A Science Diary

Look who we found in Japan!

2011-09-28T17:47:00.000-07:00

We were lucky enough to get invited to dinner with the Lt. Governor Becky Skillman (Indiana). She was in town to visit with business leaders, and also personally deliver condolences regarding the tsunami disaster back in March.

Governors from different parts of the state were also in attendance.

Inferior temporal gyrus malformation

2011-07-02T19:06:00.000-07:00

Our patient yesterday suffered from intractable epilepsy. This first image shows the malformation in the gyrus on the left side of the photo behind the eye. If you compare the two gyri, the normal one on the right has the shape of a flower with the outer edges in dark grey. The left side is more rounded.

The skull cap removed, the electrode grid here labeled 1-7 is used to map out the areas where the seizure like activity is being generated by the brain.

Tissue for the experiment was removed from electrode 6 in this image.

The Great East Japan Earthquake of 2011: the aftermath at three months.

2011-06-09T04:36:00.000-07:00

It's been nearly 3 months to the day that the North Eastern coast of Japan was rocked by the 9.0 earthquake and subsequent tsunami of 2011. The stretch of time when the earth quake reached our region in Nagoya nearly 700 km away is seared into my memory. I had just sat in the dentist chair for a check up, and several of the hygienists started squeaking, and chattering amongst themselves. At first I didn't know what was happening, and then I noticed the blinds on the window started swaying like the pendulum on a grandfather clock. Their intensity waxed until they had reached a full 40 degrees, by which time there was an intense genuine fear in the eyes of the staff as they probed the room, the rest of their fear hidden behind the alabaster sterile masks. Having only experienced 1 earth quake personally, I was relatively calm until I was struck by those fearful eyes. At once, everyone looked toward the front of the office, the closest exit, but the blinds were already starting to wane as the tremors subsided.

The aftermath was devastation in the North. More than 15,000 deaths, 125,000 buildings destroyed, 4.4 million households without electricity, and an estimated 300 billion dollars worth of damage, this is the most deadly natural disaster Japan has ever experienced. Fukushima, Sendai, Myagi, & Iwate were all struck with intense waves, some measuring an unbelievable 79 feet in height!

Locally, civilian aid has been solicited as professional rescue workers have secured the safety of most of these regions. I joined an aid group of 39 civilians from Nagoya and traveled by bus to Iwate to help with the efforts.

First, I will show you some video taken from the bus while driving through Iwate port. The video is a little bumpy, sorry in advance, but this was done as a discretionary measure as some people are moving back into these areas, and out of respect for their privacy I've taken no video openly walking down the street or any video of people living in the area. Please understand, and thank you.

For some reason Google wants to make my videos fuzzy. I'm looking into it.

Each morning our group would perform a few calisthenics together before going to work. I'm afraid I only caught the last few bits of it, but it gives you an idea of what it was like. The mood of my coworkers was hopeful, and each had a can-do attitude that was admirable given the circumstances.

At 3 months the most pervasive part of disaster is the odor. The ruble is a formidable site indeed, but imagine a garbage dump miles in every direction, and then add the acrid smell of rotting sea life that was left by the tsunami, and then cook that at about 90 degrees Fahrenheit. The breeze, when it comes, doesn't remove this odor, but only changes it's gradient. The first day we were split into groups of ten. My group was set to work in a house that was to be refurbished and lived in again.

There is a line on the wall where the waves lapped and left soil and debris, it's nearly 6 feet in the house, and more than that from the ground outside. Everything was just as it had been occupied. Food was rotting in the refrigerator, a wedding certificate was hanging high in a doorway, and clothes still hung in the closet. We removed all articles, furniture, appliances, and 5 inches of mud from the floors. The sunlight shimmered in the salt left by the sea in the dirt as it was hoisted into the back of the dump truck to be hauled away.

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Mostly, the work was removing the wretched smelling, fetid soil. Here we set up a temporary wash system to clean and replace rocks from around a home. The area was too narrow for automated machinery, and the rocks had to be dug up by hand, washed, and then replaced. A couple of inches of soil was removed with it.

Here in the back ground is the port of Iwate from the South side. The enormous green cranes are the most conspicuous objects in this photo, and in the far corner, the enormous ship sitting upright on the dock can be made out. Most of the video shot by the television crews was taken from this spot. In fact a story was being shot by a crew when I took this picture. They were doing a story on new homes being built by trees logged from nearby forests, and then towed into the bay to the city. They were filming the logs coming into the bay.

Still enormous amounts of debris, but the streets are cleared, and many sections of debris have been sectioned off for recycling by composition.

The best close-up I could get of the stranded ship. It's amazing that the dock can support this monstrous ship.

Lunch breaks were informal, the crew would find any shady spot, and take a rest from the hot sun. This home was also flooded. If you look to the top right of the image, the wall has a line left by the sea where the house was under 5 feet of water. Amazingly, this couple was in their 80's, and had moved back in within two months. They were extremely grateful and generous to us, bringing us tea (pictured) and cookies every couple of hours.

Trash and debris more than 4 feet high, and 6 feet wide was piled along roads for miles. The bags are full of soil and sand left by the sea in the houses. Shobo dan, as everyone called him, was kind of self-appointed leader in our group. We had a group leader that sometimes worked with us, but Shobo dan (fireman in Japanese) was often a usurper. Rightly so, he was senior and as a fireman had years of indispensable knowledge, plus an agreeable disposition, it just worked well, and he out-worked most of us.

The last day we cleaned a drainage tunnel that was 4X4 feet height and width, and about 100 feet in length. The drain went under a major underpass, and drained water from the mountains into the sea. The tunnel was completely clogged in four places. The first two were clogs were made up of medium sized tractors probably 30hp that had been sucked into the tunnel's by the strong currents. We removed debris and two tractors, digging them out by hand as there was no way to get machinery into the tunnel. The other two clogs were made up of dirt sticks, and oddly enough fishing nets. Imagine a 4X4 foot mound of dirt that's 8 feet deep in some places, and that is about the size of these clogs. In addition the floor of this tunnel was 8 inches deep in mud and debris for 100 feet. All of our group worked this tunnel, plus two men from the Japanese self defense force for more than 8 hours, but in the end it was spotless.

When we finished a tiny hunched over very elderly Japanese woman came down and called a few of us to follow her. We climbed up the hills crossed the road where she and three other women of her age were tending several make shift greenhouses. She paraded us down through the greenhouses muttering almost inaudible, "this is cucumber, this over here is eggplant" and on she went. The plants were impeccably tended, amid all this rubble, it was a magical moment. She took us to a large orange tub that was collecting water from the mountain, and she motioned for us to wash ourselves up a bit. The water was clean and refreshing, we thanked her, and they all got up from what they were working on and bowed to thank us as best as their tired backs would allow. Later I found out that without that drain the old women would lose their makeshift greenhouses during the rains.

Daibu is peering out over the sea. The great Buddha weathered the quake, and watched the tsunami take everything away from the locals even many lives, perched high on her mountaintop about 1 mile away.**

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Daibu's expression is still, calm, and centered.

These bells are often rung after prayer to Daibu.

Usually the first question I get in Japan is "where are you from"? I thought it would be more efficient if I just displayed it on my hard hat. To show my support I displayed the Japanese flag to the right. Now I checked beforehand what the proper flag etiquette is for displaying the US flag with another flag, and what I found was that it should always appear on the right of the displayer, which is the left of the viewer. I'm sure someone will tell me if I'm wrong, in either case, it wasn't haphazardly done.

**All measurements are in English Units so Marc won't whine.

New article

2010-12-16T16:42:00.000-08:00

As promised I've posted a link to the new article published this month in the Journal of Clinical Neurophysiology. The abstract summarizes the results which are briefly the following: some tissue from juvenile humans exhibit seizure like activity in vitro, these tissue also have aberrant neuronal avalanches.

Surgery Friday

2010-10-04T20:42:00.000-07:00

This is a photo from the surgery last Friday. The patient suffered from a deep subcortical tumor, and presented with seizures. The silvery end of the suction is pointing to the inferior temporal cortex, the region that was most epileptic during the surgery. Everything went perfectly during the experiment. The tissue was very active within a few hours after the tissue had been removed. I collected more than 6 hours of data at 20 kHz which is awesome.

OH, and the paper will be published in the December issue of Journal of Clinical Neurophysiology! Of course I'll post a link when it's hot off the press.

The title, "aberrant neuronal avalanches in tissue removed from juvenile human epileptics".

Cavernous malformation

2010-07-30T13:33:00.000-07:00

This image is of the right side of the brain just anterior to the motor cortex. The patient presented with seizures, and a cavernous malformation was found. 36% of cavernous malformations will cause seizures. The vasculature is malformed and is a purple color like a raspberry.

Recent talk

2010-07-25T17:46:00.000-07:00

I recently gave a talk which I'm placing a link to in the sidebar. The talk is a little more than 1 hour and is a whopping 40mb, just so you know before you DL. It basically sums up what I've been working on for the past few years.

Here is the title and summary:

Modeling network correlations in cortical tissue

from juvenile human epileptics

Summary

Models of neural tissue can make predictions about a real neural network, but these

predictions rely on the data to determine parameters. Hence, the model is only as good as

the data. I collected in vitro data removed from juvenile humans with refractory epilepsy,

and found human-specific spatial and temporal dynamics that are not found in rats. I will

first describe the general characteristics of the human data in comparison with rat data,

and my attempts to model these differences with three popular models of neural

networks: branching, pair-wise maximum entropy, and a forest fire model. I will

describe three key discoveries from this exploration: first, spatial dynamics are more

easily satisfied than temporal in both the rat and human tissue, second temporal

correlations are not captured by the branching or the maximum entropy model, and

thirdly, strong temporal correlations can be accounted for with the addition of a

parameter in the forest fire model. Finally I will suggest new questions that this research

has revealed about human tissue, and models of neural networks.

Surgery

2010-06-15T06:20:00.000-07:00

Yesterday we had a patient with mesial temporal lobe sclerosis. The instrument in the image is pointing at the superior temporal gyrus where the tissue for the experiment was removed from. To prove that we never know how the experiment is going to go, I didn't believe the experiment would go well (we had some delays getting the tissue), but I was wrong. Within 2 hours the first section of tissue was producing activity, and worked for 7! yes 7 hours! Thanks Rashid and Rachel for helping with the experiment (all 14 hours of it).

Jack Cowan

2010-06-11T08:16:00.000-07:00

Yesterday I put up a video of Jack Cowan giving a presentation at the Salk Institute. The video is an hour long, but well worth the time. Cowan is probably the foremost expert on statistical mechanics applied to the brain. The Salk provides a lively Q&A time, which is also interesting. I like Cowan's reply to the question about quantum mechanics. I think the lecture is very nice, and is approachable by many audiences from different backgrounds.

2010-06-10T10:40:00.000-07:00

Site under construction!

2010-06-07T19:43:00.000-07:00

Please excuse the web site, I know it looks terrible, but I thought it was time for an overhaul. Hopefully I'll be able to update everything soon.

Another update on the last patient. The patient is well, and recovering. The surgery went late, the seizure focus was removed around 7pm, so the experiment began pretty late. Interestingly, the tissue produced spikes, which is very rare for slice experiments on our array. The tissue did not exhibit a "seizure" during the experiment. These experiments are really unpredictable, which is what makes them challenging, and interesting.

Frontal Lobe Epilepsy

2010-05-20T18:51:00.000-07:00

Hello again out there in the blogosphere. Today we had a patient. Pictured here is the open skull over the left frontal lobe. To orient you, the patient's nose should be in the same plane as the fork looking instrument at the top of the image. The patient has severe epileptic seizures. The white dot is a guide that is placed into the brain to guide, the removal of bad tissue. It's not just resting on the surface, it is a long thin tube placed directly into bad tissue below the surface. Dr. Smith removes the epileptic tissue, and gives it to me. I take it back to the lab, and prepare it so we can watch seizures, and try to figure out how we can prevent them.

SFN 2008 Poster

2008-11-14T14:48:00.001-08:00

Hi,

I won't be going to the annual Society for Neuroscience meeting this year, but I do have a poster.

Basically, the poster explores the network activity of a brain under two different types of drugs. Many studies with these drugs using just one brain cell give a predictable outcome, but the network activity under these drugs have not been explored. These drugs may not be doing what they are reported to be doing. The network of brain cells don't behave like single cells do.

New President

2008-11-05T07:56:00.000-08:00

Late last night around 11:30pm Bloomington erupted in cheers as Obama was announced the winner of the Presidential election.

Throngs of people poured into the streets and marched up Kirkwood to the courthouse chanting Obama! Obama! Obama! It was an amazing event to witness, history in the making.

Patient doing great!!

2008-10-31T10:23:00.000-07:00

Here is a video of the experiment last week. Electrical events are generated by the brain tissue on the array, and appear in the video as boxes of different color. The more colors the larger the electrical event. This is 1.6 seconds of data from the seizure focus.

Surgery: Occipital lobe resection

Seizure tissue on the Micro Electrode Array

Last Wednesday we had a patient with a seizure focus in the occipital lobe. Jodi was able to remove the seizure focus, and the patient is fully recovered with no deficits!

Election Woes

2008-10-21T11:52:00.000-07:00

I'm here, alive, but I'm in the process of writing a paper. The paper will describe the results from the human experiments. It will characterize the spatiotemporal characteristics and modes of the data.

I've also been taking a course at Penn. State Neural Control Engineering with Steve Schiff. Steve, Chair of Biomedical Engineering, is a Neurosurgeon and a Physicist. His lectures are excellent, and I can interact online during the course with video.

Calvin is sick of hearing about the election and wants to know what CNN is going to cover after the election is over? Apparently nothing has happened in the world since the US presidential election.

Woods Hole Massachussetts Marine Biological Laboratory

2008-09-18T12:34:00.000-07:00

Eel pond August 17th 1am, full moon Woods Hole Mass. The day after I arrived in Woods Hole the moon was full. The course I was attending (Neuroinformatics) was directed by David Kleinfeld and Partha Mitra. The course mainly covers signal processing in terms of spectral content, and utilizing methods of transformation ie Dirichlet, Gaussian kernel, multi taper methods of recovering specified bandwidth.

I enjoyed the course, and glad to be back home. I still haven't gotten around to making a new website, but I will soon I promise.

Good News!

2008-05-21T13:40:00.000-07:00

So I'm in the process of finalizing my trip plans to Los Alamos, and I've been invited to give a presentation on behalf of the Biophysics group! This is a huge honor and I can't wait!
The second part of the good news, I just found out that I've been accepted to Woods Hole summer program in Neuroinformatics!

Back from the...

2008-05-12T10:44:00.000-07:00

I've been kicking around an idea for a while now about a new website, and I've finally made up my mind. I want to re-engineer the website completely, and the brain avalanche blog will eventually go away. I plan on consolidating my work into several central themes, and categorize them, updating whenever I have something more substantial. We've no patients scheduled until June, so there really isn't anything exciting to write about. The experiments are sort of droll, and not very entertaining, so I don't think many people will be interested in hearing about them. So the new website will be coming soon ( I hope) will read more like a resume than random spatterings of crazed scientist.

2008-04-23T06:56:00.000-07:00

My friend Rachel sent this to me. Oh my, so hilarious.

Son-Of-A-Bitch Mouse Solves Maze Researchers Spent Months Building

Can't find the monkey

2008-04-18T12:51:00.000-07:00

Sorry everyone, I've been very busy lately with experiments. I really haven't had time to write at all, and we haven't had any human surgeries, so there isn't much to (I can) tell. I can say that on the paper front we are submitting to Nature Neuroscience. We are fairly positive about our chances here.

I've ran experiments daily here, in addition to finishing the installation of our new patch clamp rig which will be mounted to a new low profile 60 electrode amplifier. We are all very excited about this, since relating population activity to single cell dynamics is a field left virtually unexplored.

The next few weeks will be even busier. I've got several trips coming up. I leave the country for two weeks, in two weeks. Then straight to Milwaukee to collaborate with some of our friends for a week. This should keep me busy until the end of May. Right now we are tentatively planning the trip to Los Alamos in mid June, so really the next few months are tied up.

Earthquake link
My first earthquake, at least the first one I've ever been aware of occurred this morning at 4:40am. What a frightening experience! (5.4 richter) I just wish I had been more conscious at the time so I could have appreciated it more. Some of my friends told me they could tell the oscillations were very periodic, and waxed and waned in intensity. How incredible that must have been to perceive the entire event with such acuity.

John Wheeler

2008-04-14T10:19:00.000-07:00

John A. Wheeler at Princeton University in 1967.

John Wheeler, the physicist that coined the term "black hole" dies at age 96.
Read the article here.

The good news, and the bad....

2008-04-08T15:09:00.001-07:00

I just found out today that Newsweek decided to drop my photos from the article. There was no reason given, in fact I had to email the editor to find out that they weren't published. No big deal really, it would have been nice, but meh.

Now for the bad news, our paper got rejected from Nature. We handed the paper to Gumbo, Nature's dancing monkey, and he really liked it. Unfortunately, Gumbo has no influence in the review process. Now the question is do we try to find Lucille; the monkey that dances for Science.

Botox on the brain...

2008-04-07T08:04:00.000-07:00

In this week's article of the Journal of Neuroscience there is an article on the potential hazards of Botox injections. The article "Could Botulinum Toxin Be Bad for You?" Ashleigh et al have found that Botox actively migrates to sites, other than the injection site, and alters nerve transmission.

Electron makes its film debut!!

2008-04-03T02:22:00.001-07:00

Electron movie from Science on Vimeo.

http://www.scientificblogging.com/news_releases/electron_caught_on_film_for_the_first_time

APRIL FOOLS!!!!

2008-04-02T08:23:00.000-07:00

Ha, well I don't think anyone believed my post yesterday. It was a fun April fools day prank.

A second life,,,

2008-04-01T06:52:00.001-07:00

After weeks of contemplation, I've decided to accept a job with second life and drop out of graduate school. In this virtual reality I plan to assume a new identity, and move on from the torment of graduate school. I'll be writing programs for a tidy sum, and have plenty of free time to enjoy the beach in California (which is where I'll be living in reality).

Dying is a lot of work!

2008-03-29T14:27:00.000-07:00

You may not have access to the journal Cell, but here is a link to the abstract for a paper by Overholtzer et al. Its bizarre to imagine dying as such an active process, but investigators are finding out just how complex the process is. Its easy, the hijakers have to land the plane sometime for fuel, and when they do, special forces will slip into the plane, shoot the bad guys and their limp and flaccid bodies fall over, lifeless.

The biochemical cascades that are initiated for death require energy, so dying is really an energetic process.

I stumbled across a good example of this today as I was hiking through Griffy park. Two trees had fallen across the path last fall, before autumn. The color in the leaves quickly faded after the trees were uprooted. However, they both still retain the shriveled up leaves. I imagine someone has thoroughly investigated the biochemical process of leaf shedding in trees, but it just occurred to me how these processes are still conserved from flora to humans.

Next book on the list...

2008-03-27T08:25:00.000-07:00

Is by Per Bak, a Dutch physicist that met with a tragic, and early death.
How Nature Works is about self organized criticality.
Here is the article: Self organized criticality, an explanation of 1/f noise.

2008-03-25T14:09:00.001-07:00

I just finished Steven Strogatz book Sync. Strogatz is in applied mathematics at Cornell. The book is about synchrony in biological oscillators (mainly) and the field of nonlinear dynamics. Strogatz gives an enthusiastic account of his own investigations, and personal interactions with Aurthur Winfree (formerly at Purdue).

2008-03-24T12:25:00.000-07:00

Back in the lab today for more experiments. The room here is kind of dark (I'm on the far right) someone forgot to bring in more candles, so the picture didn't come out to well.

Thankfully today's experiment is going well. Last Friday was a bomb, and when the experiment tanks, it is very disappointing. A day of work, and nothing to show for it, Bleh!

Cartoon

2008-03-21T07:56:00.000-07:00

This cartoon is lifted from xkcd.com. Nothing better than scientists that write cartoons, though it seems that the entire field of brainphysics has slipped past xkcd. Maybe I'll write them:)

Great News!

2008-03-19T06:30:00.000-07:00

I just got word from the editor of Newsweek magazine. Some of my photos are going to be published in an article this week. Yay! I'll fill you in on more details as I get them.

Also very good news, we had a visiting scholar this week from Los Alamos National Lab, and I was tentatively invited to spend some time collaborating out in New Mexico this summer, possibly the entire summer.

Spring Break in the desert

2008-03-17T11:06:00.001-07:00

One of many bees on a spring pollinating spree. The yellow bloom is from a brittle bush. Its hard to imagine that such beautiful flowers bloom in the desert.

I'll post more images on my photo blog soon www.focusingphotons.blogspot.com

Great news!

2008-03-05T11:52:00.000-08:00

Patient doing great, and in recovery!

The instrument in this image is pointing to the region where the tissue for our experiment came from. This is inferior temporal cortex, on the right side of the patient's head.

We collected data on the first piece of tissue, and the tissue was in normal spinal fluid. This is very rare data, in fact for three years now I have only collected two other files in normal spinal fluid. To top the night off I had activity in elevated spinal fluid, nearly 30 channels which lasted more than an hour!

The modifications I made to the slicer worked perfectly. I no longer have to hold the diffuser hose, or attach the pipe to the cart. The only thing that would make the process easier would be a quick disconnect on the hose, that will be the next modification.

Surgery Tomorrow!

2008-03-02T10:57:00.000-08:00

We have a patient scheduled for tomorrow, so I'm prep'ing for the procedure today. I'm a tiny bit nervous about tomorrow. I bought a new tissue slicer and I've never used it with human tissue. As soon as the slicer came in, I had a great idea of how to modify it to better suit our oxygenation needs. So far, the modification has worked out well.
The tube here is connected to a plastic valve which shuts on/off the gas to the clear plastic case. The tissue is attached to the metal cylinder which is normally submerged in brain juice. To diffuse the gas as it flows into the case, I inserted a sealed plastic tube (not shown) on the other side of the valve, and poked small holes in it with a needle. This also helps regulate the rate at which the gas flows into the juice.

2008-02-28T06:37:00.001-08:00

Spring time

2008-02-27T13:32:00.001-08:00

This is a shot of my street a few days ago.
Just kidding, no this is somewhere in Switzerland, but there certainly has been a substantial amount of freezing rain this year. Most of us could use some nice warm weather, and with spring break just right around the corner, I'd like provide a list of recommendations for places not to go for spring break.

Places to avoid this spring break:
1. Indiana
2. Kosovo
3. Antarctica
4. Murmansk
5. Thule

A Perl of wisdom.

2008-02-25T08:46:00.000-08:00

I feel much better today, but I'm still not over this flu. To celebrate my partial recovery, I'm going to work, YAY! Actually, I miss coding, and while sick I did a make of Perl on my Mac at home (get the source code here). It is a little more finicky than matlab, (the basic idea is the same) and I had forgotten lots of Unix commands, but it was fun nonetheless.

How to create a custom crayon widget with Perl.

Nothing to report

2008-02-22T07:20:00.000-08:00

I guess its been a good week to be sick. Last night we had an ice storm that blanketed much of the county in a thick sheet of ice. I was unaware. For the past two days I've spent more time asleep than awake. The cats are pleased, they've never seen this much of me, ever, and their favorite past time is sleeping, so we all just sleep the day away. Mid-day yesterday, I still had a fever, but I have not checked it today.

The flu

2008-02-19T19:51:00.001-08:00

As I sit here writing this I'm suffering from a +100 degree fever. Unlike Travolta, I don't feel like dancing, but then again its not Saturday night.

Friday night after I finished running the experiment I drove to Tennessee. Monday was Mom's birthday, and my brother was down visiting, so I decided at the last minute to join the party. I think I caught this virus at a gas station in Southern Indiana. I know it sounds weird, but it was late and I stopped to use the restroom. The attendant was wheezing and hacking, and I wish I had not bought that chocolate milk.

It doesn't matter now. It is full blown, and I'm down for the count. I do have a few positive things to mention. My experiment went well on Friday. Mom was ecstatic to see me, (I missed her too) and it was good to see my extended family.

The beginning of a good year.

2008-02-15T12:23:00.001-08:00

So far this year, things have been going very well. Its probably bad luck to even talk about good luck, but its okay, I'm not superstitious. If one types "luck" in the google search bar, this image of a huge tuna fish pops up that has hands growing out of it. Oh wait, no those hands belong to passersby. This Japanese tradition of placing coins on a dead tuna is said to bring good luck for the new year.

It didn't seem to work for the tuna.

I'd be lying if I said that I didn't have some superstitions. Actually, they aren't all that harmful, unless you are a tuna fish. For instance, when the turn signals quit working in my car, I at once began to turn the switch in all three different positions, and then reverted to the even more technical approach, lightly hitting the steering wheel with the back of my hand. A bulb could have been burnt out, or a wire shorted in the trunk, it could have been any number of things.

Superstitions are useful, because causality is elusive. My turn signals started working again, but long after I stopped beating my steering wheel. For whatever reason, things do work, even though reason is misplaced.

I wonder what happens if your coin slides off the fish, is that bad luck, or do you just miss out on the good luck?

Noise, enough already

2008-02-14T12:39:00.000-08:00

Monday I collected fantastic data from the tissue, hours, upon hours of data, the tissue was so robust that I were able to run DNQX on the tissue, and wash out which is really unheard of when experimenting with human tissue.

Here is where I have to thank Andrei for his advice and help with the experiment that night. You are a good friend, colleague, and comrade!

The tissue did produce activity without any manipulation, but the signal to noise ratio is very low in this portion of the data. For two days now I've been fighting with it, and it is worth coming back to, but i'm going to move on to the stronger data sets from later in the experiment, and the DNQX.

Success!

2008-02-12T07:01:00.000-08:00

Last night's surgery was a success. The patient is fine, and recovering well, and the data was fantastic. It is very unusual to collect data so soon after tissue resection. The tissue came from the inferior temporal gyrus in the right hemisphere.

{Blue line divides superior, and inferior left hemisphere}

I say unusual, but actually, I've never collected data within an hour after resection, with this one exception. The tissue was removed at 1pm, and a little after 2pm I was collecting data, what an awesome experiment!

Surgery today!!!

2008-02-11T08:09:00.000-08:00

We have a patient today, and I'm running a bit behind. I ran an experiment this weekend, and had many other things to take take care of, so that is the reason for the rush. We ordered a new piece of equipment for slicing up the brain tissue into really thin slices. That actually came in today, YAY! So I unpacked that this morning, and played with it a few minutes. I'll have to take it back to Bloomington, and practice with it for a while before I'll feel comfortable using it up here at the med. school.

What happened to the weather? It suddenly arctic-like, with 40mph winds...

How to know when your programming skills are lacking

2008-02-08T13:58:00.000-08:00

The problem with writing code is that it is not always intuitive. In fact it seldom is very intuitive. The only way to become good at writing code, is to write a lot of it. This requires patience, and time. Fortunately, I have neither of these, so the task is doubly difficult.

While juggling an experiment gone bad today, I was trying to write in some GUI into the new programs. Here is where the title comes in; if you name an internal function a working variable and that variable happens to be the clear function, you will need to shut down MatLab and start over. This may happen for several reasons, lack of creativity (working with a limited vocabulary, one may not be creative enough to produce a unique name as a variable), stupidity (no excuse here), or just plain lazy. Today's case probably includes a bit of each.

Additional programming

2008-02-07T15:14:00.000-08:00

I spent the day today sharpening up those programs and writing a new one. With some additional changes they look respectable, now all I need to do is finish data collection. I probably need to run 5 good experiments with NBQX.

One of those days,,,

2008-02-06T13:43:00.000-08:00

All I wanted to do was speed these programs up a bit, make a nice subplot output, you know streamline things. Something that should only take a few minutes, it ends up being an endless adventure.

Oh yeah, it would probably help if I slept more than 4 hours, but something was keeping me awake. I did learn that there are unique calling subroutines for subplot in log scale, and that inbred reshape calls are picky when called in subplot.

Aren't my graphs pretty?

Oh yeah, how about that, so embarrassing, this one looks better.

Guest speaker

2008-02-05T14:32:00.001-08:00

This is an image of a water strider insect taken by David Hu, Courant, NYU.
I've cut and pasted an explanation of the image from his website:

"A water layer was sprinkled with Thymol Blue, which established the Marangoni convection responsible for the evident fine-scale texture. The layer was lit from below, giving the flow a natural luminescence. Stopping vortices shed during the deceleration phase of the strider's motion are evident in Figure 2. The dipolar vortices shed by the driving legs during each stroke are evident in Figure 3, and mark the path of the strider. The starburst in Figure 3 is associated with the relatively large particle of thymol blue evident at its centre: the Thymol Blue reduces the local surface tension, thus prompting surface divergence that clears the surface of blue dye. The water striders are light-seeking, and so drawn to the starbursts."

He was the guest speaker today at the physics colloquium. Dave did his PhD in Applied Mathematics at MIT. Not only did he present his work on hydrodynamics of insects but also his newest work with locomotion of snakes. This work has little to no relation to epilepsy, but his talk was inspiring from a motivational perspective.

Presentation

2008-02-02T14:59:00.000-08:00

Very soon I have to present my findings in a public seminar for the biophysics lecture series. I have three main points that I would like to cover in the presentation.

1. Synchrony in large scale systems
2. Distributions of event sizes in these networks
3. Focal points, and distributed processes

All three of these can occur not only in a normal form, but a pathological one as well. Determining the difference is not as easy as it may seem at first glance. First, synchrony is found in the normal operations of cortex. Second, the event size distributions are non-poisson, but are inherently variable, most likely because all biological systems have noise. Third, focal points, to some degree are naturally occurring. We can visualize this by comparing say Atlanta International airport, and Indianapolis airport. Both host traffic in the form of people, but the degree of traffic is very different. The inherent weakness is if a major hub fails, the organism suffers, and may fail altogether.

Data From December 10th.

2008-01-29T08:14:00.000-08:00

This plot is from our patient on December the 10th. Neither I, nor anyone else that works with local field potential on multi electrode systems have ever seen data like this. The frequency is very high during the seizure-like event at the end of the trace. Now imagine having 64 channels of this data, that is similar on each electrode. You can imagine our surprise.

2008-01-27T10:12:00.000-08:00

I just randomly ran across this video today. I've always liked Beck, the satire in his music is deep and complex, combined with pseudo-original mixes makes for a fun and entertaining experience.

If you like the song, you can download it here.

Remember that surgery,,,,

2008-01-26T15:50:00.001-08:00

Back in December we had a really exciting data set unfold in the lab. That data set had a very low signal to noise ratio. The reasons why are two-fold: the first is because we had never really collected substantive data at Stark, and the second is because this made analysis a low level priority. Now that I had good data I was forced to write the analysis programs.

Today I think I'm finally confident that I've got a good data set from that experiment. It took hours and hours of work but in the process I've learned quite a bit about programming. I'm just trying to get caught up now, and run new experiments.

So the evil monkey is still on my back!!!

Surgery yesterday, patient doing well.

2008-01-24T13:59:00.001-08:00

Surgery yesterday, the patient is recovering, and so am I. Even though I started preparing for this surgery Tuesday, and woke early Wednesday morning for the operation, the experiment really didn't start until 9pm Wednesday night.
One word for the data, FANTASTIC! I collected hours upon hours of data from this tissue, in fact I had to call it quits and clean up because I had class this morning. When I got home around 3am I was exhausted, but I could not sleep, all I could do was think about the data.

So far I've done just a superficial sifting of the data, and its totally unique. This is why science is so compelling, just as soon as you think you can draw some conclusions about the system you are studying, wham, there goes all those ideas.

The patient has a subcortical tumor, probably oligodendroglioma, or dysembryoplastic neuroepithilial.

2008-01-22T12:04:00.000-08:00

Anyone interested in the stock market might find this interesting. It is from the NY Times today. Another interesting article a few days ago "The education of Ben Bernanke" can be found in the Times.

Picking your battles

2008-01-21T07:28:00.001-08:00

In some cultures drinking refrigerated water is frowned upon. It is common, nearly ubiquitous in US culture to serve water with ice, or water from a fountain that is refrigerated. Somehow, other cultures think that it is dangerous to drink cold water, though it seems to be very pleasing to the taste, and quenches thirst as adequately as ambient temperature H20. So in order to provide evidence that cold water was not only delicious, but healthy, I presented the proof that raising the temperature of cold water by 25 to 30 degrees takes energy. In other words, we burn calories to raise the temperature of the cold water we consume. We burn about 1.5 calories to raise 500 grams of water up to body temperature. Insignificant I admit, but its better than nothing. Some things though cannot be left to reason.

2008-01-20T20:03:00.000-08:00

MLK celebrates a b-day tomorrow

2008-01-20T16:17:00.000-08:00

Here is his famous speech. I also want to mention that this is the FIRST year that Indiana University officially recognize this as a holiday. We are a bit behind the times on this....

2008-01-20T11:58:00.000-08:00

New icon!

2008-01-17T08:20:00.000-08:00

A little bored with the blogger icon in the address bar, so I made a tiny brain, that now appears in place of the big 'B'. Its actually a picture of a real human brain, but its just really small. Is it possible to make it out? I wonder??

Experiments soon!

2008-01-16T21:50:00.000-08:00

Next week we have another patient up at the med. school. We should also be getting some new subjects for daily experiments. Hopefully 2008 will be as productive as 2007.

Last year there were many achievements, the article in J. Neuroscience (technically 08), good data collection, and many new software tools were developed.

Its always comforting to reminisce about the past, it is by nature concrete, solidified. Our fears, and insecurities are misplaced in the past; it is illogical to say, "I am afraid I won't do well on that exam last semester." This is undoubtedly why so many indulge in sentimentality.

You may remember, over Christmas break I was helping my parents work on the new house they are building. In order to find out if a particular color of exterior paint would be pleasing, Mark and I drove out to the new house to do a sort test-run with some paint they picked out. The bucket of paint was set in the center of the truck on the raised hump that houses the transmission. As the truck powered up the steep and winding section of smokies, the bucket teetered precariously on the irregular surface. My attention was fixed on the swaying bucket, waiting to intervene blocking gravity's calls. The next thing I knew we had arrived at the house, the paint did not spill, and Mark hadn't noticed the swaying bucket, or my anxious watchfulness.

You are probably thinking, I know the moral of the story, don't worry about what is out of our control, or don't fear something that could happen, but probably will not. Well, if you were thinking of those, or a slight permutation of those, you are wrong. You see when I looked at the bucket I saw each and every one of us, in the same situation, teetering, on the edge of something, sometimes we are aware of it (as was my case with the paint), and sometimes unaware(Mark). Sometimes, its just a drop of paint, others, well, the bucket overturns.

Chekhov

2008-01-14T20:09:00.000-08:00

"forests beautify the earth, that they teach man to understand beauty and induce in him a nobility of mind. Forests temper the severity of the climate. In countries where the climate is mild, less energy is wasted in the struggle with nature, so man is softer and more tender; in such countries the people are beautiful, flexible, and easily stirred, their speech is elegant, their gestures graceful. Science and art flourish among them"

Not only a literary genius, Anton Chekhov was an environmentalist before the thought of "spoiling" had ever occured. This passage is from his play, Uncle Vanya.

Chekhov was born January 17, 1860 in Taganrog on the Sea of Azov. To celebrate his upcoming birthday, I've been rereading some of my favorite works by him.

Vacation pics.

2008-01-14T05:31:00.000-08:00

Here I am on the beach.

So now I'm wondering why did I come back to work? I had it all, sunny weather, the beach, lots of books.

There was even a pirate ship loaded with tourists. You have to admit, you don't see that everyday.

Palm trees, even mountains,,,,

OOOhhhh, I remember now, that degree,,,,

So here is the story, I didn't take the big canon because I didn't want to lug around 5 kilos of camera equipment, but I did take a point and shoot. I think the difference is obvious. The town was just as I had remembered it during the day, but I had forgotten what it was like during the night. At night the locals come out and set up shop on the beach selling everything from a single piece of chocolate cake with swirling syrup topping, to fire roasted corn on the cob. This is when I missed the big canon. Those images were inspiring and brilliant. Maybe next year I'll return and share them with everyone.

We have more human experiments coming up soon so keep your eyes peeled.

Surgery yesterday.

2008-01-12T13:46:00.001-08:00

Our patient yesterday was an 8 yo female with a subcortical tumor in the hippocampal region of the right lobe. The epileptogenic tissue resected for experimentation was from the fusiform gyrus in the inferior temporal lobe about 2 cm rostral of the vein of labbe. The patient was having continuous seizure-like activity during the operation, which led us to believe that the in vitro experiments would yield valuable data. In some ways it did.

The tissue did exhibit some small ictal-like events in vitro, but did not go into large population events as some tissue does. Interestingly, the tissue did not respond to stimulation, a peculiar thing indeed.

I spoke with Dr. Smith late last night, and she said the patient well into recovery from the surgery, and is seizure free.

A new semester

2008-01-09T07:22:00.000-08:00

I made a few minor revisions to what I wrote about Mike, I'm still in shock about it by the way, and sent it to the www.idsnews.org . They phoned me last night and said they would like to publish in the paper today.

I miss taking classes. At this point I have too many things to do to take course work. In fact, I asked my prof. his opinion about my desire to audit a class, and he seriously discouraged it. Is it such a strange desire?

Is that it then? Am I supposed to only provide instruction from here on out? The deadlines, and assignments in a class provide one with a sense of duty, structure, and fulfillment, in the case of doing well in the course. I'm certainly capable of instructing, and disciplined enough to learn new things on my own, but its just not the same.
One thing is certain, I don't know of any prof. that are taking classes, or at least if they were in a class I wasn't aware of it. At some point then the transition takes place.

Other news, our article J neuroscience is in this months issue.

The loss of a friend & mentor.

2008-01-07T07:57:00.001-08:00

I had planned on creating some type of celebratory note for today, since it is the birthday of brainavalanche.com, but I'm in no mood to celebrate. I spent the last week on a beach enjoying a much needed vacation in Central America. My flight got in early this morning, and I just opened my email a few minutes ago. What I found was horrifying news. J. Michael Walker had died this past Saturday of a heart attack. He was the chair of the neuroscience department here at IU, and a great friend.

This news is especially upsetting for me, as I was his assistant instructor last semester for the graduate class N500. A few things about Mike.
As an instructor, I found his lectures on lipid signaling fascinating, and I've never thought, or will ever think about fatty acids the same way again.
As a mentor, he was not as quick to give advice as he was to provide a logical sieve. There is an important difference here, and it usually goes unappreciated.
As a friend, he was supportive and inspiring. Many traditional scientists have no use for the arts. The concept of artistic value in science is not emphasized in scientific courses; therefore it is a matter of personal development to appreciate value in these terms. Mike Walker had fully developed that value system, which is one of the reasons I think he was running the neuroscience program. Mike and I just had a conversation no less than 2 weeks ago about Henry Cartier-Bresson. The walls of his office are littered with images captured by the famous photographer. The image below is one of his most famous.

Bresson is credited with creating "the decisive moment." There is tension in this image, as the mysterious man is suspended in the air.
Mike also knew how to appreciate and live in the moment. In his own way he was an artist, wielding the brush of scientific inquiry he painted with the ultimate colors of TRUTH, each stroke revealing the secrets of nature.

You will be missed Mike.

The New old Year

2007-12-30T10:03:00.000-08:00

I've been developing new software for the machine at Stark over the last week. The general framework programs are finished, and it is possible to do analysis. The problem now is the really good data that I need to look at is noisy. Not just one type of noise, but multiple, which is impossible for a common delay tap filter, or butter to remove. I have to write my own filters, probably three, and then go back to the time domain, and somehow couple the trace segments without introducing new noise. Jumps in trace segments will have to be smoothed somehow. This is just becoming a bigger and bigger problem at each step. ARGHHHH!! Oh, wait, I'm not a pirate, UGHHHH!

Anyways, a happy early new year to all, and enjoy the classic ABBA.

Happy Belated Birthday......

2007-12-27T20:11:00.000-08:00

A hoosier hero, Eugene V. Debs had a birthday 11/5.

Besides being a hoosier, Debs ran for president 5 times, once from prison in Atlanta. Here are a couple of my favorite Debs quotes.

"Years ago I recognized my kinship with all living things, and I made up my mind that I was not one bit better than the meanest on the earth. I said then and I say now, that while there is a lower class, I am in it; while there is a criminal element, I am of it; while there is a soul in prison, I am not free."

"No war by any nation in any age has ever been declared by the people."

Xmas present from microsoft

2007-12-26T06:44:00.000-08:00

The Windows operating system, how much you have changed the world. I hope you know that everyday I get up thinking about you. The fact that I can use other operating systems, but I don't should show you how much I care. When I left you running a batch job over Christmas break, I knew you would be faithfully caching my array data for me while I was snuggled up next to the fire with a creamy hot cocoa. I trusted you with a job, that I estimated would take over 40 hours of cpu time. Like Santa in the wee hours of Christmas eve while everyone was fast asleep you delivered a present adorned with a golden bow in my array editor. Not a creature was stirring when you FAILED TO EXECUTE SAVE IN THE LAST LINE OF CODE, NOT EVEN A MOUSE COULD HAVE DONE SUCH A STUPID THING!
The final gift that you generously gave, was to such yourself off, after you failed to save.

2007-12-25T19:49:00.001-08:00

A new home

2007-12-23T08:40:00.001-08:00

Some of you may know that my parents are building a new home. Yesterday I had my first glimpse of it. It is a modest home, in a rich setting, the smoky mountains.

Just tidying up in the future kitchen.
The area is completely rural, without any near neighbors. We were there for nearly an hour, and only one car passed on the road in the front of the house.

Absent any road signs, how would one know they were in the deep south? Ask a neighbor.

Happy Holidays

2007-12-21T12:30:00.000-08:00

Best wishes, and happy holidays!

The door to our lab at Stark was decorated for the holidays this year by Yiwen. Thanks so much Yiwen I've really enjoyed working with you , and the many other delightful people at Stark. Hope you have a nice break, and I will see you all in January.

Readers, readers,,,

2007-12-19T06:16:00.001-08:00

Wow, here is a list of the countries from which brain avalanche received readers last month. Thanks you guys, oh and Serbia, no disrespect, I don't know why your flag was not picked up by my program, so here is your flag below.

My sad attempt at making a funny

2007-12-18T15:07:00.001-08:00

I definitely can't draw, but hey here is an attempt. It may not be readily apparent, from my drawing, but the dots are supposed to represent snow. This is what you do when your computer processor is working at nearly 100% for 15 minutes, and you are waiting on the results of the analysis.

Overpowered

2007-12-18T11:36:00.001-08:00

I think I posted this song a long time ago, before google made me stop using their .swf application from the browser. I like this song because it is about the brain, and I think the lyric "your data my data" is pretty much awesome.

Any C++ or Java masters out there????

2007-12-17T13:48:00.000-08:00

I've got a code glitch, that has gotten the best of me. I'm trying to use a switch case to stay in the same data set, but offer the opportunity to switch data sets after each full block evaluation. As you can see I'm prompting a figure, and this is sourced from the D object. I pull other class structures from the object, but that is irrelevant to the problem. Any suggestions, ideas?

ckFile = exist('filename');

switch(ckFile)
case 0
ckFile = 1;
prompt0 = questdlg('Would you like to choose a new directory',...
'Directory change', 'Yes', 'No','Cancel');
if strcmp(prompt0,'Yes')
clear_except prompt0;
NuDir = uigetdir(G:\, filename);
cd NuDir;
[filename] = uigetfile('*.mcd');
D = datastrm(filename);
end;

prompt = {'Enter Channel Number(1-64):',...
'Start Time:','Stop Time:'};
dlg_title = 'Search Wave Forms';
num_lines = 1;
def = {'4','0','20000'};
answer = inputdlg(prompt,dlg_title,num_lines,def);

start = str2double(answer{2});
stop = str2double(answer{3});

c = nextdata(D,'streamname','Electrode Raw Data',...
'startend', [start, stop]);
uV = getfield(D, 'MicrovoltsPerAD2');
X = getfield(D, 'ZeroADValue');
Z = find(c.data < 0);
Q = c.data;
Q(Z) = Q(Z) + 2*X;
nV = Q;
Chan = answer{1};
kern = gausskernel(0.001, 0.003);
fwave = filter(kern, 1, nV(Chan,:));
figure, plot(uV * nV(Chan,:))
hold on;
plot(uV*fwave(10:length(fwave)), 'r');

prompt0 = 0;

case 1
ckFile = 0;
if strcmp(prompt0,'No')
clear_except filename D prompt0;
end;
prompt = {'Enter Channel Number(1-64):',...
'Start Time:','Stop Time:'};
dlg_title = 'Search Wave Forms';
num_lines = 1;
def = {'4','0','20000'};
answer = inputdlg(prompt,dlg_title,num_lines,def);

start = str2double(answer{2});
stop = str2double(answer{3});

c = nextdata(D,'streamname','Electrode Raw Data',...
'startend', [start, stop]);
uV = getfield(D, 'MicrovoltsPerAD2');
X = getfield(D, 'ZeroADValue');
Z = find(c.data < 0);
Q = c.data;
Q(Z) = Q(Z) + 2*X;
nV = Q;
Chan = answer{1};
kern = gausskernel(0.001, 0.003);
fwave = filter(kern, 1, nV(Chan,:));
figure, plot(uV * nV(Chan,:))
hold on;
plot(uV*fwave(10:length(fwave)), 'r');

end;

Reply to comment.

2007-12-16T08:54:00.000-08:00

Thank you rgfanatic, for your kind and encouraging words. I'm glad to hear that Chris is doing well. I wish I could take some credit for his swift recovery, but all the credit goes to Dr. Smith and her surgical team. Dr. Smith's patients are very special, and in a very real sense are participating in the future, the future of science, medicine, and technology. This participation is "pay it forward" if you will, as better treatment, or a cure is somewhere in the future.
So we have you to thank.

It has been a hectic week...

2007-12-15T09:14:00.000-08:00

As you all know we had a surgery on Monday. Thankfully, it all went very well. We were able to collect massive amounts of data from the tissue that would have otherwise gone in the trash.

Yesterday, we had another patient. A young male, that had a mass in the opposite side of the brain from our patient on Monday. The right hippocampus, and amygdala had to be resected. Unfortunately, we were unable to collect any data from this tissue. It did produce some electrical activity but it was just not enough to discern clearly from the noise.

Here is a picture of the skull opening being drilled.

Patient recovering, experiment went well,,,

2007-12-11T07:57:00.000-08:00

The patient yesterday was a 6 year old female suffering from a mass in the left hippocampus. In order to remove the mass and prevent further epileptic seizures Dr. Smith removed a small portion of the inferior temporal cortex.

Here in the photo Dr. Patel is mapping the epileptogenic zones with a 20 electrode grid.

Dr. Smith said the patient is fine and recovering from surgery nicely.

Last night was the experiment beyond all experiments. The tissue that was resected was more epileptic than any I have ever seen. Usually when the tissue is this epileptic, it depletes the neurotransmitters in a matter of minutes (this is my guess) becomes excitotoxic and dies. Not this tissue, it kept seizing, and seizing, and seizing. It had multiple regime types, it would go through a certain series of seizures for minutes at a time, and then completely switch to a different regime. Excellent data, that completely wore me out. I got home a little after 1 am.

2007-12-09T10:23:00.000-08:00

With this weather, one could hope to be on an island in the sun...
Weezer - Island In The Sun
Uploaded by Dan_of_the_Land

Surger tomorrow.....

2007-12-09T07:26:00.000-08:00

I am in today, preparing for surgery tomorrow. I hope all goes well. The weather could turn nasty, they are predicting freezing rain.

Back to the glia

2007-12-06T08:56:00.000-08:00

Previously I posted these facts about Glia.
Sheer numbers of glia illustrate their importance.
Neurons are the original nervous system device.
Some contemporary nervous systems operate well without glia.
Glia-less nervous systems have interneurons.

This essay is not about glia. Rather I want to argue that compartmentalized interneurons are more significant in terms of their contribution to complex phenomena. Glia are important, but as I will explain, they are clearly a secondary system.
Evidence of the significance of interneurons can be found in Cnidaria, ie., hydrozoa, scyphozoa, jellyfish. Our ancient relatives have nervous systems very similar to our own. They have ionic based action potential signaling, chemical sigaling, ie., catecholamines, indoleamines, and peptides. Many of species within Cnidaria have no glia. Apparently the neurons, and interneurons are capable of many complex tasks in the absence of glia.

Cnidaria are 600 million years old, clearly they have found a niche. So what you say, they just float around in the ocean, big deal.
Cnidaria complex sensory systems do exist. Cubozoa the box jellyfish has eyes. True, camera type lens, with pigment pits, cornea, retina. That is not all, this animal has 8 eyes, and these eyes are color sensitive. Don't take my word for it, here is a Nature paper by Nilsson et al.

So here is my question: Do compartmentalized groups of interneurons give rise to consciousness; and if so, will we one day be able to model consciousness?

The Chef/Scientist

2007-12-04T10:32:00.000-08:00

I love to cook. I find the process very pleasing, in the sense that combining different substances can have completely different effects on the palette, and just the act of measuring something, it's very nice. And of course there is the reward at the end.
Cooking is a lost art. Most people find the process mystical, and feel incapable of preparing simple dishes. The process is not difficult. It takes time. Time to learn even the simple things, for instance, which type of pan to use, or which type of oil.

Cooking requires patience, as does being a scientist. In many ways the two processes are alike. In cooking, you may alter how much spice is in a recipe to see if the taste improves. In science we alter how much chemical (spice) is added to the brain, and measure the effect. The measurement isn't in taste, but a measurement all the same. Most people find science mystical, and feel incapable of understanding any scientific material.

To prove that science is not mystical I am posting my own (secret scientific) recipe for peanut-butter pumpkin pie. You should not be mystified.

Pie: 2 eggs, 200ml granule sugar, 1 tsp. cinnamon, .5 tsp of clove, .5 tsp allspice, .5 tsp of vanilla.
Mix all these ingredients well, blend on low for 2 minutes. Don't fluff the eggs too much.

Then add (either bake fresh pumpkin), or 15 oz. of pumpkin to the mix.
Heat .5 cup of water (warm) add 100 ml. of peanut butter. This should have a thick consistency, and add PB until it is nice and thick if you must.

Then blend in the PB to the rest of the mix, and voila. Bake at 425F for 15 minutes, and then lower the heat to 350F for another 35 min.

Crust: 1/2 of one sleeve of graham crackers crushed, add 3 to 5 tbs. of melted butter. Pat this into your baking pan, once it is thoroughly mixed.

I promise I'll revisit the glia renaissance soon.

WELCOME HOME MOM!!!!!!

2007-12-02T10:28:00.000-08:00

I hope you two enjoyed your vacation. I'll come visit you soon.

Love, and kisses,,, your son.

Glia, schmia,,, explain those interneurons

2007-12-01T08:38:00.000-08:00

Gfap image of astrocytes from Armstrong lab. Quite beautiful.
The renaissance of glia. Is it warranted?

Yes, for the simple fact that glia occupy 90% of the space inside your skull. Glial cells are ubiquitous in vertebrate physiology. Volumes are devoted to describing the lineage and heterogeneity of glial subtypes.

Are glia active participants in signaling? Some evidence suggests that they are.

Another question that is perhaps more pressing; where do interneurons come from.
This may seem like a ridiculous question but I would argue that it is more relevant than the entire glia renaissance that is sweeping brain research.

Consider these facts:
Sheer numbers of glia illustrate their importance.
Neurons are the original nervous system device.
Some contemporary nervous systems operate well without glia.
Glia-less nervous systems have interneurons.

Stay tuned, I'll post more soon.....

Sorry, one more post about Thanksgiving

2007-11-28T10:05:00.000-08:00

I could't resist, this video is sooooo hilarious.

Americans Enjoying Thanksgiving Tradition Of Sitting Around At Airport

Rambling thoughts,,

2007-11-27T08:27:00.000-08:00

I believe it is completely acceptable to assume that most of our ideas about how the brain functions are false.

Why do I say this? History, it has a way of making fools of us.

For example, in 1883 the American neurologist James L. Corning introduced the idea that seizures were a result of ‘venous hyperaemia’ an increased heart rate and corresponding blood pressure. Corning noted that seizures could be curtailed by restriction of the carotid artery, embracing an almost Hippocratic, Aristotelian idea of fluid imbalance as a mechanism of disease and illness (1).

Putting forward the idea of epilepsy as a symptom of high blood pressure to today's scientific community would garner laughs at best.

I've said all this to illustrate how sometimes it's not about being right, but about asking the right questions.
Last night we hosted a very important speaker, Dr. Marcus Raichle. Our lab shares very little in the way of investigation with the Raichle lab. However, I recently wrote a post that addressed the same question, Raichle posed to us last night.

Here is excerpt from Raichle's question: "evoked changes in neural activity represent a small fraction (< 10%) of functionally-relevant, ongoing brain activity as measured in terms of brain energy consumption while intrinsic functional activity consumes more than 50% of the brain's energy"

This is my post from 11/16.
While dozing off into a saturated fat induced post-lunch coma at my desk today, I had an epiphany. We require so little input. We have millions of sensors to detect heat, pressure, smell, but we rarely actively monitor them. Vision, is different of course, we are constantly monitoring, and aware of what is in the visual field. But I would argue that this really constitutes a small sample of input given the possible output. Requiring so little input, maybe we should rethink what it means to be in vitro.

1. Corning, J.L., (1883) Considerations on pathology and theraputics of epilepsy

J. Nerv. Ment. Dis. 10, 243-248.

Recall,,, recall

2007-11-25T11:53:00.000-08:00

An excellent paper if you have time to check it out.

Summary: During sleep the brain replays the days events. This replay happens in a compressed format.

Science 16 November 2007:
Vol. 318. no. 5853, pp. 1147 - 1150

Fast-Forward Playback of Recent Memory Sequences in Prefrontal Cortex During Sleep

David R. Euston, Masami Tatsuno, Bruce L. McNaughton^*

As previously shown in the hippocampus and other brain areas,patterns of firing-rate correlations between neurons in therat medial prefrontal cortex during a repetitive sequence taskwere preserved during subsequent sleep, suggesting that wakingpatterns are reactivated. We found that, during sleep, reactivationof spatiotemporal patterns was coherent across the network andcompressed in time by a factor of 6 to 7. Thus, when behavioralconstraints are removed, the brain's intrinsic processing speedmay be much faster than it is in real time. Given recent evidenceimplicating the medial prefrontal cortex in retrieval of long-termmemories, the observed replay may play a role in the processof memory consolidation.

Arizona Research Laboratories Division of Neural Systems, Memory and Aging, University of Arizona, Tucson, AZ 85724–5115, USA.

Black Friday & the characteristic malaise

2007-11-24T10:22:00.000-08:00

Ouch! Getting a good deal can be painful.

I found a similar video.

Next year, I'll be taking bets on who the sale items will go to.

Black Friday

2007-11-23T10:38:00.000-08:00

Black Friday, a day of blitzkrieg for the consumer where the few and lucky win their prize. It may mean good deals to a consumer now, it certainly did not in September of 1869.

Black Friday did not find its beginnings at the outpost general store in early America. September 24, 1869, not long after the civil war, the country came dreadfully close to financial collapse.

Two speculators Jay Gould, and James Fisk were cornering the gold market, with the belief that the government would buy back paper notes circulated during the war with gold. This caused the price of gold to inflate. When Grant found out what was happening, he flooded the market with U.S. gold. This saturation, led to a huge sell off that left many people penniless.

Now if only I could talk someone into standing in line for me at Best Buy.

2007-11-22T09:19:00.000-08:00

"THE NEW COLOSSUS"

a poem by Emma Lazarus

Not like the brazen giant of Greek fame, With conquering limbs astride from land to land; Here at our sea-washed, sunset gates shall stand A mighty woman with a torch, whose flame Is the imprisoned lightning, and her name Mother of Exiles. From her beacon-hand Glows world-wide welcome; her mild eyes command The air-bridged harbor that twin cities frame. "Keep, ancient lands, your storied pomp!" cries she With silent lips.

"Give me your tired, your poor, Your huddled masses yearning to breathe free, The wretched refuse of your teeming shore. Send these, the homeless, tempest-tost to me, I lift my lamp beside the golden door!"

If the pilgrims arrived today in Plymouth Massachussetts, I wonder, how would they be received?

Happy Thanksgiving

2007-11-22T06:53:00.001-08:00

Shinya Yamanaka reprograms human adult cells

2007-11-20T11:24:00.001-08:00

An incredible announcement today by the Yamanaka lab in Japan. Yamanaka et al. have successfully reprogrammed adult cells into pluripotent stem cells.

The moral battle over the use/destruction of stem cells from fertilized eggs, has swiftly and unceremoniously become moot.

What does this mean?

If you can afford it, a molecular biology lab will extract skin cells from any part of your body, and then these cells could then be turned into cells that can change into any type of cell. They would do this with an exact match of the person's DNA. Hence, no anti-rejection drug therapy would be needed.

When I first read this, I instantly thought of the most desperate, and needy people who could benefit from this discovery. And I hope Michael Jackson gets a nose as soon as possible.

2007-11-20T06:22:00.000-08:00

Information is the currency of scientific research. Communicating that information clearly is crucial. Here are some tips that I have found useful.

Techniques for Clear Scientific Writing and Editing

Gary Westbrook, Senior Editor, The Journal of Neuroscience
Linda Cooper, McGill University Everyone has experienced the joy of reading about exciting research. Unfortunately, in many cases, such findings can be buried in obscure language. Writing that is clear and simple enables researchers to share their interesting findings with a wide audience; this is particularly relevant in a highly interdisciplinary field such as neuroscience.
In previous articles, we reviewed suggestions for effective writing (see past editions of the SFN Newsletter). To extend the principles of clear writing in science, here are a few editing techniques to help researchers write concise and effective manuscripts.

Tips for revising sentences
Overuse of the passive voice is a common problem in writing. Although the passive has its place—for example, in the Methods section—in many instances it makes the manuscript dull by failing to identify the author’s role in the research. Other weak writing practices are the overuse of prepositional phrases, the verb “to be,” nominalizations, and noun strings. Using too many prepositional phrases causes information overload that can confuse readers. Overuse of the weak linking verb “to be” creates unnecessarily long and imprecise sentences. Sentences with many nominalizations (noun forms of verbs) result in texts that are difficult to understand. Energize your text by transforming the noun forms of verbs back into verbs and avoid noun strings (nouns modifying nouns), which result in too much compressed information that is confusing to readers. Consider, too, where to put new and important information. Generally, readers look for new information at the end of sentences, the end of paragraphs, and the end of abstracts. Help the reader locate your most important point by placing it in these stress positions.

Examples of Principles at Work

1. Use direct, active-voice sentences.
Original: Only at synaptic sites the co-localization of GLu1 and NR1 with the PSD-95 complex was observed.
Revised: We observed that GLu1 and NR1 co-localize with the PSD-95 complex only at synaptic sites.

2. Limit prepositional phrases.
Original: This growth factor is important to the survival of the motoneurons in the spinal cord but not in the cranial nucleus in the brainstem.
Revised: This growth factor helps motoneurons survive in the spinal cord but not in the cranial nucleus.

3. Limit use of the verb "to be."
Original: This mechanism is an important factor in our understanding of cytomegaloviral infections in the brain.
Revised: This mechanism will help us understand how cytomegaloviruses infect the brain.

4. Avoid noun forms of verbs (nominalizations)
Original: Significant ipsilateral cortical activation was seen with stimulation in previous PET studies.
Revised: Previous PET studies show that stimuli activate the ipsilateral cortex.

5. Limit noun strings
Original: Community information feedback mechanisms are important if governments want scientists to explain how they spend taxpayers’ money.
Revised: Governments should create effective mechanisms for scientists to explain how they spend taxpayers’ money.

6. Put new and important information toward the end of sentences.
Original: Whereas mutating four CREs in the promoter did not block up-regulation, site-directed mutagenesis of all five CREs in the promoter blocked this up-regulation almost completely.
Revised: Site-directed mutagenesis of all five CREs in the promoter blocked this up-regulation almost completely, whereas mutating four of them had no effect.

Learn more at the annual meeting
At the Society’s Annual Meeting, we cover these and other writing techniques in a workshop called “Writing, Editing, and Publishing in Science.” For more information about the San Diego workshop, contact Linda.Cooper@McGill.CA.

Oligodendroglioma

2007-11-18T11:56:00.000-08:00

Anonymous said...

I have had a Oligodendroglioma tumor for 7 years now. I went through 2 craniotomies within one year apart. After the second operation it started to grow back faster, so they sent me through radiation,and I am still taking temedar for my chemo. They do MRI's on me every 2 months. My question is do you see these type tumors to be hard to control? Will I still be around in 20 years? I am only 36 and have had it since i was 30.

November 17, 2007 8:13 PM

Dear Anonymous,

Thank you for writing. I want to first commend you for your courage and bravery in enduring so much. You have my sincere sympathy.

Here is my disclaimer; I am not a medical doctor, your personal physician(s) know your case, and they should be consulted in any and all matters concerning your health.

My research is designed to flesh out the differences between network-based animal models of epilepsy and human epilepsy. I know very little about the molecular mechanisms of oligodendroglioma, rather I study the epilepsy that results from the growth of the tumor.

That said, given the information you've provided I can offer you some information about the most current studies regarding the medication you are currently taking, and some medications that are still in early development phase.

You mentioned that your are currently taking Temedar. There is a recent article by Jun et al that you might find interesting. "Treatment with temozolomide combined with AMG 102 resultedin increased inhibition of cell growth in vitro compared withtreatment with either single agent alone." Jun et al have found that combining these two compounds for treatment arrest the growth of the tumor signficantly.

Carmustine (BCNU, NSC 409962)BCNU was the first generation of alkylating agents.
A newly developed analog of Carmustine is the Gliadel Wafer. It was developed by NCDDG, headed by Henry Brem of Johns Hopkins University. BCNU is impregnated in a wafer composed of a polyanhydride biodegradable polymer invented by Robert Langer of the Massachusetts Institute of Technology. From what I can tell (I've never seen this procedure performed) the wafer is implanted in the region of the tumor, and the drug is delivered directly to the site.

The good news, if there can be any about central nervous system tumors, is that oligos. are slow growing. Stupp et al recently published survival statistics for Oligos.; mean survival of 14.6 months from the time of diagnosisand a less than 30% survival rate at 2 years (1).

Hang in there Anonymous! Since the 1950's research in medicine has made incredible strides, and within the last 15 years there has literally been an explosion in molecular biochemistry. You are doing the best thing you can possibly do, and that is learn everything you can about oligodendroglioma.

Anonymous, thank you for sharing.

1. Stupp R, van den Bent MJ, Hegi ME. Optimal role of temozolomide in the treatment of
malignant gliomas. Curr Neurol Neurosci Rep 2005;5:198–206.[Medline]

My domain, all mine,

2007-11-17T08:41:00.000-08:00

Recently I passed the 150th blog mark. This is actually the 154th blog I've written, and its been almost a year. I want to thank my loyal readers, and the visitors for stopping in to take a peak at science diary.

To celebrate the fact that I've babbled at least 150 times in the past year I purchased my domain name. If you look at the address in your browser search field, it now reads www.brainavalanche.com instead of www.brainavalanche.blogspot.com. I felt that I've invested so much time and effort into the site that I should assume full ownership. It really matters very little since all the old links should work if I migrated everything properly.

I'd like to have a birthday party for baby brainavalanche on the one year proper, maybe I can get some celebration ideas from my readers?

Very little input.

2007-11-16T15:25:00.000-08:00

While dozing off into a saturated fat induced post-lunch coma at my desk today, I had an epiphany. We require so little input. We have millions of sensors to detect heat, pressure, smell, but we rarely actively monitor them. Vision, is different of course, we are constantly monitoring, and aware of what is in the visual field. But I would argue that this really constitutes a small sample of input given the possible output. Requiring so little input, maybe we should rethink what it means to be in vitro.

We live in an exciting time. The average desktop computer with a Pentium 5 cpu has 100 million transistors. The human brain has about 100 billion transistors, is Skynet in our future?

Junichi Takeno and his team at Meiji University built a robot whom named "Egobot." Egobot is "self-aware", and can determine if it is interacting with a doppelganger or a mirror image of itself.

SFN again,,,

2007-11-15T09:34:00.000-08:00

During my poster presentation I was approached by an individual that, to put it bluntly, told me I was an uninformed moron. In retrospect, I take offense to that, --who is he calling uninformed?

This guy, looks at me besmirchingly and says Cohen, Science 2002. I'm befuddled to say the least. What, I asked him? He just walked away with this quirky smile on his face without answering. There were other people at my poster at this time, and they both shared the same look of disdain, like I handled this thing so poorly.

Well science comment guy, this article doesn't have anything to do with my poster! Rarely, if ever are any "papers" the final definitive answer or proof of anything in that regard, but this paper shares little if any similarities to my research.

If you had stuck around science comment guy I would have explained to you that I am interested in large network, population phenomenon, and this paper is targeted towards elucidating the contributions of GABA systems to ictal events.

1.My poster is about animal models of epilepsy, and how well they map onto human epilepsy.

2.My poster never mentions the activity of a single brain cell.
1 brain cell = 1 bit buddy, and that is not a network.

SFN,,,,

2007-11-13T12:25:00.000-08:00

The convention center architecture reminded me of a gerbil cage, an extraordinarily large one, made for humans. It was fully stocked with food stuffs and starbucks thankfully. Traversing from one end of the convention center to the other at a brisk pace me more than 13 minutes.

I spent most of my days going to presentations: Presidential lectures, Slide presentations, Mini Symposiums. Many presentations left me bewildered. Being an outstanding scientist does not make you by default a great presenter.

Here is my list of great scientists who are great presenters*:
K. D. Harris
Sebastian Seung
Kevin Staley
Fred Rieke

* indicates no particular order

Just down right peculiar:
The convention center employees could be identified by their sailor uniforms. << The one time I leave my sailor uniform at home,,,, damn!!

The identities in this picture have been protected for reasons I think should be obvious. I'd like to compare and contrast the two posters here side by side. The one on the right looks presentable. The poster on the left? Really? Seriously? I wanted to run and hide when I saw this poster, in fact, soon after I took the picture, I was frantically biting my nails in the fetal position on the floor, drooling on myself.

A night at the Salk

2007-11-11T18:48:00.001-08:00

Of course every day was an adventure in San Diego. A pulsing city with a vibrant atmosphere makes for a lovely setting for the annual meeting. An invitation to a party at the Salk though, was over the top. Schmoozing with the likes of Igor Timofeev, Peter Latham, and Terry Sejnowski was an amazing opportunity, and a grand social occasion as well. The blurred figures in the photo are an interesting affect.