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[0] Matsuzaka Y, Picard N, Strick PL, Skill representation in the primary motor cortex after long-term practice.J Neurophysiol 97:2, 1819-32 (2007 Feb)

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ref: -2012 tags: parvalbumin interneurons V1 perceptual discrimination mice date: 03-06-2019 01:46 gmt revision:0 [head]

PMID-22878719 Activation of specific interneurons improves V1 feature selectivity and visual perception

  • Lee SH1, Kwan AC, Zhang S, Phoumthipphavong V, Flannery JG, Masmanidis SC, Taniguchi H, Huang ZJ, Zhang F, Boyden ES, Deisseroth K, Dan Y.
  • Optogenetic Activation of PV+ interneurons improves neuronal feature selectivity and improves perceptual discrimination (!!!)

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

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

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

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ref: -0 tags: betzig sparse and composite coherent lattices date: 02-14-2019 00:00 gmt revision:1 [0] [head]

Sparse and composite coherent lattices

  • Focused on the math:
    • Linear algebra to find the wavevectors from the Bravais primitive vectors;
    • Iterative maximization @ lattice points to find the electric field phase and amplitude
    • (Read paper for details)
  • High NA objective naturally converts plane wave to a spherical wave; this can be used to create spherically-constrained lattices at the focal point of objectives.

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ref: -0 tags: Kato fear conditioning GABA auditory cortex mice optogenetics SOM PV date: 02-04-2019 19:09 gmt revision:0 [head]

PMID-29375323 Fear learning regulates cortical sensory representation by suppressing habituation

  • Trained mice on CS+ and CS --> lick task.
    • CS+ = auditory tone followed by tailshock
    • CS- = auditory tone (both FM modulated, separated by 0.5 - 1.0 octave).
    • US = licking.
  • VGAT2-ChR2 or PV-ChR2
  • GABA-ergic silencing of auditory cortex through blue light illumination abolished behavior difference following CS+ and CS-.
  • Used intrinsic imaging to locate A1 cortex, then AAV - GCaMP6 imaging to lcoated pyramidal cells.
  • In contrast to reports of enhanced tone responses following simple fear conditioning (Quirk et al., 1997; Weinberger, 2004, 2015), discriminative learning under our conditions caused no change in the average fraction of pyramidal cells responsive to the CS+ tone.
    • Seemed to be an increase in suppression, and reduced cortical responses, which is consistent with habituation.
  • Whereas -- and this is by no means surprising -- cortical responses to CS+ were sustained at end of tone following fear conditioning.
  • ----
  • Then examined this effect relative to the two populations of interneurons, using PV-cre and SOM-cre mice.
    • In PV cells, fear conditioning resulted in a decreased fraction of cells responsive, and a decreased magnitude of responses.
    • In SOM cells, CS- responses were enhanced, while CS+ were less enhanced (the main text seems like an exaggeration c.f. figure 6E)
  • This is possibly the more interesting result of the paper, but even then the result is not super strong.

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

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

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

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ref: -0 tags: NET probes SU-8 microfabrication sewing machine carbon fiber electrode insertion mice histology 2p date: 12-29-2017 04:38 gmt revision:1 [0] [head]

PMID-28246640 Ultraflexible nanoelectronic probes form reliable, glial scar–free neural integration

  • SU-8 asymptotic H2O absorption is 3.3% in PBS -- quite a bit higher than I expected, and higher than PI.
  • Faced yield problems with contact litho at 2-3um trace/space.
  • Good recordings out to 4 months!
  • 3 minutes / probe insertion.
  • Fab:
    • Ni release layer, Su-8 2000.5. "excellent tensile strength" --
      • Tensile strength 60 MPa
      • Youngs modulus 2.0 GPa
      • Elongation at break 6.5%
      • Water absorption, per spec sheet, 0.65% (but not PBS)
    • 500nm dielectric; < 1% crosstalk; see figure S12.
    • Pt or Au rec sites, 10um x 20um or 30 x 30um.
    • FFC connector, with Si substrate remaining.
  • Used transgenic mice, YFP expressed in neurons.
  • CA glue used before metabond, followed by Kwik-sil silicone.
  • Neuron yield not so great -- they need to plate the electrodes down to acceptable impedance. (figure S5)
    • Measured impedance ~ 1M at 1khz.
  • Unclear if 50um x 1um is really that much worse than 10um x 1.5um.
  • Histology looks realyl great, (figure S10).
  • Manuscript did not mention (though the did at the poster) problems with electrode pull-out; they deal with it in the same way, application of ACSF.

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ref: Wilson-2006.12 tags: parkinsons burst firing MPTP mice STN DBS date: 01-26-2012 17:25 gmt revision:6 [5] [4] [3] [2] [1] [0] [head]

PMID-16973296[0] Subthalamic nucleus neurones in slices from MPTP-lesioned mice show irregular, dopamine-reversible firing pattern changes, but without synchronous activity

  • loss of dopamine in parkinson-model rats (not MPTP!) induces synchronized low-frequency oscillatory burst-firing in subthalamic nucleus neurons
  • MPTP mice, neurons fire slower, and more irregularly
  • only dopamine varied (increased) firing rate.
  • the STN & GP are insufficient to generate the abberant firing patterns in the STN, by itself - the disease is more than just dopamine depletion.


[0] Wilson CL, Cash D, Galley K, Chapman H, Lacey MG, Stanford IM, Subthalamic nucleus neurones in slices from 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mice show irregular, dopamine-reversible firing pattern changes, but without synchronous activity.Neuroscience 143:2, 565-72 (2006 Dec 1)

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ref: Verloop-1984.08 tags: recording electrode arrays MEA epoxy teflon simple mold slice cultures date: 01-03-2012 00:57 gmt revision:2 [1] [0] [head]

PMID-6492861[0] A simple method for the construction of electrode arrays.

  • It is simple!
  • of note: "Therefore arrays of equidistant electrodes have been developed for superficial and depth recording. During the last decade the construction of many of these multiple electrodes for in vivo and in vitro measurements is based o n thin film techniques (Wise a n d Angell, 1975; Pickard, 1979; Pochay et al., 1979; Prohaska et al., 1979; Kuperstein and Whittington, 1981).
    • Have to go back and check these thin-film attempts.
  • See also: PMID-7248818[1] A flexible high density multi-channel electrode array for long-term chronic implantation. (surface recording).


[0] Verloop AJ, Holsheimer J, A simple method for the construction of electrode arrays.J Neurosci Methods 11:3, 173-8 (1984 Aug)
[1] Weissman AD, Schwartz EL, A flexible high density multi-channel electrode array for long-term chronic implantation.Brain Res Bull 6:6, 543-6 (1981 Jun)

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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: notes-0 tags: ice hydrophones glissando recording sound date: 01-19-2010 16:41 gmt revision:0 [head]

http://silentlistening.wordpress.com/2008/05/09/dispersion-of-sound-waves-in-ice-sheets/ -- amazing!

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ref: Gilbert-2009.03 tags: human prediction estimation social situation neighbor advice affective forecasting date: 06-10-2009 15:13 gmt revision:2 [1] [0] [head]

PMID-19299622[0] The Surprising Power of Neighborly Advice.

  • quote (I cannot say this any better!): "People make systematic errors when attempting to predict their affective reactions to future events, and these errors have social (1–3), economic (4–8), legal (9, 10), and medical (11–22) consequences. For example, people have been shown to overestimate how unhappy they will be after receiving bad test results (23), becoming disabled (14, 19–21), or being denied a promotion (24), and to overestimate how happy they will be after winning a prize (6), initiating a romantic relationship (24), or taking revenge against those who have harmed them (3). Research suggests that the main reason people mispredict their affective reactions to future events is that they imagine those events inaccurately (25). For example, people tend to imagine the essential features of future events but not the incidental features (26–28), the early moments of future events but not the later moments (17, 24), and so on. When mental simulations of events are inaccurate, the affective forecasts that are based on them tend to be inaccurate as well."
  • solution, ala François de La Rochefoucauld: "Before we set our hearts too much upon anything," he wrote, "let us first examine how happy those are who already possess it"
    • this is surrogation ; it relies not on mental simulation, hence is immune to the associated systematic errors.
    • problem is that people differ. paper agues that, in fact, they don't all that much - the valuations & affective reactions are produced by evolutionarily ancient physiological mechanisms. Furthermore, people's neighbors, friends, and peers are likely to all be similar in personality and preference via self-selection and social reinforcement - hence their reactions to a situation will be similar.
  • They used a speed-dating scenario in their experiments, from which they observe: "Women made more accurate predictions about how much they would enjoy a date with a man when they knew how much another woman in their social network enjoyed dating the man than when they read the man's personal profile and saw his photograph."
  • Next, they employ personality-evaluation "Men and women made more accurate predictions about how they would feel after being evaluated by a peer when they knew how another person in their social network had felt after being evaluated than when they previewed the evaluation itself."
  • Conclusion: "But given people's mistaken beliefs about the relative ineffectiveness of surrogation and their misplaced confidence in the accuracy of their own mental simulations (39), it seems likely that in everyday life, La Rochefoucauld's advice—like the advice of good neighbors—is more often than not ignored.
  • Editorializing: I'm not quite convinced that 'neighborly advice' is an accurate predictor of our absolute reaction to a situation as much as it socially informs us of reaction we are *supposed* to have. Society by consensus - that's what some of my European friends dislike about (some parts of) American culture. They need to run some controls in other cultures (?)


[0] Gilbert DT, Killingsworth MA, Eyre RN, Wilson TD, The surprising power of neighborly advice.Science 323:5921, 1617-9 (2009 Mar 20)

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ref: Debarnot-2009.03 tags: sleep motor imagery practice date: 03-24-2009 15:32 gmt revision:3 [2] [1] [0] [head]

PMID-18835655[0] Sleep-related improvements in motor learning following mental practice.

  • shows that after both physical practice and mental imagery on day 1, sleep improves test performance in both when testing on day 2.


[0] Debarnot U, Creveaux T, Collet C, Gemignani A, Massarelli R, Doyon J, Guillot A, Sleep-related improvements in motor learning following mental practice.Brain Cogn 69:2, 398-405 (2009 Mar)

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ref: Matsuzaka-2007.02 tags: skill learning M1 motor control practice cortex date: 03-20-2009 18:31 gmt revision:1 [0] [head]

PMID-17182912[0] Skill Representation in the Primary Motor Cortex After Long-Term Practice

  • The acquisition of motor skills can lead to profound changes in the functional organization of the primary motor cortex (M1) yes
  • 2 task modes: random target acquisition, and one of 2 repeating sequences (predictable, repeating mode)
  • 2 years of training -> 40% of units were differentially active during the two task modes
  • variations in movement types in the two classes did not fully explain the difference in activity between the 2 tasks
    • M1 neurons are more influence by the task than the actual kinematics.


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ref: Porro-1996.12 tags: motor imagery fMRI practice date: 02-19-2009 22:50 gmt revision:0 [head]

PMID-8922425 Primary Motor and Sensory Cortex Activation during Motor Performance and Motor Imagery: A Functional Magnetic Resonance Imaging Study.

  • says exactly what you might expect: that the motor cortex is active during motor imagery, and the regions active during motor performance and motor imagery are overlapping.

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ref: bookmark-0 tags: windows service pack date: 02-15-2008 14:06 gmt revision:1 [0] [head]

windows is retarded:


I got this error installing service pack 2 on a triple-boot MacBook.

  • I agree! I also agree that if (computer) geeks would make a more user-friendly linux with better open office, we would all switch to linux. But for now we'll have to stick with the retarded windows :( -- ana/poison

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ref: bookmark-0 tags: WiMax Wifi radio spectrum licensing FCC date: 12-04-2007 23:45 gmt revision:0 [head]

spectrum options for broadband wireless

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ref: notes-0 tags: iceweasel firefox acroread uninstall debian linux mozplugger date: 11-10-2007 04:39 gmt revision:1 [0] [head]

Adobe acrobat reader 7.0 leaks a prodigious amount of memory on my linux system (Debian Etch, stable). However, some pdfs will only open in acroread, so i want to keep the application around for occasional use. Because of the memory leaks, it is not good to have it loaded by default by iceweasel / firefox (evince or xpdf is better). To do this:

  1. quit your browser (not sure if this is necessary, but perhaps it is a good idea).
  2. open /etc/mozpluggerrc and comment out (#) all the sections that reference acroread. There are 3 macro lines, as well as one line in in the pdf / x-pdf content handling list.
  3. goto ~/.mozilla and remove pluginreg.dat ; do the same for ~/.mozilla/firefox
  4. go to /usr/lib/iceweasel/plugins and move / remove / rename nppdf.so (if it is there) (this is what tripped me up for a while - i had to look at the automatically-generated pluginreg.dat to figure out that acroread was being loaded without mozplugger via this plugin).

that's it! :)

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ref: bookmark-0 tags: blackfin coding practice software engineering institute Carnegie mellon ucalgary date: 10-17-2007 14:26 gmt revision:0 [head]

Little Stupid Details - what they are, and how to avoid them

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ref: notes-0 tags: Duke Licensing patents university royalty royalties intellectualproperty date: 10-12-2007 17:41 gmt revision:4 [3] [2] [1] [0] [head]

What I have learned about licensing & Duke (or really, licensing at universities in general), in no particular order:

  • Licensing fees split up: 50% to the inventors, 10% to the lab, 10% to the department, 30% to the dean
    • The 50% inventors' fees are split up based on what is determined fair by the inventors themselves, or if that fails, by the Office of Licensing & Ventures (OLV) itself. If there are several patents in a licensing, then it is split between patents based on relevance / contribution, then between each of the inventors. Royalties are split in the same way.
    • The OLV & patent's budget is indirectly paid through these licensing fees.
  • Universities are granted ownership of any intellectual property developed by graduate students & other employees under federal funding through the 1980/1984 Bayh-Dole Act. Universities assume ownership of IP developed through privately funded work, though there is no one law for this.
    • Graduate students are considered employees under the law, hence IP retained, even if no formal contract was signed.
  • Even if an independent inventor (e.g. me) files a invention disclosure form to Duke in good faith, and upon investigation the OLV agrees that the claim of independence is supported, this does not prevent future litigation.
    • If the fields of invention and research overlap, as is probably true for me, then OLV & Duke are likely to protest (money is at stake, after all).
  • Patents require a servicing fee every 3-5 years - have to learn more about this!
  • Almost certainly want a patent on a device. without it, it is very easy to steal :/
    • Can patent software 'ideas' or 'methods' that have utility, but not the actual software. The text of the software is copyrighted, like a book.
  • If a patent has people on it who were not involved in the invention, the patent can be legally contested and voided. Conversely, if the patent does not have all the inventors on it, then it can also be contested by an outside party, and voided.
  • Duke will pay the legal fees for patents & writing up a licensing contract
    • Duke will also pay the fees to patent in other countries (where the patenting fees are much higher), depending on market.
      • The European Union has no centralized patent office - patents must be filed in each country and translated to & from the official language. The legal and translation fees & time spent on this can be very high, so usually companies only file in a few largest markets, if at all.
    • Concerning the named inventors on a patent, above, Duke determines who is involved usually by asking the PI, without delving into the internal politics of a lab. This may or may not be an issue.
  • Typical licensing fees $25k - $1M, depending on what is being patented.
  • Duke can revoke the licensing agreement if the company is not using it / making progress within a period specified by the licensing contract, e.g. 6 - 9 months.
  • Duke typically licenses multiple patents at a time to startups; startups typically need more than one patent.
  • Duke typically pursues non-exclusive licenses on biological models (e.g. Gouping Feng's OCD mouse), and exclusive licenses on devices (like this, i suppose)
    • In some fields, device licensing is exclusive to a field - e.g. one company licenses for Parkinson's application, another for Alzheimer's, etc.
  • Once a patent is licensed to a company, it typically becomes gradually 'diluted' as the company & employees invests more in the idea/technology. If the initial royalty level was 5%, and the company makes significant changes & improvements, then the company will re-negotiate the royalty percentage.
    • Oftent the licensing agreement specifies the maximum amount of dilution / the minimum royalty level, as ultimately the university was involved in the first step to commercialization, without which anything else could have happened.
  • Similarly, if the company licensing University IP needs to give a certain royalty percentage to another patent holder & cannot remain solvent without decreasing University share, then the company and University will negotiate a lower royalty rate.


  • Everything is fluid & up for negotiation, depending on the desires and situations of each of the parties.
    • Typically, the university and inventor are on the same side, but that is not true for me.
  • Need a lawyer to navigate the maze!

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


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

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ref: bookmark-0 tags: Linux device_drivers memory virtual_memory PCI address_translation date: 0-0-2006 0:0 revision:0 [head]