A Researcher Wrote About Why Neural Networks Like Picdescbot Hallucinate So Many Sheep – And Yet Will

New technique captures the activity of an entire brain in a snapshot

When it comes to measuring brain activity, scientists have tools that can take a precise look at a small slice of the brain (less than one cubic millimeter), or a blurred look at a larger area. Now, researchers at The Rockefeller University have described a new technique that combines the best of both worlds—it captures a detailed snapshot of global activity in the mouse brain.

(Image caption: Sniff, sniff: This density map of the cerebral cortex of a mouse shows which neurons get activated when the animal explores a new environment. The lit up region at the center (white and yellow) represents neurons associated with the mouse’s whiskers)

“We wanted to develop a technique that would show you the level of activity at the precision of a single neuron, but at the scale of the whole brain,” says study author Nicolas Renier, a postdoctoral fellow in the lab of Marc Tessier-Lavigne, Carson Family Professor and head of the Laboratory of Brain Development and Repair, and president of Rockefeller University.

The new method, described in Cell, takes a picture of all the active neurons in the brain at a specific time. The mouse brain contains dozens of millions of neurons, and a typical image depicts the activity of approximately one million neurons, says Tessier-Lavigne. “The purpose of the technique is to accelerate our understanding of how the brain works.”

Making brains transparent

“Because of the nature of our technique, we cannot visualize live brain activity over time—we only see neurons that are active at the specific time we took the snapshot,” says Eliza Adams, a graduate student in Tessier-Lavigne’s lab and co-author of the study. “But what we gain in this trade-off is a comprehensive view of most neurons in the brain, and the ability to compare these active neuronal populations between snapshots in a robust and unbiased manner.”

Here’s how the tool works: The researchers expose a mouse to a situation that would provoke altered brain activity—such as taking an anti-psychotic drug, brushing whiskers against an object while exploring, and parenting a pup—then make the measurement after a pause. The pause is important, explains Renier, because the technique measures neuron activity indirectly, via the translation of neuronal genes into proteins, which takes about 30 minutes to occur.

The researchers then treat the brain to make it transparent—following an improved version of a protocol called iDISCO, developed by Zhuhao Wu, a postdoctoral associate in the Tessier-Lavigne lab—and visualize it using light-sheet microscopy, which takes the snapshot of all active neurons in 3-D.

To determine where an active neuron is located within the brain, Christoph Kirst, a fellow in Rockefeller’s Center for Studies in Physics and Biology, developed software to detect the active neurons and to automatically map the snapshot to a 3-D atlas of the mouse brain, generated by the Allen Brain Institute.

Although each snapshot of brain activity typically includes about one million active neurons, researchers can sift through that mass of data relatively quickly if they compare one snapshot to another snapshot, says Renier. By eliminating the neurons that are active in both images, researchers are left only those specific to each one, enabling them to home in on what is unique to each state.

Observing and testing how the brain works

The primary purpose of the tool, he adds, is to help researchers generate hypotheses about how the brain functions that then can be tested in other experiments. For instance, using their new techniques, the researchers, in collaboration with Catherine Dulac and other scientists at Harvard University, observed that when an adult mouse encounters a pup, a region of its brain known to be active during parenting—called the medial pre-optic nucleus, or MPO—lights up. But they also observed that, after the MPO area becomes activated, there is less activity in the cortical amygdala, an area that processes aversive responses, which they found to be directly connected to the MPO “parenting region.”

“Our hypothesis,” says Renier, “is that parenting neurons put the brake on activity in the fear region, which may suppress aversive responses the mice may have towards pups.” Indeed, mice that are being aggressive to pups tend to show more activity in the cortical amygdala.

To test this idea, the next step is to block the activity of this brain region to see if this reduces aggression in the mice, says Renier.

The technique also has broader implications than simply looking at what areas of the mouse brain are active in different situations, he adds. It could be used to map brain activity in response to any biological change, such as the spread of a drug or disease, or even to explore how the brain makes decisions. “You can use the same strategy to map anything you want in the mouse brain,” says Renier.

Zoos prevent extinction. This is why I support zoos. This is why the world should support zoos.

Meme credit goes to the zookeepers at www.facebook.com/ZoosSavingSpecies @zoossavingspecies

from the Fresh Paleomemes fb group

Physicists Detect Gravitational Waves, Proving Einstein Right

On Thursday (Feb. 11, 2016) at 10:30 a.m. ET, the National Science Foundation will gather scientists from Caltech, MIT and the LIGO Scientific Collaboration in Washington D.C. to update the scientific community on the efforts being made by the Laser Interferometer Gravitational-wave Observatory (LIGO) to detect gravitational waves.

But why is this exciting? And what the heck are “gravitational waves”?

Keep reading

Perfect magnets

Reblog if you ARE a woman in STEM, SUPPORT women in STEM, or ARE STILL BITTER about Rosalind Franklin not getting credit for discovering the structure of DNA and the Nobel prize going to Watson and Crick instead.

New York City Has Genetically Distinct ‘Uptown’ and ‘Downtown’ Rats

A graduate student sequenced rats all over Manhattan, and discovered how the city affects their genetic diversity.

whoa-o-o-o-o-oh-oh

WHOA-O-O-O-O-OH-OH

UPTOWN RAT

Today is Copernicus’s 540th birthday. You may remember Copernicus as the man who said “Hey, what if the Earth went around the sun?” To which the Catholic Church replied “Hey, what if we set you on fire?” 

Chemical Elements as Humans by Brightside

Neuroscientist Discovers Potential New Source for Pain Inhibition

A UT Dallas scientist has found a new neurological mechanism that appears to contribute to a reduction in pain.

According to Dr. Ted Price, associate professor in the School of Behavioral and Brain Sciences, the discovery of neuroligin-2 as a cause exacerbating chronic pain is significant for the research community. Although the findings likely won’t immediately lead to new pain therapies, the findings offer a potential new therapeutic direction to investigate, he said.

Price’s research on the topic has recently been published online in Pain, the journal of the International Association for the Study of Pain.

The study focused on the body’s inhibitory networks — a series of biochemical reactions that decrease certain neurological activity, such as pain. Price said a great deal of previous research in this area has focused on the activity of the neurotransmitter GABA, a chemical released by nerve cells in the brain.

Normally, a GABA neurotransmitter acts to inhibit neuronal activity, such as pain. However, when pain becomes chronic there is strong evidence that a process called GABAergic plasticity can cause GABA to lose its inhibitory activity, sometimes making the pain even worse.

The source of these excitatory actions in neuronal circuits has been broadly attributed to chloride ions, but Price’s research has found another potential cause of GABAergic plasticity: synaptic adhesion molecules called neuroligin-2.

“From a basic science perspective, we’re really excited about it because it demonstrates that the types of GABAergic plasticity that can occur in the setting of chronic pain are more diverse than we’ve appreciated before,” he said.

Price, who heads the undergraduate research program in neuroscience in the school, focuses much of his research on understanding the neuroscience behind pain, particularly chronic pain. He said individuals with chronic pain typically don’t receive the pain-reduction benefits delivered by inhibitory systems. Instead, they often experience increased pain.

“When you hit your hand with a hammer, almost everybody has the same reflex reaction — that is, to rub your finger which, in turn, helps to reduce pain. The reason that works is because it increases GABAergic inhibition in the spinal cord,” Price said. “However, people who have chronic pain — if they do the same thing — find that rubbing it actually makes the pain worse. That’s because the GABAergic system loses its efficacy and, in fact, can become excitatory.”

Price said the research is another step in determining why the GABAergic system stops working correctly in some people and provides a second theory for what drives the system.

“Having two ideas and different models will allow us to determine what the therapeutic opportunities are — creating something that will change that back to normal. The lack of performance in the inhibitory system is very detrimental to those who are in chronic pain,” he said.

Price said the development of chronic pain is, in essence, one’s body “learning” something that is bad.

“It’s changing the way the body functions — it’s learning. That learning, in the case of chronic pain, is aberrant — it’s causing the situation to get worse. If we can figure out what that form of learning was, then we can potentially reverse it. Understanding that the GABAergic system changes during this form of learning potentially offers a new therapeutic avenue,” he said.