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

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

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

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ref: -0 tags: 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 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: 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: 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: 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: 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: 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____

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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: 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.

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

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

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ref: 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!