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ref: -0 tags: optogenetics micro LED flexible electrodes PET rogers date: 12-28-2017 03:24 gmt revision:9 [8] [7] [6] [5] [4] [3] [head]

PMID-23580530 Injectable, cellular-scale optoelectronics with applications for wireless optogenetics.

  • Supplementary materials
  • 21 authors, University Illinois at Urbana-Champaign, Tufts, China, Northwestern, Miami ..
  • GaN blue and green LEDs fabricated on a flexible substrate with stiff inserter.
    • Inserter is released in 15 min with a dissolving silk fibrin.
    • made of 250um thick SU-8 epoxy, reverse photocured on a glass slide.
  • GaN LEDS fabricated on a sapphire substrate & transfer printed via modified Karl-Suss mask aligner.
    • See supplemental materials for the intricate steps.
    • LEDs are 50um x 50um x 6.75um
  • Have integrated:
    • Temperature sensor (Pt serpentine resistor) / heater.
    • inorganic photodetector (IPD)
      • ultrathin silicon photodiode 1.25um thick, 200 x 200um^2, made on a SOI wafer
    • Pt extracellular recording electrode.
        • This insulated via 2um thick more SU-8.
  • Layers are precisely aligned and assembled via 500nm layer of epoxy.
    • Layers made of 6um or 2.5um thick mylar (polyethylene terephthalate (PET))
    • Layers joined with SU-8.
    • Wiring patterned via lift-off.
  • Powered via RF scavenging at 910 Mhz.
    • appeared to be simple, power in = light out; no data connection.
  • Tested vs control and fiber optic stimulation, staining for:
    • Tyrosine hydroxylase (makes l-DOPA)
    • c-fos, a neural activity marker
    • u-LEDs show significant activation.
  • Also tested for GFAP (astrocytes) and Iba1 (activated microglia); flexible & smaller devices had lower gliosis.
  • Next tested for behavior using a self-stimulation protocol; mice learned to self-stimulate to release DA.
  • Devices are somewhat reliable to 250 days!

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ref: -0 tags: Peter Ledochowitsch ECoG parylene fabrication MEMS date: 09-25-2014 16:54 gmt revision:0 [head]

IEEE-5734604 (pdf) Fabrication and testing of a large area, high density, parylene MEMS µECoG array

  • Details 5-layer platinum parylene process for high density ECoG arrays.

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ref: -0 tags: microelectrodes original metal pipette glass recording MEA date: 01-31-2013 19:46 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

IEEE-4065599 (pdf) Comments on Microelectrodes

  • The amplifiers themselves, even back in 1950's, posed no problems -- low bandwidth. All that is required is low noise and high input impedance.
  • KCl Glass electrodes are LPF (10M resistive + 10pf parasitic capacitance); metal HPF (capacitive).
    • The fluid tip will not see external triphasic spikes of vertebrate axons above the noise level.
  • Metal probe the most useful.
  • Pt electrode in CSF behaves like a capacitor at low voltage across a broad frequency range. CSF has compounds that retard oxidation; impedance is more resistive with physiological saline.
  • Noise voltage generated by a metal electrode best specified by equivalent noise resistance at room temperature, E rmsnoise=4kTR nδF R_n should equal the real part of the electrode impedance at the same frequency.
  • Much of electrochemistry: solid AgCl diffuses away from an electrode tip with great speed and can hardly be continuously formed with an imposed current. Silver forms extremely stable complexes with organic molecules having attached amino and sulfhydril groups which occur in plenty where the electrode damages the tissue. Finally, the reduction-oxidation potential of axoplasm is low enough to reduce methylene blue, which places it below hydrogen. AgCl and HgCl are reduced.
  • The external current of nerve fibers is the second derivative of the traveling spike, the familiar triphasic (??) transient.
  • Svaetichin [1] and Dowben and Rose [3] plated with Platinum black. This increases the surface area.
    • Very quickly it burns onto itself a shell of very adherent stuff. It is kept from intimate contact with the tissue around it by a shell.
    • We found that if we add gelatin to the chloroplatinic acid bath from which we plate the Pt, the ball is not only made adherent to the tip but is, in a sense, prepoisoned and does not burn a shell into itself.
  • glass insulation using woods metal (which melts at a very low temperature). Platinum ball was plated onto 2-3um pipette tip. 3um gelatinized platinum black ball, impedance 100kOhm at 1kHz.
    • Highly capacitive probe: can be biased to 1 volt by a polarizing current of 1e-10 amp. (0.1nA).
  • Getting KCl solution into 1um pipettes is quite hard! They advise vacuum boiling to remove the air bubbles.
  • Humble authors, informative paper.

____References____

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ref: Ledochowitsch-2011.01 tags: Ledochowitsch transparent micro ECoG Peter date: 01-30-2013 07:01 gmt revision:2 [1] [0] [head]

PMID-22254956[0] A transparent μECoG array for simultaneous recording and optogenetic stimulation.

  • We present a 49-channel μECoG array with an electrode pitch of 800 μm and a 16-channel linear μECoG array with an electrode pitch of 200 μm.
  • The backing material was Parylene C. Transparent, sputtered indium tin oxide (ITO) was used in conjunction with e-beam evaporated gold to fabricate the electrodes

____References____

[0] Ledochowitsch P, Olivero E, Blanche T, Maharbiz MM, A transparent μECoG array for simultaneous recording and optogenetic stimulation.Conf Proc IEEE Eng Med Biol Soc 2011no Issue 2937-40 (2011)

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ref: Fuentes-2009.03 tags: Nicoelis DCS spinal cord stimulation PD Fuentes Petersson 6-OHDA date: 03-03-2012 02:46 gmt revision:3 [2] [1] [0] [head]

PMID-19299613[0] Spinal cord stimulation restores locomotion in animal models of Parkinson's disease.

  • Motivation: different levels of cortical oscillation during movement and rest (LFO decreased, medium-high freq increased); PD associated with abnormal synchronous corticostriatal oscillations.
  • In epilepsy patients, stimulation of peripheral nerve afferents is effective in desychronizing low-frequency neural activity, reducing the frequency and duration of seizures (8,9,10) PMID-11050139[1] PMID-16886985[2] PMID-18188148[3]
  • DCS (dorsal column stimulation)
    • Epidural, longitudal electrodes, horizontal electrical field.
    • Upper thoracic, mice.
    • 300Hz.
    • simpler and safer than brain surgery.
    • [24] DCS induces no increase in arousal. (Wall, PD. Brain 1970; 93:505.
  • used the tyrosine hydroxyalse inhibitor AMPT
  • M1 LFP: Osc around 1.5-4Hz and 10-15Hz enhanced; osc > 25Hz subdued.
  • DCS increased locomotion by 29x in depleted animals, and 4.9x in normal animals.
  • Also titrated L-DOPA with DAT-KO mice. Without dopamine, there is no movement.
    • DCS increased L-DOPA effectiveness by 5x (1/5 the dose was required)
  • Verified in a 6-OHDA lesion model in rats.
    • Lesioned animals moved more, sham moved less.
  • Activation of locomotion is via striatal medium spiny neurons projecting to the output nuclei of the basal ganglia [26 PMID-8402406[4] ,27 PMID-1695404[5]].
  • In PD, with reduced striatal dopamine levels, the activation threshold of the projection neurons from the striatum is significantly increased [25] PMID-17916382[6].

____References____

[0] Fuentes R, Petersson P, Siesser WB, Caron MG, Nicolelis MA, Spinal cord stimulation restores locomotion in animal models of Parkinson's disease.Science 323:5921, 1578-82 (2009 Mar 20)
[1] Fanselow EE, Reid AP, Nicolelis MA, Reduction of pentylenetetrazole-induced seizure activity in awake rats by seizure-triggered trigeminal nerve stimulation.J Neurosci 20:21, 8160-8 (2000 Nov 1)
[2] DeGiorgio CM, Shewmon A, Murray D, Whitehurst T, Pilot study of trigeminal nerve stimulation (TNS) for epilepsy: a proof-of-concept trial.Epilepsia 47:7, 1213-5 (2006 Jul)
[3] George MS, Nahas Z, Bohning DE, Lomarev M, Denslow S, Osenbach R, Ballenger JC, Vagus nerve stimulation: a new form of therapeutic brain stimulation.CNS Spectr 5:11, 43-52 (2000 Nov)
[4] Brudzynski SM, Wu M, Mogenson GJ, Decreases in rat locomotor activity as a result of changes in synaptic transmission to neurons within the mesencephalic locomotor region.Can J Physiol Pharmacol 71:5-6, 394-406 (1993 May-Jun)
[5] DeLong MR, Primate models of movement disorders of basal ganglia origin.Trends Neurosci 13:7, 281-5 (1990 Jul)
[6] Grillner S, Wallén P, Saitoh K, Kozlov A, Robertson B, Neural bases of goal-directed locomotion in vertebrates--an overview.Brain Res Rev 57:1, 2-12 (2008 Jan)

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ref: Hilker-2004.01 tags: STN subthalamic DBS stimulation cortex cerebellum PET PD parkinsons date: 01-24-2012 05:38 gmt revision:1 [0] [head]

PMID-14688612[0] Subthalamic Nucleus Stimulation Restores Glucose Metabolism in Associative and Limbic Cortices and in Cerebellum: Evidence from a FDG-PET Study in Advanced Parkinson's Disease

  • cortical depression of glucose metabolism
  • hypermetabolic state in the left rostral cerebellum (?!)
  • DBS generally remedies this imbalance, restoring glucose metabolism to the cortex associative/motor/frontal as well as to the thalamus distant from the stimulation site.

____References____

[0] Hilker R, Voges J, Weisenbach S, Kalbe E, Burghaus L, Ghaemi M, Lehrke R, Koulousakis A, Herholz K, Sturm V, Heiss WD, Subthalamic nucleus stimulation restores glucose metabolism in associative and limbic cortices and in cerebellum: evidence from a FDG-PET study in advanced Parkinson's disease.J Cereb Blood Flow Metab 24:1, 7-16 (2004 Jan)

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ref: Lilly-1950 tags: Lilly original MEA glass pipette date: 01-04-2012 01:52 gmt revision:4 [3] [2] [1] [0] [head]

bibtex:Lilly-1950 A Method of Recording the Moving Electrical Potential Gradients in the Brain. The 25-Channel Bavatron and Electro-Iconograms.

  • images/1017_2.pdf
  • Every cell in the cortex is within 25 um of a capillary (!). Really?
  • You can already see him wanting to record from whales / dolphins.
  • Used electrode arrays and photocathode tubes to record from cat.
  • 8x8mm array, 2mm spacing, 100um tip opening in the glass pipettes.
    • Pipettes could slide up & down to rest gently on the pia.
    • Were filled via capilary action
    • Both acute and chronic recording.
  • 1mm spacing of electrodes would still record on the order of 5,000 neurons; good thing there is exponential space dependence.
    • Resistance 50k, low so that thermal noise has little effect.
  • recorded 3,500 feet of film (!!); 1,200 feet of film accumulates in two minutes; this takes 48 minutes to see once.
  • Results in preparation ... were they ever published? where? Must have been nearly impossible to analyze without a computer!

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ref: -0 tags: meta learning Artificial intelligence competent evolutionary programming Moshe Looks MOSES date: 08-07-2010 16:30 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

Competent Program Evolution

  • An excellent start, excellent good description + meta-description / review of existing literature.
  • He thinks about things in a slightly different way - separates what I call solutions and objective functions "post- and pre-representational levels" (respectively).
  • The thesis focuses on post-representational search/optimization, not pre-representational (though, I believe that both should meet in the middle - eg. pre-representational levels/ objective functions tuned iteratively during post-representational solution creation. This is what a human would do!)
  • The primary difficulty in competent program evolution is the intense non-decomposability of programs: every variable, constant, branch effects the execution of every other little bit.
  • Competent program creation is possible - humans create programs significantly shorter than lookup tables - hence it should be possible to make a program to do the same job.
  • One solution to the problem is representation - formulate the program creation as a set of 'knobs' that can be twiddled (here he means both gradient-descent partial-derivative optimization and simplex or heuristic one-dimensional probabilistic search, of which there are many good algorithms.)
  • pp 27: outline of his MOSES program. Read it for yourself, but looks like:
  • The representation step above "explicitly addresses the underlying (semantic) structure of program space independently of the search for any kind of modularity or problem decomposition."
    • In MOSES, optimization does not operate directly on program space, but rather on subspaces defined by the representation-building process. These subspaces may be considered as being defined by templates assigning values to some of the underlying dimensions (e.g., they restrict the size and shape of any resulting trees).
  • In chapter 3 he examines the properties of the boolean programming space, which is claimed to be a good model of larger/more complicated programming spaces in that:
    • Simpler functions are much more heavily sampled - e.g. he generated 1e6 samples of 100-term boolean functions, then reduced them to minimal form using standard operators. The vast majority of the resultant minimum length (compressed) functions were simple - tautologies or of a few terms.
    • A corollary is that simply increasing syntactic sample length is insufficient for increasing program behavioral complexity / variety.
      • Actually, as random program length increases, the percentage with interesting behaviors decreases due to the structure of the minimum length function distribution.
  • Also tests random perturbations to large boolean formulae (variable replacement/removal, operator swapping) - ~90% of these do nothing.
    • These randomly perturbed programs show a similar structure to above: most of them have very similar behavior to their neighbors; only a few have unique behaviors. makes sense.
    • Run the other way: "syntactic space of large programs is nearly uniform with respect to semantic distance." Semantically similar (boolean) programs are not grouped together.
  • Results somehow seem a let-down: the program does not scale to even moderately large problem spaces. No loops, only functions with conditional evalutation - Jacques Pitrat's results are far more impressive. {815}
    • Seems that, still, there were a lot of meta-knobs to tweak in each implementation. Perhaps this is always the case?
  • My thought: perhaps you can run the optimization not on program representations, but rather program codepaths. He claims that one problem is that behavior is loosely or at worst chaotically related to program structure - which is true - hence optimization on the program itself is very difficult. This is why Moshe runs optimization on the 'knobs' of a representational structure.

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

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

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ref: bookmark-0 tags: petaflop gigaflop RIKEN protein folding MDGRAPE date: 09-17-2007 14:55 gmt revision:0 [head]

pretty impressive project, especially considering how much time and money they spent ($15 m, 6 man-months to do the verilog (only!)) http://www.hotchips.org/archives/hc16/3_Tue/1_HC16_Sess6_Pres1_bw.pdf

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ref: Blankertz-2006.06 tags: BMI EEG ECoG competiton 2006 date: 0-0-2007 0:0 revision:0 [head]

PMID-16792282 http://hardm.ath.cx:88/pdf/BCIcompetition2006.pdf