Tag Archives: Scientific Literature

Blue Brain Project Simulates 30,000 Neurons of Rat Brain

October 9th, 2015 | Brain

FIGURE 13_Spontaneous activity v3

The European Blue Brain Project to simulate the rat brain has finally bore its first fruit. Researchers spent over 20 years of biological experimentation and 10 years of computational science work to get to this point.
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The project has been hotly contested across the science world.
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Last year, more than one hundred neuroscientists threatened to boycott the project unless significant changes were made. More than 1 billion euro was funneled into the project by the European Commission, and many scientists wondered if anything useful would be created.

But alas, the first findings were published October 8 in the journal Cell, in an article entitled, “Reconstruction and Simulation of Neocortical Microcircuitry.”

“[We] find a spectrum of network states with a sharp transition from synchronous to asynchronous activity, modulated by physiological mechanisms,” wrote the authors. “The spectrum of network states, dynamically reconfigured around this transition, supports diverse information processing strategies.”

This first simulation is meant to represent a “scaffold” on which many more layers of complexity can be added. I think it’s a good first step and hopefully this work can lead to a deeper understanding of the human brain.
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-RSB

80,000 Neurons Firing in the Brain of a Zebrafish

July 29th, 2014 | Brain

Labeled_Zebrafish_80000_neuronsA team led by Drs. Jeremy Freeman and Misha Ahrens recently recorded the activity of approximately 80,000 neurons firing in the brain of a zebrafish larvae. The technique they implemented is called light-sheet microscopy. Briefly, the scientists genetically engineer zebrafish neurons to emit a fluorescent signal just after the neuron fires. Laser beams are the shot through the fish so that the activated neurons will glow and an overhead microscope records the whole thing. Of course, this technique only works because the zebrafish are entirely transparent, so don’t expect to have your brain scanned in this manner any time soon.

“At the beginning of the movie, the fish is resting and the forebrain region on the far-right is flashing away. That may represent whatever the fish is thinking about when it’s just hanging out.

Scientists then created the illusion that the fish was drifting backwards by sliding bars in front of its eyes.
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Its intent to swim to catch up was measured with electrodes on its muscles. When the bars start sliding, a few neurons sitting just behind the eyes light up followed by a huge cascade of activity, including massive pulses initiating swimming.”

“There must be fundamental principles about how large populations of neurons represent information and guide behavior,” says neuroscientist Jeremy Freeman of Janelia Farm Research Campus in Ashburn, Virginia. “In this system, where we record from the whole brain, we might start to understand what those rules are.”

We know that the processing of sensory input and the generation of behavior involves large networks of neurons, and Dr. Freeman believes that observing networks with this sort of technology will enable us to gain deeper insight to how the brain functions.
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It is important to note that the temporal resolution is fast enough to identify which neurons are involved in a given behavior but too slow to count how many times they fire. Thus, there is no way that this technique could ever decipher the neural computations that take place at the millisecond timescale in the human brain.

I think we’ll probably need nanobots to ever fully decode the brain…
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Find the full article here… if you have a subscription :/

-RSB

[via Wired]

Another Case of Bad Science and Science Reporting on Marijuana

April 22nd, 2014 | Brain

Autosave-File vom d-lab2/3 der AgfaPhoto GmbH

You may have recently stumbled across one of the recent headlines in the media that look something like this:

Casual marijuana use linked with brain abnormalities, study finds

Casual marijuana use may damage your brain

Even Recreational Marijuana May Be Linked To Brain Changes

The scientific paper they are all referring to is linked here (although you can’t read it without a subscription, which brings up a totally different problem in access to science):

When I first read these headlines, I was understandably intrigued. Had someone REALLY found good evidence in MRI data that there are differences in the brains of casual marijuana smokers? The idea is not totally far fetched. Alcohol is known to be neurotoxic and it can shrink the size of the brain through dehydration, but this is mostly corrected after you quit drinking. Carbon monoxide in cigarette smoke is also a known neurotoxin, but I’ve never read about any changes in the size of anatomical regions of the brain from smoking tobacco, unless you count brain tumors. However, no one has ever really found evidence to support major anatomical changes in the brain following marijuana use. So could this really be true?

Even before reading the paper, my intuition said the answer was no… brain imaging research is notoriously fraught with spurious findings linked to inappropriate use of statistics.

I gave the paper a casual read, and immediately, I noticed problems, MAJOR problems. First of all, sample size… only 20 people were included in the cross-sectional study. That is low. A cross-sectional study means that they had no within-subject comparisons. In other words, all of the data was collected at one time. A much stronger approach would have been to image subjects before they smoke and then through time as they begin to “casually smoke” marijuana. Of course, this is much more difficult, but with a study design containing so many potential confounds (see below), it’s pretty much required (imho) to say anything definitively.

Second of all, the confounds… the investigators did not control for various other aspects of these people’s lives that may cause changes in brain anatomy. How much did each subject drink? smoke tobacco? do other drugs? etc… These all could be equally correlated to the differences in brain anatomy which they discovered. Or it could something entirely different like genetics?

And lastly, the statistics… I came across this article by computational biologist Lior Pachter, and that was sort of the nail in the coffin. I suggest reading through it because Lior does a great job of highlighting the problems with multiple comparison statistics, causation vs. correlation, and many other mistakes.

He even calls it  “quite possibly the worst paper [he’s] read all year.” The Journal of Neuroscience is a rather prestigious journal, so this is all the more upsetting.

I do not study the effects of marijuana use on the brain, so I can’t tell you how it may or may not cause harm. I am absolutely positive it has some effect. But it’s important to remember that pretty much everything you do creates changes in your brain. Reading a book, riding a bike, talking with your friends…
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these all create lasting memories that are encoded in your neurons. However, after reading this most recent article, there is ABSOLUTELY NO WAY you can assert that marijuana use is harmful, or creates anatomical changes, or anything really…

It’s just another case of sensationalist reporting of poorly conducted science.
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-RSB

See-Through Brain Developed

April 10th, 2013 | Brain

See-Through-Brain-CLARITY-1

See-Through-Brain-CLARITY-2

See-Through-Brain-CLARITY-3

See-Through Brain Development

The world’s very first See-Through Brain has been developed by a team at Stanford University led by Karl Deisseroth (M.D., Ph.D.).  Deisseroth is well-known for his critical role in the development of Optogenetics, a tool used to control individual neurons with light.  Optogenetics is normally limited to surface neurons because the light has trouble reaching deeper areas, but the see-through brain may greatly enhance its efficacy.

The new method (termed CLARITY) involves removing the fat that provides structure but also blocks light.  The brain is soaked in a chemical that forms a nanoporous hydrogel-hybridized mesh in the brain.  This mesh can then support all the tissue so the fat can be washed away, resulting in the incredible see-through brain.

Unfortunately, the new technique can’t be used in living animals, but it still represents a huge advancement for neuroanatomists.  No longer will there be much need to cut the brain into tiny slices (an extremely time-consuming process) to observe connectivity.

The announcement comes just a week after President Barack Obama announced a $100 million BRAIN initiative, and this new step forward surely offers a taste of the sort of technological breakthroughs the initiative hopes to achieve.

And all the Leaders in Neuroscience seem to be weighing in on this one:

“I can’t make any official statement, but I can say that this is exactly the type of technology one would hope to develop for the [BRAIN] project” – Dr. Michelle Freund, a program manager with the National Institutes of Mental Health

“If the entire mouse brain is transparent, that makes a very large fraction of neuroscience research much easier”  – Dr. R. Clay Reid of the Allen Institute for Brain Science in Seattle.

This technique “is a giant step forward from having to slice the mouse brain into 1,000 pieces and looking at them each individually, then trying to reconstruct the relationships of all those slices” – Dr. Cori Bargmann of Rockefeller University, a co-leader of Obama’s brain initiative.

“It’s exactly the technique everyone’s been waiting for”- Dr. Terry Sejnowski of the Salk Institute.

Karl_Deisseroth_Stanford

 Karl Deisseroth, mastermind of the CLARITY technique

It is certainly an exciting time to be a Neuroscientist.

You can find the full article here.

-RSB

The First Brain-to-Brain Interface

March 11th, 2013 | Brain

Brain-To-Brain-Interface

Scientists have created a Brain-to-Brain interface that allows two different animals to pass neural information from one brain to the next without ever seeing each other.  The study, published on February 28th in Scientific Reports, is the first of its kind.  The internet has been going crazy about it so I thought I’d offer my two cents and try to explain in layman’s terms exactly what happened.

Who Conducted the Experiment?

The lab of Miguel Nicolelis from Duke University performed the experiment with some collaborators in Natal, Brazil.  This lab was one of the first teams to study the restoration of movement for paraplegics through the use of Brain-to-Machine interfaces.

How Does the Experiment Work?

First of all, electrodes must be implanted in 2 different rats’ brains.  It looks like this:

A rat with a brain-to-brain implant

The electrodes record electrical activity from neurons in the brain in the form of spikes. These spikes represent information (thoughts) and their number and timing are recorded and then transmitted through those wires into a nearby computer. The computer then converts the spikes into a representation that can be stimulated into the second rat’s brain. The hope is that the pattern that is stimulated into the second brain will make the rat respond in the same way as the first rat. In more detail: The first rat is signaled by an LED light to either go Left or Right (you can see in the yellow circle above).  The brain information from rat #1 is recorded and transferred to rat #2, and then he has to go in the same direction as the first rat, but without seeing an LED light to let him know which way to go.  He can only know which way to go if he uses the information that is being pumped into his brain through the wires.

So really, it is a brain-to-computer-to-brain interface.  Here’s a schematic of what I just described:

Brain-to-Brain Interface Experimental Design

An important point of this experimental design is that the original rat (labeled “Encoder”) received a reward if the second rat (“Decoder”) could perform the task successfully.  This means that the 1st rat could change its thoughts a little bit if the second rat was not working correctly, and this effectively trained the network to operate more effectively.
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One really cool thing about this study is that this all worked over very large distances.
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One rat was in a cage in Brazil while the other one was in America!

So How Do We Know it Worked?

The second rat was able to pick the right lever 70% of the time, a performance significantly better than chance, suggesting that the information was successfully transferred and understood.  If the information wasn’t transferring properly, the performance would have been around 50%, meaning that the second rat had no idea which direction to go.  You can see that graphically in the image below.  The Encoder rat is the 1st rat and the Decoder rat is the second rat that is trying to use the first rat’s thoughts to complete the task.

Brain-to-Brain Interface Results

Why Is This Brain-to-Brain Interface Important?

I have been pondering the implications of the study for the past week or so. Nicolelis pointed out that, in theory, such a system is not limited to a pair of brains, but instead could include a network of brains, which he named a “Brain-Net.” Researchers at Duke and at the ELS-IINN are now working on experiments to link multiple animals cooperatively to solve more complex behavioral tasks.   “We cannot even predict what kinds of emergent properties would appear when animals begin interacting as part of a brain-net. In theory, you could imagine that a combination of brains could provide solutions that individual brains cannot achieve by themselves.” Such a connection might even mean that one animal would incorporate another’s sense of “self,” he said.

To me, this paper says that it’s possible to take information from one brain and pump it into another brain to assist the second brain to do something.  I think to make this really useful, it will be necessary to record from many more neurons at a time to get a more accurate representation of the neural information.  We also have to have a better understanding of how thoughts are encoded in those spikes so we really know what information we’re transferring.

Maybe one day we’ll see bees flying in formation or cows herding themselves…  And when they find a way to translate this technology to humans, we could ultimately see some sort of telepathic communication in action.
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Exciting times ahead!

-RSB