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Scientists unveil ‘wiring diagram’ for a tiny bit of brain

Neuroscientists from Seattle’s Allen Institute and other research institutions have wrapped up a five-year, multimillion-dollar project with the release of a high-resolution 3-D map showing the connections between 200,000 cells in a clump of mouse brain about as big as a grain of sand.

The data collection, which is now publicly available online, was developed as part of the Machine Intelligence From Cortical Networks program, or MICrONS for short. MICrONS was funded in 2016 with $100 million in federal grants to the Allen Institute and its partners from the Intelligence Advanced Research Projects Activity, the U.S. intelligence community’s equivalent of the Pentagon’s DARPA think tank.

MICrONS is meant to clear the way for reverse-engineering the structure of the brain to help computer scientists develop more human-like machine learning systems, but the database is likely to benefit biomedical researchers as well.

“We’re basically treating the brain circuit as a computer, and we asked three questions: What does it do? How is it wired up? What is the program?” R. Clay Reid, senior investigator at the Allen Institute and one of MICrONS’ lead scientists, said today in a news release. “Experiments were done to literally see the neurons’ activity, to watch them compute.”

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Cosmic Science

Muon mystery, MindPong and a lost city revealed

Egyptian archaeologists unearth a 3,000-year-old lost city, magnetic readings from muons could lead to new physics, and Elon Musk’s Neuralink venture has monkeys playing video games with neural impulses. Get the details on the Web:

‘Lost Golden City’ found in Luxor

Egypt’s best-known archaeologist, Zahi Hawass, announced today that the long-lost ruins of a 3,000-year-old city have been found in Luxor. The sprawling settlement dates to the reign of Amenhotep III and his son, Akhenaten. Egypt’s Ministry of Tourism and Antiquities says it continued to be used by Tutankhamun and his successor, King Ay.

The city was at one time called “The Rise of Aten,” reflecting the religious shift brought about by Akhenaten. Today it’s being called the “Lost Golden City.” During the past seven months of excavation, several neighborhoods have been uncovered, but the administrative and residential district hasn’t yet been brought forth from the sands. “The discovery of this lost city is the second most important archaeological discovery since the tomb of Tutankhamun,” said Betsy Bryan, an Egyptologist at Johns Hopkins University.

Previously: ‘Lost cities’ teach lessons for future cities

Muon anomaly sparks deep questions

Anomalous results from a Fermilab experiment have added to the suspicion that scientists have finally found a flaw in one of their most successful theories, the Standard Model of particle physics. The anomalies have to do with the strength of the magnetic field for a weightier cousin of the electron, known as the muon. Data from Fermilab’s Muon g-2 experiment supported previous findings from Brookhaven National Laboratory that the muon’s magnetism is ever-so-slightly stronger than predicted by the Standard Model — just 2.5 parts per billion stronger.

If the results hold up, physicists might have to consider far-out explanations — for example, the existence of scads of particles that haven’t yet been detected, or a totally new take on the foundations of physics. But the findings will require further confirmation. Grand discoveries, like 2012’s detection of the Higgs boson, typically have to be confirmed to a confidence level of 5-sigma. Now the muon findings have hit 4.2-sigma — which doubters would say is still substandard.

Previously: Could the God Equation be our ultimate salvation?

Elon Musk touts mind control

Neuralink, the brain-implant venture funded by tech billionaire Elon Musk, is showing off an AI system that lets a macaque monkey play a game of Pong with its mind alone. Researchers monitored the monkey’s neural impulses as it operated a joystick to play the game, and then correlated the firing patterns of the neurons with the gameplay. Eventually, the brain-monitoring system eliminated the need for the monkey to use the joystick at all.

In a Twitter exchange, Musk said human trials of the mind-reading system would begin, “hopefully, later this year.” He said Neuralink’s first brain-implant product would enable someone with paralysis to use a smartphone with their mind faster than someone using thumbs. “Later versions will be able to shunt signals from Neuralinks in brain to Neuralinks in body motor/sensory neuron clusters, thus enabling, for example, paraplegics to walk again,” Musk tweeted.

Previously: ‘Three Little Pigs’ demonstrate Neuralink’s brain implant

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GeekWire

‘Three Little Pigs’ demonstrate Neuralink’s brain implant

With grudging assistance from a trio of pigs, Neuralink co-founder Elon Musk showed off the startup’s state-of-the-art neuron-reading brain implant and announced that the system has received the Food and Drug Administration’s preliminary blessing as an experimental medical device.

During today’s demonstration at Neuralink’s headquarters in Fremont, Calif., it took a few minutes for wranglers to get the swine into their proper positions for what Musk called his “Three Little Pigs demonstration.”

One of the pigs was in her natural state, and roamed unremarkably around her straw-covered pen. Musk said the second pig had been given a brain implant that was later removed, showing that the operation could be reversed safely.

After some difficulty, a third pig named Gertrude was brought into her pen. As she rooted around in the straw, a sequence of jazzy electronic beeps played through the sound system. Musk said the tones were sounded whenever nerves in the pig’s snout triggered electrical impulses that were picked up by her brain implant.

“The beeps you’re hearing are real-time signals from the Neuralink in Gertrude’s head,” he said.

Eventually, Neuralink’s team plans to place the implants in people, initially to see if those who have become paralyzed due to spinal cord injuries can regain motor functions through thought alone.

Musk said the implant received a Breakthrough Device designation from the FDA last month. That doesn’t yet clear the way for human clinical trials, but it does put Neuralink on the fast track for consultation with the FDA’s experts during preparations for such trials.

Neuralink has received more than $150 million in funding, with roughly two-thirds of that support coming from Musk himself. Today he said the venture had about 100 employees. He expects that number to grow. “Over time, there might be 10,000 or more people at Neuralink,” he said.

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GeekWire

Scientists will map effects of Alzheimer’s disease

A $40.5 million collaborative research center headquartered at Seattle’s Allen Institute aims to create high-resolution maps of brains ravaged by Alzheimer’s disease, to trace new paths to early diagnosis and treatment.

The center will draw upon expertise not only at the institute, but also at UW Medicine and Kaiser Permanente Washington Health Research Institute. Funding for the next five years comes from the National Institute on Aging, part of the National Institutes of Health.

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GeekWire

Study spotlights 3-D mouse brain atlas

The third time’s the charm for the Allen Institute for Brain Science’s 3-D atlas of the mouse brain.

Version 3 of the atlas, known as the Allen Mouse Brain Common Coordinate Framework or CCFv3, is the subject of a research paper published today in the journal Cell. It builds on a partial brain map that focused on the mouse cortex and was released in 2016.

Previous versions of the atlas were rendered with lower-resolution 3-D maps. The latest high-resolution maps are fine enough to pinpoint the locations of individual brain cells — which is crucial for interpreting datasets that contain thousands or millions of pieces of information.

“In the old days, people would define different regions of the brain by eye. As we get more and more data, that manual curation doesn’t scale anymore,” Lydia Ng, senior director of technology at the Seattle-based Allen Institute for Brain Science, explained in a news release. “Just as we have a reference genome sequence, you need a reference anatomy.”

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GeekWire

Allen Institute reorganizes brain science division

Allen Institute sculpture
A sculpture titled “MIRALL” stands sentry at the Allen Institute’s headquarters in Seattle’s South Lake Union district. (GeekWire Photo / Kurt Schlosser)

Seattle’s Allen Institute is heading into a new phase of research into neuroscience — a phase that includes reorganizing its current activities as well as adding new ones.

The Allen Institute for Brain Science, which is the largest division under the institute’s umbrella, was established by Microsoft co-founder Paul Allen in 2003 and has continued on its mission since Allen’s death in 2018. It’s grown to more than 300 scientists and staff members who work in two broad research areas.

One program, known as Cell Types, focuses on mapping out a “periodic table” of brain cells. The Allen Institute’s new 16-year plan calls for the Allen Institute for Brain Science to focus solely on studying brain cell types and neural connectivity.

The second program, known as MindScope, seeks to understand how the brain’s neural circuits produce the sense of vision. That field of study, along with the Allen Brain Observatory, will transition out of the Allen Institute for Brain Science to become a separate program at the Allen Institute.

A new division, due for launch in 2022, will focus on research related to neural computation and dynamics.

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GeekWire

Scientists capture a rare brain cell recording

The von Economo neuron is a large and distinct looking brain cell that has been found in only a few animals, including humans. (Allen Institute Photo)

Researchers at Seattle’s Allen Institute for Brain Science have captured the first-ever recording of electrical spikes from von Economo neurons — a rare kind of cell that’s found deep in the human brain and may be associated with social intelligence.

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GeekWire

Movie-watching mice pose a neurological mystery

Jerome Lecoq
The Allen Institute’s Jerome Lecoq, one of the lead authors of a mouse-brain study, works on one of the 2-photon microscopes that was used to record neural activity in more than 200 mice. (Allen Institute Photo)

For years, neuroscientists have been monitoring the brain activity of mice as they looked at a wide range of images — including the film-noir classic “Touch of Evil” — in hopes of discovering deep insights about the workings of the visual system. Now they’ve come upon a plot twist worthy of director Orson Welles himself.

The latest results, reported today in the journal Nature Neuroscience by researchers at Seattle’s Allen Institute for Brain Science and at the University of Washington, suggest that more than 90% of the neurons in the visual cortex don’t work the way scientists thought.

“We thought that there are simple principles according to which these neurons process visual information, and those principles are all in the textbooks,” Christof Koch, the brain institute’s chief scientist and president, said in a news release. ”But now that we can survey tens of thousands of cells at once, we get a more subtle — and much more complicated picture.”

Not that there’s anything wrong with that.

“To me, that’s the business. In some sense, that’s the exciting thing,” Michael Buice, an associate investigator at the Allen Institute and one of the study’s lead authors, told GeekWire. “We’re in a more interesting place than we thought.”

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GeekWire

Allen Institute maps out ‘org chart’ for brain

Allen Institute researchers
Researchers Hongkui Zeng, Julie Harris and Hannah Choi check out a brain connectivity image at the Allen Institute for Brain Science. (Allen Institute Photo)

Researchers at Seattle’s Allen Institute say a new and improved map of the mouse brain reveals not only how different regions are connected, but how those connections are ordered in a hierarchical way.

They add that the mapping techniques behind their study, which was published today by the journal Nature, could shed light on how diseases like Alzheimer’s, Parkinson’s or schizophrenia tangle up connections in the human brain.

The map produced by the study is technically known as a medium-scale “connectome.” It’s been variously compared to a wiring diagram, organizational chart or subway map for the brain. An initial version of the map was published five years ago — and at the time, it was hailed as a landmark for brain science.

Like that earlier version of the Allen Mouse Brain Connectivity Atlas, the newly published map was created by injecting glow-in-the-dark viruses into the brains of mice, and then tracking how brain impulses lit up different types of brain cells.

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GeekWire

Brain wave recording goes into overdrive

Neuropixels researchers
Severine Durand and Tamina Ramirez, researchers at the Allen Institute for Brain Science, review data collected from mice using the Neuropixels brain-probing system. (Allen Institute Photo)

Seattle’s Allen Institute for Brain Science is sharing 70 trillion bytes’ worth of data documenting electrical activity in mouse brains, collected by a new type of silicon probe that can monitor hundreds of neurons simultaneously.

The Neuropixels system, developed by an international collaboration that includes the Allen Institute, could be adapted to record brain activity in human patients as well, said Josh Siegle, a senior scientist at the institute who works with the probes.

“The application I’m most interested in is decoding the communication patterns of the brain, and really understanding how information is transmitted between regions,” Siegle told GeekWire. “What are the transmission protocols?”

Neuropixels has already produced insights into the brain’s inner workings, Siegle said. This week, the institute is due to publish findings on the BioRxiv preprint server that confirm hierarchical patterns of connectivity in the brain.

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