So, a year and a half ago I bought a green 1995 900 SE convertible for $600. At that time, it didn't move or go in reverse. Since then, I've been fixing up random things here an there (or just straight modifying / breaking the car by other standards) and recently realized that I had better start keeping track of everything that's been done, in case my memory lapses or i need to know where some random part came from. I doubt this will be useful to anyone else - next time, pictures!

Things that I've done to the green convertible, in approximate chronological order:

1. replaced the clutch cable. previous owner says that the clutch was relatively new; verified when i swapped the transmission.
2. replaced the turbo transmission with one from a 900 S n/a; new transmission has slightly shorter final drive ratio, which is fun. Both transmissions have approximately the same number of miles on them (again, the original tranny had no reverse).
1. The subframe brace bolts were seized on this car - it took several weeks off and on + heat + rust solvent to remove both large 18mm bolts. I recommend replacing them with new ones if possible (these look fine, they are very heavy bolts).
2. In the process of doing this, I stripped one captive nut used for the transmission mount, and had to drill it out & replace it with a 3/8" grade 8 bolt & double nut affair from home cheapo. Be careful when threading these bolts in, or you'll have to do the same!
3. replaced the rubber boots on the control-arm ball joints, and in turn repacked the ball joints with grease. This takes a lot of patience.
4. installed a new gas filler hose from the plastic filler line to the gas tank. Previous one was held on with zip-ties. (yes, zip-ties: after i filled the damn thing up, i noticed that it was leaking excessively, and had to drive it around until the gas was burned through & unlikely to drip all over the ground once the car was parked.)
5. removed turbo silencer prior intercooler.
6. installed a new passenger side headlamp assembly.
7. replaced the thermostat.
8. replaced and gapped all 4 spark plugs.
9. reflashed the ECU to stage 2.5 or so - 1.4 bar peak boost @ 3k rpm, 1.2 bar above 4k rpm, no boost limit in 2nd gear. This was done via Trionic5 suite, available from http://ecuproject.com/
10. replaced both front struts & shocks with parts from a junkyard 1997 900 SE; previous ones had a loose / faulty wheel bearing. Very worthy upgrade.
11. replaced all brake pads + front brake rotors to fit the struts/shocks/bearing hubs from the 97 900 SE. (the hubs are incompatible with 1995 disc rotors - different internal flange diameter.)
12. replaced both front brake calipers. The previous 1995-version calipers did not mate well with '97 struts and '97 discs. Initially bought used calipers off of ebay, but the damn bleeder valve was sheared off at the nut, so I took the pads off them and installed remaned ones. Brake feel is much, much better now.
13. added internal bracing / roll cage, though without the top hoop. removed most of the upholstery & seats in the back to fit this.
14. oil and filter changed at 161k.
15. adjusted some of the window seals - but they still need to be replaced eventually.
16. removed condenser and AC compressor.
17. replaced / changed the serpentine belt to a 71" / 1805mm 6-tooth duralast belt - aka AC delete belt ref. Water pump is only 25% engaged with the belt now, but seems to work just fine (and the internet verifies this.)
18. repainted some rust spots on the trunk lid.
19. installed plenty of grease on the upholstery -- oops :P
20. Got two used tires from America's discount tires; rear tires still shady. Will get around to replacing them; have already gotten around to destroying the front ones with second-gear burnouts to 60 :)
21. Resurfaced flywheel, replaced clutch disc with one from a Jeep Wagoneer (though not the pressure plate -- it looked fine, no signs of cracking).
22. Replaced drivers side main crankcase seal.
23. Replaced drivers side transaxle output bushing + drivers and passengers transaxle output seals
24. Removed oil pan, cleaned pickup, and re-did oil pan seal.
25. Welded a new stud on the turbo, applied with anti-seize this time! always use anti-seize on exhaust parts, they get hot!
26. Removed head, had it ground to fix a minor valve leak and milled flat (increasing the compression ratio a bit). Cleaned the block top surface, intake manifold, fuel injectors, piston heads, and cylinders as best I could. Removed & replaced the broken stud underneath the power steering pump. In the course of having the head out, replaced the relevant seals:
1. Valve stem seals
2. Head gasket
3. Intake gasket
4. Exhaust gasket
27. Replaced upper and lower radiator hoses.
28. As of May 1 2012, I no longer own the car -- I'm off to California, and can't take it with me. May the new owner enjoy it as much as I have!

Things that need to be done to the 'vert:

1. There is still a click in the rear drivers-side brake, should inspect it; likely brake pads.
2. New rear tires (!!).
3. hood gas springs are shot. Meh.

Now, wonders of wonders, I have another of these cars - though a sedan, not a convertible. It cost much more (about 8x as much), and is hence in much better shape. That said, I've had to do the following:

1. Replaced the rear drivers side brake caliper. In the rain; should have waited for a sunny day, as this took longer than expected. (Everything does.)
2. New front disc rotors & pads Dec 2008. As of July 2010, they should be replaced soon.
3. Replaced the clutch + throwout bearing. The latter was making terrible noises back when I drove to Atlanta fall 2008; I nearly didn't make it back.
4. Removed a "Saab saver" steering rack brace installed by a previous owner. To install this brace, you need to drill through the wheel well, which allows (possibly salty) water to touch the bare metal. As a result of this + stress upon metal that was not engineered to bear it, the wheel well cracked almost to the point where the shock mount was about to go through the hood! I'm glad I caught this while the car was parked, and not while i was going 70!
5. welded the wheel well back together with 2x1/4" steel strap. I tried to weld to the major braces of the unibody, and later covered everything with plenty of paint and spray-on rubber soundproofing compound. Still, I worry about the opposite side of the metal, where the heat from the welding undoubtably removed rust-preventing paint. Seems reliable so far.
6. replaced drivers side inner CV joint boot & of course repacked the CV joint grease. You need to take the CV joint completely apart to fit the thing - it won't stretch!
7. Built a tool for removing the differential output bushing from the transmission. As the output of the differential is only a bushing, and it's put under a lot of stress during hard acceleration (especially peel outs - one wheel spinning much faster than the other = lots of strain on diff), the bushing wears out quickly. It is a pressure fit sleeve, so I reasoned that it could be removed by pressure - not quite. It must be cut out, very tediously, using a single-ended hacksaw. To keep metal debris out of the diff housing, insert a rag into where the CV axle was, and flush the tranny throughly after installing a new bushing.
1. This is all rather difficult, so don't peel out!
2. The passengers side half-axle is supported by a bearing by the alternator, so it does not have the same levels of stress & does not wear as quickly.
8. Four new tires. $560 - beh.
9. Replaced front brake discs Nov 2010
10. New front strut inserts + reground front brakes May 2012 -- in Albuquerque.
11. Flushed transmission oil in the desert outside of Lake Powell; the heat of Phoenix did it in & shifting was starting to be very sticky. Also adjusted the clutch cable, which later snapped while driving in SF. (Fortunately, was able to first gear it to a parking garage, where I fixed it on the spot).
12. Fan control relay went out in the desert of Utah; ended up shorting it closed with a bit of wire. Said wire must be removed after turning off the car, otherwise the fan will run indefinitely!
13. Sold car February 2013. May the next owner enjoy her well!

And now the blue 1998 saab 900, sold to Adam:

1. Replaced front oxygen sensor
2. Replaced rear transmission mount (had to take off the subframe for this, yuck)
3. Fixed front passengers side window regulator (ish).
4. Adjusted clutch master cylinder. The linkage between the pedal and the master cylinder was plastic and badly worn, which was causing the clutch to never fully disengage, in turn gradually leading to third gear synchro wearing out. Adjusted the stop on the pedal to compensate for this; it should ultimately be replaced, though works fine now.
5. Replaced front drivers side headlight.

Next, the saab 9000 aero:

1. Swapped wastegate / APC control valve with one from my 900 to remedy overboost issues.
2. Replaced alternator brushes. Thing was a bear to remove -- had to jack up the engine a bit to get it out!
3. Re-soldered alternater to battery charging and starting wire
4. Re-soldered engine-to-chassis grounding wire; transmission to battery wire seemed fine.
5. Replaced tubing from blow-off valve, PCV, and fuel pressure regulator to intake manifold with aftermarket silicone tubing.
6. Installed new radio.
7. Replaced headlight relay.
8. Replaced turn signal relay.
9. Replaced thermostat.
10. Replaced rear lower panhard rod bushing; was falling out and rubbing against the rear axle.
1. All of the other rear-end suspension bushings looked fine!
11. Gapped all 4 spark plugs.
12. New tires @ 120k miles; will need to rotate them.
13. Cut wire from glass break sensor to security / immobilizer module, as passing buses were setting off the car alarm.
14. Bought new IAC valve off ebay, put it in (difficult compared to a NG900!), but it idled too high (perhaps I needed to reset the ECU?). Therefore I took the new one out, cleaned and lubricated the old one, and re-installed it. The car still idles high for ~10 seconds when put in neutral, but it comes down, and I suppose I'll live with that for now.
15. Blocked off the evap & PCV & instrument boost gauge intake manifold barbs in the process of debugging the high idle (figured that there were vacuum leaks).
16. Replaced central lock relay with a used one from ePartsLand.
17. Installed new drivers-side wheel bearing. Note you need to take the axle out to get access to the hex-head bolts which hold the hub in. Thankfully, it's not hard once this is done.
18. New front/rear brakes/rotors.
1. Front brakes were easy; rear brakes have a hidden retraction allen key.
1. Follow the directions here. To fit a new rotor and pads, the whole brake caliper needs to be taken apart!
19. Removed A/C and installed a short belt 2325 mm length.
1. Note: tensioner pully is threaded backwards to prevent pulley rotation from loosening it.
2. Note: to disengage the tensioner, you don't need a special tool - just put a breaker bar on a 19mm socket & use that as a lever.
20. Rear shocks were replaced with Bilstein HD types from thesaabsite.com
21. Installed new heater core, and all but one of the hoses leading to it.
22. New fuel filter 121k
23. Headgasket job April 21-25:
1. New headgasket + new headbolts. One of them did not torque up to the right 'feel' following the saab-specificed procedure (33ft-lbs, 44ft-lbs, 90deg torque-to-yield. I'm going to replace that one with a M12 12.9 grade bolt from Mcmaster; have ordered 110, 120, and 130mm length & will see which fits best. Original stretch bolts are grade 10.9.
2. New radiator
3. New idler pulley
4. New head gasket + head bolts; only cleaned the block and head, did not have them ground. Seems OK so far!
5. Flushed oil, though it still took a few hours at temperature to boil off the remaining antifreeze that had leaked into the engine oil.
6. Kept the timing chain + guides, though it's stretched near the limit; will have to replace next time I have the thing disassembled.
7. New exhaust manifold. Pain to install, as I didn't remove the turbo when removing the head. Still quite possible.
8. New urethane engine torque mount. Just cut out the old rubber inserts with a hacksaw -- not too hard. Be careful which way you put in the new blue inserts -- they are asymmetrical.
9. One new hood gas strut = enough.
10. New plugs. Old ones were filthy.
24. Todo
1. Windshield & Por-15 the frame around it; I bet the previous installer scratched the paint.
2. Camber bolts to help the tires last longer.

PMID-1601445 Factors influencing the biocompatibility of insertable silicon microshafts in cerebral cortex.

• Relatively early assessment of tissue reaction to silicon electrodes.
• Noted 'severe' reaction at electrode tip; recommend recording along the shaft, Michigan style.
• Noted microhematoma formation.
• Recommend fast insertion.
• Bending of the shafts (e.g. they exert lateral force) causes lateral tissue damage.
• Problem with fast insertion is that it may cause the needle to bend a bit -- resulting in lateral 'kill zone'.
• Ultimate speed must be a compromise.
• Advocate shearing blade tip or chisel point to sever microtubules, rather than a conical tip pushing them to a annular ring that can grab to the sides of the needle.
• 
• Good paper, reviews the relevant cellular anatomy...

Quick review of electrode area / impedance within m8ta:

• {895} 500um^2
• {311} 490um^2 nominal; 900k
• {1040} 108um^2, plated from 5M to 1M.
• Neuronexus: 177, 413um, 700um, and 1250um.
• Suggest 177um for SUA, 413um for MUA.
• Community consensus seems to be that these electrodes don't last as long, though.
• {823} 122um^2 nominal
• {736} 500um^2
• {1027} (Utah) 1600um^2.

At Cornell I took a VLSI design class taught by Rajit Manohar (*), and even then - 2002/2003 - he was very excited about asynchronous circuit design. I was uncertain about the technology at the time, but generally I trusted his instinct. Seems that there is certainly some oil in those hills - Octasic has just released a new basestation IC based on asynchronous processor cores: http://www.octasic.com/en/products/oct2200/oct2224w.php

The associated product-brief/technology whitepaper gives some good motivations for why asynchronous design is superior to classical synchronous design: (I'll quote, since I find this fascinating, hope they don't mind!)

• Elimination of clock trees - Synchronous high-speed processors require large clock trees to keep sequential blocks synchronized. These clock trees require high-power buffers to drive complex high-capacitance networks that cover most of the chip. Clocks change state twice per cycle, consuming power on both positive and negative edges. These clock trees do not perform any information processing, thus provide no useful computing work, yet they consume a significant portion of the total power. Eliminating the clock trees alone can reduce power consumption by as much as 40% in a high-performance processor.
• Elimination of pipeline state elements - Modern synchronous high-performance processors rely heavily on pipeline design techniques. Those pipelines require the use of a very large number of inter-stage flip-flops and state elements to support a high clock frequency operation. However, these inter-stage flip-flops and state elements also dont contribute to the actual data processing and computing tasks performed by the processor. In an asynchronous design these storage elements are discarded, saving the silicon space they occupy and the large amount of power they consume.
• Elimination of lost margin timing - These inter-stage flip-flops require set-up and hold times which force a significant portion of the time between clock edges to be unusable for computation in high-frequency synchronous designs. Moreover given that each sub-micron technology shrink tends to increase path timing uncertainty, this further shortens the active period that can be used to achieve useful work between clock edges. This also means that in a synchronous design, the inter-stage circuit logic needs to be designed to operate increasingly faster than a single clock period to perform the same work. This requires the increased use of larger, higher power buffers in the datapath. In an asynchronous processor design, the logic does not have to deal with such small time steps. They can be built using slower, smaller and lower power circuits, while still delivering the same level of overall performance. Because the gates can be slower, it allows more use of low-leakage high-threshold voltage (HVT) gates, which drastically reduces leakage and further reduces power consumption and die area.
• Reducing wire interconnect length -The silicon area savings discussed above translate into even more power savings, because wires connecting two elements get shorter as the circuits between these elements shrink. Shorter wires have less capacitance, thus switching them requires less power by using smaller buffers

Cool! I expect to see these techniques in many processors in the future - from embedded, very power sensitive MCUs to GPUs!

(*) Rajit was a cool guy. Not only did he give us a good grade, but he even drove us 'downtown' (in the sense of down the hill, Ithaca doesn't really have a downtown) at one point to pick up some resistors and other electronic parts so we could test out MOSIS-fabricated ASIC.

PMID-101388[0] Fine control of operantly conditioned firing patterns of cortical neurons.

• hand-arm area of M1, 11 or 12 chronic recording electrodes, 3 monkeys.
• but, they only used one unit at a time in the conditioning task (i think)
• conditioning in 77% of single units and 65% of combined units (multiunits?).
• trained to move a handle to a position indicated by 8 annular cursor lights.
• cursor was updated at 50hz -- this was just a series of lights! talk about simple feedback...
• Investigated different smoothing: too fast, FR does not stay in target; too slow, cursor acquires target too slowly.
• My gamma function is very similar to their lowpass filter used for smoothing the firing rates.
• 4 or 8 target random tracking task
• time out of 8 seconds
• run of 40 trials
• the conditioning reached a significant level of performance after 2.2 runs of 40 trials (in well-trained monkeys); typically, they did 18 runs/day.
• recordings:
• 
• scalar mapping of unit firing rate to cursor position.
• filtered 600-6kHz
• each accepted spike triggered a generator that produced a pulse of of constant amplitude and width -> this was fed into a lowpass filter (1.5 to 2.5 & 3.5Hz cutoff), and a gain stage, then a ADC, then (presumably) the PDP.
• can determine if these units were in the pyramidal tract by measuring antidromic delay (stimulate muscles??)
• recorded one neuron for 108 days!!
• neuronal activity is still being recorded from one monkey 24 months after chronic implantation of the microelectrodes.
• average period in which conditioning was attempted was 3.12 days.
• successful conditioning was always associated with specific repeatable limb movements
• "However, what appears to be conditioned in these experiments is a movement, and the neuron under study is correlated with that movement." YES.
• the monkeys clearly learned to make (increasingly refined) movement to modulate the firing activity of the recorded units.
• the monkey learned to turn off certain units with specific limb positions; the monkey used exaggerated movements for these purposes.
• e.g. finger and shoulder movements, isometric contraction in one case.
• Trained some monkeys or > 15 months; animals got better at the task over time.
• PDP-12 computer!
• Information measure: 0 bits for missed targets, 2 for a 4 target task, 3 for 8 target task; information rate = total number of bits / time to acquire targets.
• 3.85 bits/sec peak with 4 targets, 500ms hold time
• with this, monkeys were able to exert fine control of firing rate.
• damn! compare to Paninski! [1]
• 4.29 bits/sec when the same task was performed with a manipulandum & wrist movement
• they were able to condition 77% of individual neurons and 65% of combined units.
• Implanted a pyramidal tract electrode in one monkey; both cells recorded at that time were pyramidal tract neurons, antidromic latencies of 1.2 - 1.3ms.
• failures had no relation to over movements of the monkey.
• Fetz and Baker [2,3,4,5] found that 65% of precentral neurons could be conditioned for increased or decreased firing rates.
• and it only took 6.5 minutes, on average, for the units to change firing rates!
• Summarized in [1].

____References____

PMID-21228307 Ultrasmall and customizable multichannel electrodes for extracellular recordings

• 7um carbon fiber electrodes.
• It has been estimated that insertion of a 50 um wire in the adult rat hippocampus CA1 area could damage 90% of the neurons that would otherwise be recordable by the electrode (Claverol-Tinture and Nadasdy 2004)
• Highlight the tetrode effect: it's like beam forming.
• Carbon fibers from Goodfellow Cambridge.
• Insulated with a pulled micropipette.
• Added insulation with cathodic electrodeposition paint (Claerclad HSR)
• focused ion beam milling (FIB) (Qiao et al 2005) -- working resolution below 10nm.
• The carbon fibers were fond to be stiff enough to penetrate the fly 'dura'.
• 

PMID-23428842 Chronic intracortical microelectrode arrays induce non-uniform, depth-related tissue responses.

• Woolley AJ, Desai HA, Otto KJ.
• One timepoint, 4 weeks.
• Laser confocal microscopy
• after tissue clearing (optical index of refraction matching) in a 60% sucrose solution.
• Single-shank iridium contact silicon substrate MEA.
• Device cut level with surface of brain after insertion.
• Intact MEAs via device-capture histology, DHhist (Woolley et al 2011)
• 350-450um tissue explanted with device.
• They promote their technique.
• Tissue surrounding microdevices exhibited two major depth-related phenomena:
• a non-uniform microglial coating along the device length and
• a dense mass of cells surrounding the implant in cerebral cortical layers I and II.
• The dense mass of cells contained vimentin, a protein not typically expressed highly in CNS cells, evidence that non-CNS cells likely descended down the face of the penetrating devices from the pial surface.
• But no Iba1 (activated microglia) per se in the tissue mass.
• 
• Hoe342 -- cell marker.
• This mass was apparently consistent across animals!
• Cells in the mass were VIM positive -- fibroblasts -- meninges?
• low GFAP = not an astrocytic scar.
• This study provides further evidence that a progressive invasion of non-CNS cells contributes substantially to the chronic phase of the tissue response around intracortical MEAs.
• Again, might be from BBB distruption {1237}

• {1193} -- microglia response not correlated to electrode failure, but correlated to ferritin immunoresponse
• {781} -- also note that menigeal fibroblasts migrate down electrode tracts.
• {1028} -- measured vimentin, GFAP, and ED1 (not Iba1). Found Vim+ and GFAP+, suggesting reactive astrocytes and not meningeal cells. ED1 aka CD68 is specific to macrophages and not microglia, so these may be blood-derived cells.
• {1200} -- chronic contact with the meninges v.s intraparenchymal correlated with Vim+ encapsulation.
• {1210} -- old paper showing the same result near surface of implant.
• {1196} -- more against GFAP & pro BBB disruption
• {1204} -- GFAP uncorrelated (!) with NeuN intensity
• {307} -- all initial tests of utah arrays showed fibrous encapsulation; one array was completely explanted. This is why now they put gore-tex over the implant -- to prevent fibroblast migration (i guess).

PMID-19963267 Quantitative analysis of the tissue response to chronically implanted microwire electrodes in rat cortex.

• Winslow BD, Tresco PA.
• The spatial distribution of biomarkers associated with the foreign body response to insulated microwires placed in rat cerebral cortex was analyzed 2, 4, and 12 weeks after implantation using quantitative methods.
• We found no evidence that reactive gliosis increases over time or that neuronal loss is progressive, we did find evidence of persistent inflammation and enhanced BBB permeability at the electrode brain tissue interface that extended over the 3 month indwelling period and that exhibited more animal to animal variability at 3 months than at 2 and 4 weeks.

PLoS One:

PMID-23251670 Ultra-Bright and -Stable Red and Near-Infrared Squaraine Fluorophores for In Vivo Two-Photon Imaging

• Podgorski K, Terpetschnig E, Klochko OP, Obukhova OM, Haas K.
• between 750 and 950 nm, where absorption and scattering by tissues is minimized
• Near-infrared (NIR) probes are ideal for biological imaging because few endogenous molecules in organisms absorb or emit in the NIR region: there is little background autofluorescence to contend with.
• Squaraine-based fluorescent sensors have been developed for a variety of analytes including Ca2+ [20], pH [21], protein and DNA, and squaraine-based labels exhibit an increase in fluorescence intensity and lifetime upon binding to biomolecules [22], [23]. The photostability of squaraine dyes is comparable to those of conventional cyanine dyes [23], but can be substantially increased by the synthesis of a squaraine-rotaxane [24], an interlocked structure wherein a macrocycle encases the electrophilic squarylium core, preventing its exposure to nucleophilic attack in solution (Fig. 1a).
• See also (this seems a growing trend):
• PMID-23292608 Choi, H.S. et al. Targeted zwitterionic near-infrared fluorophores for improved optical imaging. Nat. Biotechnol. 31, 148–153 (2013).
• focus on low background emission for maximizing SNR & image-guided surgery on tumors.
• Lukinavičius, G. et al. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat. Chem. 5, 132–139 (2013).

PMID-22056675 A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins

• Kleinlogel S, Terpitz U, Legrum B, Gökbuget D, Boyden ES, Bamann C, Wood PG, Bamberg E.
• Push-pull (excitation and inhibition) or complementary (white light) optogenetics.
• Fused with a gastric chloride pump for good membrane localization.

PMID-22056675 Substantial Generalization of Sensorimotor Learning from Bilateral to Unilateral Movement Conditions

• Kleinlogel S, Terpitz U, Legrum B, Gökbuget D, Boyden ES, Bamann C, Wood PG, Bamberg E.
• These findings collectively suggest a substantial overlap between the neural processes underlying bilateral and unilateral movements, supporting the idea that bilateral training, often employed in stroke rehabilitation, is a valid method for improving unilateral performance.

PMID-23408972 Credit Assignment during Movement Reinforcement Learning

• Chadderdon GL, Neymotin SA, Kerr CC, Lytton WW. -- SUNY Downstate
• A Bayesian credit-assignment model with built-in forgetting accurately predicts their [humans] trial-by-trial learning.

PMID-23382796 Visuomotor Learning Enhanced by Augmenting Instantaneous Trajectory Error Feedback during Reaching

• Patton JL, Wei YJ, Bajaj P, Scheidt RA.
• Learning in the gain 2 and offset groups was nearly twice as fast as controls. not surprising.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054771 Flexible Switching of Feedback Control Mechanisms Allows for Learning of Different Task Dynamics

• unimanual / bimanual tasks.

PMID-23365648 Recognizing Sights, Smells, and Sounds with Gnostic Fields

• Christopher Kanan UCSD
• Jerzy Konorski proposed a theoretical model in his final monograph in which competing sets of “gnostic” neurons sitting atop sensory processing hierarchies enabled stimuli to be robustly categorized, despite variations in their presentation.
• Gnostic: of or relating to knowledge.
• Supervised learning.
• "The algorithm can be implemented in a few hours".
• 
• Tested by classifying contemporary artists from emulated auditory nerve responses. 78% accuracy.
• Tested for image recognition w/ standardized datasets.
• 
• Method:
• Feature-extraction.
• PCA based whitening.
• Coarse template matching within the gnostic units via dot product.
• Feature vector is learned via unsupervised clustering of the whitened training features for each channel and category.
• Numbre of gnostic units per category set by fn of number of festure vectors and their dimensionality.
• Take the unit with the largest activity (inhibitive competition).
• This is a highly nonlinear function
• which normalizes based on population variability (contraharmonic mean -- weights the inverse of the SNR, effectively).
• Sum over time.
• Decode using a linear classifier over the gnostic units.
• Trained using Balanced Winnow algorithm. (multiplicative and not additive weight updates, allegedly neurally inspired)

PMID-23300606 Decoding Hindlimb Movement for a Brain Machine Interface after a Complete Spinal Transection

• Manohar A, Flint RD, Knudsen E, Moxon KA.
• SC transection resulted in a 40% decrease in M1 information content & a persistent reduction in neuronal firing rates.
• Very similar to Niolelis & Chapin 1999. Meh.
• See Wyler 1980 {909}

Journal of Neural Engineering:

PMID-23449002 Model-based rational feedback controller design for closed-loop deep brain stimulation of Parkinson's disease.

• Goal: rational design of stimulation pattern based on control theory.
• Needed a model of PD, of course -- opted for a thalamic relay controlled by GPi inhibition.
• Full PID controller

PMID-23428966 Improving brain-machine interface performance by decoding intended future movements.

• Goal: improve BMI performance by minimizing the deleterious effects of delay in the BMI control loop.
• We mitigate the effects of delay by decoding the subject's intended movements a short time lead in the future.

PMID-23428937 An implantable wireless neural interface for recording cortical circuit dynamics in moving primates.

• Borton DA, Yin M, Aceros J, Nurmikko A. Brown.
• 24Mbps, attached to Utah probe, discussed this with Schwarz.
• Inductive recharging of li-ion battery.
• Pigs, etc.
• 
• 

PMID-23428877 Local-learning-based neuron selection for grasping gesture prediction in motor brain machine interfaces.

• Nonlinear neural activities are decomposed into a set of linear ones in a weighted feature space.
• Used a margin to segregate different gestures and L1 normalization to remove irrelevant neurons.

PMID-22954906 Sparse decoding of multiple spike trains for brain-machine interfaces.

• Tankus A, Fried I, Shoham S.
• Similar idea as above --
• This method is based on sparse decomposition of the high-dimensional neuronal feature space, projecting it onto a low-dimensional space of codes serving as unique class labels.
• Tested against a range of existing methods using simulations and recordings of the activity of 1592 neurons in 23 neurosurgical patients who performed motor or speech tasks.

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

• Prasad A, Xue QS, Sankar V, Nishida T, Shaw G, Streit WJ, Sanchez JC.
• {1193}

PMID-23283391 Performance of conducting polymer electrodes for stimulating neuroprosthetics.

• Green RA, Matteucci PB, Hassarati RT, Giraud B, Dodds CW, Chen S, Byrnes-Preston PJ, Suaning GJ, Poole-Warren LA, Lovell NH.
• PEDOT is a fine electrode substrate. Surprising?
• Can deliver ~ 20x the charge of Pt.

PMID-23160018 Properties and application of a multichannel integrated circuit for low-artifact, patterned electrical stimulation of neural tissue.

• Hottowy P, Skoczeń A, Gunning DE, Kachiguine S, Mathieson K, Sher A, Wiącek P, Litke AM, Dąbrowski W.
• Made a 64-channel 'Stimchip'
• Each channel has a DAC-driven configurable voltage or current source.
• Has additional artifact-minimization circuitry.
• Designed for MEAs :-/

Nature Methods:

PMID-23524393 Whole-brain functional imaging at cellular resolution using light-sheet microscopy

• Ahrens MB, Keller PJ.
• 
• Here we use light-sheet microscopy to record activity, reported through the genetically encoded calcium indicator GCaMP5G, from the entire volume of the brain of the larval zebrafish in vivo at 0.8 Hz, capturing more than 80% of all neurons at single-cell resolution.
• 5um slices, 4um thick light sheet.
• We determined an average signal-to-noise ratio of 180 ± 11 (mean ± s.e.m., n = 31; not considering the signal-to-noise ratio of the calcium indicator itself, see Online Methods) for neurons in different regions of the light sheet–based whole-brain recording. Owing to this high ratio and the short volumetric imaging interval, which was comparable to the time course of GCaMP5G at room temperature, the occurrence of action potentials within the recording interval was detectable in most cases.
• We used the albino (slc45a2) mutant
• The mouse brain is significantly bigger, is largely impenetrable to visible light and is surrounded by a skull. Realistically, we may not see methods that enable whole brain activity mapping in mammals at the cellular level for quite a while.
• Moved the laser light beam in 2 dimensions & the objective in one; laser was scanned via piezoelectric mirrors, and the objective was also peizo-electric control.
• 
• Used segmentation to tease apart co-active ensembles.
• Understanding of actual function not too deep, but then again neither was my reading of the paper.
• 
• Prominent feature is the autonomous hindbrain oscillator.

PMID-23142873 Two-photon optogenetics of dendritic spines and neural circuits

• In neocortical slices.
• C1V1 -- combination of ChR1 and VChR1. Slower kinetics more suitable for galvanometer based scanning.
• AAV virus injected P21 mice, 400um from pial surface of somatosensory cortex.
• measured currents via patch-clamp.
• Also tested two-photon spatial light modulator (SLM)-based microscopy, a holographic method that enables optical targeting of groups of neurons or spines located in arbitrary three-dimensional (3D) positions
• goal: several neurons can be selectively or simultaneously activated in three dimensions—an approach that could enable the optical dissection of the function of microcircuits with single-cell precision.

Nanowires, useful for Flip's idea.

• These from [editorial http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1961.html]
• PMID-22231664 Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
• Robinson JT, Jorgolli M, Shalek AK, Yoon MH, Gertner RS, Park H. Harvard.
• looks like it's limited to slices & 100's of neurons atm.
• 
• Compared to patch-pipe, of course.
• Lithographic fabrication; pillars were thinned via thermal oxidation and wet chemical etching. Sounds very tricky.
• 3um microwire length.
• HEK293 and rat cortical neurons.
• PMID-22179566 Intracellular recordings of action potentials by an extracellular nanoscale field-effect transistor
• PMID-22327876 Intracellular recording of action potentials by nanopillar electroporation

Of personal interest:

Richardson-Lucy (RL) deconvolution for sub-diffraction limit imaging.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056624 Collaborative Filtering for Brain-Computer Interaction Using Transfer Learning

• Taylor the language of human-computer interaction to the users, based on k-NN in previous data.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0055518 Brain Training Game Boosts Executive Functions, Working Memory and Processing

• 'Brain Age' is effective in a double-blind study.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061390 Cognitive Training Improves Sleep Quality and Cognitive Function among Older Adults with Insomnia

• Debatable causality.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054402 Perceived Multi-Tasking Ability, Impulsivity, and Sensation Seeking

• The findings indicate that the persons who are most capable of multi-tasking effectively are not the persons who are most likely to engage in multiple tasks simultaneously. To the contrary, multi-tasking activity as measured by the Media Multitasking Inventory and self-reported cell phone usage while driving were negatively correlated with actual multi-tasking ability
• Finally, the findings suggest that people often engage in multi-tasking because they are less able to block out distractions and focus on a singular task. Participants with less executive control - low scorers on the Operation Span task and persons high in impulsivity - tended to report higher levels of multi-tasking activity.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052500 Learning and Long-Term Retention of Large-Scale Artificial Languages

• We report data from a large-scale learning experiment that demonstrates that adults can learn words from unsegmented input in much larger languages than previously documented and that they retain the words they learn for years. These results suggest that statistical word segmentation could be scalable to the challenges of lexical acquisition in natural language learning.
• A unique artificial language was generated for each participant. Each language had 1000 word types and 60,000 word tokens (for 10 hours of speech). Frequencies of words were distributed via a Zipfian frequency distribution: , where is the frequency of word and is its rank, such that there were a few highly frequent words and many more with lower frequencies (max = 8000, min = 10 tokens) [30].

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052042 Non-Hebbian Learning Implementation in Light-Controlled Resistive Memory Devices

• Light and voltage controlled memsistors. Interesting.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058284 Attractor Metabolic Networks

• We have found that the systemic enzymatic activities are governed by attractors with capacity to store functional metabolic patterns which can be correctly recovered from specific input stimuli. The network attractors regulate the catalytic patterns, modify the efficiency in the connection between the multienzymatic complexes, and stably retain these modifications. Here for the first time, we have introduced the general concept of attractor metabolic network, in which this dynamic behavior is observed.
• Used a Hopfield network via a Boltzman machine.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059196 Prenatal Exposure to a Polychlorinated Biphenyl (PCB) Congener Influences Fixation Duration on Biological Motion at 4-Months-Old: A Preliminary Study

• infants exposed to PCBs have delayed / impaired development. Expected, but still sad.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060437 Hunger in the Absence of Caloric Restriction Improves Cognition and Attenuates Alzheimer's Disease Pathology in a Mouse Model

• Ghrelin, a hunger-inducing drug attenuates AD pathology, in the absence of caloric restriction, and the neuroendocrine aspects of hunger also prevent age-related cognitive decline.

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).
• Yet stiff enough to penetrate the dura of rats.
• Lithographic patterning process pretty clever, actually.
• Device dissolves within three minutes of implantation.
• Probes are tiny -- 10um wide, 2.7um thick, coated in parylene-X.
• No histology. Follow-up?

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

• [www.sciencemag.org/cgi/content/full/340/6129/211/DC1 Supplementary materials]
• 21 authors, University Illinois at Urbana-Champaign, Tufts, China, Northwestern, Miami ..
• GaN blue and green LEDs farbricated on a flexible substrate with stiff inserter.
• Inserter is released in 15 min with a dissolving silk fibroin.
• 250um SU-8, reverse photocured on a glass slide.
• GaN LEDS fabricated on a sapphire substrate & transfer printed.
• 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 more SU-8.
• Layers are precisely aligned and assembled via 500nm layer of epoxy.
• Layers made of 6um thick mylar (polyester)
• 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!

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).

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?

PMID-22832283 Stab injury and device implantation within the brain results in inversely multiphasic neuroinflammatory and neurodegenerative responses.

• Here we present a detailed quantitative study of the cellular events and the stability of the blood-brain barrier (BBB) following intracortical microelectrode implantation and cortical stab injury in a chronic survival model
• For chronically implanted animals, we observed a biphasic paradigm between blood-derived/trauma-induced and CNS-derived inflammatory markers driving neurodegeneration at the interface.
• In contrast, stab injured animals demonstrated a CNS-mediated neurodegenerative environment.
• Showed controls for once!
• Large difference in GFAP & IgG in chronic vs. stab wound.

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 polymide 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____

http://docs.lib.purdue.edu/dissertations/AAI3444877/

• Several different projects --
• Stretchable PDMS electrodes
• PDMS-parylene ECoG
• Transmitting parallel neural data via free-space optical link
• semi-flexible hydrogel-parylene neural electrode.
• The parylene electrodes with selectively patterned hydrogel provide stiff mechanical properties for easy penetration into the brain tissues and subsequent flexibility after insertion upon swelling of the hydrogel.
• advanced packaging system with using a composite inorganic parylene combination.
• Atomic layer deposited alumina-zirconia (Al2O3–ZrO2) composite layer can provide a conformal and nano-laminated coating on parylene surface in neural packaging systems in order to improve the hermeticity for long term implantations
• Can't get the entire PDF. annoying.

A New Multi-Site Probe Array with Monolithically Integrated Parylene Flexible Cable for Neural Prostheses

• 
• Use DRIE to etch the back of the wafer after patterning the front. Clever!

PMID-21240559 Highly-compliant, microcable neuroelectrodes fabricated from thin-film gold and PDMS

• 
• 
• he microcable electrodes were also electromechanically tested, with measurable conductivity (220 kΩ) at an average 8% strain (n = 2) after the application of 200% strain.

Bay area hikes:

• Mt. Umunhum. Near Los Gatos.

PMID-16425835Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex

• claim that they have done a logitudinal development series that included 39 array implants in 18 monkeys.
• can get reliable recordings out to 3 months (only? probably the array was forced out of the brain?)
• however, it seems that their recording quality did not decrease dramatically over those 3 months.
• excellent methods section.
• also {1027}

____References____