Map Of The Developing Human Brain Shows Where Problems Begin (NPR)

Our ability to image the brain is becoming quite extraordinary. How we use those images and the agenda of which they are a piece are, however, somewhat concerning. It's wonderful to see how the brain can go wrong in development, but it's FAR more important to understand WHY the brain goes wrong - and the single greatest factor, far more important than genetics, is adverse childhood experience, especially neglect, abuse, and incest.

If we could put an end to those three experiences, the rates of mental illness would be a fraction of the current numbers.

Map Of The Developing Human Brain Shows Where Problems Begin

by Jon Hamilton
April 02, 2014
3 min 53 sec

Play the story
Download


Images of the developing fetal brain show connections among brain regions. Allen Institute for Brain Science
A high-resolution map of the human brain in utero is providing hints about the origins of brain disorders including schizophrenia and autism.

The map shows where genes are turned on and off throughout the entire brain at about the midpoint of pregnancy, a time when critical structures are taking shape, researchers reported Wednesday in the journal Nature.

"It's a pretty big leap," says Ed Lein, an investigator at the Allen Institute for Brain Science in Seattle who played a central role in creating the map. "Basically, there was no information of this sort prior to this project."

Having a map like this is important because many psychiatric and behavioral problems appear to begin before birth, "even though they may not manifest until teenage years or even the early 20s," says Dr. Thomas Insel, director of the National Institutes of Mental Health.

The human brain is often called the most complex object in the universe. Yet its basic architecture is created in just nine months, when it grows from a single cell to more than 80 billion cells organized in a way that will eventually let us think and feel and remember.

"We're talking about a remarkable process," a process controlled by our genes, Lein says. So he and a large team of researchers decided to use genetic techniques to create a map that would help reveal this process. Funding came from the 2009 federal stimulus package. The project is part of the BrainSpan Atlas of the Developing Brain.

The massive effort required tens of thousands of brain tissue samples so small that they had to be cut out with a laser. Researchers used brain tissue from aborted fetuses, which the Obama administration has authorized over the objections of abortion opponents.

Researchers tested each sample to see which genes were turned on and off in each tiny bit of brain. This helped the team figure out which types cells were present at specific points in the brain and what those cells were doing, Lein says.

The resulting map, which is available to anyone who wants to use it, has already led to at least two important findings, Lein says. "The first is that many genes that are associated with brain disorders are turned on early in development, which suggests that these disorders may have their origin from these very early time points."

And the map tells researchers who study these disorders where in the brain they should be looking for signs of trouble, Lein says.

For example, the map shows that genes associated with autism appear to be acting on a specific type of brain cell in a part of the brain called the neocortex. That suggests "we should be looking at this particular type of cell in the neocortex, and furthermore that we should probably be looking very early in the prenatal stages for the origin of autism," Lein says.

The second important finding from the mapping project, Lein says, is that the human brain is different from a mouse brain in ways researchers didn't know before. These differences could explain why a number of brain drugs that work well in mice have failed badly in people.

The map also reveals just how little scientists had known about the brain of a fetus.

"It's an enormous surprise to us that the genes that get expressed in the fetal brain don't look anything like what we would have expected from the adult brain," Insel says. "It's almost as if the fetal brain is a different organ altogether."

That realization is already helping to explain the complex role that genes often play in brain disorders, Insel says.

For example, researchers have been puzzled by some of the genes that appear to be involved in autism and schizophrenia because their function in the adult brain didn't seem to have anything to do with the disorders.

"But when you look at these new maps we have of what's happening in the fetal brain," Insel says, suddenly much of this begins to make sense."

Carl Zimmer - Secrets of the Brain

Here is a very cool article from Carl Zimmer at National Geographic - the developments in brain imaging that are helping us gain better understanding of how the brain functions.

Secrets of the Brain

New technologies are shedding light on biology’s greatest unsolved mystery: how the brain really works.

Text by Carl Zimmer | February 2014
Photographs by Robert Clark

Brain Terrain The human brain is a three-pound wad of flesh able to explore the universe, imagine a better world, and ponder its own nature. Armed with far more sophisticated imaging techniques, scientists today are reaching toward an ultimate understanding of what makes us us. U.S. National Library of Medicine, Visible Human Project

Van Wedeen strokes his half-gray beard and leans toward his computer screen, scrolling through a cascade of files. We’re sitting in a windowless library, surrounded by speckled boxes of old letters, curling issues of scientific journals, and an old slide projector that no one has gotten around to throwing out.

“It’ll take me a moment to locate your brain,” he says.

On a hard drive Wedeen has stored hundreds of brains—exquisitely detailed 3-D images from monkeys, rats, and humans, including me. Wedeen has offered to take me on a journey through my own head.

“We’ll hit all the tourist spots,” he promises, smiling.

This is my second trip to the Martinos Center for Biomedical Imaging, located in a former ship-rope factory on Boston Harbor. The first time, a few weeks ago, I offered myself as a neuroscientific guinea pig to Wedeen and his colleagues. In a scanning room I lay down on a slab, the back of my head resting in an open plastic box. A radiologist lowered a white plastic helmet over my face. I looked up at him through two eyeholes as he screwed the helmet tight, so that the 96 miniature antennas it contained would be close enough to my brain to pick up the radio waves it was about to emit. As the slab glided into the cylindrical maw of the scanner, I thought of The Man in the Iron Mask.

Mind Machine An engineer wears a helmet of sensors at the Martinos Center for Biomedical Imaging—part of a brain scanner requiring almost as much power as a nuclear submarine. Antennas pick up signals produced when the scanner’s magnetic field excites water molecules in the brain. Computers convert this data into brain maps like the one below.

The magnets that now surrounded me began to rumble and beep. For an hour I lay still, eyes closed, and tried to keep myself calm with my own thoughts. It wasn’t easy. To squeeze as much resolution as possible out of the scanner, Wedeen and his colleagues had designed the device with barely enough room for a person of my build to fit inside. To tamp down the panic, I breathed smoothly and transported myself to places in my memory, at one point recalling how I had once walked my nine-year-old daughter to school through piles of blizzard snow.

As I lay there, I reflected on the fact that all of these thoughts and emotions were the creation of the three-pound loaf of flesh that was under scrutiny: my fear, carried by electrical impulses converging in an almond-shaped chunk of tissue in my brain called the amygdala, and the calming response to it, marshaled in regions of my frontal cortex. My memory of my walk with my daughter was coordinated by a seahorse-shaped fold of neurons called the hippocampus, which reactivated a vast web of links throughout my brain that had first fired when I had clambered over the snowbanks and formed those memories.

I was submitting to this procedure as part of my cross-country reporting to chronicle one of the great scientific revolutions of our times: the stunning advances in understanding the workings of the human brain. Some neuroscientists are zooming in on the fine structure of individual nerve cells, or neurons. Others are charting the biochemistry of the brain, surveying how our billions of neurons produce and employ thousands of different kinds of proteins. Still others, Wedeen among them, are creating in unprecedented detail representations of the brain’s wiring: the network of some 100,000 miles of nerve fibers, called white matter, that connects the various components of the mind, giving rise to everything we think, feel, and perceive. The U.S. government is throwing its weight behind this research through the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. In an announcement last spring President Barack Obama said that the large-scale project aimed to speed up the mapping of our neural circuitry, “giving scientists the tools they need to get a dynamic picture of the brain in action.”

 

Centuries of study have provided increasingly detailed understanding of human brain anatomy. Now scientists are turning their attention to the complex circuits that connect the brain’s many regions—some 100,000 miles of fibers called white matter, enough to circle the Earth four times. In this image taken at the Martinos Center, pink and orange bundles transmit signals critical for language. VAN WEEDEN AND L. L. WALD, MARTINOS CENTER FOR BIOMEDICAL IMAGING, HUMAN CONNECTOME PROJECT; BRAIN PREPARATION PERFORMED AT ALLEN INSTITUTE FOR BRAIN SCIENCE

As they see the brain in action, neuroscientists can also see its flaws. They are starting to identify differences in the structure of ordinary brains and brains of people with disorders such as schizophrenia, autism, and Alzheimer’s disease. As they map the brain in greater detail, they may learn how to diagnose disorders by their effect on anatomy, and perhaps even understand how those disorders arise.

On my return trip to his lab Wedeen finally locates the image from my session in the scanner. My brain appears on his screen. His technique, called diffusion spectrum imaging, translates radio signals given off by the white matter into a high-resolution atlas of that neurological Internet. His scanner maps bundles of nerve fibers that form hundreds of thousands of pathways carrying information from one part of my brain to another. Wedeen paints each path a rainbow of colors, so that my brain appears as an explosion of colorful fur, like a psychedelic Persian cat.

Wedeen focuses in on particular pathways, showing me some of the circuitry important to language and other kinds of thought. Then he pares away most of the pathways in my brain, so that I can more easily see how they’re organized. As he increases the magnification, something astonishing takes shape before me. In spite of the dizzying complexity of the circuits, they all intersect at right angles, like the lines on a sheet of graph paper.

“It’s all grids,” says Wedeen.

 

Anatomy of a Mystery New technologies let scientists peer deep into the hidden structure of the brain. A high-resolution view of the image above reveals white matter fibers arranged in a mysterious grid structure, like longitude and latitude lines on a map. Van Wedeen and L. L. Wald, Martinos Center for Biomedical Imaging, Human Connectome Project

When Wedeen first unveiled the grid structure of the brain, in 2012, some scientists were skeptical, wondering if he’d uncovered only part of a much more tangled anatomy. But Wedeen is more convinced than ever that the pattern is meaningful. Wherever he looks—in the brains of humans, monkeys, rats—he finds the grid. He notes that the earliest nervous systems in Cambrian worms were simple grids—just a pair of nerve cords running from head to tail, with runglike links between them. In our own lineage the nerves at the head end exploded into billions but still retained that gridlike structure. It’s possible that our thoughts run like streetcars along these white matter tracks as signals travel from one region of the brain to another.

“There’s zero chance that there are not principles lurking in this,” says Wedeen, peering intently at the image of my brain. “We’re just not yet in a position to see the simplicity.”

Scientists are learning so much about the brain now that it’s easy to forget that for much of history we had no idea at all how it worked or even what it was. In the ancient world physicians believed that the brain was made of phlegm. Aristotle looked on it as a refrigerator, cooling off the fiery heart. From his time through the Renaissance, anatomists declared with great authority that our perceptions, emotions, reasoning, and actions were all the result of “animal spirits”—mysterious, unknowable vapors that swirled through cavities in our head and traveled through our bodies.

The scientific revolution in the 17th century began to change that. The British physician Thomas Willis recognized that the custardlike tissue of the brain was where our mental world existed. To understand how it worked, he dissected brains of sheep, dogs, and expired patients, producing the first accurate maps of the organ.

It would take another century for researchers to grasp that the brain is an electric organ. Instead of animal spirits, voltage spikes travel through it and out into the body’s nervous system. Still, even in the 19th century scientists knew little about the paths those spikes followed. The Italian physician Camillo Golgi argued that the brain was a seamless connected web. Building on Golgi’s research, the Spanish scientist Santiago Ramón y Cajal tested new ways of staining individual neurons to trace their tangled branches. Cajal recognized what Golgi did not: that each neuron is a distinct cell, separate from every other one. A neuron sends signals down tendrils known as axons. A tiny gap separates the ends of axons from the receiving ends of neurons, called dendrites. Scientists would later discover that axons dump a cocktail of chemicals into the gap to trigger a signal in the neighboring neuron.

 

Intimate View Two hundred sections of a piece of mouse brain, each less than 1/1,000 the thickness of a human hair, are readied to be imaged by an electron microscope. Arranged in stacks, 10,000 such photomicrographs form a 3-D model no larger than a grain of salt (in tweezers). A human brain visualized at this level of detail would require an amount of data equal to all the written material in all the libraries of the world.

Jeff Lichtman, a neuroscientist, is the current Ramón y Cajal Professor of Arts and Sciences at Harvard, carrying Cajal’s project into the 21st century. Instead of making pen-and-ink drawings of neurons stained by hand, he and his colleagues are creating extremely detailed three-dimensional images of neurons, revealing every bump and stalk branching from them. By burrowing down to the fine structure of individual nerve cells, they may finally get answers to some of the most basic questions about the nature of the brain. Each neuron has on average 10,000 synapses. Is there some order to their connections to other neurons, or are they random? Do they prefer linking to one type of neuron over others?

To produce the images, Lichtman and his colleagues load pieces of preserved mouse brain into a neuroanatomical version of a deli meat slicer, which pares off layers of tissue, each less than a thousandth the thickness of a strand of human hair. The scientists use an electron microscope to take a picture of each cross section, then use a computer to order them into a stack. Slowly a three-dimensional image takes shape—one that the scientists can explore as if they were in a submarine traveling through an underwater kelp forest.

“Everything is revealed,” says Lichtman.

The only problem is the sheer enormity of “everything.” So far the largest volume of a mouse’s brain that Lichtman and his colleagues have managed to re-create is about the size of a grain of salt. Its data alone total a hundred terabytes, the amount of data in about 25,000 high-definition movies.

01:39

00:31

05:57

A Voyage Into the Brain Thought, feeling, sense, action—all derive from unimaginably complex interactions among billions of nerve cells. A section of mouse brain no larger than a grain of salt serves as a window into this hidden world.

Go read the rest of the article.

Connectome Update (Brain Science Podcast 103) with Olaf Sporns

On last month's Brain Science Podcast, your host, Dr. Ginger Campbell, spoke with neuroscientist Olaf Sporns, author of Discovering the Human Connectome, to get an update on connectome research.

Connectome Update (BSP 103)

November 22, 2013
Ginger Campbell, MD


OLAF SPORNS, PHD

• Download mp3 
• Download Episode Transcript

The Human Connectome is a description of the structural connectivity of the human brain, but according to Olaf Sporns, author of Discovering the Human Connectome, this description must include a description of the brain's dynamic behavior. I first talked with Sporns back in BSP 74, but BSP 103 gave us a chance to talk about recent progress in connectomics.

Sporns sees the study of the brain's connections as fundamental to understanding how the brain works.

"It will allow us to ask new questions that perhaps we couldn’t ask before. It will be a foundational data set for us, just like the genome is. We will not be able to imagine neuroscience going back to a time when we did not have the connectome, but it will not give us all the answers.”

In his first book, Networks of the Brain, Sporns described how Network Theory provides important tools for dealing with the large data sets that are created by studying complex systems like the human brain. In BSP 103 we discuss both the challenges and the promise of Discovering the Human Connectome.

Harvard’s George Whitesides Gives Brilliant Critique of Mammoth U.S. Brain Project

Not everyone in the neuroscience and psychology worlds are excited by President Obama's $100 million Brain Activity Map Project—or the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. George Whitesides (Harvard chemist and veteran of big government ventures in support of nanotechnology) recently gave a very good critique of the BRAIN Initiative.

Harvard’s Whitesides Gives Brilliant Critique of Mammoth U.S. Brain Project

By Gary Stix | May 29, 2013

George Whitesides

The Obama administration’s Big Brain project—$100 million for a map of some sort of what lies beneath the skull—has captured the attention of the entire field of neuroscience. The magnitude of the cash infusion can’t help but draw notice, eliciting both huzzahs mixed with gripes that the whole effort might sap support for other perhaps equally worthy neuro-related endeavors.

The Brain Activity Map Project—or the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative—is intended to give researchers tools to elicit the real-time functioning of neural circuits, providing a better picture of what happens in the brain when immersed in thought or when brain cells are beset by a degenerative condition like Parkinson’s or Alzheimer’s. Current technologies are either too slow or lack the resolution to achieve these goals.

One strength of the organizers—perhaps a portent of good things to come—is that they don’t seem to mind opening themselves to public critiques. At a planning meeting earlier this month, George Whitesides, the eminent Harvard chemist and veteran of big government ventures in support of nanotechnology, weighed in on how the project appeared to an informed outsider. Edited excerpting of some of his comments follows. This posting is a bit long, but Whitesides is eloquent and it’s worth reading what he has to say because his views apply to any large-scale sci-tech foray.

Whitesides began his talk after listening to a steady cavalcade of big-name neuroscientists furnish their personal wish lists for the program: ultrasound to induce focal lesions, more fruit fly studies to find computational nervous system primitives, more studies on zebra fish, studies on wholly new types of model organisms, avoiding too much emphasis on practical applications and so on.

“Listening to you this morning has been intensely interesting for me,” Whitesides began. “It has very much the flavor of a thousand flowers blooming. That is to say a problem which we all agree is intensely important: what is the brain how does it think, what is mind. It fits right there with issues such as what is life and where does life come from. It fits with the great problems of the next century.” 

“The question of whether people outside understand what is going on and where it leads is more complicated,” he continued. “I’ll just make a point to set a starting point. When I first heard about…the brain map I checked with a bunch of people who are good scientists and neurobiologists and everybody’s opposed, almost universally…There’s very deep skepticism that this approach, physical mapping at that scale, is going to work and lead to something.”

To promote the program, Whitesides emphasized the critical need to get non-neuroscientists to understand the problem being addressed—and to think carefully about something as simple as what the project should be called. Would the name “brain map” convey anything intelligible to someone not conversant with technical papers that bear titles like “Climbing Fiber Input Shapes Reciprocity of Purkinje Cell Firing”?

Whitesides suggested reverting to first principles in trying to describe to the world at large the importance of spending $100 million to gain better insight into the minutiae of neural circuitry. He recommended a cross-disciplinary collaboration by drawing upon knowledge, not from geneticists or bioengineers, but by borrowing across the divide of C.P. Snow’s Two Cultures: In other words, bringing in the English teachers. Going as basic as it gets, Whitesides told a room packed with full professors from elite universities that they should craft the story of the Big Brain project with the structural elements of a murder mystery.

“You have to have a puzzle or problem: Who killed lady of house? Was it the butler or somebody else? There has to be a puzzle or conflict or problem you want to resolve. The second element, a journey or trek, how you get there. You’ve spent much time talking here about that: what technical methods to get data or to formulate experiments. 

“The third component: There has to be a surprise. If you don’t have a surprise nobody’s interested. You have to catch the attention of people. To say [you want to come up with] a theory of mind is too far off. You want something shorter term that people can get a grip on. Finally, you need a resolution. The cat killed the lady of house, not the butler…But you need a resolution. Often in science you call it an application. 

“If you don’t have those components, you don’t have much to work with when talking to people who are not neuroscientists. Everybody’s fascinated by the particular tack they take to a particular piece of research. Outside it’s a different story. People want to know what you’re all doing and it has to be simple enough for people to understand that. It’s very difficult to do. 

“It’s very, very difficult to do and one of the issues here is to start hammering out that story. In genomics, it was: ‘we’re going to understand genomics, and based on the genome we’re going to understand cancer, and based on that understanding we’re going to cure cancer; and based on that your mother is going to live for a longer period of time.’ 

“Now it’s turned out to be more complicated than that as everything is in biology is. But here you’ve got an even more complicated problem. So how do you simplify this very complicated problem with top and bottom-level stories in such a fashion that I as an outsider can understand what the field is going to be doing, what it’s deliverables are going to be? … 

“Now in that context there are just a couple of things to remember. One of them is the question of ‘Why now?’ This problem has been around for a long time. And this is hardly the first group that’s thought about the nature of the brain. So why is now the time where we expect something astonishing to happen? With genomics, it happened because the technology of sequencing became so good that virtually anyone could generate floods of data and then begin to think about what could be done with that. What’s the corresponding thing here? I don’t know the answer to that. 

“The second issue which is in the same general issue of ‘why now’ is ‘Who cares?’” Obviously you care because you care about problems. But outside of this room with people who are not neuroscientists, what do they care about? What is the problem that you say you’re going to solve that they care about and I don’t think there are any shortage of these problems, all the way from alleviating tremor in Parkinson’s to beginning to think about depression, which is one of the great problems in public health.”

Whitesides then went on to talk about other considerations for structuring the project so that it retains some relevance beyond the neuroscience community. “I think that it’s really important to have deliverables and outcomes.” he said. “They don’t have to be the things that have the characteristic that they have to be the ultimate goal, but you need milestones along the way so you can go to the outside world and say we have done this. It’s not a compelling case to say that we’re here and in 100 years we’ll have a theory of mind and there’s nothing to show you in between because it’s all too complicated to understand. So what are they going to be and what do they look like?

“Second there’s a question of reductionism vs. higher-level stuff. If you think that a theory of mind is going to come by understanding the function of individual synapses and then building up from there, that tends not to work too well with really complicated systems. It works well with engineered systems like transistors or integrated circuits or devices or the Internet or Facebook. Those systems are engineered systems. Picking really complicated systems apart is hard to do. So what often one does is go from the end and look at higher-level behaviors in terms of black boxes and if you have good working models, you can pick those black boxes apart. 

“Just to give you an example of how the fully reductionist approach can run into difficulties, again we can go to genomics. If you talk now to the people in the pharmaceutical industry, what they will say is they’re moving massively away from target-based medicine to phenotypic assays. That is to say, if you want to find out whether a mouse gets better, you give a mouse stuff and see what happens, you don’t ask too many detailed questions. The detailed questions haven’t worked out very well. Here I don’t have a sense where the dividing line is between things that are best done at high-level and things that are best done by going reductionist. But there’s probably a place for everything.” 

“Zebra fish are a nice transparent model, but they’re probably not going to tell us very much about depression. People are probably more interested in depression than they are in zebra fish outside the room. That’s an interesting question. 

“The third point is about balance and inclusion. We are at the tail end of a pretty successful program in the United States on nanoscience or nanotechnology. And the question of why was this successful is complicated. But one of the reasons is that when this program emerged, it was phrased in such a way that virtually every area of science saw there was something in it for them; that is, the chemists, the biologists, the physicists, the device guys; everybody saw that there was some value in nanoscience for them. 

“And there was a supporting enormously important technology which is the technology of integrated circuits. And what’s happened over the course of time is what the engineers at Intel have done which is almost beyond belief in terms of its sophistication. Two generations or maybe one generation from now, microprocessors will have minimum feature sizes that are on the order of maybe 8 nanometers. I still can’t believe this and that’s using 190 nanometer light. 

So they provided an enormous practical push for this area and then everybody had something interesting to do at the nanoscale. The question is how to does one open this community in such a fashion that everyone thinks there’s something interesting and important…[For the brain project], it has to include engineering, it has to include clinical medicine it has to include the molecular it has to include cells and animals. The whole story has to be there somehow but making the story inclusive will make a much stronger case for building a strong community. 

The last point I’ll make is inclusion of industry…Let me tell you another short story which comes from a component of genomics that was Illumina, the sequencer that has been as important as many other things in genomics. The inventor of the technology at the very beginning was David Walt of Tufts…I was at a seminar with David in which one of the people in the audience at the end asked the following question: [which was] ‘how do you handle the conflict of interest problem in an academic lab. when you’re working on this and a company is working on the same thing’ and he [Walt] said ‘there’s never a problem and the reason there’s never a problem is that once industry takes up an idea; and good engineers, mature engineers, begin to work on it, an academic laboratory can never compete.’ 

“Now the relevance to this [the brain project] if you think about what Illumina and other sequencers made possible in genomics you can ask the question: are there corresponding things in this area where really good, skilled industrial engineers can make a capability available to the community in a way that makes it possible to collect all the data, all the structure, function, the measurements that you want to collect because it’s going to be vastly, vastly easier if it’s done as a centralized function, with real people paying real dollars to get it done really, really well. 

“And it may be premature to do it at this point. I don’t know the answer to that but it’s something for you to think about. And I think the earlier you get people who are professional engineers and, on the other end, clinicians actively involved in the work that you’re doing; the more likely you are to find components that you can use and motivations for using them that will help keep the field strong. 

“So it’s a fantastic area, unbelievably complicated. Outside it looks less straightforward than it looks to you inside and inside it looks pretty chaotic, so you can imagine what it looks like from outside.”

~ About the Author: Gary Stix, a senior editor, commissions, writes, and edits features, news articles and Web blogs for SCIENTIFIC AMERICAN. His area of coverage is neuroscience. He also has frequently been the issue or section editor for special issues or reports on topics ranging from nanotechnology to obesity. He has worked for more than 20 years at SCIENTIFIC AMERICAN, following three years as a science journalist at IEEE Spectrum, the flagship publication for the Institute of Electrical and Electronics Engineers. He has an undergraduate degree in journalism from New York University. With his wife, Miriam Lacob, he wrote a general primer on technology called Who Gives a Gigabyte? Follow on Twitter @gstix1.


The views expressed are those of the author and are not necessarily those of Scientific American.

The Human Connectome Project (HCP) consortium is led by David C. Van Essen, PhD (Washington University School of Medicine), and Kamil Ugurbil, PhD, (University of Minnesota). They have released some new brain data including brain imaging scans and behavioral information -- individual differences in personality, cognitive capabilities, emotional characteristics and perceptual function -- obtained from 68 healthy adult volunteers.

Very cool - and all of their data is freely available, including a full package of 3 terabytes of data (for the cost of the storage device on which they send it to you).

Connectome Project Releases Brain Data

A map of average “functional connectivity” in human cerebral cortex (including subcortical gray matter). Regions in yellow are functionally connected to a “seed” location in the parietal lobe of the right hemisphere, whereas regions in red and orange are weakly connected or not connected at all. (Credit: Image courtesy of Washington University in St. Louis)

Mar. 5, 2013 — The Human Connectome Project, a five-year endeavor to link brain connectivity to human behavior, has released a set of high-quality imaging and behavioral data to the scientific community. The project has two major goals: to collect vast amounts of data using advanced brain imaging methods on a large population of healthy adults, and to make the data freely available so that scientists worldwide can make further discoveries about brain circuitry.

The initial data release includes brain imaging scans plus behavioral information -- individual differences in personality, cognitive capabilities, emotional characteristics and perceptual function -- obtained from 68 healthy adult volunteers. Over the next several years, the number of subjects studied will increase steadily to a final target of 1,200. The initial release is an important milestone because the new data have much higher resolution in space and time than data obtained by conventional brain scans.

The Human Connectome Project (HCP) consortium is led by David C. Van Essen, PhD, Alumni Endowed Professor at Washington University School of Medicine in St. Louis, and Kamil Ugurbil, PhD, Director of the Center for Magnetic Resonance Research and the McKnight Presidential Endowed Chair Professor at the University of Minnesota.

"By making this unique data set available now, and continuing with regular data releases every quarter, the Human Connectome Project is enabling the scientific community to immediately begin exploring relationships between brain circuits and individual behavior," says Van Essen. "The HCP will have a major impact on our understanding of the healthy adult human brain, and it will set the stage for future projects that examine changes in brain circuits underlying the wide variety of brain disorders afflicting humankind."

The consortium includes more than 100 investigators and technical staff at 10 institutions in the United States and Europe. It is funded by 16 components of the National Institutes of Health via the Blueprint for Neuroscience Research.

"The high quality of the data being made available in this release reflects an intensive, multiyear effort to improve the data acquisition and analysis methods by this dedicated international team of investigators," says Ugurbil.

The data set includes information about brain connectivity in each individual, using two distinct magnetic resonance imaging (MRI) approaches. One, called resting-state functional connectivity, is based on spontaneous fluctuations in functional MRI signals that occur in a complex pattern in space and time throughout the gray matter of the brain. Another, called diffusion imaging, provides information about the long-distance "wiring" -- the anatomical pathways traversing the brain's white matter. Each method has its own limitations, and analyses of both functional connectivity and structural connectivity in each subject should allow deeper insight than by either method alone.

Each subject is also scanned while performing a variety of tasks within the scanner, thereby providing extensive information about "Task-fMRI" brain activation patterns. Behavioral data using a variety of tests performed outside the scanner are being released along with the scan data for each subject. The subjects are drawn from families that include siblings, some of whom are twins. This will enable studies of the heritability of brain circuits.

The imaging data set released by the HCP takes up about two terabytes (2 trillion bytes) of computer memory -- the equivalent of more than 400 DVDs -- and is stored in a customized database called "ConnectomeDB."

"ConnectomeDB is the next-generation neuroinformatics software for data sharing and data mining. It's a convenient and user-friendly way for scientists to explore the available HCP data and to download data of interest for their research," says Daniel S. Marcus, PhD, assistant professor of radiology and director of the Neuroinformatics Research Group at Washington University School of Medicine. "The Human Connectome Project represents a major advance in sharing brain imaging data in ways that will accelerate the pace of discovery about the human brain in health and disease."

Further information: http://www.humanconnectome.org/

TED Talks - 7 Talks on Mapping the Human Brain

In honor of President Obama's efforts to create a second "Decade of the Brain," in which he hopes to do for neuroscience what the human genome project did for genetics, the TED Blog editors have posted seven talks that deal with mapping the human brain.

Enjoy!

7 talks on mapping the human brain

Posted by: Tedstaff

February 22, 2013

In his State of the Union address, US President Barack Obama teased the importance of mapping the human brain, hinting that it could be a good investment in the future. According to The New York Times, the president will soon announce a decade-long plan to support the comprehensive rendering of the brain as part of his budget proposal. The project, which is being called the Brain Activity Map, will reportedly involve federal agencies, private foundations and scores of neuroscientists. The plan could cost in the upwards of billions of dollars.

Mapping the human brain is an endeavor several TED speakers have already begun embarking on. Here, a look at talks about how this mapping can take place — and why it’s a scientific priority.

Sebastian Seung: I am my connectomeSebastian Seung has proposed an incredibly ambitious goal: mapping all the connections between neurons in the brain, a map he calls the “connectome.” There are questions about whether we have the technology to accomplish his goal, but it is clearly a dream that would have enormous repercussions if it becomes real.

* * * 

Allan Jones: A map of the brainAllan Jones is approaching the mapping from a different perspective: which genes are turned on in which part of the brain. They mapped which of 25,000 genes are active in each of a multitude of tiny regions of the brain, producing an extraordinary data set that scientists are only beginning to delve into.

* * * 

Henry Markram: A brain in a supercomputerHenry Markram talked in 2009 about an idea to simulate a brain in a supercomputer. He previously ran the “Blue Brain” project to simulate about a million neurons. His new initiative, the Human Brain Projectis far more ambitious — it will attempt to simulate a brain capable of learning, and just received a commitment of half a billion Euros to complete.

* * *

Erin Schuman: How neurons reach out to each otherIf we’re going to understand how our brains create us, we will need to know how our brains build themselves at the smallest levels. It’s no easy feat: each neuron can have 100,000 synapses. But using some of the same methods you could use to count the number of fish in a pond, Erin Schuman shows how neurons distribute the assembly work in a decentralized way — and how understanding those decentralized systems could further our understanding of all kinds of successful networks.

* * *

Gero Miesenbach reengineers a brainIn the quest to map the brain, many scientists have attempted the incredibly daunting task of recording the activity of each neuron. Gero Miesenboeck works backward — manipulating specific neurons to figure out exactly what they do, through a series of stunning experiments that reengineer the way fruit flies percieve light.

* * *

Ralph Adolphs: The social brainWe humans can’t help but attribute our social qualities our non-human companions. Anyone who’s yelled at their computer can attest to that. Ralph Adolphs studies that kind of social behavior, both when it’s normal and when it’s not. In this fascinating talk, he shares how we know which regions of our brains are essential to social interactions and sheds light on the behavioral loop in which our actions and feelings affect our perceptions of social situations as much as the realities of those situations.

* * *

Andres Lozano: Turning dials in the brainSometimes, when you want to learn how something works, you need poke it with an electrode. Andres Lozano does that to living brains, albeit with far more precision and control than you may think is possible — and he’s alleviated symptoms of crippling neurological disorders, like dystonia and Parkinson’s, along the way. Telling uplifting success stories, he shows you how he does it and previews his promising next steps — attempting to “turn the lights back on” in Alzheimer’s patients.

David Van Essen, PhD - The Human Connectome Project: Progress and Perspectives

This video comes from the NIH Center for Information Technology - David Van Essen, PhD discusses the Human Connectome Project: Progress and Perspectives. If the video doesn't work, the link here will take you to the site, where you can watch the video.



Description: Neuroscience Seminar Series

For more information go to http://neuroseries.info.nih.gov 

Author: David Van Essen, PhD 

Runtime: 01:08:40 

Download: Download Video 

How to download a Videocast 

Caption Text: Download Caption File

Brain and Neuroscience in the News

Here are a few recent articles that I have not had time to post individually, but these deserve some attention. I'm offering a taste of each one and I hope you seek out and explore the ones that interest you - follow the link in the title to see the whole article.

Weak Brain Connections Found in People with Anxiety Disorder

By Traci Pedersen Associate News Editor
Reviewed by John M. Grohol, Psy.D. on September 5, 2012 

 

 

The brains of people with generalized anxiety disorder (GAD) have weaker connections between a brain region in charge of emotional response and the amygdala.  

This suggests that the brain’s “panic button” may be chronically pushed down due to lack of regulation, according to a new University of Wisconsin-Madison imaging study.

GAD, which is characterized by excessive, uncontrollable worry, affects nearly 6 percent of the population.

The findings support the hypothesis that reduced communications between parts of the brain result in the extreme anxiety felt by people with GAD, said lead author Jack Nitschke, Ph.D., associate professor of psychiatry.

 * * * * *

Neuroscience: Idle minds

Neuroscientists are trying to work out why the brain does so much when it seems to be doing nothing at all.

• Kerri Smith

19 September 2012

For volunteers, a brain-scanning experiment can be pretty demanding. Researchers generally ask participants to do something — solve mathematics problems, search a scene for faces or think about their favoured political leaders — while their brains are being imaged.

But over the past few years, some researchers have been adding a bit of down time to their study protocols. While subjects are still lying in the functional magnetic resonance imaging (fMRI) scanners, the researchers ask them to try to empty their minds. The aim is to find out what happens when the brain simply idles. And the answer is: quite a lot.

Some circuits must remain active; they control automatic functions such as breathing and heart rate. But much of the rest of the brain continues to chug away as the mind naturally wanders through grocery lists, rehashes conversations and just generally daydreams. This activity has been dubbed the resting state. And neuroscientists have seen evidence that the networks it engages look a lot like those that are active during tasks.

Resting-state activity is important, if the amount of energy devoted to it is any indication. Blood flow to the brain during rest is typically just 5–10% lower than during task-based experiments¹. And studying the brain at rest should help to show how the active brain works. Research on resting-state networks is helping to map the brain's intrinsic connections by showing, for example, which areas of the brain prefer to talk to which other areas, and how those patterns might differ in disease.

But what is all this activity for? Ask neuroscientists — even those who study the resting state — and many will sigh or shrug. “We're really at the very beginning. It's mostly hypotheses,” says Amir Shmuel, a brain-imaging specialist at McGill University in Montreal, Canada. Resting activity might be keeping the brain's connections running when they are not in use. Or it could be helping to prime the brain to respond to future stimuli, or to maintain relationships between areas that often work together to perform tasks. It may even consolidate memories or information absorbed during normal activity.

* * * * * 

Beyond the Brain

by Tanya Marie Luhrmann 
 

In the 1990s, scientists declared that schizophrenia and other psychiatric illnesses were pure brain disorders that would eventually yield to drugs. Now they are recognizing that social factors are among the causes, and must be part of the cure.

By the time I met her, Susan was a success story. She was a student at the local community college. She had her own apartment, and she kept it in reasonable shape. She did not drink, at least not much, and she did not use drugs, if you did not count marijuana. She was a big, imposing black woman who defended herself aggressively on the street, but she had not been jailed for years. All this was striking because Susan clearly met criteria for a diagnosis of schizophrenia, the most severe and debilitating of psychiatric disorders. She thought that people listened to her through the heating pipes in her apartment. She heard them muttering mean remarks. Sometimes she thought she was part of a government experiment that was beaming rays on black people, a kind of technological Tuskegee. She felt those rays pressing down so hard on her head that it hurt. Yet she had not been hospitalized since she got her own apartment, even though she took no medication and saw no psychiatrists. That apartment was the most effective antipsychotic she had ever taken.

Twenty years ago, most psychiatrists would have agreed that Susan had a brain disorder for which the only reasonable treatment was medication. They had learned to reject the old psychoanalytic ideas about schizophrenia, and for good reasons. When psychoanalysis dominated American psychiatry, in the mid-20th century, clinicians believed that this terrible illness, with its characteristic combination of hallucinations (usually auditory), delusions, and deterioration in work and social life, arose from the patient’s own emotional conflict. Such patients were unable to reconcile their intense longing for intimacy with their fear of closeness. The science mostly blamed the mother. She was “schizophrenogenic.” She delivered conflicting messages of hope and rejection, and her ambivalence drove her child, unable to know what was real, into the paralyzed world of madness. It became standard practice in American psychiatry to regard the mother as the cause of the child’s psychosis, and standard practice to treat schizophrenia with psychoanalysis to counteract her grim influence. The standard practice often failed.

The 1980s saw a revolution in psychiatric science, and it brought enormous excitement about what the new biomedical approach to serious psychiatric illness could offer to patients like Susan. To signal how much psychiatry had changed since its tweedy psychoanalytic days, the National Institute of Mental Health designated the 1990s as the “decade of the brain.” Psychoanalysis and even psychotherapy were said to be on their way out. Psychiatry would focus on real disease, and psychiatric researchers would pinpoint the biochemical causes of illness and neatly design drugs to target them.

Schizophrenia became a poster child for the new approach, for it was the illness the psychoanalysis of the previous era had most spectacularly failed to cure. Psychiatrists came to see the assignment of blame to the schizophrenogenic mother as an unforgivable sin. Such mothers, they realized, had not only been forced to struggle with losing a child to madness, but with the self-denigration and doubt that came from being told that they had caused the misery in the first place. The pain of this mistake still reverberates through the profession. In psychiatry it is now considered not only incorrect but morally wrong to see the parents as responsible for their child’s illness. I remember talking to a young psychiatrist in the late 1990s, back when I was doing an anthropological study of psychiatric training. I asked him what he would want non-psychiatrists to know about psychiatry. “Tell them,” he said, “that schizophrenia is no one’s fault.” 
    
It is now clear that the simple biomedical approach to serious psychiatric illnesses has failed in turn. At least, the bold dream that these maladies would be understood as brain disorders with clearly identifiable genetic causes and clear, targeted pharmacological interventions (what some researchers call the bio-bio-bio model, for brain lesion, genetic cause, and pharmacological cure) has faded into the mist. To be sure, it would be too strong to say that we should no longer think of schizophrenia as a brain disease. One often has a profound sense, when confronted with a person diagnosed with schizophrenia, that something has gone badly wrong with the brain.

* * * * *

The Creativity of the Wandering Mind

New research suggests engaging in simple tasks that allow the mind to wander facilitates creative thinking.

September 4, 2012 • By Tom Jacobs 

Do you have a numbingly dull job, one so monotonous that you frequently find your mind wandering? Well, congratulations: without realizing it, you have boosted your creative potential.

Mindless tasks that allow our thoughts to roam can be catalysts for innovation. That’s the conclusion of a research team led by Benjamin Baird and Jonathan Schooler of the University of California, Santa Barbara’s META Lab (which focuses on Memory, Emotion, Thought and Awareness).

Their research, published in the journal Psychological Science, suggests putting a difficult problem in the back of your mind won’t, by itself, lead to creative thinking. The key seems to be performing some simple chore while it’s lodged there.

Baird and his colleagues describe an experiment featuring 135 people, ages 19 to 35. Their creativity was measured by performance on the classic Unusual Uses Task, in which each participant is given two minutes to come up with as many uses as possible for a specific item, such as a brick. Besides the sheer number of responses, their answers are judged on originality, flexibility, and level of detail.

All the participants began by tackling two such problems. One-quarter of them then spent 12 minutes on an intellectually demanding task, which demanded constant attention. Another quarter spent that same amount of time on an undemanding task, which only required them to provide “infrequent responses.” Another quarter was instructed to rest for 12 minutes, while the rest went directly to the next task without a break.

All then tackled four additional rounds of the Unusual Uses Task. Two were repeats of the tests they performed earlier, and two featured objects that were new to them.

Those who had performed the undemanding task in the interim had significantly higher scores than those in any of the other categories (including the people who had simply rested for 12 minutes). However, this jump in creativity occurred only for the items they were tackling for a second time. They did not score any better than the others when presented with a new object.

This suggests their success in coming up with creative solutions “resulted from an incubation process” which was “characterized by high levels of mind wandering,” the researchers write.

 * * * * *

Neuroscience mapping brain connections

Discoveries could yield an understanding of and treatments for disorders such as autism, schizophrenia, depression and Parkinson's disease.

A brain scan of white matter fibers, color-coded by direction. (Courtesy of the Laboratory of Neuro Imaging at UCLA and Martinos Center for Biomedical Imaging at MGH www.humanconnectomeproject.org / September 5, 2012)

By Cassandra Willyard

September 13, 2012

Inside the human skull lies a 3-pound mystery. The brain — a command center composed of tens of billions of branching neurons — controls who we are, what we do and how we feel.

"It's the most amazing information structure anybody has ever been able to imagine," says Dr. Walter Koroshetz, deputy director of the National Institute of Neurological Disorders and Stroke in Bethesda, Md.

For centuries, the brain's inner workings remained largely unexplored. But all that is changing. With the help of new tools, researchers are delving deeper into this complex organ than ever before. We're in a brainy age of discovery that could change our understanding of how the brain works and why, in some cases, it fails to do its job.

Scientists already have an intimate knowledge of brain anatomy, from the hippocampus to the amygdala. "We've mapped these in exquisite detail," says Arthur Toga, director of the Laboratory of Neuro Imaging at UCLA.

But those maps don't show how the regions connect. And it's this connectivity that enables the complex behaviors our brains perform so seamlessly.

Sebastian Seung and the Connectome: Does Brain Wiring Make Us Who We Are?

The RSA posted a video clip of Sebastian Seung talking about his book, Connectome: How the Brain's Wiring Makes Us Who We Are. The clip is short, at about 16 minutes, but there is a link to the audio of the full talk. I have also included two other videos of Seung talking about his work with mapping the human brain.

Connectome: How the brain's wiring makes us who we are

Rising star in the field of neuroscience Sebastian Seung argues that our identity lies not in our genes but in the connections between our brain cells -- and he describes the monumental task of mapping these "connectomes", neuron by neuron, synapse by synapse.

Listen to the podcast of the full event including audience Q&A: http://www.thersa.org/events/audio-and-past-events/2012/connectome-how-the-br...

Find out more about the Eyewire Game: http://wiki.eyewire.org/en/Instructions

* * * * * * *

Connectomics: Sebastian Seung vs. Tony Movshon, Columbia 2012

Does the brain's wiring make us who we are?
Neuroscientists Sebastian Seung and Anothony Movshon debate minds, maps, and the future of their field.

Moderated by Robert Krulwich and Carl Zimmer
Introduction by Stuart Firestein

Columbia University
April 2, 2012

* * * * * * *

Sebastian Seung: Caroline Werner Gannett Series

TEDxHendrixCollege (2011) - What Can Your Mind Do for You?

The TEDx event at Hendrix College (Arkansas) was focused on the topic, What Can Your Mind Do for You? There are five good videos here on topics ranging from connectome, glial cells, functionalism, and the impact of modern technology on the brain. Good stuff.

Below are the talks from TEDxHendrixCollege 2011: What Can Your Mind Do for You?




Dr. Doug Fields: The Other Brain

In this talk, Dr. Doug Fields discusses glia, or "glue," which make up 85% of the cells in the human brain. New discoveries about these glial cells are revolutionizing the way that scientists view the brain, and Dr. Fields gives us a glimpse into this burgeoning area of neuroscience.

R. Douglas Fields, Ph.D., is the Chief of the Section on Nervous System Development and Plasticity at the National Institute of Child Health and Human Development, a part of the National Institutes of Health (NIH), and Adjunct Professor in the Neuroscience and Cognitive Science Program at the University of Maryland, College Park. He is author of the new book The Other Brain, which gives readers an eyewitness view of the discovery of brain cells, called glia, that communicate without using electricity. He is an internationally recognized authority on neuron-glia interactions, brain development, and the cellular mechanisms of memory. In 2004 Dr. Fields founded the scientific journal Neuron Glia Biology, where he is the Editor-in-Chief, and he serves on the editorial board of several other neuroscience journals. The author of over 150 articles in scientific journals, Dr. Fields also enjoys writing about science for the general public. He is a scientific advisor to Scientific American Mind and Odyssey magazines. He has written articles for Outside Magazine, the Washington Post and other, and he writes on-line columns for the Huffington Post, Psychology Today and Scientific American. Dr. Fields received advanced degrees at UC Berkeley (B.A.), San Jose State University (M.A.), and in 1985 he received the Ph.D. degree from the University of California, San Diego, jointly from the Neuroscience Department, in the Medical School and the Neuroscience Group, at the Scripps Institute of Oceanography. He held postdoctoral fellowships at Stanford University, Yale University, and the National Institutes of Health before starting his research laboratory at the NIH in 1994. In addition to science he enjoys building guitars, rock-climbing, and scuba diving.

Dr. Andy James: The Cognitive Connetome

Dr. Andy James is exploring individual differences in cognition using fMRI. By developing a cognitive connectome, or a map of connections in the brain that are involved in cognition, Dr. James hopes to identify the cognitive differences between healthy individuals to help understand cognition in both healthy and clinical populations.

Dr. Andrew James is an assistant professor in the Brain Imaging Research Center of the Psychiatric Research Institute at the University of Arkansas for Medical Sciences.  After receiving bachelor degrees in Chemistry and Applied Psychology at the Georgia Institute of Technology in 1999, he pursued graduate studies in neuroscience at the University of Florida. There he was introduced to functional magnetic resonance imaging, which combined his passions for analytic instrumentation and cognition. After receiving his Neuroscience Ph.D. in 2005, he spent four years as a postdoctoral fellow at Emory University and the Georgia Institute of Technology before accepting a professorship at the University of Arkansas for Medical Sciences.

Dr. James's research focuses upon developing novel experimental designs and statistical analyses to push the methodological boundaries of functional neuroimaging. His past research has encompassed a broad range of topics including age-related changes in neural networks mediating motor learning, the neural encoding of aftertaste perception, the reorganization of motor networks following stroke, and modeling inter- and intra-subject variability in emotion-regulating networks with major depressive disorder.  His recent work focuses on how the brain encodes individual differences in reasoning and personality, where he seeks to bridge the gap between well-validated neuropsychological measures of cognition and the brain's functional networks.

Dr. Jack Lyons: Why You Need a Brain (and Why You Don’t)

In this entertaining talk, philosopher Dr. Jack Lyons outlines his version of functionalism and asks the audience if they really do need a brain.

Dr. Jack Lyons is Associate Professor of Philosophy at the University of Arkansas in Fayetteville. He got his bachelor's degree from Valparaiso University in Indiana and his PhD in philosophy with a minor in cognitive science from the University of Arizona. He taught at Florida State University for two years before coming to Arkansas. He works mainly in epistemology, cognitive science, and philosophy of mind. Recent projects concern various issues in the foundations of cognitive science, including modularity, the nature of representation, multiple realizability, and the recent neoreductionist movement in the philosophy of mind. Most of his current work has involved the epistemology of perception. He has published several journal articles on epistemology and philosophy of psychology/cognitive science and has a recent book on Oxford University Press, entitled Perception and Basic Beliefs. He is an associate editor for the journal Episteme: A Journal of Individual and Social Epistemology.

Carl Schoonover: Portraits of the Mind

Carl Schoonover's talk at TEDxHendrixCollege took the audience on a visually stunning journey through the history of neuroscience, showcasing the gorgeous results of the various methods that have been used to study the brain from antiquity through the 21st century.

Carl Schoonover is a neuroscience PhD candidate and National Science Foundation graduate fellow at Columbia University, and the author of Portraits of the Mind. He has written for The Huffington Post, Scientific American, Design Observer, Science Magazine, Le Figaro, Commentaire, Boing Boing and LiveScience, and cofounded NeuWrite, a collaborative working group for scientists, writers, and those in between. He hosts a radio show on WKCR 89.9FM, which focuses on opera, classical music, and their relationship to the brain.

Dr. Sandra Aamodt: The Wired Brain: How Modern Life Is Changing Your Mind

Sandra Aamodt reveals how technology is changing the development of the next generation in our increasingly modernizing world, both for the better and the worse.

Sandra Aamodt is a former editor in chief of Nature Neuroscience, the leading scientific journal in the field of brain research. She received her undergraduate degree in biophysics from the Johns Hopkins University, and her doctorate in neuroscience from the University of Rochester. After four years of postdoctoral research at Yale University, she joined Nature Neuroscience at its founding in 1998 and was editor in chief from 2003 to 2008, when she left to spend a year sailing across the Pacific Ocean. She lives in Northern California with her husband, one cat, and three chickens.

During her editorial career, she read over three thousand neuroscience papers and wrote dozens of editorials on neuroscience and science policy. She also gave lectures at twenty universities, and attended forty-five scientific meetings in ten countries. Her science writing has been published in The New York Times, the Washington Post, El Mundo and the Times of London. Her first book, Welcome to Your Brain: Why You Lose Your Car Keys But Never Forget How to Drive and Other Puzzles of Everyday Life (coauthored with Sam Wang), won the 2009 American Association for the Advancement of Science/Subaru SB&F Prize for Excellence in Science Books. Welcome to Your Child's Brain: How the Mind Grows from Conception to College, by the same authors, will be published in September 2011.