A new microscopy technique could begin providing valuable 3D data on living cells. There are many different microscopy techniques out there. Unfortunately, the really cool ones require the cell to be dead. Electron, dye contrast, fluorescence can all give excellent results but all require the specimen to be dead. Electron microscopy in particular requires difficult preparation and can occasionally influence the structure of the specimen due to the addition of heavy metals. Phase contrast (think high school light microscope) allows living specimens but cells are generally poor at absorbing light.

That all could change. A new technique from MIT uses the refractive properties of the cell to generate a 3D image. It is essentially a cellular version of a CT scan. Computed Tomography (CT) has been used by clinical medicine for years now but has been relegated to large specimens like your lung or kidney due to resolution and speed. The technique works by taking hundreds of images using x-rays, all at different angles. Each slice of the specimen is then reconstructed on the computer to form a complete 3D model.

The MIT team has successfully managed to shrink CT equipment enough to image specimens on the cellular level. Three dimensional models take about 1/10th of a second, meaning you can watch a cell in real time.

A movie of the 3D models created by this technique can be found here

Epilepsy and glaucoma could be a thing of the past. Well, that could be a bit sensationalistic but research coming out of Purdue University is showing some promise. A recent press release highlights three astounding projects. One measures epileptic brain activity while a seizure is occurring, another dispenses GABA neurotransmitters to calm localized seizures. The last measures pressure buildup in glaucoma patients.

Details after the jump.
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Non-technical version: DN now uses the database to load and save data. Hooray! It eats RAM like candy but that is expected and can be somewhat fixed. Speed is still a concern but real optimization will come later once the codebase is solid.

Next step is to begin working on the client in earnest and get some simulations running! Gruesome technical details for those that care after the jump
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This is the first of many posts in the new category “Design Decisions”. These posts will chronicle my thought process as I work through various problems, both technical and philosophical.

The first problem that should pop up in any brain simulation project is also one of the most difficult to answer. How does a brain grow? Is the particular structure of the human brain required for intelligence?

Discussion after the jump.
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Decreased blood flow in the brain may be a useful symptom to diagnose depression. A research team in Israel visually confirmed that depression patients often had decreased cerebral blood flow, even more so if the patient was undergoing electroconvulsive therapy (administration of electricity to induce controlled seizures).

The data was gathered using SPECT (single photon emission computed tomography). The images created from SPECT are three dimensional and confirmed previous studies. Depressed patients often had decreased blood flow in the frontal, limbic and subcortical regions of the brain. It is hoped that this imaging technique will be able to diagnose depression before treatment options are chosen, so that the patient may have the highest likelihood of recovery.

“Currently, clinical psychiatry is based almost solely on subjective observer-based judgment. Our findings suggest that objective imaging evaluations could support subjective clinical decisions”

Interesting, effective anti-depressant medication increases blood flow in the brain, which may partially explain why anti-depressants work. It was noted, however, that electroconvulsive therapy did not increase blood flow despite having a track record of helping severe depression patients. Conversely, this may be why electroconvulsive patients have a tendency to relapse after several months.

Maybe this technique will help the over prescription of anti-depressant drugs. I personally know several people that are likely not clinically depressed (just my own guesses) but are on medication regardless. Depression medication is rapidly becoming the single most prescribed medication.

You are an aggregate collection of billions and billions of cells, enzymes, hormones, and various other organic substances. In a moment of clarity, you realize that each of these things is neither more or less than a physical object, obeying entirely knowable rules. You enjoy no more a privileged existence than any other machine. You are more than the sum of your parts, yes: you are their product. Now contemplate free-will. Does the fact that a decision is based on the complex interplay of neurotransmitters, that it - in theory - is predictable with certainty negate the fact that a decision is made? No. We are machines. And that’s beatiful.

I stumbled on this quote and quite like it.

Female mice aggressively mounting males? Scientific American is reporting on a study coming from Harvard University turning gentle female mice into aggressive alpha-males. Details (and a movie!) after the jump.
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As I was working on the new unified file format today, I couldn’t help but think to myself “Wouldn’t a relational database be great right now?”. But of course, relational databases are exclusive to server environments.

I had completely forgotten, until today, about SQLite. SQLite is a wonderful flat file relational database. I have used it previously in another project (funnily enough, another distributed project - Distributed Backup System). It supports the majority of the SQL protocol, is ACID compliant and is super simple to use. There is even a C++ wrapper so you don’t have to use the C style function calls. To top it off, there is a free database editor GUI available.

Frankly, I am ecstatic right now. This will cut a tremendous amount of time off saving/loading code and will be more flexible to boot. Because of the database, I’ll be able to save statistics and useful data much easier, meaning more scientific value from the project (and less headache for me). I am now planning on including some features I was hesitant about because of the hassle in programming (such as crossover mutations).

The one concern I have is physical size. With the power of databases come the inevitable increase in physical hard drive usage. Hopefully I can find a happy medium so volunteers are not required to sacrifice a large chunk of HDD space for data collection and storage.

Discover Magazine has a decent piece on the top 10 unsolved mysteries of the brain. The first point, “How is information coded in neural activity?”, technically covers the other nine because all other functions of the brain (memory, emotion, motor control, etc) is the result of information encoded inside the brain. But I may be trifling at details.

It is a good read and light on technical terminology with plenty of links to relevant articles.

The endocannabinoid system is a fascinating and complex system. It has received little attention until relatively recently, where it is now becoming clear that it is a vital and important regulatory system in our CNS. Often associated with marijuana and then routinely ignored, the endocannabinoid system has been recently shown to play a critical role in regulating and protecting neurons, modulate mood, stimulate stem cell differentiation and inhibit nicotine addiction. Details and corresponding papers after the jump.

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