Neuronal ensemble bursting in the basal forebrain encodes salience irrespective of valence.Neuron 59:1, 138-49 (2008 Jul 10)

[0] Isoda M, Hikosaka O, Switching from automatic to controlled action by monkey medial frontal cortex.Nat Neurosci 10:2, 240-8 (2007 Feb)

[0] Fetz EE, Volitional control of neural activity: implications for brain-computer interfaces.J Physiol 579:Pt 3, 571-9 (2007 Mar 15)

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

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ref: -2020 tags: dreamcoder ellis program induction ai tenenbaum date: 10-10-2021 17:32 gmt revision:2 [1] [0] [head]

DreamCoder: Growing generalizable, interpretable knowledge with wake-sleep Bayesian program learning

  • Kevin Ellis, Catherine Wong, Maxwell Nye, Mathias Sable-Meyer, Luc Cary, Lucas Morales, Luke Hewitt, Armando Solar-Lezama, Joshua B. Tenenbaum

This paper describes a system for adaptively finding programs which succinctly and accurately produce desired output. These desired outputs are provided by the user / test system, and come from a number of domains:

  • list (as in lisp) processing,
  • text editing,
  • regular expressions,
  • line graphics,
  • 2d lego block stacking,
  • symbolic regression (ish),
  • functional programming,
  • and physcial laws.
Some of these domains are naturally toy-like, eg. the text processing, but others are deeply impressive: the system was able to "re-derive" basic physical laws of vector calculus in the process of looking for S-expression forms of cheat-sheet physics equations. These advancements result from a long lineage of work, perhaps starting from the Helmholtz machine PMID-7584891 introduced by Peter Dayan, Geoff Hinton and others, where onemodel is trained to generate patterns given context (e.g.) while a second recognition module is trained to invert this model: derive context from the patterns. The two work simultaneously to allow model-exploration in high dimensions.

Also in the lineage is the EC2 algorithm, which most of the same authors above published in 2018. EC2 centers around the idea of "explore - compress" : explore solutions to your program induction problem during the 'wake' phase, then compress the observed programs into a library by extracting/factoring out commonalities during the 'sleep' phase. This of course is one of the core algorithms of human learning: explore options, keep track of both what worked and what didn't, search for commonalities among the options & their effects, and use these inferred laws or heuristics to further guide search and goal-setting, thereby building a buffer attack the curse of dimensionality. Making the inferred laws themselves functions in a programming library allows hierarchically factoring the search task, making exploration of unbounded spaces possible. This advantage is unique to the program synthesis approach.

This much is said in the introduction, though perhaps with more clarity. DreamCoder is an improved, more-accessible version of EC2, though the underlying ideas are the same. It differs in that the method for constructing libraries has improved through the addition of a powerful version space for enumerating and evaluating refactors of the solutions generated during the wake phase. (I will admit that I don't much understand the version space system.) This version space allows DreamCoder to collapse the search space for re-factorings by many orders of magnitude, and seems to be a clear advancement. Furthermore, DreamCoder incorporates a second phase of sleep: "dreaming", hence the moniker. During dreaming the library is used to create 'dreams' consisting of combinations of the library primitives, which are then executed with training data as input. These dreams are then used to train up a neural network to predict which library and atomic objects to use in given contexts. Context in this case is where in the parse tree a given object has been inserted (it's parent and which argument number it sits in); how the data-context is incorporated to make this decision is not clear to me (???).

This neural dream and replay-trained neural network is either a GRU recurrent net with 64 hidden states, or a convolutional network feeding into a RNN. The final stage is a linear ReLu (???) which again is not clear how it feeds into the prediction of "which unit to use when". The authors clearly demonstrate that the network, or the probabalistic context-free grammar that it controls (?) is capable of straightforward optimizations, like breaking symmetries due to commutativity, avoiding adding zero, avoiding multiplying by one, etc. Beyond this, they do demonstrate via an ablation study that the presence of the neural network affords significant algorithmic leverage in all of the problem domains tested. The network also seems to learn a reasonable representation of the sub-type of task encountered -- but a thorough investigation of how it works, or how it might be made to work better, remains desired.

I've spent a little time looking around the code, which is a mix of python high-level experimental control code, and lower-level OCaml code responsible for running (emulating) the lisp-like DSL, inferring type in it's polymorphic system / reconciling types in evaluated program instances, maintaining the library, and recompressing it using aforementioned version spaces. The code, like many things experimental, is clearly a work-in progress, with some old or unused code scattered about, glue to run the many experiments & record / analyze the data, and personal notes from the first author for making his job talks (! :). The description in the supplemental materials, which is satisfyingly thorough (if again impenetrable wrt version spaces), is readily understandable, suggesting that one (presumably the first) author has a clear understanding of the system. It doesn't appear that much is being hidden or glossed over, which is not the case for all scientific papers.


With the caveat that I don't claim to understand the system to completion, there are some clear areas where the existing system could be augmented further. The 'recognition' or perceptual module, which guides actual synthesis of candidate programs, realistically can use as much information as is available in DreamCoder as is available: full lexical and semantic scope, full input-output specifications, type information, possibly runtime binding of variables when filling holes. This is motivated by the way that humans solve problems, at least as observed by introspection:
  • Examine problem, specification; extract patterns (via perceptual modules)
  • Compare patterns with existing library (memory) of compositionally-factored 'useful solutions' (this is identical to the library in DreamCoder)* Do something like beam-search or quasi stochastic search on selected useful solutions. This is the same as DreamCoder, however human engineers make decisions progressively, at runtime so-to-speak: you fill not one hole per cycle, but many holes. The addition of recursion to DreamCoder, provided a wider breadth of input information, could support this functionality.
  • Run the program to observe input-output .. but also observe the inner workings of the program, eg. dataflow patterns. These dataflow patterns are useful to human engineers when both debugging and when learning-by-inspection what library elements do. DreamCoder does not really have this facility.
  • Compare the current program results to the desired program output. Make a stochastic decision whether to try to fix it, or to try another beam in the search. Since this would be on a computer, this could be in parallel (as DreamCoder is); the ability to 'fix' or change a DUT is directly absent dreamcoder. As an 'deeply philosophical' aside, this loop itself might be the effect of running a language-of-thought program, as was suggested by pioneers in AI (ref). The loop itself is subject to modification and replacement based on goal-seeking success in the domain of interest, in a deeply-satisfying and deeply recursive manner ...
At each stage in the pipeline, the perceptual modules would have access to relevant variables in the current problem-solving context. This is modeled on Jacques Pitrat's work. Humans of course are even more flexible than that -- context includes roughly the whole brain, and if anything we're mushy on which level of the hierarchy we are working.

Critical to making this work is to have, as I've written in my notes many years ago, a 'self compressing and factorizing memory'. The version space magic + library could be considered a working example of this. In the realm of ANNs, per recent OpenAI results with CLIP and Dall-E, really big transformers also seem to have strong compositional abilities, with the caveat that they need to be trained on segments of the whole web. (This wouldn't be an issue here, as Dreamcoder generates a lot of its own training data via dreams). Despite the data-inefficiency of DNN / transformers, they should be sufficient for making something in the spirit of above work, with a lot of compute, at least until more efficient models are available (which they should be shortly; see AlphaZero vs MuZero).

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ref: -2021 tags: gated multi layer perceptrons transformers ML Quoc_Le Google_Brain date: 08-05-2021 06:00 gmt revision:4 [3] [2] [1] [0] [head]

Pay attention to MLPs

  • Using bilinear / multiplicative gating + deep / wide networks, you can attain similar accuracies as Transformers on vision and masked language learning tasks! No attention needed, just a in-network multiplicative term.
  • And the math is quite straightforward. Per layer:
    • Z=σ(XU),,Z^=s(Z),,Y=Z^V Z = \sigma(X U) ,, \hat{Z} = s(Z) ,, Y = \hat{Z} V
      • Where X is the layer input, σ\sigma is the nonlinearity (GeLU), U is a weight matrix, Z^\hat{Z} is the spatially-gated Z, and V is another weight matrix.
    • s(Z)=Z 1(WZ 2+b) s(Z) = Z_1 \odot (W Z_2 + b)
      • Where Z is divided into two parts along the channel dimension, Z 1Z 2Z_1 Z_2 . 'circleDot' is element-wise multiplication, and W is a weight matrix.
  • You of course need a lot of compute; this paper has nice figures of model accuracy scaling vs. depth / number of parameters / size. I guess you can do this if you're Google.

Pretty remarkable that an industrial lab freely publishes results like this. I guess the ROI is that they get the resultant improved ideas? Or, perhaps, Google is in such a dominant position in terms of data and compute that even if they give away ideas and code, provided some of the resultant innovation returns to them, they win. The return includes trained people as well as ideas. Good for us, I guess!

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ref: -2018 tags: luke metz meta learning google brain sgd model mnist Hebbian date: 08-05-2021 01:07 gmt revision:2 [1] [0] [head]

Meta-Learning Update Rules for Unsupervised Representation Learning

  • Central idea: meta-train a training-network (a MLP) which trains a task-network (also a MLP) to do unsupervised learning on one dataset.
  • The training network is optimized through SGD based on small-shot linear learning on a test set, typically different from the unsupervised training set.
  • The training-network is a per-weight MLP which takes in layer input, layer output, and a synthetic error (denoted η\eta ), and generates a and b, which are then fed into an outer-product Hebbian learning rule.
  • η\eta itself is formed through a backward pass through weights VV , which affords something like backprop -- but not exactly backprop, of course. See the figure.
  • Training consists of building up very large, backward through time gradient estimates relative to the parameters of the training-network. (And there are a lot!)
  • Trained on CIFAR10, MNIST, FashionMNIST, IMDB sentiment prediction. All have their input permuted to keep the training-network from learning per-task weights. Instead the network should learn to interpret the statistics between datapoints.
  • Indeed, it does this -- albeit with limits. Performance is OK, but only if you only do supervised learning on the very limited dataset used in the meta-optimization.
    • In practice, it's possible to completely solve tasks like MNIST with supervised learning; this gets to about 80% accuracy.
  • Images were kept small -- about 20x20 -- to speed up the inner loop unsupervised learning. Still, this took on the order of 200 hours across ~500 TPUs.
  • See, as a comparison, Keren's paper, Meta-learning biologically plausible semi-supervised update rules. It's conceptually nice but only evaluates the two-moons and two-gaussian datasets.

This is a clearly-written, easy to understand paper. The results are not highly compelling, but as a first set of experiments, it's successful enough.

I wonder what more constraints (fewer parameters, per the genome), more options for architecture modifications (e.g. different feedback schemes, per neurobiology), and a black-box optimization algorithm (evolution) would do?

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ref: -0 tags: DNA paint FRET tag superresolution imaging oligos date: 02-20-2020 16:28 gmt revision:1 [0] [head]

Accelerated FRET-PAINT Microscopy

  • Well isn't that smart -- they use a FRET donor, which is free to associate and dissociate form a host DNA strand, and a more-permanently attached DNA acceptor, which blinks due to FRET, for superresolution imaging.
  • As FRET acceptors aren't subject to bleaching (or, perhaps, much less subject to bleaching), this eliminates that problem...
  • However, the light levels used ~1kW / cm^2, does damage the short DNA oligos, which interferes with reversible association.
  • Interestingly, CF488 donor showed very little photobleaching; DNA damage was instead the limiting problem.
    • Are dyes that bleach more slowly better at exporting their singlet oxygen (?) or aberrant excited states (?) to neighboring molecules?

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ref: Gage-2005.06 tags: naive coadaptive control Kalman filter Kipke audio BMI date: 09-13-2019 02:33 gmt revision:2 [1] [0] [head]

PMID-15928412[0] Naive coadaptive Control May 2005. see notes

____References____

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ref: -0 tags: optical gain media lasers cross section dye date: 06-13-2019 15:13 gmt revision:2 [1] [0] [head]

Eminently useful. Source: https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-974-fundamentals-of-photonics-quantum-electronics-spring-2006/lecture-notes/chapter7.pdf

Laser Dye technology by Peter Hammond

  • This paper is another great resource!
  • Lists the stimulated emission cross-section for Rhodamine-6G as 4e-16 @ 550nm, consistent with the table above.
  • At a (high) concentration of 2mMol (1 g/l), 1/e penetration depth is 20um.
    • Depending on the solvent, there may be aggregation and stacking / quenching.
  • Tumbling time of Rhodamine 6G in ethanol is 20 to 300ps; fluorescence lifetime in oscillators is 10's of ps, so there is definitely polarization sensitive amplification.
  • Generally in dye lasers, the emission cross-section must be higher than the excited state absorption, σ eσ \sigma_e - \sigma^\star most important.
  • Bacteria can actually subsist on rhodamine-similar sulfonated dyes in aqueous solutions! Wow.

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ref: -2019 tags: lillicrap google brain backpropagation through time temporal credit assignment date: 03-14-2019 20:24 gmt revision:2 [1] [0] [head]

PMID-22325196 Backpropagation through time and the brain

  • Timothy Lillicrap and Adam Santoro
  • Backpropagation through time: the 'canonical' expansion of backprop to assign credit in recurrent neural networks used in machine learning.
    • E.g. variable rol-outs, where the error is propagated many times through the recurrent weight matrix, W TW^T .
    • This leads to the exploding or vanishing gradient problem.
  • TCA = temporal credit assignment. What lead to this reward or error? How to affect memory to encourage or avoid this?
  • One approach is to simply truncate the error: truncated backpropagation through time (TBPTT). But this of course limits the horizon of learning.
  • The brain may do BPTT via replay in both the hippocampus and cortex Nat. Neuroscience 2007, thereby alleviating the need to retain long time histories of neuron activations (needed for derivative and credit assignment).
  • Less known method of TCA uses RTRL Real-time recurrent learning forward mode differentiation -- δh t/δθ\delta h_t / \delta \theta is computed and maintained online, often with synaptic weight updates being applied at each time step in which there is non-zero error. See A learning algorithm for continually running fully recurrent neural networks.
    • Big problem: A network with NN recurrent units requires O(N 3)O(N^3) storage and O(N 4)O(N^4) computation at each time-step.
    • Can be solved with Unbiased Online Recurrent optimization, which stores approximate but unbiased gradient estimates to reduce comp / storage.
  • Attention seems like a much better way of approaching the TCA problem: past events are stored externally, and the network learns a differentiable attention-alignment module for selecting these events.
    • Memory can be finite size, extending, or self-compressing.
    • Highlight the utility/necessity of content-addressable memory.
    • Attentional gating can eliminate the exploding / vanishing / corrupting gradient problems -- the gradient paths are skip-connections.
  • Biologically plausible: partial reactivation of CA3 memories induces re-activation of neocortical neurons responsible for initial encoding PMID-15685217 The organization of recent and remote memories. 2005

  • I remain reserved about the utility of thinking in terms of gradients when describing how the brain learns. Correlations, yes; causation, absolutely; credit assignment, for sure. Yet propagating gradients as a means for changing netwrok weights seems at best a part of the puzzle. So much of behavior and internal cognitive life involves explicit, conscious computation of cause and credit.
  • This leaves me much more sanguine about the use of external memory to guide behavior ... but differentiable attention? Hmm.

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ref: -0 tags: Airy light sheet microscopy attenuation compensation LSM imaging date: 02-19-2019 04:51 gmt revision:1 [0] [head]

Light-sheet microscopy with attenuation-compensated propagation-invariant beams

  • Ah ... beautiful illustration of the airy light sheet concept.
  • In practice, used a LCOS SLM to generate the beam (as .. phase matters!) plus an AOM to scan the beam.
    • Microscope can operate either in SPIM (single plane imaging microscope) or DSLM (digital scanning light sheet microscope),
  • Improves signal-to-background ratio (SBR) and contrast-to-noise ratio (CNR) (not sure why they don't use SNR..?)

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ref: -0 tags: tissue response indwelling implants dialysis kozai date: 04-04-2018 00:28 gmt revision:1 [0] [head]

PMID-25546652 Brain Tissue Responses to Neural Implants Impact Signal Sensitivity and Intervention Strategies

  • (Interesting): eight identical electrode arrays implanted into the same region of different animals have shown that half the arrays continue to record neural signals for >14 weeks while in the other half of the arrays, single-unit yield rapidly degraded and ultimately failed over the same timescale.
  • In another study, aimed at uncovering the time course of insertion-related bleeding and coagulation, electrodes were implanted into the cortex of rats at varying time intervals (−120, −90, −60, −30, −15, and 0 min) using a micromanipulator and linear motor with an insertion speed of 2 mm/s.40 The results showed dramatic variability in BBB leakage that washed out any trend (Figure 3), suggesting that a separate underlying cause was responsible for the large inter- and intra-animal variability.

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ref: -0 tags: recurrent cortical model adaptation gain V1 LTD date: 03-27-2018 17:48 gmt revision:1 [0] [head]

PMID-18336081 Adaptive integration in the visual cortex by depressing recurrent cortical circuits.

  • Mainly focused on the experimental observation that decreasing contrast increases latency to both behavioral and neural response (latter in the later visual areas..)
  • Idea is that synaptic depression in recurrent cortical connections mediates this 'adaptive integration' time-constant to maintain reliability.
  • Model also explains persistent activity after a flashed stimulus.
  • No plasticity or learning, though.
  • Rather elegant and well explained.

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ref: Gilgunn-2012 tags: kozai neural recording electrodes compliant parylene flexible dissolve date: 12-28-2017 03:50 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

IEEE-6170092 (pdf) An ultra-compliant, scalable neural probe with molded biodissolvable delivery vehicle

    • Optical coherence tomography is cool.
  • Large footprint - 150 or 300um, 135um thick (13500 or 40500 um^2; c.f. tungsten needle 1963 (50um) or 490 (25um) um^2.)
  • Delivery vehicle is fabricated from biodissolvable carboxy-methylcellulose (CMC).
    • Device dissolves within three minutes of implantation.
    • Yet stiff enough to penetrate the dura of rats (with what degree of dimpling?)
    • Lithographic patterning process pretty clever, actually.
    • Parylene-X is ~ 1.1 um thick.
    • 500nm Pt is patterned via ion milling with a photoresist mask.
    • Use thin 20nm Cr etch mask for both DRIE (STS ICP) and parylene etch.
  • Probes are tiny -- 10um wide, 2.7um thick, coated in parylene-X.
  • CMC polymer tends to bend and warp due to stress -- must be clamped in a special jig.
  • No histology. Follow-up: {1399}

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ref: -0 tags: kozai CMC dissolving insertion shuttle parylene date: 12-28-2017 03:19 gmt revision:1 [0] [head]

PMID-25128375 Chronic tissue response to carboxymethyl cellulose based dissolvable insertion needle for ultra-small neural probes.

  • CMC = carboxymethyl cellulose, commonly used as a food additive, in toothpaste, etc.
  • To address CMC dissolution, we developed a sophisticated targeting, high speed insertion (∼80 mm/s), and release system to implant shuttles.
  • Cross section of the probes are large, 300 x 125um and 100 x 125um.
  • Beautiful histology: the wound does gradually close up as the CMC dissolves, but no e-phys.

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ref: Kozai-2009.11 tags: electrodes insertion Kozai flexible polymer momolayer date: 12-28-2017 02:59 gmt revision:12 [11] [10] [9] [8] [7] [6] [head]

PMID-19666051[0] Insertion shuttle with carboxyl terminated self-assembled monolayer coatings for implanting flexible polymer neural probes in the brain.

  • This study investigated the use of an electronegative (hydrophillic) self-assembled monolayer (SAM) as a coating on a stiff insertion shuttle to carry a polymer probe into the cerebral cortex, and then the detachment of the shuttle from the probe by altering the shuttle's hydrophobicity.
    • Used 11-mercaptoundecanoic acid.
    • Cr/Au (of course) evaporated on 15um thick Si shuttle.
    • SAM attracts water once inserted, causing the hydrophobic polymer to move away.
      • Why not make the polymer hydrophillic?
      • Is this just soap?
  • Used agarose brain model.
  • Good list of references for the justification of soft electrodes, and researched means for addressing this, mostly usnig polymer stiffeners.
    • "Computer models and experimental studies of the probe–tissue interface suggest that flexible and soft probes that approach the brain’s bulk material characteristics may help to minimize micromotion between the probe and surrounding tissue ({737}; {1203}; {1102}; {1200}; LaPlaca et al., 2005; {1216}; Neary et al., 2003 PMID-12657694; {1198})"
  • "However, polymer probes stick to metallic and silicon surfaces through hydrophobic interactions, causing the polymer probe to be carried out of the brain when the insertion shuttle is removed. The solution is to use a highly hydrophillic, electronegative, self-assembled monolayer coating on the shuttle.
  • Biran et al 2005 suggests that incremental damage due to stab wounds from the shuttle (needle) should be minor.
  • Probes: 12.5 um thick, 196 um wide, and 1.2cm long, polymide substrate and custom designed lithographed PDMS probes.
  • Polymer probes were inserted deep - 8.5 mm.
  • PDMS probes inserted with non-coated insertion shuttle resulted in explantation of the PDMS probe.

____References____

[0] Kozai TD, Kipke DR, Insertion shuttle with carboxyl terminated self-assembled monolayer coatings for implanting flexible polymer neural probes in the brain.J Neurosci Methods 184:2, 199-205 (2009 Nov 15)

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ref: -2016 tags: Kozai carbon fiber microelectrodes JNE PEDOT PSS pTS date: 04-27-2017 01:42 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-27705958 Chronic in vivo stability assessment of carbon fiber microelectrode arrays.

  • showed excellent recording characteristics and nearly zero glial scarring.
  • 6.4um carbon fiber + 800nm parylene-C = 8.4um.
    • Cytec Thoronel T-650 CF, Youngs modulus = 255 GPa, tensile strength = 4.28 GPa, PAN-based.
  • Everything protected with our wonderful phenol epoxy 353NDT, heat-cure.
  • Used two coating solutions:
    • Solution of 0.01 M 3,4-ethylenedioxythiophene (483028, Sigma-Aldrich, St. Louis, MO): 0.1 M sodium p-toluenesulfonate (152536, Sigma-Aldrich, St. Louis, MO).
      • pTS is not that dissimilar from it's alkyl cousin, SPS, {1353}. Likely a soapy chemical due to the opposed methyl and sulfonic acid group; benzine will take up less room in the polymer c.f. SDS & may lower the oxidation potential of EDOT.
      • Tosylates have been explored as a EDOT counterion : PMID-22383043 Characterization of poly(3,4-ethylenedioxythiophene):tosylate conductive polymer microelectrodes for transmitter detection. and PEDOT-TMA
    • Solution was composed of 0.01 M 3,4-ethylene-dioxythiophene (483028, Sigma-Aldrich, St. Louis, MO):0.1 M polystyrene sulfonate (m.w. 70.000, 222271000, Acros, NJ).
    • For each solution the electrodeposition was carried out by applying 100 pA/channel for 600 s to form a layer of poly(3,4-ethylenedioxythiophene):sodium p-toluenesulfonate (PEDOT:pTS) or poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS).
      • Weird, would use voltage control here..
  • According to works by Green et al [45] and Hukins et al [46], equation (1) can be used to determine the aging time that
the fibers have undergone: t 37=t TQ10 T37)/10 t_{ 37} = t_T Q10^{T-37)/10} where t 37 t_{ 37} is the simulated aging time at 37 °C, t T t_T is the amount of real time that the samples have been kept at the elevated temperature, T T , and Q10 Q10 is an aging factor that is equal to 2, according to ASTM guidelines for polymer aging [47].
  • Show > 2MOhm impedance of the small-area electrodes. At the aging endpoint, PEDOT:pTS had about half the impedance of PEDOT:PSS.
    • 4M PSS, 7M pTS, both plated down to ~ 130k initial, went up to 2M pSS, 840k pTS.
  • Recording capability quite stellar
  • Likewise for the glial response.

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ref: -0 tags: gold micrograin recording electrodes electroplating impedance date: 10-17-2016 20:28 gmt revision:5 [4] [3] [2] [1] [0] [head]

PMID-23071004 Gold nanograin microelectrodes for neuroelectronic interfaces.

  • We report a single-cell sized microelectrode, which has unique gold nanograin structures, using a simple electrochemical deposition method.
  • Fabricated microelectrode had a sunflower shape with 1-5 (um of micropetals along the circumference of the microelectrode and 500 nm nanograins at the center.
  • The nanograin electrodes had 69-fold decrease of impedance and 10-fold increase in electrical stimulation capability compared to unmodified flat gold microelectrodes.
  • images/1270_1.pdf pdf
  • The deposition was conducted with an aqueous solution containing 25 mM HAuCl (HAuCl · 3H O, Sigma-Aldrich, MO, 4 4 2USA) and 20 g/L polyvinylpyrrolidone (surfactant, stabilizing agent)

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

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ref: -0 tags: 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: Cosman-2005.12 tags: microstimulation RF pain neural tissue ICMS date: 09-04-2014 18:10 gmt revision:14 [13] [12] [11] [10] [9] [8] [head]

One of the goals/needs of the lab is to be able to stimluate and record nervous tissue at the same time. We do not have immediate access to optogenetic methods, but what about lower frequency EM stimulation? The idea: if you put the stimulation frequency outside the recording system bandwidth, there is no need to switch, and indeed no reason you can't stimulate and record at the same time.

Hence, I very briefly checked for the effects of RF stimulation on nervous tissue.

  • PMID-16336478[0] Electric and Thermal Field Effects in Tissue Around Radiofrequency Electrodes
    • Most clinical response to pulsed RF is heat ablation - the RF pulses can generate 'hot spots' c.f. continuous RF.
    • Secondary effect may be electroporation; this is not extensively investigation.
    • Suggests that 500kHz pulses can be 'rectified' by the membrane, and hence induce sodium influx, hence neuron activation.
    • They propose that some of the clinical effects of pulsed RF stimulation is mediated through LTD response.
  • {1297} -- original!
  • PMID-14206843[2] Electrical Stimulation of Excitable Tissue by Radio-Frequency Transmission
    • Actually not so interesting -- deals with RF powered pacemakers and bladder stimulators; both which include rectification.
  • Pulsed and Continous Radiofrequency Current Adjacent to the Cervical Dorsal Root Ganglion of the Rat Induces Late Cellular Activity in the Dorsal Horn
    • shows that neurons are activated by pulsed RF, albeit through c-Fos staining. Electrodes were much larger in this study.
    • Also see PMID-15618777[3] associated editorial which calls for more extensive clinical, controlled testing. The editorial gives some very interesting personal details - scientists from the former Soviet bloc!
  • PMID-16310722[4] Pulsed radiofrequency applied to dorsal root ganglia causes a selective increase in ATF3 in small neurons.
    • used 20ms pulses of 500kHz.
    • Small diameter fibers are differentially activated.
    • Pulsed RF induces activating transcription factor 3 (ATF3), which has been used as an indicator of cellular stress in a variety of tissues.
    • However, there were no particular signs of axonal damage; hence the clinically effective analgesia may be reflective of a decrease in cell activity, synaptic release (or general cell health?)
    • Implies that RF may be dangerous below levels that cause tissue heating.
  • Cellphone Radiation Increases Brain Activity
    • Implies that Rf energy - here presumably in 800-900Mhz or 1800-1900Mhz - is capable of exciting nervous tissue without electroporation.
  • Random idea: I wonder if it is possible to get a more active signal out of an electrode by stimulating with RF? (simultaneously?)
  • Human auditory perception of pulsed radiofrequency energy
    • Evicence seems to support the theory that it is local slight heating -- 6e-5 C -- that creates pressure waves which can be heard by humans, guinea pigs, etc.
    • Unlikely to be direct neural stimulation.
    • High frequency hearing is required for this
      • Perhaps because it is lower harmonics of thead resonance that are heard (??).

Conclusion: worth a shot, especially given the paper by Alberts et al 1972.

  • There should be a frequency that sodium channels react to, without inducing cellular stress.
  • Must be very careful to not heat the tissue - need a power controlled RF stimulator
    • The studies above seem to work with voltage-control (?!)

____References____

[0] Cosman ER Jr, Cosman ER Sr, Electric and thermal field effects in tissue around radiofrequency electrodes.Pain Med 6:6, 405-24 (2005 Nov-Dec)
[1] Alberts WW, Wright EW Jr, Feinstein B, Gleason CA, Sensory responses elicited by subcortical high frequency electrical stimulation in man.J Neurosurg 36:1, 80-2 (1972 Jan)
[2] GLENN WW, HAGEMAN JH, MAURO A, EISENBERG L, FLANIGAN S, HARVARD M, ELECTRICAL STIMULATION OF EXCITABLE TISSUE BY RADIO-FREQUENCY TRANSMISSION.Ann Surg 160no Issue 338-50 (1964 Sep)
[3] Richebé P, Rathmell JP, Brennan TJ, Immediate early genes after pulsed radiofrequency treatment: neurobiology in need of clinical trials.Anesthesiology 102:1, 1-3 (2005 Jan)
[4] Hamann W, Abou-Sherif S, Thompson S, Hall S, Pulsed radiofrequency applied to dorsal root ganglia causes a selective increase in ATF3 in small neurons.Eur J Pain 10:2, 171-6 (2006 Feb)

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ref: -0 tags: hike tamalpais kent lake california date: 08-24-2014 19:17 gmt revision:1 [0] [head]

Pretty solid hike yesterday. 25.25 miles (or likely more, given the limited resolution of my tracing) in about 7.5 hours for an average speed of 3.4 mph. Lots of different terrain and eosystems along the way -- redwoods to lakeside to golden grassy hilltops to manzanita / scrub forest. Would be good for mountain biking.

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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: spectroscopy frequency domain PMT avalanche diode laser Tufts date: 02-25-2014 19:02 gmt revision:0 [head]

Frequency-domain techniques for tissue spectroscopy and imaging

  • 52 pages, book chapter
  • Good detail on bandwidth, tissue absorption, various technologies.

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ref: -0 tags: polyimide platinum electrodes Spain longitudinal intrafasicular adhesion delamination date: 10-05-2013 22:24 gmt revision:4 [3] [2] [1] [0] [head]

PMID-17278585 Assessment of biocompatibility of chronically implanted polyimide and platinum intrafascicular electrodes. 2007

  • Designed platinum/polyimide longitudinal intrafasicular electrodes (LIFEs)
    • 25um PT/Ir, insulated to 60-75um diameter. PT/IR has a young's modulus of 202 Gpa.
      • Plated with platinum black under sonication, as this forms a tougher surface than without sonication.
      • See also: PMID-20485478 Improving impedance of implantable microwire multi-electrode arrays by ultrasonic electroplating of durable platinum black. Desai SA, Rolston JD, Guo L, Potter SM. 2010
    • Polyimide PI2611, 10um thick, 50mm long, 220um wide in the electrode segment.
  • Implanted into rat sciatic nerve for 3 months.
  • These electrodes have been tested in people for two days:
    • Electrical stimulation through the implanted electrodes elicited graded sensations of touch, joint movement, and position, referring to the missing limb. This suggested that peripheral nerve interfaces could be used to provide amputees with prosthetic limbs with sensory feedback and volitional control that is more natural than what is possible with current myoelectric and body-powered prostheses.
  • CMAPs = compound muscle action potentials.
  • CNAPs = compound nerve action potentials.
  • Platinum wire LIFE performed very similarly to the thin-film polyimide LIFE in most all tests, with slightly higher potentials recorded by the larger polyimide probe.
  • 'Higher encapsulation with the polyimide probes! Geometry?
  • However, the polyimide LIFEs induced less functional decline than the wire LIFEs.
  • Other polyimide studies [14] [16] [24] -- one of which they observed a 70% reduction of tensile strength after 11 months of implantation.
    • [14] F. J. Rodríguez, D. Ceballos, M. Schüttler, E. Valderrama, T. Stieglitz, and X. Navarro, “Polyimide cuff electrodes for peripheral nerve stimulation,” J. Neurosci. Meth., vol. 98, pp. 105–118, 2000.
    • [16] N. Lago, D. Ceballos, F. J. Rodríguez, T. Stieglitz, and X. Navarro, “Long term assessment of axonal regeneration through polyimide regenerative electrodes to interface the peripheral nerve,” Biomaterials, vol. 26, pp. 2021–2031, 2005.
    • [24] M. Schuettler, K. P. Koch, and T. Stieglitz, “Investigations on explanted micromachined nerve electrodes,” in Proc. 8th Annu. Int. Conf. Int. Functional Electrical Stimulation Soc., Maroochydore, Australia, 2003, pp. 306–310.
      • The technology of sandwiching a metallization layer between two layers of polyimide seems to be suitable, because no delamination of the polyimide layers was observed even after 11 months. The right choice of metals for building the electrical conductive elements of the microelectrodes is crucial. Ti/Au/Ti/Pt layers tend to flake off from polyimide while delamination of Ti/Pt layers was not observed. However, adhesion of Ti/Pt layers was investigated after 2.5 months of implantation while Ti/Au/Ti/Pt layers were exposed after 11 months to the biological system. In previous research projects, surgeons also reported on delamination of Ti/Au layers from polyimide substrate after three months. Unfortunately, we had no possibility of inspecting these microelectrodes in our laboratory.
      • See also {1250}

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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: Prasad-2012.1 tags: tungsten microwire electrodes histology insulation failure sanchez microwire tungsten date: 06-27-2013 22:40 gmt revision:12 [11] [10] [9] [8] [7] [6] [head]

PMID-23010756[0] Comprehensive characterization and failure modes of tungsten microwire arrays in chronic neural implants.

  • c.f. [1]
  • microwire implant, durations that ranged from acute to up to 9 months in 25 rats.
  • First 2-3 weeks electrode impedance + recording quality fluctuated the most widely.
  • Electrode recording site deterioration continued for the long-term animals as insulation damage occurred and recording surface became more recessed over time.
  • Activated microglia were found near electrode tracts in all chronic animals.
    • High ferritin expression, intraparenchymal bleeding, microglial degeneration suggesting presence of excessive oxidative stress via Fenton chemistry.
      • Wikipedia: Free iron is toxic to cells as it acts as a catalyst in the formation of free radicals from reactive oxygen species via the Fenton Reaction.[11] Hence vertebrates use an elaborate set of protective mechanisms to bind iron in various tissue compartments.
  • Ferritin expression sometimes associated with blebbing / cytorrhexis. (in figures 7-8)
    • Interestingly, during the first few hours after implantation many microglial cells are undergoing cytoplasmic fragmentation (cytorrhexis) which indicates ongoing degeneration of these cells as their cytoplasm literally breaks apart. Cytorrhexis has been previously observed in the aged human brain where it becomes particular prominent in subjects with Alzheimer’s disease.
  • Could not discriminate abiotic (insulation, recording site size) and biotic (inflammatory response) causes of failure.
    • Microglial response not correlated with prolonged performance.
  • Tungsten TDT microwire arrays. 50um diameter, 10um polyimide insulation.
  • SEM imaging pre and prior implantation.
  • Antibodies marking microglia:
    • Iba1 marks all microglia.
    • ED1 stain against CD68 to identify active macrophages [80], but not necessarily all activated microglia since many activated cells are not engaged in phagocytosis and thus are ED1-negative.
    • Anti-ferritin staining to identify those microglia involved in the sequestration of free iron that may leak as a result of BBB compromize.
      • Issue: ferritin is expressed in all tissues ..
    • OX-6 to identify antigen-presenting MHC-II (immune) cells, e.g. microglia or blood-borne immune cells.
  • Found the immunohistoheamistry not terribly convincing.
    • Above, arrows show withdrawn electrode tips.
  • Working with the FDA to promote good laboratory practice (GLP) and good manufacturing practice (GMP). Can mention the same.
  • No evidence of infection in rats.
    • Not true in monkeys..

____References____

[0] Prasad A, Xue QS, Sankar V, Nishida T, Shaw G, Streit WJ, Sanchez JC, Comprehensive characterization and failure modes of tungsten microwire arrays in chronic neural implants.J Neural Eng 9:5, 056015 (2012 Oct)
[1] Freire MA, Morya E, Faber J, Santos JR, Guimaraes JS, Lemos NA, Sameshima K, Pereira A, Ribeiro S, Nicolelis MA, Comprehensive analysis of tissue preservation and recording quality from chronic multielectrode implants.PLoS One 6:11, e27554 (2011)

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

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

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

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ref: Lee-2005.12 tags: micromotion silicon michigan array simulation strain date: 01-28-2013 03:13 gmt revision:1 [0] [head]

PMID-16317231[0] Biomechanical analysis of silicon microelectrode-induced strain in the brain.

  • Simulation.
  • Our analysis demonstrates that when physical coupling between the electrode and the brain increases, the micromotion-induced strain of tissue around the electrode decreases as does the relative slip between the electrode and the brain.
  • Argue that micromotion and shear cause lost recording sensitivity due to inflammation and astroglial scarring around the electrode.
    • This seems to be the scientific consensus ATM.

____References____

[0] Lee H, Bellamkonda RV, Sun W, Levenston ME, Biomechanical analysis of silicon microelectrode-induced strain in the brain.J Neural Eng 2:4, 81-9 (2005 Dec)

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ref: -0 tags: brain micromotion magnetic resonance imaging date: 01-28-2013 01:38 gmt revision:0 [head]

PMID-7972766 Brain and cerebrospinal fluid motion: real-time quantification with M-mode MR imaging.

  • Measured brain motion via a clever MR protocol. (beyond my present understanding...)
  • ventricles move at up to 1mm/sec
  • In the Valsava maneuver the brainstem can move 2-3mm.
  • Coughing causes upswing of the CSF.

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ref: Chen-2004.08 tags: brain phantoms agar agarose proxy date: 07-13-2012 01:39 gmt revision:3 [2] [1] [0] [head]

Regarding brain phantoms:

Pia:

Also, both hydrophilic and hydrophobic cleaning appears to be superior to bare tungsten, with the hydrophillic surface treatment slightly superior -- PMID-16686416[2]

____References____

[0] Chen ZJ, Gillies GT, Broaddus WC, Prabhu SS, Fillmore H, Mitchell RM, Corwin FD, Fatouros PP, A realistic brain tissue phantom for intraparenchymal infusion studies.J Neurosurg 101:2, 314-22 (2004 Aug)
[1] Ritter RC, Quate EG, Gillies GT, Grady MS, Howard MA 3rd, Broaddus WC, Measurement of friction on straight catheters in in vitro brain and phantom material.IEEE Trans Biomed Eng 45:4, 476-85 (1998 Apr)
[2] Jensen W, Yoshida K, Hofmann UG, In-vivo implant mechanics of flexible, silicon-based ACREO microelectrode arrays in rat cerebral cortex.IEEE Trans Biomed Eng 53:5, 934-40 (2006 May)

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ref: RodriguezOroz-2001.09 tags: STN SNr parkinsons disease single unit recording spain 2001 tremor oscillations DBS somatotopy organization date: 02-22-2012 18:24 gmt revision:12 [11] [10] [9] [8] [7] [6] [head]

PMID-11522580[0] The subthalamic nucleus in Parkinson's disease: somatotopic organization and physiological characteristics

  • Looks like they discovered exactly what we have discovered ... only in 2001. This is both good and bad.
    • From the abstract: "Neurones responding to movement were of the irregular or tonic type, and were found in the dorsolateral region of the STN. Neurones with oscillatory and low frequency activity did not respond to movement and were in the ventral one-third of the nucleus. Thirty-eight tremor-related neurones were recorded."
  • Again, from the abstract: "The findings of this study indicate that the somatotopic arrangement and electrophysiological features of the STN in Parkinson's disease patients are similar to those found in monkeys."
  • It may be that we want to test differential modulation / oscillation: look for differences between rest and activity, if there is sufficient support for both these in the files we have.
  • These people were much, much more careful about localization of their single-electrode tracks. E.g. they calculated electrode location relative the DBS electrode stereotatically, and referenced this to the postoperative MRI location of the treatment electrode.
  • Many more (32% of 350 neurons) responded to active or passive movement.
  • Of this same set, 15% (31 neurons) had a firing rate with rhythmical activity; 38 neurons had rhythmic activity associated with oscillatory EMG, but most of these were responsive to passive stimulation.
  • Autocorrelation of the neuronal bursting and tremor peaked at mean 7Hz, while autocorr. of EMG peaked at mean 5Hz.
  • This whole paragraph is highly interesting: ''The neuronal response associated with active movements was studied by simultaneous recording of neuronal EMG activity of the limbs. Five tremor-related neurons, recorded while a voluntary movement was performed, were available for analysis. Voluntary activation of a particular limb segment arrested the tremor. This was associated with a change in the discharges of the recorded neuron, which fired at a slower rate and in synchrony with the voluntary movement. On occasions, freezing of the voluntary movement ensued and tremor reappeared, changing the neuronal activity back to the typical 4-5Hz tremor-related activity. The cross-correlation analysis of two such neurons showed a peak frequency of 4.63 and 4.88 Hz for tremor-related activity, and 1.5 to 1.38 Hz during voluntary movement. Whether neuronal discharges in the STN preceded or followed EMG activity of the limbs could not be precisely established under the present conditions.
  • Somatotopic representation in the STN is expected from normal and MTPT-treated monkeys. Indeed, somatotopy is enhanced int he GPm of MTPT-treated monkeys.
    • This somatotopy is likely to result from organized afferent from the primary motor cortex (M1) to dorsolateral STN; this is the target of DBS treatment. Ventral and medial STN seems to project to associative and limbic cortical regions.
    • It seems they think the STN is generally not diseased, it is just a useful target for stimulating without evoked movement as in M1. This is consistent with optogenetic studies by Deisseroth [1].
    • Supporting this: "DBS of STN in Parkinson's disease improves executive motor functions, but aggravates conditional associative learning.
  • Interesting: In Parkinson's disease patients with tremor, Levy and colleagues found synchronization and a high firing rate (>10Hz) while recording pairs of neurons >600um apart.
  • Recordings of cortical activity through EEG and STN LFP showed significant coherence in the beta and gamma frequency bands during movement - consistent with corticosubthalamic motor projection. ... and suggest that the STN neurons involved in parkinsonian tremor are the same as the ones ativated during the performance of a voluntary movement. (! -- I agree with this.)
  • More: The reciprocal inhibitory-excitatory connections tightly linking the GPe and the STN may generate self-perpetuating oscillations.

Old notes:

  • this paper concentrates on STN electrophysiology in PD.
    • has a rather excellent list of references.
  • found a somatotopic organization in the STN, with most motor-related units more irregular and in the dorsolateral STN.
  • found a substantial fraction of tremor-synchronized neurons.
  • conclude that the somatotopic organization is about the same as in monkeys (?) (!)
  • M1 projects to STN, as verified through anterograde tracing studies. [1] These neurons increase their firing rate in response to passive movements.
  • there appears to be a relatively-complete representation of the body in the dorsolateral STN.

____References____

[0] Rodriguez-Oroz MC, Rodriguez M, Guridi J, Mewes K, Chockkman V, Vitek J, DeLong MR, Obeso JA, The subthalamic nucleus in Parkinson's disease: somatotopic organization and physiological characteristics.Brain 124:Pt 9, 1777-90 (2001 Sep)
[1] Gradinaru V, Mogri M, Thompson KR, Henderson JM, Deisseroth K, Optical deconstruction of parkinsonian neural circuitry.Science 324:5925, 354-9 (2009 Apr 17)

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ref: RodriguezOroz-2011.01 tags: DBS dopamine impulse control spain pamplona ventral beta date: 02-22-2012 17:02 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-21059746[0] Involvement of the subthalamic nucleus in impulse control disorders associated with Parkinson’s disease

  • recorded LFP in the STN of 28 patients.
    • of these 10 had impulse control disorders, 9 had dyskinesias, and 9 had no complications.
  • compared ON and OFF medication.
  • no difference between groups in off states.
  • large differences in ON states.
    • Impulse control problems: theta-alpha activity(4-10 Hz) 6 Hz mean.
      • Larger coherence with frontal regions 4-7.5 Hz.
    • Dyskinesias: higher frequency theta-alpha 8 Hz mean.
      • Higher coherence with motor areas, 7.5 - 10Hz.
    • No problems: no noticeable LFP oscillations (?).
  • PD patients often have side-effects of Punding and hobbyism.
    • Does meth treat PD? Selegiline does. Fascinating history there regarding combining MAOI + amphetamine --> effective PD drug.
    • Why does both meth and levodopa induce impulsivity?
    • Some of the other effects of L-DOPA treatment: hypersexuality, manic behavior or shopping.
    • Lesion of the subthalamic nucleus by infarction or tumor is associated with behavioral alterations including agitation, manic states and logorrhoea, with or without hemiballismus.
  • In some patients with ICD (impulse control disorders) induced by subthalamic nucleus deep brain stimulation, the abnormal behavior was provoked by stimulation with a ventral contact and suppressed by switching it off. (dorsal region is more motor).
    • In three patients with ICD, stimulation through the ventral contact induced a euphoric state -- PPN?
  • STN recordings from rats and monkeys modify their frequency in response to reward related tasks (Aron and Poldrack 2006); in humans the STN is active during an inhibition task (LI et al 2008).
  • LFP recordings from the treatment electrode were very low! 16uV.
  • Typical results show large differences between ON and OFF: ON show more activity > 60 Hz, OFF more < 60 Hz (Brown et al 2001; Brown 2003 Gatev et al 2006).
  • LFP recordings in PD patients from the STN showed that emotional stimulus led to a decrease in alpha power in the ventral contacts (Brucke et al 2007), whereas active movement led to a decrease in the beta power recorded in the dorsal subthalamic nucleus (Alegre et al 2005).
  • Original work on STN mediating impulsivity: Delong 1983 PMID-6422317 The neurophysiologic basis of abnormal movements in basal ganglia disorders.
    • Single cell studies in the basal ganglia of behaving animals have revealed specific relations of neuronal activity to movements of individual body parts and a relation to specific parameters of movement, particularly direction, amplitude, and velocity. (no fulltext available).

____References____

[0] Rodriguez-Oroz MC, López-Azcárate J, Garcia-Garcia D, Alegre M, Toledo J, Valencia M, Guridi J, Artieda J, Obeso JA, Involvement of the subthalamic nucleus in impulse control disorders associated with Parkinson's disease.Brain 134:Pt 1, 36-49 (2011 Jan)

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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: QingBai and Wise-2001.08 tags: Bai Wise buffered MEA recording electrodes Michigan date: 01-05-2012 04:53 gmt revision:5 [4] [3] [2] [1] [0] [head]

IEEE-936367 (pdf) Single-unit neural recording with active microelectrode arrays

  • Design neural probes with on-chip unity-gain amplifiers. Proven to not degrade recordings (indeed, it should help!)
  • 200ohm output impedance
  • 11uV RMS noise, 100Hz-10kHz.
  • Multiplexer adds 8uV rms noise. noise from clock transitions 2ppm.
  • Also built amplifiers with 40db voltage gain (100x).

____References____

Qing Bai and Wise, K.D. Single-unit neural recording with active microelectrode arrays Biomedical Engineering, IEEE Transactions on 48 8 911 -920 (2001)

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

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

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

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ref: DOTY-1965.07 tags: Doty 1965 stimulation herpes restraint date: 01-03-2012 06:56 gmt revision:1 [0] [head]

PMID-14347624[0] Conditioned reflexes elicited by Eletrical Stimulation of the Brain in Macaques

  • "The relation of neural to mental processes is nowhere more clearly and directly deominstrated than in the elicitation of subjective experience in human patients by electrical stimluation of their brains"
  • Difference between sensory and motor thresholds heretofore unexplained. I guess they were in S1 -- and higher current activates more axons (?)
  • Ewald (42) perfected the means, introduced by Simonoff (40) of stimulating the brain in freely moving, unanesthetized animals. Have to look this up.
    • Movement could be elicited by stimulation of any part of the cerebral cortex of dogs.
  • Loucks: any neocortical or subcortical locus could serve as a CS in rats.
  • permanent chairing due to fear of herpes B: "With ten laboratory workers dying in the past decade if virus B encephalitis following monkey bites (11), it was felt that all possible steps should be taken to protect techinall personel form this danger, and the monkeys were permanently restrained." (in a chair)
    • Several changes had to be made to the chair to fix this.
    • even the pigtail monkeys, which are more gentile, would become aggressive and recalcitrant when the task became more difficult.
  • Simple classical conditioning test in monkeys.
    • CR = lever pressing to aviod US (shock).
  • All electrical stimuli were fed through RF isolation units to prevent ground loop.
  • Beast of a study: Stimulation proved effective as SA-or FRCS in all areas of the brain assayed, covering 38 cortical (Table 1 and Fig. 2) and 31 subcortical loci. The latter included the optic tract, lateral and medial geniculate nuclei, pulvinar, lateral posterior nucleus, posterior hypothalamus, tegmentum dorsal to nucleus ruber, brachium of the superior colliculus, and the periaqueductal gray.
  • Threshold for response varied with both time (facilitation and habituation) and with the attentive & motivational state of the animal.
  • Can discriminate electrodes 1-3mm apart.
  • Quote: Judicious and limited use of punishment (electric shock) was required to mantain performance without making the monkey "neurotic". (This as they were testing various currents, and some were below threshold).
    • A fully trained monkey can respond to one pulse.
    • Hard to train monkeys on anything below 20Hz. (Recall anything in the ~6Hz range puts cats to sleep).
  • Subthreshold precentral ICMS would induce movement if activation was increased, eg. US, or a loud and unfamiliar sound, e.g. a truck horn.
  • Much lower threshold for ICMS in monkeys as compared to cats. But they were not controlling the critical parameter, e.g. current intensity or delivered charge.

____References____

[0] DOTY RW, CONDITIONED REFLEXES ELICITED BY ELECTRICAL STIMULATION OF THE BRAIN IN MACAQUES.J Neurophysiol 28no Issue 623-40 (1965 Jul)

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

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

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

____References____

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

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ref: Fontani-2007.12 tags: mental training skilled motor control date: 01-03-2012 02:33 gmt revision:2 [1] [0] [head]

PMID-18229536[0] Effect of mental imagery on the development of skilled motor actions.

  • with trained subjects (performing something called Ura-Shuto-Uchi (Japanese? but the researchers are Italian)) showed a decrease in reaction time and EMG activity, as well as a increase in movement speed, muscle strength, power, and work. These results did not apply to untrained individuals. EEG also apparently changed vs. the untrained condition.

____References____

[0] Fontani G, Migliorini S, Benocci R, Facchini A, Casini M, Corradeschi F, Effect of mental imagery on the development of skilled motor actions.Percept Mot Skills 105:3 Pt 1, 803-26 (2007 Dec)

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

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

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

____References____

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

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ref: Wyrwicka-1966.01 tags: ICMS brainstem stimulation feeding prey chasing VTA date: 12-28-2011 20:44 gmt revision:2 [1] [0] [head]

PMID-5941514[0] Feeding induced in cats by electrical stimulation of the brain stem.

  • tested in cats.
  • stimulation points in the lateral hypothalamus (makes sense, controlls hunger)
  • half in ventral tegmental area (VTA)
  • aphygia is induced by lesions of the lateral hypothalamus.
  • in one experiment, the meat in the bowl was replaced with a banana. "Upon stimulation the cat quickly approached the bowl, sniffed the banana, turned away (in some disgust and frustration!?), searched the chamber, returned to the banana etc, but would not eat the banana."

____References____

[0] Wyrwicka W, Doty RW, Feeding induced in cats by electrical stimulation of the brain stem.Exp Brain Res 1:2, 152-60 (1966)

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ref: Bassett-2009.07 tags: Weinberger congnitive efficiency beta band neuroimagaing EEG task performance optimization network size effort date: 12-28-2011 20:39 gmt revision:1 [0] [head]

PMID-19564605[0] Cognitive fitness of cost-efficient brain functional networks.

  • Idea: smaller, tighter networks are correlated with better task performance
    • working memory task in normal subjects and schizophrenics.
  • Larger networks operate with higher beta frequencies (more effort?) and show less efficient task performance.
  • Not sure about the noisy data, but v. interesting theory!

____References____

[0] Bassett DS, Bullmore ET, Meyer-Lindenberg A, Apud JA, Weinberger DR, Coppola R, Cognitive fitness of cost-efficient brain functional networks.Proc Natl Acad Sci U S A 106:28, 11747-52 (2009 Jul 14)

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ref: -0 tags: new gmail layout date: 12-23-2011 23:23 gmt revision:0 [head]

The new layout does not do full-bleed messages, which annoys me. Were gmail not so useful I would switch to another program.

Considering gmail claims to be about email, only 23% of the screen is devoted to .. email.

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

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

in the author's own words:

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

____References____

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

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ref: photo-0 tags: Roan Mountain Tracy Michelle Cristy date: 12-07-2011 02:51 gmt revision:2 [1] [0] [head]

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ref: -0 tags: iceland mountains lost adventure date: 07-08-2011 23:00 gmt revision:2 [1] [0] [head]

Just got back from a trek through the volcanic mountains of Iceland. The landscape is extremely dramatic; though it’s not nearly the scale of Alaska or the Rockies, it presents itself as such, as the largest plant is thick moss or stubble grass (in places); everything is bare, the vistas unobstructed. (What do you do if you get lost in an Icelandic forest? Stand up.). There are no trees for size reference, indeed it seemed so alien for a bit that I was amazed that I could still breathe the air.

The first day of exploring I had a pretty serious scare. Was walking, very light and fast as usual, with just enough to protect against rain, just enough food to keep me from eating moss. I elected to take the less-popular route back, which lead across a high muddy (no plants) gray (all the snow is ashen) scree-filled plain, to a hunchback of a mountain, and down into the river valley where I was camped. The first part was fine, though searingly desolate and wind-shorn. The problem came when I rounded the final peak and discovered that the trail was covered by a gray wind-sculpted snowmass. It was at an angle too steep for my shit shoes and lack of ice-tools, and the slopes everywhere else were critical: free a rock and it will tumble 100‘. Free a Tim and he will also tumble 100 feet .. or more. I didn’t want to hike the 17km back the way I came without an attempt at re-finding the trail, so I set off, gingerly, over the ice and gravel, alone.

The ash actually saved me, as it coated the snowfields, and made them passable in the late late afternoon warmth (the sun ‘sets’ around midnight and rises at 2.). This lead to a pinnacle from which I could *see* the campsite! But there was only slide-to-death venues for descent, until I noticed a set of footprints heading up a steep snowbank to my left. I was elated - a trace of humanity! I set off with renewed vigor, and did a semi-controlled fall down the ice; the foot-holes kept me under control.

But they were not foot holes. I noticed quickly that the holes were irregular in spacing and shape, and shortly after I passed the steepest wind sculpted section of snowbank, realized that they were made by a large rock falling off the mountain, picking up speed as it dented the ice shell. I kept going, mostly because I could not stop, though eventually it leveled off. Had that rock not fallen, I don’t think I would have had the psychological wherewithal to try the slope, nevermind foot purchase to slow my descent.

As a stream gets broader its slope generally decreases, given constant resistance from the rock / earth, so as I descended the valleys broadened and became less treacherous. I made the remainder of the way back on a riverbed, albeit with wet feet. It was exciting, and i felt fully in the world as i was trying to get off that trail-less mountain, but I’m not sure if I want to do it again; the following day while hiking up neighboring peaks I felt a heightened sense of caution, vertigo.

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

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

A Step toward and Artificial Scientist

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

Artificial beings - his book.

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ref: Inzlicht-2009.03 tags: uncertainty religion conviction decision science date: 02-02-2010 20:39 gmt revision:3 [2] [1] [0] [head]

The Neural Markers of Religious Conviction PMID-19291205

Recently a friend pointed this article out to me, and while I found the scientific results interesting though slightly questionable - that religious people have less anterior cingulate cortex activation upon error - the introduction and discussion were stimulating. What follows are a few quotes and my interpretation and implications of the authors' viewpoint.

"The absence of a cognitive map providing clear standards and goals is uncomfortable and leads people to search for and assert belief systems that quell their anxiety by allowing for clearer goal pursuit (McGregor, Zanna, Holmes, & Spencer, 2001)." I would argue that uncertainty itself is highly uncomfortable - whether it is uncertainty as to how much food you will have in the future, or uncertainty as to the best behavior. In this sense, of course religion decreases anxiety - it provides a structured way to think about this disordered and highly undecidable world, a filter to remove or explain away many of the random parts of our lives. In my personal experience, conviction is usually easier than trying to hold accurate probabalistic models in your mind - conviction is pleasurable, even if it is wrong.

I find their short review of cognitive science in the introduction interesting - they claim that the septo-hippocampal system is concerned with the detection and correction of errors associated with concrete behaviors and goals, while in humans (and other primates?) the ACC allows error and feedback based operations on concepts and higher-order goals. The need for a higher-level error detection circuit makes sense in humans, as we are able to bootstrap our behavior to very complicated limits, but it also begs to question - what trains the ACC? To some degree, it must train itself in the via the typical loopy feedback-based brain way, but this only goes so far, as (at least in the modern world) the space of all possible behaviors, longterm and short term, given stochastic feedback is too large to be either decidable or fully parseable/generalizable into an accurate global model, even given a lifetime of experience. Religion, as this paper and many others posits, provides this global model against which behaviors and perceptions can be measured.

But why does a uncertainty challenge causes a compensatory increase in the strength of convictions, almost to the point of zealousness (how is this adaptive? just as a means of reducing anxiety?); I've seen it happen, but why. From a Bayesian point of view, increased uncertainty necessitates decreased certainty, or fewer convictions. From a pragmatic point of view, increased uncertainty requires increased convictions purely because the convictions have to make up for the lack of environmental information from which to make a decision. Any theory must include the cost of not making a decision, the cost of delaying a decision, and the principle of sunk costs.

There are other solutions to the 'undecidable' problems of life than religion - literary culture and science come to mind. The principle behind all may be that, while individual experience and intellect is possibly insufficient for generating global rules to guide behavior, the condensed experience of thousands/millions/billions of people is. This assumes that experience, as a random variable/signal, scales according to the laws of large numbers - noise decreases monotonically as sample size increases. This may not actually be true, it depends on the structure of the distributions, and the extent to which people's decisions/behaviors are orthogonal, and the fidelity of the communication / aggregation channels which operate on the data. I think the dimensionality increase afforded by larger sample size is slower than the concomitant noise decrease, hence (valid) global rules guiding behavior can be extracted from large populations of people. Regarding the communication channels, it seems there were always high fidelity channels of experience - e.g. Homer, Benjamin Franklin's transatlatic trips, the royal Society of London, (forgive my western pov) - and now, there are even more (the internet)! The latter invention should, at least within the framework here, allow larger groups of people to make 'harder' or 'more undecidable' decisions by virtue of greater information. Fairly standard rhetoric to the internet crowd (c.f. forums), I know.

I would argue that this is better than using convictions... but the result of communication / aggregation is convictions anyway, so eh. Getting back to the uncertainty issue, the authors point out that conservative cultures there is usually greater uncertainty (which way is the arrow of causality?), and increasing uncertainty bolsters support zealous action, e.g. war.

"For example, contemporary social psychological research indicates that uncertainty threats can cause people to become more extreme in their opinions, so that they exaggerate their religious convictions and become more willing to support a war to defend those convictions (McGregor, Haji, Nash, & Teper, 2008). In fact, even nonbelievers bolster their personal convictions to near-religious levels in order to reduce uncertainty-related distress (McGregor et al., 2001). Thus, in terms of feedback-loop models, the standards and predictions provided by religious convictions are strong enough that they can resist any discrepant feedback that might alert the comparator system."

This, I believe, is fairly accurate, and it implies several dramatic things: if a despot or leader wishes to engender support for a war, particularly a religious war, then he should make the lives of his constituents uncertain. If their lives are stable and certain sans ideology, then they will be less likely to have the convictions ('the other side is bad!') to fight certain wars. (It of course depends on who/what the other side is!). Take Europe vs. America as an example - America has far fewer social support systems and greater uncertainty in life than in Europe. The Economist frequently phrases American businesses' penchant for hiring and firing people quickly and seemingly at whim, as it encourages creative reuse, economic flexibility, and better allocation of capital, but it has a clear downside - increased anxiety, uncertainty. We (well, not me, but many Americans) deal with this via religion, the article would argue (that said, I should guess that there are a great many other reasons people are religious). Still, in western Europe has less uncertainty in life, is more secular, and less tolerant of ideological wars. Hence the antidote for war is to give people stable, significant lives. More common-sense rhetoric.

On to another suggestive point made by the article: "In terms of feedback-loop models, this explanation suggests that the standards and predictions provided by religion are inadequate and should, in fact, result in prediction errors; however, because religious beliefs are rigid, inconsistent information is reinterpreted in such a way that it becomes assimilated to preexisting convictions, further sustaining beliefs (Park, 2005)."

I would be interested in an actual test of this hypothesis - if it is possible without bias (perhaps another EEG study? perhaps it has been already done?) The authors actually prove the opposite point, that religions people are more likely to answer correctly on the Stroop test. They take more time, but seem to be more careful. This reminds me of Matteo Ricci, who allegedly used his Jesuit training in sustained concentration and memorization to master the Chinese language; clearly religion is far more than just a means of reducing perceived uncertainty about the world.

To loop the argument back on its tail - this is the 'meta' blog, afterall - one may question if the theory (looking at behavior in terms of the unpleasantness of uncertainty and the need for decidability) is a good way of looking at things, just as we questioned if religion is a good theory of the world. I think it generalizes; for example, Solaiman mentioned that the European children of the revolution of 1968 had parents who notably applied very little guidance to their lives; they were like the American hippies. These people grew up disliking their parents, and sought far more structure in their lives and in parenting their own children. One may imagine that they disliked the vast uncertainty their parents bluntly exposed them to, and paucity of guiding principles - something that the parents, after years of living in the world, probably had. Secondly, Solaiman recalled that all his favorite teachers were those that were strictest, strongest in their conviction, and most structured in their pedagogy. People seek to make decisions decidable whether through parents, teachers, religion, science or even art and literature.

To summarize, uncertainty engenders convictions by the pragmatic principle. Best thing we can do is to either reduce uncertainty or found those convictions on aggregate data(*)


(*) Google publication. The principle of data is our zeitgist, but history suggests that independent of what we think now it will not be the last.

comments? edit this, write below.

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ref: -0 tags: foreign car repair stories date: 12-15-2009 04:53 gmt revision:0 [head]

I find this particular study of how things fail fascinating - http://foreignaffairs.us/solutions.php

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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]

http://www.carolinamtnclub.com/%5CHiking%5Cgoogle%5C511.htm

awesome place! but watch out for the cows!

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ref: -0 tags: Vanity Fair American dream control theory in politics and society date: 05-03-2009 17:11 gmt revision:3 [2] [1] [0] [head]

Rethinking the American Dream by David Kamp

  • check out the lights in the frame at the bottom, and the kid taking a picture center-right (image courtesy of Kodak, hence.)

  • (quote:) "Still, we need to challenge some of the middle-class orthodoxies that have brought us to this point—not least the notion, widely promulgated throughout popular culture, that the middle class itself is a soul-suffocating dead end."
    • Perhaps they should teach expectations management in school? Sure, middle class should never die - I hope it will grow.
  • And yet, this is still rather depressive - we all want things to continuously, exponentially get better. I actually think this is almost possible, we just need to reason carefully about how this could happen: what changes in manufacturing, consumption, energy generation, transportation, and social organization would gradually effect widespread improvement.
    • Some time in individual lives (my own included!) is squandered in pursuit of the small pleasures which would be better used for purposeful endeavor. Seems we need to resurrect the idea of sacrifice towards the future (and it seems this meme itself is increasingly popular).
  • Realistically: nothing is for free; we are probably only enjoying this more recent economic boom because energy (and i mean oil, gas, coal, hydro, nuclear etc), which drives almost everything in society, is really cheap. If we can keep it this cheap, or make it cheaper through judicious investment in new technologies (and perhaps serendipity), then our standard of living can increase. That is not to say that it will - we need to put the caloric input to the economy to good use.
    • Currently our best system for enacting a general goal of efficiency is market-based capitalism. Now, the problem is that this is an inherently unstable system: there will be cheaters e.g. people who repackage crap mortgages as safe securities, companies who put lead paint on children's toys, companies who make unsafe products - and the capitalistic system, in and of itself, is imperfect at regulating these cheaters (*). Bureaucracy may not be the most efficient use of money or people's lives, but again it seems to be the best system for regulating/auditing cheaters. Examined from a control feedback point-of-view, bureaucracy 'tries' to control axes which pure capitalism does not directly address.
    • (*) Or is it? The largest problem with using consumer (or, more generally, individual) choice as the path to audit & evaluate production is that there is a large information gradient or knowledge difference between producers and consumers. It is the great (white?) hope of the internet generation that we can reduce this gradient, democratize information, and have everyone making better choices.
      • In this way, I'm very optimistic that things will get continuously better. (But recall that optimality-seeking requires time/money/energy - it ain't going to be free, and it certainly is not going to be 'natural'. Alternately, unstable-equilibrium-maintaining (servoing! auditing!) requires energy; democracy's big trick is that it takes advantage of a normal human behavior, bitching, as the feedstock. )
  • Finally (quote:) "I’m no champion of downward mobility, but the time has come to consider the idea of simple continuity: the perpetuation of a contented, sustainable middle-class way of life, where the standard of living remains happily constant from one generation to the next. "
    • Uh, you've had this coming: stick it. You can enjoy 'simple continuity'. My life is going to get better (or at least my life is going to change and be interesting/fun), and I expect the same for everybody else that I know. See logic above, and homoiconic's optimism

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ref: bookmark-0 tags: moral saints ethics personal Kant date: 05-01-2009 19:49 gmt revision:1 [0] [head]

Moral Saints by Susan Wolf

  • yes.
  • (to paraphrase:) "nothing is a good substitute for compelling personal ideals. "
  • (quote:) Perhaps what I have already said is enough to make some people begin to regard the absence of moral saints in their lives as a blessing. For there comes a point in the listing of virtues that a moral saint is likely to have that one might naturally begin to wonder whether the moral saint isn't, after all, too good - if not too good for his own good, but rather too good for hiw own well being. For the moral virtues [...] are apt to crowd out the nonmoral virtues, as well as many of the interests and personal characteristics that we generally think contribute to a healthy, well-rounded, richly developed character.
    • I agree with this, and it feels good to read this - it feels good to be justified in being another somewhat selfish, somewhat altruistic human. I imagine what she is trying to say is that extreme morality, perhaps like any extreme (and I'm cautious in apply this very broad generalization), is bad.
  • Roughly, perfectly moral people never discover anything really interesting, because discovery like this requires passion and selfishness of purpose: selfishess to pursue one's own intense interests.
  • (paraphrase) One would hope that moral figures, paragons even, would be not just moral but accomplished and attractive in nonmoral ways too. The attractiveness of most celebrities certainly does not hinge on their morality - rather it hinges on simply, how unusual, impassioned, and dominant in personality they are; yet they are not characteristically immoral.
    • Again I think this favors the mixture model..
    • On prefers the blunt, tactless, and opinionated Betsy Trotwood to the unfailingly kind and patient Agnes Copperfield.
  • (quote:) There seems to be a limit to the ammount of morality that we can stand.
  • (quote:) Morality itself does not seem to be a suitable object of passion.
    • cf. music or sports - Things which give us immense and immediate pleasure. This is what I think is necessary to sustain passion.
    • When someone gives up personal pleasures for moral obligations, one wonders not at how moral that person is, but rather how little he she loves the other things.
    • This may be because moral saints are unattractive because they make us feel uncomfortable - they expose our thoughts, vices, and flaws. Well, we don't want to give up activities that we enjoy (for more moral occupations). duh.
  • A utilitarian saint may observe that personal goals and interests are practically moral because the both enhance the happiness of the owner, as well as the happiness of those with whom the owner associates. Maximize integral given a realistic model of human behavior, yea mofos.
    • A utilitarian moral saint would then encourage others to pursue goals that are happiness-producing and attainable with a normal person's reach.
    • Ultimately this forces the argument that the utilitarian moral saint should give up sainthood (if not utilitarianism?)
    • It is to say that the hierarchy of valuations of actions, ideals, opinions, and judgments, is not exclusively hierarchal with morality at the top. Morality may be the most important, but it is not the only important criteria.
      • Morality may be the consequence of (some) humans desire to reduce things too much - to overfit the model, so to speak. It's like applying {723} to your life.
      • (quote:) The role morality plays in the development of our characters and the shape of our practical deliberations need neither be that of a universal medium through which all other values must be translated nor of an ever-present filter through which all other values must pass.
  • This is all observed from a very western viewpoint - but what about Zen Buddism? (subtext: I think is that these people are still seeking something through their studies and meditations (it is still goal directed behavior). They are frustrated by the temporal-difference structure of the reward signaling in us mammals, but abrogating it's activity does nothing to change it's homeostasis. Or maybe it does??)

{652}
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ref: notes-0 tags: policy gradient reinforcement learning aibo walk optimization date: 12-09-2008 17:46 gmt revision:0 [head]

Policy Gradient Reinforcement Learning for Fast Quadrupedal Locomotion

  • simple, easy to understand policy gradient method! many papers cite this on google scholar.
  • compare to {651}

{645}
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ref: bookmark-0 tags: goodbrush paintings favorite date: 11-24-2008 03:03 gmt revision:4 [3] [2] [1] [0] [head]

hopefully these links don't move..

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

{614}
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ref: Froemke-2007.11 tags: nucleus basalis basal forebrain acetylcholine auditory cortex potentiation voltage clamp date: 10-08-2008 22:44 gmt revision:2 [1] [0] [head]

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

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

____References____

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ref: Lin-2008.07 tags: basal forebrain salience sclin date: 10-05-2008 01:26 gmt revision:3 [2] [1] [0] [head]

PMID-18614035[0] Neuronal ensemble bursting in the basal forebrain encodes salience irrespective of valence.

  • Here, we show that both reward- and punishment-predicting stimuli elicited robust bursting of many noncholinergic basal forebrain (BF) neurons in behaving rats...

____References____

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ref: Isoda-2007.02 tags: SMA saccade basal_forebrain executive function 2007 microstimulation SUA cortex sclin date: 10-03-2008 17:12 gmt revision:2 [1] [0] [head]

PMID-17237780[0] Switching from automatic to controlled action by monkey medial frontal cortex.

  • SCLIN's blog entry
  • task: two monkeys were trained to saccade to one of two targets, left/right pink/yellow. the choice was cued by the color of the central fixation target; when it changed, they should saccade to the same-colored target.
    • usually, the saccade direction remained the same; sometimes, it switched.
    • the switch could either occur to the same side as the SUA recording (ipsilateral) or to the opposite (contralateral).
  • found cells in the pre-SMA that would fire when the monkey had to change his adapted behavior
    • both cells that increased firing upon an ipsi-switch and contra-switch
  • microstimulated in SMA, and increased the number of correct trials!
    • 60ua, 0.2ms, cathodal only,
    • design: stimulation simulated adaptive-response related activity in a slightly advanced manner
    • don't actually have that many trials of this. humm?
  • they also did some go-nogo (no saccade) work, in which there were neurons responsive to inhibiting as well as facilitating saccades on both sides.
    • not a hell of a lot of neurons here nor trials, either - but i guess proper statistical design obviates the need for this.
  • I think if you recast this in tems of reward expectation it will make more sense and be less magical.
  • would like to do shadlen-similar type stuff in the STN
questions
  1. how long did it take to train the monkeys to do this?
  2. what part of the nervous system looked at the planned action with visual context, and realized that the normal habitual basal-ganglia output would be wrong?
    1. probably the whole brain is involved in this.
    2. hypothetical path of error trials: visual system -> cortico-cortico projections + context activation -> preparatory motor activity -> basal ganglia + visual context (is there anatomical basis for this?) -> activation of some region that detects the motor plan is unlikely to result in reward -> SMA?

____References____

{329}
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ref: Fetz-2007.03 tags: hot fetz BMI biofeedback operant training learning date: 09-07-2008 18:56 gmt revision:7 [6] [5] [4] [3] [2] [1] [head]

PMID-17234689[0] Volitional control of neural activity: implications for brain-computer interfaces (part of a symposium)

  • Limits in the degree of accuracy of control in the latter studies can be attributed to several possible factors. Some of these factors, particularly limited practice time, can be addressed with long-term implanted BCIs. YES.
  • Accurate device control under diverse behavioral conditions depends significantly on the degree to which the neural activity can be volitionally modulated. YES again.
  • neurons (50%) in somatosensory (post central) cortex fire prior to volitional movement. interesting.
  • It should also be noted that the monkeys activated some motor cortex cells for operant reward without ever making any observed movements See: Fetz & Finocchio, 1975, PMID-810359.
    • Motor cortex neurons that were reliably associated with EMG activity in particular forelimb muscles could be readily dissociated from EMG when the rewarded pattern involved cell activity and muscle suppression.
    • This may be realated to switching between real and imagined movements.
  • Biofeedback worked well for activating low-threshold motor units in isolation, but not high threshold units; attempts to reverse recruitment order of motor units largely failed to demonstrate violations of the size principle.
  • This (the typical BMI decoding strategy) interposes an intermediate stage that may complicate the relationship between neural activity and the final output control of the device
    • again, in other words: "First, the complex transforms of neural activity to output parameters may complicate the degree to which neural control can be learned."
    • quote: This flexibility of internal representations (e.g. to imagine moving your arm, train the BMI on that, and rapidly directly control the arm rather than gonig through the intermediate/training step) underlies the ability to cognitively incorporate external prosthetic devices in to the body image, and explains the rapid conceptual adaptation to artificial environments, such as virtual reality or video games.
      • There is a high flexibility of input (sensory) and output (motor) for purposes of imagining / simulating movements.
  • adaptive learning algorithms may create a moving target for the robust learning algorithm; does it not make more sense to allow the cortex to work it's magic?
  • Degree of independent control of cells may be inherently contrained by ensemble interactions
    • To the extent that internal representations depend on relationships between the activities of neurons in an ensemble, processing of these representations involves corresponding constraints on the independence of those activities.
  • quote: "These factors suggest that the range and reliability of neural control in BMI might increase significantly when prolonged stable recordings are acheived and the subject can practice under consistent conditions over extended periods of time.
  • Fetz agrees that the limitation is the goddamn technology. need to fix this!
  • there is evidence of favortism in his citations (friends with Miguel??)

humm.. this paper came out a month ago, and despite the fact that he is much older and more experienced than i, we have arrived at the same conclusions by looking at the same set of data/papers. so: that's good, i guess.

____References____

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

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

{579}
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ref: notes-0 tags: software debian xpaint maxima math mathematica date: 07-02-2008 14:37 gmt revision:3 [2] [1] [0] [head]

oldies but goodies:

  • Maxima a computer algebra system, almost like a free version of Mathematica!
    • be sure to install maxima-emacs to get LaTeX prettyprinting.
  • [xpaint] Has a cool spring-mass-friction system where the length of the spring (the distance between cursor and paint brush) controls the width of the paint brush. see below!

Both are in Debian of course :)

{577}
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ref: notes-0 tags: grain protein growing framing feed oats alfalfa barley corn wheat date: 06-18-2008 15:14 gmt revision:0 [head]

I found this on my computer tucked away into a dusty corner. Such fascinating information should not be left hidden -

{550}
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ref: notes-0 tags: cairo ocaml cvs date: 03-11-2008 02:36 gmt revision:3 [2] [1] [0] [head]

cairo-ocaml is broken in Debian (lenny) in that it is incompatible with liblabl-gtk2 in the repository; to compile ocaml programs (e.g. Geoproof) that depend on it, you need to :

  1. sudo apt-get install liblablgtk2-ocaml-dev
  2. get http://cairographics.org/snapshots/cairo-1.5.12.tar.gz, unpack, configure, make, make install.
  3. get the cvs version of cairo-ocaml (which apparently has not been touched in a few years..)
    1. cvs -d :pserver:anoncvs@cvs.cairographics.org:/cvs/cairo co cairo-ocaml (cvs syntax is confusing. I'm glad we have svn now)
    2. aclocal -I support
    3. autoconf
    4. ./configure (ignore complaints about LIBSVG_CAIRO)
    5. make
  4. oh, and make note of this (essential if you are using ocamlopt, the native compiler)

{531}
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ref: notes-0 tags: patent maintenance fee date: 01-06-2008 17:23 gmt revision:0 [head]

http://www.uspto.gov/go/pac/doc/general/

  • A maintenance fee is due 3 1/2, 7 1/2 and 11 1/2 years after the original grant for all patents issuing from the applications filed on and after December 12, 1980

{527}
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ref: bookmark-0 tags: Ruby gmail imap migration date: 12-20-2007 18:03 gmt revision:0 [head]

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

{513}
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ref: bookmark-0 tags: perl rails ruby CGI BBC date: 12-03-2007 15:55 gmt revision:0 [head]

BBC deploys perl-on-rails in their highly restricted production environment.

  • faster than ruby (of course)
  • good discussion on the page - references things like http://open.nytimes.com/
  • one comment suggests TAR & gzipping your webpages to avoid a filesystem overloaded by too many files. You can index to the TARed files with a simple byte offset -- neat!!
  • also references perl Catalyst and CGI::Application

{486}
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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}


Hello,

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

{442}
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ref: bookmark-0 tags: language learning year french brain hack date: 09-03-2007 04:13 gmt revision:2 [1] [0] [head]

http://mirror.mricon.com/french/french.html -- "how i learned french in a year"

  • verbiste : verb conjugator for linux (Gnome)
  • When talking about software, it was FredBrooks in TheMythicalManMonth who said that people will always reinvent the wheel because it is intrinsically easier and more fun to write your own code than it is read someone else's code.

{385}
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ref: bookmark-0 tags: linux dual boot grub chainloader windows date: 05-31-2007 16:55 gmt revision:0 [head]

http://www.faqs.org/docs/Linux-HOWTO/Linux+Win9x+Grub-HOWTO.html

{321}
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ref: programming-0 tags: hair rendering GPU date: 04-07-2007 22:55 gmt revision:1 [0] [head]

http://www-evasion.imag.fr/Publications/2007/WBKMCL07/surveyHair.pdf

  • the NVidia example looks particuarly interesting & beautiful!
  • mostly hairy (hah) women in the author biography section

{167}
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ref: GarciaRill-1991.01 tags: PPN pedunculopontine nucleus brainstem sleep locomotion consciousness 1991 date: 0-0-2007 0:0 revision:0 [head]

PMID-1887068 The Pedunculopontine nucleus

  • extensive review!

{128}
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ref: bookmark-0 tags: neuroanatomy pulvinar thalamus superior colliculus image gray brainstem date: 0-0-2007 0:0 revision:0 [head]

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

{77}
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ref: Kilgard-1998.03 tags: dopamine basal_forebrain nucleus_basalis cortical_plasticity date: 0-0-2007 0:0 revision:0 [head]

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

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

http://www2.chass.ncsu.edu/garson/PA765/logistic.htm

  • transform probabilities into logarithmic variables = logits

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ref: notes-0 tags: MCMC Monte carlo markov chain date: 0-0-2006 0:0 revision:0 [head]

In a MCMC, the invariant distribution is a eigenvector of the state transition matrix whose eigenvalue is 1!

page 372 of http://www.inference.phy.cam.ac.uk/itprnn/book.pdf

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ref: bookmark-0 tags: training neural_networks with kalman filters date: 0-0-2006 0:0 revision:0 [head]

with the extended kalman filter, from '92: http://ftp.ccs.neu.edu/pub/people/rjw/kalman-ijcnn-92.ps

with the unscented kalman filter : http://hardm.ath.cx/pdf/NNTrainingwithUnscentedKalmanFilter.pdf