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Scientists enlist AI to decipher what rodents say

Mouse cartoon
University of Washington researchers have developed an AI program that uses machine learning in an effort to decipher the ultrasonic vocalizations made by mice. (UW Medicine Illustration / Alice Gray)

Researchers at the University of Washington School of Medicine have developed a software program that enlists artificial intelligence to decipher the ultrasonic vocalizations made by mice and rats.

The “DeepSqueak” program, described today in a study published by the journal Neuropsychopharmacology, focuses on squeaks and whistles that are well above the range of human hearing.

Software converts the audio signals into visual graphs, or sonograms, and then puts those images through the kinds of machine-vision algorithms that are used for autonomous vehicles.

“DeepSqueak uses biomimetic algorithms that learn to isolate vocalizations by being given labeled examples of vocalizations and noise,” Russell Marx, one of the study’s authors, explained in a news release.

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Allen Institute expands into immunology

Thomas Bumol in lab
Thomas Bumol, far left, executive director of the Allen Institute for Immunology, meets with his team prior to the institute’s launch. When fully staffed, the institute will have 60 to 70 employees. (Allen Institute Photo)

Billionaire philanthropist Paul Allen died two months ago, but before he passed away, he passed along a $125 million commitment to a new research frontier: the Allen Institute for Immunology.

The Allen Institute’s newest division, unveiled today at the institute’s Seattle headquarters, will focus on the human immune system and how it can be tweaked to fight cancer and autoimmune diseases such as rheumatoid arthritis.

“None of this would have been possible without the extraordinary vision and generosity of our late founder, Paul Allen,” Allan Jones, president and CEO of the Allen Institute, said at the unveiling. “Paul challenged us to go after the really hard problems, to unravel the complexities of biology, and make a lasting impact on science that advances health.”

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Human gene-editing experiment put on hold

He Jiankui
Chinese researcher He Jiankui addresses the Second International Summit on Human Genome Editing in Hong Kong. (National Academies via Twitter)

The Chinese researcher behind a controversial experiment to produce gene-edited children took the stage at a Hong Kong conference to explain his work, and acknowledged that the international outcry has brought a halt to the experiment.

“The clinical trial was paused due to the current situation,” He Jiankui, a biomedical researcher at the Southern University of Science and Technology in Shenzhen, said today at the Second International Summit on Human Genome Editing.

The university says He (pronounced “Heh”) has been on unpaid leave since January, and today Chinese news outlets reported that his lab on campus has been shut down and sealed off for investigation.

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Reports of gene-edited babies spawn investigations

CRISPR mechanism
CRISPR-Cas9 technology uses “molecular scissors” to cut and splice DNA. (UC-Berkeley Graphic)

Multiple investigations are being sought in the wake of reports that a Chinese laboratory facilitated the birth of twin girls whose genes had been edited to protect them against the HIV virus that causes AIDS.

The first-of-its-kind experiment, which took advantage of the CRISPR gene-editing technique, came to light in reports published late Sunday by MIT Technology Review and The Associated Press. The researcher in charge of the project, He Jiankui of the Southern University of Science and Technology in Shenzhen, also published a series of videos explaining the gene-editing project.

There has been no outside confirmation of He’s claims, but geneticists and health policymakers say such claims raise grave ethical issues — including the prospect of creating designer babies, enhancing traits and even introducing exotic new traits.

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First gene-edited babies reportedly born in China

He Jiankui
Chinese researcher He Jiankui discusses his lab’s effort to produce babies whose genes have been altered to protect them from future HIV infection. (The He Lab via YouTube)

A Chinese researcher says his lab facilitated the first birth of gene-edited children — twin girls who are said to possess genetic alterations that could protect them from HIV, the virus that causes AIDS.

“Two beautiful little Chinese girls, named Lulu and Nana, came crying into this world as healthy as any other babies a few weeks ago. The girls are home now,” He Jiankui, a researcher at the Southern University of Science and Technology in Shenzhen, said in a YouTube video.

If confirmed, the report is certain to bring the ethical issues surrounding human genetic engineering into sharp focus, and could lead either to rapid developments in the technology or regulatory limits.

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$43 million effort targets brain-blood connection

Salk researchers
Rusty Gage and Carol Marchetto study brain cells at the Salk Institute. Gage will lead one of three teams taking part in a $43 million research initiative created by the American Heart Institute and the Allen Institute’s Paul G. Allen Frontiers Group. (Salk Institute Photo)

Medical researchers know all about the blood-brain barrier, but Seattle’s Allen Institute and the American Heart Association have selected three teams to participate in a $43 million initiative to study the blood-brain connection.

The American Heart Association-Allen Initiative in Brain Health and Cognitive Impairment initiative, launched in May, is aimed at merging research focusing on the brain and on the blood circulation system to develop a new understanding of age-related brain disorders such as Alzheimer’s disease — and find new ways to counter such disorders.

Today the heart association and the Paul G. Allen Frontiers Group, a division of the Allen Institute, announced which researchers will take part in the effort. The three teams are headquartered at the Salk Institute for Biological Studies and the Stanford University School of Medicine in California; and at University Hospitals Cleveland Medical Center in Ohio.

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Paul Allen set aside funds to fight his disease

Matthias Stephan
Matthias Stephan, who studies lymphoma at Seattle’s Fred Hutchinson Cancer Research Center, is among 10 newly named Allen Distinguished Investigators. (Fred Hutch News Service Photo / Robert Hood)

It’s notable that the newest class of Allen Distinguished Investigators, announced today by the Paul G. Allen Frontiers Group, includes researchers who are developing new treatments for lymphoma. Lymphoma is the type of blood cancer that led to the death of Microsoft co-founder Paul Allen, the namesake and funder of the research program.

The decision to focus on that disease — along with nuclear biophysics, neuroimmunology, brain cells and Alzheimer’s disease, and cellular development and aging — was made last year, long before the billionaire philanthropist was diagnosed with a recurrence of his non-Hodgkin’s lymphoma. Nevertheless, the choice is in line with Allen’s willingness to tackle the toughest challenges in bioscience.

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Stem cells help fix damaged hearts in monkeys

Heart stem cells
Heart cells grown in the lab from human embryonic stem cells can restore lost heart function for macaque monkeys. Will they do the same for humans? (UW Medicine via YouTube)

Medical researchers have restored the function of damaged hearts in macaque monkeys, using heart muscle cells derived from human embryonic stem cells. Now they want to do the same for humans.

The technique, detailed today in the journal Nature Biotechnology, could go into human clinical trials as early as 2020, said senior study author Charles Murry, director of the Institute for Stem Cell and Regenerative Medicine at the University of Washington School of Medicine.

“I’ve been in research since 1984, and this worked better than anything I’ve ever seen for the treatment of heart failure,” he told GeekWire.

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How robots and mini-organs can save real humans

Kidney organoids
This is a bird’s-eye view of a microwell plate containing kidney organoids that were produced from human stem cells by a robotic system. The yellow boxed region is shown at higher magnification to reveal individual organoids. Red, green and yellow colors mark distinct segments of 3-D kidney tissue. (UW Medicine Photo / Freedman Lab)

Good news, everybody: Robots can now create human mini-organs from stem cells. What could possibly go wrong?

The method may sound like a nightmare from HBO’s AI thriller “WestWorld,” but researchers from the University of Washington School of Medicine say it really is good news.

“This is a new ‘secret weapon’ in our fight against disease,” Benjamin Freedman, a medical researcher at the UW Institute for Stem Cell and Regenerative Medicine and the Kidney Research Institute, said in a news release.

The robotic system could accelerate the production and use of organ tissues that don’t have to be cut out of an actual human but are nevertheless suitable for research and drug discovery. The system is described in a study published online today in the journal Cell Stem Cell.

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Protein designers get a boost for flu vaccine project

David Baker
David Baker heads the University of Washington’s Institute for Protein Design. (UW Medicine Photo)

The University of Washington’s Institute for Protein Design has won an $11.3 million grant from the Open Philanthropy Project to cook up a public health breakthrough: a universal flu vaccine.

This marks the San Francisco-based nonprofit group’s first gift to a research effort in the Seattle area, and one of its largest gifts to date. Open Phil’s main funders are Facebook co-founder Dustin Moskovitz and philanthropist Cari Tuna, a husband-and-wife team.

The grant will accelerate the institute’s efforts to advance the field of protein design and put it to use in real-world applications.

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