Friday, August 7, 2020

Emory students win Amazon's Alexa Prize for AI with strategy of caring about others

Jinho Choi (center), the faculty advisor for the Emory Alexa Prize team, with graduate students James Finch (left), and Sarah Fillwock, the team leader.

A team of Emory University students won Amazon’s 2020 Alexa Prize, a global competition to create the most engaging chatbot to advance the field of artificial intelligence. The team earned $500,000 for taking first place with their chatbot named Emora.

The students designed Emora to provide comfort and warmth to people interacting with Amazon’s voice-activated Alexa-enabled devices, whether they wanted to discuss movies, sports and their pets or their concerns for themselves and their families amid the COVID-19 pandemic.

The Emory team consisted of 14 students led by graduate student Sarah Fillwock and faculty advisor Jinho Choi, assistant professor in the Department of Computer Science. They christened their chatbot Emora because it sounds like a feminine version of “Emory” and is similar to a Hebrew term for a sage skilled in eloquence.

Even as they celebrate their win, the Emory team is looking ahead to how they can apply the concepts they developed to benefit everything from education to people suffering from depression and social isolation.

The annual Alexa Prize, launched in 2016, challenges university students to make breakthroughs in the design of chatbots, or social bots — software apps that simplify interactions between humans and computers by allowing them to talk with one another. Emory used a unique strategy to beat out nine other universities and take the top spot in this year’s competition, the most hotly contested ever. 

“Normally people think of a chatbot as being an intelligent assistant, to answer questions or provide a customer service,” Fillwock says. “We designed a more socially oriented chatbot that could actually show interest in an individual user and provide comfort to people if they wanted it.”

Read the full story.

Related:
Emory team vies for best social bot via Amazon's Alexa Prize

Wednesday, July 29, 2020

Butterfly genomics: Monarchs fly differently, but meet up and mate

An eastern monarch butterfly rests in Saint Marks, Florida, on its way to overwinter in Mexico. (Photo by Venkat Talla)

Each year, millions of monarch butterflies migrate across eastern North America to fly from as far north as the U.S.-Canadian border to overwinter in central Mexico — covering as much as 3,000 miles. Meanwhile, on the other side of the Rocky Mountains, western monarchs generally fly 300 miles down to the Pacific Coast to spend the winter in California. It was long believed that the eastern and western monarchs were genetically distinct populations.

A new study, however, confirms that while the eastern and western butterflies fly differently, they are genetically the same. The journal Molecular Ecology published the findings, led by evolutionary biologists at Emory University.

“It was surprising,” says Jaap de Roode, Emory professor of biology and senior author of the study. His lab is one of a handful in the world that studies monarch butterflies.

“You would expect that organisms with different behaviors and ecologies would show some genetic differences,” de Roode says. “But we found that you cannot distinguish genetically between the western and eastern butterflies.”

Read the whole story here.

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Thursday, July 16, 2020

Beautyberry leaf extract restores drug's power to fight 'superbug'

"We decided to investigate the chemical properties of the American beautyberry because it was an important medicinal plant for Native Americans," says Emory ethnobotanist Cassandra Quave, a senior author of the study. (Photo by Tharanga Samarakoon)

By Carol Clark

Scientists discovered a compound in the leaves of a common shrub, the American beautyberry, that boosts an antibiotic’s activity against antibiotic-resistant staph bacteria. Laboratory experiments showed that the plant compound works in combination with oxacillin to knock down the resistance to the drug of methicillin-resistant Staphylococcus aureus, or MRSA.

The American Chemical Society's ACS Infectious Diseases published the finding, led by scientists at Emory University and the University of Notre Dame.

The American beautyberry, or Callicarpa americana, is native to the southern United States. Prolific in the wild, the shrub is also popular in ornamental landscaping. It’s known for showy clusters of bright purple berries that begin to ripen in the summer and are an important food source for many species of birds.

“We decided to investigate the chemical properties of the American beautyberry because it was an important medicinal plant for Native Americans,” says Cassandra Quave, co-senior author of the study and an assistant professor in Emory University’s Center for the Study of Human Health and Emory School of Medicine’s Department of Dermatology. Quave is also a member of the Emory Antibiotic Resistance Center and a leader in the field of medical ethnobotany, studying how indigenous people incorporate plants in healing practices to uncover promising candidates for new drugs.

Micah Dettweiler, a recent Emory graduate and a staff member of the Quave lab, is first author of the study. Christian Melander, professor of chemistry at Notre Dame, is co-senior author.

The Alabama, Choctaw, Creek, Koasati, Seminole and other Native American tribes relied on the American beautyberry for various medicinal purposes. Leaves and other parts of the plant were boiled for use in sweat baths to treat malarial fevers and rheumatism. The boiled roots were made into treatments for dizziness, stomachaches and urine retention, while bark from the stems and roots were made into concoctions for itchy skin.

Previous research found that extracts from the leaves of the beautyberry deter mosquitoes and ticks. And a prior study by Quave and colleagues found that extracts from the leaves inhibit growth of the bacterium that causes acne. For this study, the researchers focused on testing extracts collected from the leaves for efficacy against MRSA.

“Even a single plant tissue can contain hundreds of unique molecules,” Quave says. “It’s a painstaking process to chemically separate them out, then test and retest until you find one that’s effective.”

The researchers identified a compound from the leaves that slightly inhibited the growth of MRSA. The compound belongs to a group of chemicals known as clerodane diterpenoids, some of which are used by plants to repel predators.

Since the compound only modestly inhibited MRSA, the researchers tried it in combination with beta-lactam antibiotics.

“Beta-lactam antibiotics are some of the safest and least toxic that are currently available in the antibiotic arsenal,” Quave says. “Unfortunately, MRSA has developed resistance to them.” 

Laboratory tests showed that the beautyberry leaf compound synergizes with the beta-lactam antibiotic oxacillin to knock down MRSA’s resistance to the drug.

The next step is to test the combination of the beautyberry leaf extract and oxacillin as a therapy in animal models. If those results prove effective against MRSA infections, the researchers will synthesize the plant compound in the lab and tweak its chemical structure to try to further enhance its efficacy as a combination therapy with oxacillin.

“We need to keep filling the drug-discovery pipeline with innovative solutions, including potential combination therapies, to address the ongoing and growing problem of antibiotic resistance,” Quave says.

Each year in the U.S., at least 2.8 million people get an antibiotic-resistant infection and more than 35,000 people die, according to the Centers for Disease Control and Prevention.

“Even in the midst of the COVID-19, we can’t forget about the issue of antibiotic resistance,” Quave says. She notes that many COVID-19 patients are receiving antibiotics to deal with secondary infections brought on by their weakened conditions, raising concerns about a later surge in antibiotic-resistant infections.

Co-authors of the study include Emory post-doctoral fellow Gina Porras; Emory graduate students Caitlin Risener and Lewis Marquez; Tharanga Samarakoon, collections manager of the Emory Herbarium; and Roberta Melander from the University of Notre Dame.

The work was supported by the National Institute of Allergy and Infectious Disease, the National Institute of General Medical Sciences, the Jones Ecological Research Center and Emory University.

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Civil War plant medicines blast drug-resistant bacteria
The plant hunters

Friday, July 10, 2020

Georgia Coast Atlas: A portal to hidden stories

The rich biodiversity of the Georgia coast includes the roseate spoonbill, shown in a marsh on Sapelo Island. Photo by Anthony Martin.

The Georgia Coast Atlas is a public, online gateway to the dynamic ecosystems and intriguing history of the state’s 100-mile-long coast and barrier islands. Emory University’s Department of Environmental Sciences and the Emory Center for Digital Scholarship launched the ambitious project. It showcases scholarship in science and the humanities, weaving together research, fieldwork and technology to create an unprecedented resource for educators, conservationists, students and the general public.

The interactive trove — made up of stunning flyover video, oral and written stories and annotated maps — keeps expanding through the efforts of Emory students and faculty.

“The main aim of the Atlas is to show how special the Georgia coast is as a place,” says Anthony Martin, a professor of practice in Environmental Sciences. “Secondly, it documents how the region is rapidly changing.”

Read the whole story here.

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Wednesday, July 1, 2020

World Zoonoses Day: 'We have to act now to avoid even bigger catastrophes'

"The primary risks for future spillover of zoonotic diseases are deforestation of tropical environments and large-scale industrial farming of animals, specifically pigs and chickens at high density," says Emory disease ecologist Thomas Gillespie. (Getty Images)

By Carol Clark

On July 6 in 1885, Louis Pasteur successfully administered the first vaccine against rabies, one of the most feared diseases of that time. The bite of an infected animal transmits the rabies virus to humans, leading to an agonizing death without the vaccine.

World Zoonoses Day, held July 6 every year, marks this major breakthrough in the fight against zoonoses — diseases caused by germs that spread between animals and people. And yet, 135 years later, despite tremendous advances in science and medicine, the world is struggling to respond to the novel coronavirus — the latest devastating pathogen to spill over from animals.

“We are at a crisis point,” says Thomas Gillespie, associate professor in Emory University’s Department of Environmental Sciences and Rollins School of Public Health. “We have to act now. We cannot forsake this moment. If we don’t radically change our attitudes toward the natural world, things are going to get much, much worse. Pandemics will become increasingly common. What we are experiencing now will seem mild by comparison.”

Gillespie served as an expert reviewer for a report by the United Nations Environmental Program and partners, “Preventing future zoonotic disease outbreaks: Protecting the environment, animals and people in a post-COVID-19 world,” to be released July 6.

“The primary risks for future spillover of zoonotic diseases are deforestation of tropical environments and large-scale industrial farming of animals, specifically pigs and chickens at high density,” Gillespie says.

A disease ecologist, Gillespie studies how germs jump between wildlife, domesticated animals and people. Through this “One Health” approach, he aims to protect humans, ecosystems and biodiversity.

"We're all feeling the impact of the COVID-19 pandemic," Gillespie says. "That's created a sense of urgency that we haven't seen with past discussions of climate change and land-use change."

While vaccine development is important, pathogens can leap from animals to humans much faster than scientists can develop vaccines and treatments. “We also need complementary approaches that focus on the environment,” Gillespie notes. “It’s far cheaper to invest in the prevention of infectious disease outbreaks than to deal with the consequences of a pandemic.”

Gillespie is contributing his “One Health” expertise to an upcoming United Nations forum on the U.N. Sustainable Development Goals.

“The silos have broken down,” Gillespie says. “There is growing awareness that we don’t need a separate forum on climate change and another one for pandemics. Discussions about the environment and health should be integrated and not considered separately so that we can gain momentum. We really need to be sprinting right now. Climate change and the increase in pandemics are both signals that we have reached a tipping point.”

Genetic sequencing links the novel coronavirus that causes COVID-19 to horseshoe bats in China. The first detected outbreak sprang from a live animal market in Wuhan. Gillespie points out, however, that the coronavirus may have been circulating in remote, rural areas before it was detected in Wuhan, a city of 10 million where population density fueled rapid transmission.

He notes that no one has studied the ecological impacts of China’s Three Gorges Dam project. The world’s largest hydroelectric power station, it was built on the Yangtze River on what was previously a mix of secondary forest and agricultural land.

“Live animal markets are definitely dangerous places when it comes to spillover events,” Gillespie says, “but shutting all of them down won’t solve the bigger issue. The markets are just a small piece of a much bigger problem.”

Deforestation to make way for palm oil plantations, which changed the roosting habits of bats, was linked to a major Nipah virus outbreak in Malaysia. Evidence suggests that similar deforestation in West Africa for palm oil production may have played a role in outbreaks of Lassa fever and Ebola.

A meta-analysis by Gillespie and colleagues quantified how fragmentation of forests by agriculture facilitates the spread of pathogens from wildlife. Optimal rates of spillover occur once 40 percent of the forest cover disappears. “That opens a window where you’re going to see more germs jumping species,” Gillespie says. “And tropical environments are at primary risk for pathogen spillover due to simple mathematics — there is a much richer diversity of species living in the tropics than in other environments.”

In the developed world, and rapidly developing parts of the world, people are eating more animal protein and fried food than is recommended for human health. To meet the demand, corporations are clearing natural habitats for cattle ranches, for soybean fields to feed the cattle, and oil palm plantations for cooking oil.

Many species are endangered by these actions. Habitat loss, poaching and disease are the primary threats to the remaining great apes, Gillespie says. COVOID-19 poses a particularly dire situation for apes in danger of extinction, he adds, including bonobos, chimpanzees, gorillas and orangutans. Due to genetic similarities, they are highly susceptible to human respiratory diseases. Gillespie serves as an adviser on great apes to the International Union for Conservation of Nature (IUCN), and has worked to develop IUCN guidelines during the pandemic to limit human contact with the animals while also protecting them from poachers. Gillespie and colleagues created the “Non-human Primate COVID-19 Information Hub” to serve as a real-time resource on the issue.

Current policies fail to factor in the costs of wholesale extraction of resources and the destruction of natural habitats, Gillespie warns. Nature will persist, he adds, even as biodiversity diminishes.

“Nature will push forward, evolution will happen, without regard to human suffering,” Gillespie says. “Meanwhile, we’re ignoring how dependent we are on nature and how fragile we are in the grand scheme of things.”

Gillespie starts off his undergraduate Conservation Biology class with a quiz. Among the questions: How many people are there on the planet? Has the world reached its human carrying capacity?

The last item on the quiz asks students to list 10 species that occur in Atlanta. “None of the students ever writes Homo Sapiens,” Gillespie says. “Many people don’t think of themselves as part of nature anymore. They have this artificial sense that we’re apart from it.”

The pandemic is shifting perspectives. “We’re all feeling the impact of the COVID-19 pandemic,” Gillespie says. “That’s created a sense of urgency that we haven’t seen with past discussions on climate change and land-use change. People are recognizing the linkages between our financial and agricultural systems, the environment and our health. It’s critical right now to make the message as understandable as possible to as many people as possible.”

Follow Thomas Gillespie on Twitter: @BiodiversHealth.

Related:
Great apes and COVID-19: Experts raise the alarm for endangered species
Spillover: Why germs jump species from animals to people
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