AI detects new class of genetic mutations behind autism

Agencies
May 30, 2019

Using Artificial Intelligence (AI), researchers have discovered new genetic flaws that contribute to autism in people.

Most previous research on the genetic basis of disease has focused on the 20,000 known genes and the surrounding sections of DNA that regulate those genes.

However, even this enormous amount of genetic information makes up only slightly more than one per cent of the 3.2 billion chemical pairs in the human genome.

The other 99 per cent has conventionally been thought of as "dark" or "junk," although recent research has begun to disrupt that idea.

In their new finding, detailed in the journal Nature Genetics, the research team offers a method to make sense of this vast array of genomic data.

The system uses an AI technique called deep learning in which an algorithm performs successive layers of analysis to learn about patterns that would otherwise be impossible to discern.

The algorithm teaches itself how to identify biologically relevant sections of DNA and predicts whether those snippets play a role in any of more than 2,000 protein interactions that are known to affect the regulation of genes.

"This method provides a framework for doing this analysis with any disease," said Olga Troyanskaya, Professor at Princeton University in the US.

The approach could be particularly helpful for neurological disorders, cancer, heart disease and many other conditions that have eluded efforts to identify genetic causes.

In the case of autism, the researchers analysed the genomes of 1,790 families with "simplex" autism spectrum disorder, meaning the condition is apparent in one child but not in other members of the family.

The method sorted among 120,000 mutations to find those that affect the behaviour of genes in people with autism.

Among this sample, fewer than 30 per cent of the people affected by autism spectrum disorder had a previously identified genetic cause.

The newly found mutations are likely to significantly increase that fraction, the researchers said.

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International New York Times
July 7,2020

The coronavirus can stay aloft for hours in tiny droplets in stagnant air, infecting people as they inhale, mounting scientific evidence suggests.

This risk is highest in crowded indoor spaces with poor ventilation, and may help explain superspreading events reported in meatpacking plants, churches and restaurants.

It’s unclear how often the virus is spread via these tiny droplets, or aerosols, compared with larger droplets that are expelled when a sick person coughs or sneezes, or transmitted through contact with contaminated surfaces, said Linsey Marr, an aerosol expert at Virginia Tech.

Follow latest updates on the Covid-19 pandemic here

Aerosols are released even when a person without symptoms exhales, talks or sings, according to Marr and more than 200 other experts, who have outlined the evidence in an open letter to the World Health Organization.

What is clear, they said, is that people should consider minimizing time indoors with people outside their families. Schools, nursing homes and businesses should consider adding powerful new air filters and ultraviolet lights that can kill airborne viruses.

What does it mean for a virus to be airborne?

For a virus to be airborne means that it can be carried through the air in a viable form. For most pathogens, this is a yes-no scenario. HIV, too delicate to survive outside the body, is not airborne. Measles is airborne, and dangerously so: It can survive in the air for up to two hours.

For the coronavirus, the definition has been more complicated. Experts agree that the virus does not travel long distances or remain viable outdoors. But evidence suggests it can traverse the length of a room and, in one set of experimental conditions, remain viable for perhaps three hours.

How are aerosols different from droplets?

Aerosols are droplets, droplets are aerosols — they do not differ except in size. Scientists sometimes refer to droplets fewer than 5 microns in diameter as aerosols. (By comparison, a red blood cell is about 5 microns in diameter; a human hair is about 50 microns wide.)

From the start of the pandemic, the WHO and other public health organizations have focused on the virus’s ability to spread through large droplets that are expelled when a symptomatic person coughs or sneezes.

These droplets are heavy, relatively speaking, and fall quickly to the floor or onto a surface that others might touch. This is why public health agencies have recommended maintaining a distance of at least 6 feet from others, and frequent hand washing.

But some experts have said for months that infected people also are releasing aerosols when they cough and sneeze. More important, they expel aerosols even when they breathe, talk or sing, especially with some exertion.

Scientists know now that people can spread the virus even in the absence of symptoms — without coughing or sneezing — and aerosols might explain that phenomenon.

Because aerosols are smaller, they contain much less virus than droplets do. But because they are lighter, they can linger in the air for hours, especially in the absence of fresh air. In a crowded indoor space, a single infected person can release enough aerosolized virus over time to infect many people, perhaps seeding a superspreader event.

For droplets to be responsible for that kind of spread, a single person would have to be within a few feet of all the other people, or to have contaminated an object that everyone else touched. All that seems unlikely to many experts: “I have to do too many mental gymnastics to explain those other routes of transmission compared to aerosol transmission, which is much simpler,” Marr said.

Can I stop worrying about physical distancing and washing my hands?

Physical distancing is still very important. The closer you are to an infected person, the more aerosols and droplets you may be exposed to. Washing your hands often is still a good idea.

What’s new is that those two things may not be enough. “We should be placing as much emphasis on masks and ventilation as we do with hand washing,” Marr said. “As far as we can tell, this is equally important, if not more important.”

Should I begin wearing a hospital-grade mask indoors? And how long is too long to stay indoors?

Health care workers may all need to wear N95 masks, which filter out most aerosols. At the moment, they are advised to do so only when engaged in certain medical procedures that are thought to produce aerosols.

For the rest of us, cloth face masks will still greatly reduce risk, as long as most people wear them. At home, when you’re with your own family or with roommates you know to be careful, masks are still not necessary. But it is a good idea to wear them in other indoor spaces, experts said.

As for how long is safe, that is frustratingly tough to answer. A lot depends on whether the room is too crowded to allow for a safe distance from others and whether there is fresh air circulating through the room.

What does airborne transmission mean for reopening schools and colleges?

This is a matter of intense debate. Many schools are poorly ventilated and are too poorly funded to invest in new filtration systems. “There is a huge vulnerability to infection transmission via aerosols in schools,” said Don Milton, an aerosol expert at the University of Maryland.

Most children younger than 12 seem to have only mild symptoms, if any, so elementary schools may get by. “So far, we don’t have evidence that elementary schools will be a problem, but the upper grades, I think, would be more likely to be a problem,” Milton said.

College dorms and classrooms are also cause for concern.

Milton said the government should think of long-term solutions for these problems. Having public schools closed “clogs up the whole economy, and it’s a major vulnerability,” he said.

“Until we understand how this is part of our national defense, and fund it appropriately, we’re going to remain extremely vulnerable to these kinds of biological threats.”

What are some things I can do to minimize the risks?

Do as much as you can outdoors. Despite the many photos of people at beaches, even a somewhat crowded beach, especially on a breezy day, is likely to be safer than a pub or an indoor restaurant with recycled air.

But even outdoors, wear a mask if you are likely to be close to others for an extended period.

When indoors, one simple thing people can do is to “open their windows and doors whenever possible,” Marr said. You can also upgrade the filters in your home air-conditioning systems, or adjust the settings to use more outdoor air rather than recirculated air.

Public buildings and businesses may want to invest in air purifiers and ultraviolet lights that can kill the virus. Despite their reputation, elevators may not be a big risk, Milton said, compared with public bathrooms or offices with stagnant air where you may spend a long time.

If none of those things are possible, try to minimize the time you spend in an indoor space, especially without a mask. The longer you spend inside, the greater the dose of virus you might inhale.

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News Network
March 5,2020

Bergen, Mar 5: Divorce of parents may impact the academics of children negatively, suggests a new study.

According to the study, parental divorce is associated with a lower grade point average (GPA) among adolescents, with a stronger association seen in teens with more educated mothers.

The study was published in the journal PLOS ONE.

Children and adolescents with divorced or separated parents are known to do less well in school than adolescents with nondivorced parents and to be less well-adjusted, on average, across a spectrum of physical and mental health outcomes.

In the new study, researchers used data from the youth@hordaland study, a population-based survey of adolescents aged 16-19 conducted in the spring of 2012 in Hordaland County, Norway.

19,439 adolescents were invited to participate and 10,257 agreed; of those, 9,166 are included in the current study.

Overall, adolescents with divorced parents had a 0.3 point lower GPA (standard error 0.022, p<0.01) than their peers.

Controlling for parental education reduced the effect by 0.06 points to 0.240 (SE 0.021, p<0.01). This heterogeneity was predominantly driven by maternal education levels, the researchers found.

After controlling for paternal education and income measures, divorce was associated with a 0.120 point decrease in GPA among adolescents whose mothers had a secondary school education level; a 0.175 point decrease when mothers had a Bachelor's level education; and a 0.209 point decrease when mothers had a Master's or PhD level education (all estimates relative to adolescents with a mother who had a basic level of education, such as ISCED 0-2).

Due to the cross-sectional structure of the study, researchers could not investigate specific changes between pre- and post-divorce family life, and future studies are needed to investigate potential mechanisms (such as reduced parental monitoring or school-involvement) which might drive this finding.

Nonetheless, this study provides new evidence that the negative association between divorce and teens' GPA is especially strong in families with more educated mothers.

"Among Norwegian adolescents, parental divorce was hardly associated with GPA among youth whose parents have low educational qualifications. In contrast, among adolescents with educated or highly educated mothers, divorce was significantly associated with lower GPA," said the authors.

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News Network
July 9,2020

Washington, Jul 9: Ayurvedic practitioners and researchers in India and the US are planning to initiate joint clinical trials for Ayurveda formulations against the novel coronavirus, the Indian envoy here has said.

In a virtual interaction with a group of eminent Indian-American scientists, academicians, and doctors on Wednesday, Indian Ambassador to the US Taranjit Singh Sandhu said the vast network of institutional engagements have brought scientific communities between the two countries together in the fight against Covid-19.

 “Our Institutions have also been collaborating to promote Ayurveda through joint research, teaching and training programs. Ayurvedic practitioners and researchers in both the countries are planning to initiate joint clinical trials of Ayurvedic formulations against Covid-19,” Sandhu said.

“Our scientists have been exchanging knowledge and research resources on this front,” he said.

The Indo-US Science Technology Forum (IUSSTF) has always been instrumental in promoting excellence in science, technology, and innovation through collaborative activities.

To address Covid-19-related challenges, the IUSSTF had given a call to support joint research and start-up engagements. A large number of proposals are being reviewed on fast track mode by the experts on both the sides, he said.

“Indian pharmaceutical companies are global leaders in producing affordable low-cost medicines and vaccines and will play an important role in the fight against this pandemic,” Sandhu said.

According to the ambassador, there are at least three ongoing collaborations between Indian vaccine companies with US-based institutions.

These collaborations would be beneficial not just to India and the US, but also for the billions who would need to be vaccinated against Covid-19 across the world, he noted.

Asserting that innovation will be the key driver in pandemic response and recovery, he said tech-companies and start-ups have already begun to take the lead in this direction.

"Telemedicine and telehealth will evolve as will other digital platforms across sectors," he said.

Noting that there has been a longstanding collaboration between India and the US in the health sector, he said scientists have been working together in several programs to understand important diseases at the basic and clinical level.

Many such programs have been focused on translational research to develop new therapeutics and diagnostics.

There are over 200 ongoing NIH funded projects in India involving 20 institutions from NIH network and several eminent institutions in India engaged in a wide spectrum of research areas to create health care solutions, the senior diplomat said.

The collaboration under Vaccine Action Program (VAP) resulted in the development of ROTAVAC vaccine against rotavirus which causes severe diarrhea in children.

The vaccine was developed by an Indian company (Bharat Biotech) at an affordable cost. It has been commercialised and introduced in the Expanded Program on Immunisation.

Development of many other vaccines such as TB, Influenza, Chikungunya are also in progress under the VAP, he said.

 “As I speak, the VAP meeting is in progress where experts from both countries are deeply engaged in technical discussions to expedite development of Covid-19 vaccine,” Sandhu said in his remarks.

During the interaction, the eminent experts appreciated India's handling of the Covid-19 pandemic and offered their valuable suggestions and best practices in this regard.

They shared their ideas on deepening the knowledge partnership between India and the US.

The experts who took part in the interaction, were drawn from wide-ranging fields including artificial intelligence, quantum information science, biomedical engineering, robotics, mechanical engineering, earth and ocean science, virology, physics, astrophysics, and health sciences.

Prominent among those who attended the virtual interaction were Subhash Kak Regents Professor at Oklahoma State University, Dr Vijay Kuchroo, Samuel L Wasserstrom Professor of Neurology at Harvard Medical School, Dr Ashish M Kamat, Professor of Urology at MD Anderson Cancer Center, Ashutosh Chilkoti, Alan L Kaganov Professor of Biomedical Engineering and Chair of the Department of Biomedical Engineering at Duke University; and Prof Manu Prakash, a professor in Department of Bioengineering at Sandford University, among others.

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