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ref: -2017 tags: two photon holographic imaging Arch optogenetics GCaMP6 date: 09-12-2019 19:24 gmt revision:1 [0] [head]

PMID-28053310 Simultaneous high-speed imaging and optogenetic inhibition in the intact mouse brain.

  • Bovetti S1, Moretti C1, Zucca S1, Dal Maschio M1, Bonifazi P2,3, Fellin T1.
  • Image GCamp6 in either scanned mode (high resolution, slow) or holographically (SLM, redshirt 80x80 NeuroCCD, activate opsin Arch, simultaneously record juxtasomal action potentials.

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ref: -3000 tags: DBS STN oscillations beta gamma research date: 02-21-2012 16:51 gmt revision:22 [21] [20] [19] [18] [17] [16] [head]

There seems to be an interesting connection between excessive grip force, isometric muscle contraction causing coherence between motor cortex and EMG, lack of inhibition on delayed response and go-no-go task, and experiments with STN lesioned rats, and the high/low oscillation hypothesis. Rather tenuous, I suppose, but let me spell it out. ( My personal impression, post-hoc, is that this is an epiphenomena of something else; evidence is contradictory.)

  1. PD patients, STN DBS impairs ability to match force characteristics to task requirements both in terms of grip force {88}, and when lifting heavy and light objects {88-2}. This is consistent with GPi function controlling the vigor or scaling of muscle responses
  2. Isometric force creation frequently engages the piper rhythm between cortex and muscles {1066}, which may be a means of preserving motor state {1066-4}.
  3. In PD patients there is marked increase in beta oscillation and synchronization {1064}, which decreases during movement {829}. Some suggest that it may be a non-coding resting state {969}, though beta-band energy is correlated with PD motor symptoms PMID-17005611, and STN DBS attenuates the power in the beta band {710-2},{753},{1073}, and DCS is likely to do the same PMID-21039949. Alternatively synchrony limits the ability to encode meaningful information. The beta band activity does not seem associated with rest tremor {1075}. Furthermore, beta band decreases prior and during movement, and with the administration of levodopa oscillation shifts to higher frequency -- the same frequency as the piper rhythm {1075}. Closed-loop stimulation with a delay (80ms) designed to null the beta oscillations is more effective than continuous high frequency DBS {967}.
  4. PD patients have deficits in inhibition on go-no-go and delayed response tasks that is exacerbated by STN DBS {1077-3}, as well as expedited decision making in conflict situations {1077} Lesioning the STN in rats has similar effect on delayed reward task performance, though it's somewhat more complicated. (and their basal ganglia is quite a bit different). {677}.
  5. The <30 Hz and >30Hz bands are inversely affected by both movement and dopamine treatment. {1069}

footnote: how much is our search for oscillations informed by our available analytical techniques?

Hypothesis: Impulsivity may be the cognitive equivalent of excess grip force; maintenance of consistent 'force' or delayed decision making benefits from Piper-band rhythms, something which PD abolishes (gradually, through brain adaptation). DBS disrupts the beta (resting, all synchronized) rhythm, and thereby permits movement. However it also effectively 'lesions' the STN, which leads to cognitive deficits and poor force control. (Wait .. DBS plus levodopa improves 40-60Hz energy -- this would argue against the hypothesis. Also, stroke in the STN in normal individuals causes hemiballismus, which resolves gradually; this is not consistent with oscillations, but rather connectivity and activity.)

Testing this hypothesis: well, first of all, is there beta-band oscillations in our data? what about piper band? We did not ask the patients to delay response, so any tests thereof will be implicit. Can look at relative energy 10Hz-30Hz and 30Hz-60Hz in the spike traces & see if this is modulated by hand position. (PETH as usual).

So. I made PETHs for beta / gamma power ratio of the spiking rate, controlled by shuffling the PETH triggers. Beta power was between 12 and 30 Hz; gamma between 30 and 75 Hz, as set by a noncausal IIR bandpass filter. The following is a non-normalized heatmap of all significant PETHs over all sessions triggered when the hand crossed the midpoint between targets. (A z-scored heatmap was made as well; it looked worse).

X is session number, Y time, 0 = -1 sec. sampling rate = 200 Hz. In one file (the band) there seems to be selective gamma inhibition about 0.5 sec before peak movement. Likely it is an outlier. 65 neurons of 973 (single and multiunits together) were significantly 'tuned' = 6.6%; marginally significant by binomial test (p=0.02). Below is an example PETH, with the shuffled distribution represented by mean +- 1 STD in blue.

The following heatmap is created from the significant PETHs triggered on target appearance.

80 of the 204 significant PETHs are from PLEX092606005_a. The total number of significant responses (204/1674, single units and multiunits) is significant by the binomial test p < 0.001, with and without Sept. 26 removed. Below is an example plot (092606005). Looks pretty damn good, actually.

Let's see how stable this relationship is by doing a leave-half out cross-validation, 10 plies, in red below (all triggers plotted in black)

Looks excellent! Problem is we are working with a ratio, which is prone to spikes. Fix: work in log space.

Aggregate response remains about the same. 192 / 1674 significant (11.5%)

In the above figure, positive indicates increased β\beta power relative to γ\gamma power. The square shape is likely relative to (negative lags) hold time and (positive lags) reaction time, though the squareness is somewhat concerning. Recording is from VIM.

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ref: bookmark-0 tags: machine_learning research_blog parallel_computing bayes active_learning information_theory reinforcement_learning date: 12-31-2011 19:30 gmt revision:3 [2] [1] [0] [head]

hunch.net interesting posts:

  • debugging your brain - how to discover what you don't understand. a very intelligent viewpoint, worth rereading + the comments. look at the data, stupid
    • quote: how to represent the problem is perhaps even more important in research since human brains are not as adept as computers at shifting and using representations. Significant initial thought on how to represent a research problem is helpful. And when it’s not going well, changing representations can make a problem radically simpler.
  • automated labeling - great way to use a human 'oracle' to bootstrap us into good performance, esp. if the predictor can output a certainty value and hence ask the oracle all the 'tricky questions'.
  • The design of an optimal research environment
    • Quote: Machine learning is a victim of it’s common success. It’s hard to develop a learning algorithm which is substantially better than others. This means that anyone wanting to implement spam filtering can do so. Patents are useless here—you can’t patent an entire field (and even if you could it wouldn’t work).
  • More recently: http://hunch.net/?p=2016
    • Problem is that online course only imperfectly emulate the social environment of a college, which IMHO are useflu for cultivating diligence.
  • The unrealized potential of the research lab Quote: Muthu Muthukrishnan says “it’s the incentives”. In particular, people who invent something within a research lab have little personal incentive in seeing it’s potential realized so they fail to pursue it as vigorously as they might in a startup setting.
    • The motivation (money!) is just not there.

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ref: notes-0 tags: Barto Hierarchal Reinforcement Learning date: 02-17-2009 05:38 gmt revision:1 [0] [head]

Recent Advancements in Hierarchal Reinforcement Learning

  • RL with good function-approximation methods for evaluating the value function or policy function solve many problems yet...
  • RL is bedeviled by the curse of dimensionality: the number of parameters grows exponentially with the size of a compact encoding of state.
  • Recent research has tackled the problem by exploiting temporal abstraction - decisions are not required at each step, but rather invoke the activity of temporally extended sub-policies. This is somewhat similar to a macro or subroutine in programming.
  • This is fundamentally similar to adding detailed domain-specific knowledge to the controller / policy.
  • Ron Parr seems to have made significant advances in this field with 'hierarchies of abstract machines'.
    • I'm still looking for a cognitive (predictive) extension to these RL methods ... these all are about extension through programmer knowledge.
  • They also talk about concurrent RL, where agents can pursue multiple actions (or options) at the same time, and assess value of each upon completion.
  • Next are partially observable markov decision processes, where you have to estimate the present state (belief state), as well as a policy. It is known that and optimal solution to this task is intractable. They propose using Hierarchal suffix memory as a solution ; I can't really see what these are about.
    • It is also possible to attack the problem using hierarchal POMDPs, which break the task into higher and lower level 'tasks'. Little mention is given to the even harder problem of breaking sequences up into tasks.
  • Good review altogether, reasonable balance between depth and length.

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ref: -0 tags: perl one-liner search files cat grep date: 02-16-2009 21:58 gmt revision:2 [1] [0] [head]

In the process of installing compiz - which I decided I didn't like - I removed Xfce4's window manager, xfwm4, and was stuck with metacity. Metacity probably allows focus-follows-mouse, but this cannot be configured with Xfce's control panel, hence I had to figure out how to change it back. For this, I wrote a command to look for all files, opening each, and seeing if there are any lines that match "metacity". It's a brute force approach, but one that does not require much thinking or googling.

find . -print | grep -v mnt | \
perl -e 'while($k = <STDIN>){open(FH,"< $k");while($j=<FH>){if($j=~/metacity/){print "found $k";}}close FH;}' 
This led me to discover ~/.cache/sessions/xfce4-session-loco:0 (the name of the computer is loco). I changed all references of 'metacity' to 'xfwm4', and got the proper window manager back.

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ref: notes-0 tags: kicad C++ design hierarchy date: 01-18-2008 22:06 gmt revision:1 [0] [head]

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ref: bookmark-0 tags: architecture travel places to see Spencer Tunic date: 09-18-2007 14:28 gmt revision:1 [0] [head]

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

http://www.mat.univie.ac.at/~neum/

very nice collection of links!!

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ref: notes-0 tags: SQL fulltext search example date: 0-0-2006 0:0 revision:0 [head]

SELECT * FROM `base` WHERE MATCH(`From`, `To`) AGAINST('hanson') ORDER BY `Date` DESC Limit 0, 100

  • you need to have a fulltext on the column set provided as a parameter to the MATCH() keyword. Case does not matter so log as the coalition is correct.

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ref: notes-0 tags: architecture aesthetic light date: 0-0-2006 0:0 revision:0 [head]

http://www.thomaslockehobbs.com/ -- interetsing photoblog of a globetrotter & laconic harvard intellectual

http://www.uni-weimar.de/architektur/InfAR/lehre/Entwurf/Patterns/107/ca_107.html Modern buildings are often shaped with no concern for natural light - they depend almost antirely on artificial light. But buildings which displace natural light as the major source of illumination are not fit places to spend the day.

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ref: bookmark-0 tags: job_search professional employment wisdom date: 0-0-2006 0:0 revision:0 [head]

http://www.tcnj.edu/~rgraham/wisdom.html