Wednesday, May 16, 2018

Chemistry students sing their studies, hoping for a good reaction



By Carol Clark

On the last day of the spring semester, during Bill Wuest’s “Principles of Reactivity” course, loud noises rattle the Atwood Chemistry Center’s Atomic Classroom. It isn’t explosions — it’s pop music mixed with bursts of laughter.

“This bond’s alright!” a group of Emory first-year students belts out on a YouTube video playing on screens before the class. Backed by the music of “Oh, What a Night,” they dance before a periodic table, write on a white board and mix chemicals in a lab while singing lyrics they wrote themselves: “Now I use a base to synthesize. It can readily be hydrolyzed. Mechanisms, what a sight!”

In just under four minutes, the students sing key lessons they learned over the semester about carbonyl mechanisms.

“It’s basically describing how reactions go,” explains Rebecca Henderson, one of the performers. “A reaction is not normally just putting two chemicals together and — BOOM — a product comes out. There’s a lot of different steps involved and we wanted to describe some of them, and why a reaction goes down one pathway and not another.”

Henderson created the video with classmates Carson Brooks, Lauren Cohen, Justine Griego and Alex Kim. They all played themselves in the video — except for Kim, who used powder to create a white patch in his hair and portray the professor.

“I love it when they mock me, they get extra points for that,” says Wuest, who has a natural, white streak of hair running through the center of his close-cropped dark hair.

Wuest, who joined Emory in the fall of 2017 as a Georgia Research Alliance Distinguished Investigator, directs an organic chemistry lab along with teaching undergraduates. He started having students make music parody videos while he was at Temple University.

“A lot of people think that chemistry is dry and boring but there’s a lot of creativity involved in it and that’s often overlooked in classrooms,” Wuest says.

The videos fit in well with Emory’s curriculum. Last fall, Emory became one of the first major research universities to completely overhaul how chemistry is taught, from introductory courses to capstone seminars. The new program, called Chemistry Unbound, moves away from teaching a narrow slice of chemistry every year to jumping into a big-picture understanding of chemistry’s central role across the sciences.



The video assignment helps with those big-picture concepts, Wuest says. Students form groups of up to six to make a two-to-four-minute educational video about some aspect of what they’ve learned in class. The video can either take the form of a musical parody of a well-known song or — for the less adventurous — a more straightforward lesson in the style of the Khan Academy website.

While Wuest is not the first to have chemistry students make videos, he is one of the few to actually measure their effect. With the help of his wife, Liesl Wuest, an educational analyst who also works at Emory, he has compared learning outcomes — in the form of exam performance before and after the videos — and found a strong correlation to improved scores.

His Temple students received extra credit, but not a grade, for making videos. Out of 130 students, 25 percent of them opted to do the videos. The average score for the class on an exam before the video project and an exam following the video project found that those who made videos had an average of 50 percent more improvement in their scores compared to those who opted out.

“Making the videos forces students to think about the material in new ways,” Wuest says. “It also makes the material more memorable to help it stick with them long term.”

Wuest refined the criteria for the video project and turned it into a graded requirement for his Emory classes. The top videos, based on accuracy and execution, will be housed on the Canvas learning management system so that future students can use them for inspiration and study aids.



“I was really impressed with the level of the videos this semester,” Wuest says. “They showcase the quality and the diversity of the students at Emory.”

Wuest plans to continue measuring the effect of the videos on learning. Many of the students, meanwhile, have given the video assignment a big thumb’s up.

“Not only do you learn the material, but it’s a fun experience,” says Dennis Jang, a first-year student.

Jang helped make a video called “I’ll Make a Chemist Out of You,” set to the song “I’ll Make a Man Out of You” from the Disney movie “Mulan.” The other first year students in his group included Muhammad Dhanani, Alex Fukunaga, Gaby Garcia and Jessie Kwong.

“The hardest part of this project was balancing the content and the comedy,” Jang says. “We presented some broad aspects of what we learned in class and some more specific aspects. And then we added humor to keep the audience watching.”

The formula worked. An informal vote following the screening of the videos in class, based on laughter and applause, showed “I’ll Make a Chemist Out of You” was the clear audience favorite.

“As we were watching all of the videos together we were laughing and just really enjoying being together,” Henderson says. “It was the final wrap-up of a great semester. Bill really knows how to make a true community out of a classroom.”

You can watch more of the videos by clicking here. 


Related:
Chemistry synthesizes radical overhaul of undergraduate curriculum

Monday, May 14, 2018

Study reveals how the brain decides to make an effort

"Understanding how the brain works normally when deciding to expend effort provides a way to pinpoint what's going on in disorders where motivation is reduced," says Emory psychologist Michael Treadway, whose lab conducted the study.

By Carol Clark

From deciding to quit hitting the snooze button and get out of bed in the morning to opting to switch off the TV and prepare for sleep at night, the mind weighs the costs versus benefits of each choice we make. A new study reveals the mechanics of how the brain makes such effortful decisions, calculating whether it is worth expending effort in exchange for potential rewards.

The Proceedings of the National Academy of Sciences (PNAS) published the findings by psychologists at Emory University.

“We showed that the brain’s ventromedial prefrontal cortex, which was not previously thought to play a key role in effort-based choices, actually appears to be strongly involved in the formation of expectations underlying those choices,” says Emory psychologist Michael Treadway, senior author of the paper.

Treadway’s lab focuses on understanding the molecular and circuit-level mechanisms of psychiatric symptoms related to mood, anxiety and decision-making.

“Understanding how the brain works normally when deciding to expend effort provides a way to pinpoint what’s going on in disorders where motivation is reduced, such as depression and schizophrenia,” he says.

Previous research had observed three brain regions in decision-making; the dorsal anterior cingulate cortex (dACC), the anterior insula (aI) and the ventromedial prefrontal cortex (vmPFC). Studies had pointed to the vmPFC as central to the computation of subjective value during probability decision-making. But prior evidence also suggested that when it comes to decisions about effort expenditure, those subjective value estimates were not computed by the vmPFC but by the other two brain regions.

A limitation to previous studies on effort-based choices is that they simultaneously presented the costs and benefits of a choice to experimental subjects.

“In the real world, however, we usually have to make decisions based on incomplete information,” says Amanda Arulpragasam, first author of the PNAS paper and a psychology PhD candidate in Treadway’s lab.

Arulpragasam designed a study that allowed the researchers to model distinct neural computations for effort and reward.

Subjects underwent functional magnetic resonance imaging (fMRI) while performing an effort-based decision-making task where the effort costs and rewards of a choice were presented separately over time.

The subjects could choose to make no effort and receive $1, or make some level of physical effort in exchange for monetary rewards of varying magnitude, up to $5.73. The physical effort involved rapid button pressing at varying percentages of each participant’s maximum button pressing rate. Participants were required to press the button using their non-dominant pinkie finger, making the task challenging enough to be unpleasant, although not painful.

In the effort-first trials, participants were shown a vertical bar representing the percentage of their maximum button pressing rate that would be required to do the task. They were then shown the size of the reward for performing the task. The reward-first trials presented the information in the opposite order.

After receiving both sets of information, participants were prompted to choose the no-effort option or the effort option.

The experimental design allowed the researchers to tease apart the effects of recent choices on the formation of value expectations of future decisions.

The results revealed a clear role for the vmPFC in encoding an expected reward before all information had been revealed. The data also suggested that the dACC and aI are involved in encoding the difference between what participants were expecting and what they actually got, rather than effort-cost encoding.

“Some have argued that decisions about effort have a different neural circuitry than decisions about probability and risk,” Treadway says. “We’ve showed that all three brain regions come into play, just in a different way than was previously known.”

Co-authors of the PNAS paper include Jessica Cooper, a post-doctoral fellow in the Treadway lab and Makiah Nuutinen, a research interviewer in the lab.

Related:
Twitter reveals how future-thinking Americans are and how that affects their decisions

Friday, May 11, 2018

Dengue 'hot spots' provide map to chikungunya and Zika outbreaks

A street scene in Merida, Mexico, a city of about one million in the Yucatan Peninsula where the study was based. Merida had a little over 40,000 reported dengue cases during 2008 to 2015 and nearly half of them were clustered in 27 percent of the city.

By Carol Clark

Identifying dengue fever “hot spots” can provide a predictive map for outbreaks of chikungunya and Zika — two other viral diseases that, along with dengue, are spread by the Aedes aegypti mosquito.

PLOS Neglected Tropical Diseases published the findings, the first confirmation of the spatial-temporal overlap for outbreaks of the three diseases, led by Emory University.

“We had hypothesized that we would see some overlap between these diseases, but we were surprised at the strength of that overlap,” says Gonzalo Vazquez-Prokopec, a disease ecologist in Emory’s Department of Environmental Sciences and lead author of the study. “The results open a window for public health officials to do targeted, proactive interventions for emerging Aedes-borne diseases. We’ve provided them with a statistical framework in the form of a map to guide their actions.”

The analysis drew from eight years of data from Merida, Mexico, on symptomatic cases. A city of one million located in the Yucatan Peninsula, Merida had about 40,000 reported dengue cases during 2008 to 2015, and nearly half of them were clustered in 27 percent of the city. The neighborhoods comprising these dengue hot spots contained 75 percent of the first chikungunya cases reported during the outbreak of that disease in 2015 and 100 percent of the first Zika cases reported during the Zika outbreak in 2016.

“Currently, most mosquito control efforts are not done until cases of mosquito-borne diseases are detected,” Vazquez-Prokopec says. “But by the time you detect a virus in an area, it has likely already begun to spread beyond that area.”

Mosquito control efforts generally involve outdoor spraying that covers broad swaths of a city, further reducing efficacy, he adds. Outdoor spraying is particularly ineffective for the Aedes aegypti mosquito. “This mosquito is highly adapted to urban environments,” Vazquez-Prokopec says. “It likes to live inside houses and to feed on people.”

A targeted approach would make it more feasible to implement time-consuming and costly interventions such as indoor residual spraying.

A technician sprays the ceiling and walls of a home in Merida. Indoor residual spraying is effective, but is not practical for large areas of a city, due to the time and expense involved. Photo by Nsa Dada.

“The statistical framework that we have developed allows public health officials to harness the power of big data to do more effective and efficient mosquito control by focusing on high-risk areas — even before an epidemic begins,” Vazquez-Prokopec says.

The study used disease case reports at the household level and then scaled them up to neighborhoods to protect individuals’ privacy in the final map. The hot spots for reported dengue cases were confirmed by data from laboratory blood tests of a cohort of 5,000 people. The analysis showed that people living in a dengue hot spot had twice the rate of infection of those outside of the hot spots.

The research team included scientists from the Autonomous University of Yucatan and health officials from the state and federal level in Mexico. Other members of the team were scientists from seven other universities and health research institutions, including the U.S. Centers for Disease Control and Prevention.

The researchers are now working with the Pan American Health Organization (PAHO) to develop a manual and training materials, based on open-access software, for mapping risks of Aedes-borne diseases to guide proactive interventions throughout urban areas of the developing world.

More than one third of the world’s population lives in areas at high risk for infection with the dengue virus, a leading cause of illness and death in the tropics and subtropics, according to the Centers for Disease Control and Prevention. Dengue fever is sometimes called “break bone fever” due to the excruciating pain that is among its symptoms.

The chikungunya virus emerged in the Americas in 2013, sweeping through many countries where dengue is endemic. Common symptoms of chikungunya infection may include headache, muscle pain, joint swelling and rash.

Zika virus followed in 2016, causing little alarm at first due to its relatively mild symptoms. It soon became apparent, however, that the Zika virus could cause birth defects in the babies of pregnant women who were infected.

“You tend to see transmission go down right after large numbers of a population are infected with these Aedes-borne viruses, leading to herd immunity,” Vazquez-Prokopec says. “But these viruses do not disappear. They keep circulating and can reappear later.”

Meanwhile, new Aedes-borne viruses are likely to emerge, he adds, as rapid urbanization and a warming climate help the mosquito thrive.

Vaccines are not yet available for chikungunya or Zika, and efforts to roll out a vaccine for dengue are complicated by the fact that the virus comes in different serotypes.

“Although effective vaccines would be the ultimate line of defense against these diseases, we cannot give up on mosquito control,” Vazquez-Prokopec says.

Related:
Contact tracing, with indoor spraying, can curb dengue outbreak
Zeroing in on 'super spreaders' and other hidden patterns of epidemics
Human mobility data may help curb epidemics

Monday, May 7, 2018

Bonding over bones, stones and beads


By Carol Clark

"I've really been into bones since I was little. I don't know why," says Emory University senior Alexandra Davis, an anthropology major. "Not fresh bodies, though. No soft tissues or blood. Just bones."

In fact, Davis loves bones so much that she was willing to spend seven weeks in Malawi with Emory anthropologist Jessica Thompson and four more of her students last summer, excavating bones and other artifacts in ancient hunter-gatherer sites, assisted by a team of locals.

Thompson will return to Malawi in July with another team of students to continue excavation of two sites that were started last summer. "We want to get into the deeper layers, because in both cases we did not come close to reaching the bottom of the sites," Thompson says. "Then, we want to find out how old they are."

Read more about the project.

Related:
Malawi yields oldest-known DNA from Africa
Have skull drill, will travel

Friday, May 4, 2018

'Dog-nition' research set for Science Friday



Come. Sit. Stay. And listen to Science Friday's interview at 3:30 pm E.T. today with Emory neuroscientist Gregory Berns, who is exploring the inner workings of the canine mind. Two of the questions the program plans to explore: Do dogs have a concept of time? And how do our furry companions make sense of the world?

You can tweet questions you'd like answered to @scifri. The radio program is based at WNYC Studios, distributed to public radio stations across the United States, and is also accessible online.

Related:
A dog's dilemma: Do canines prefer praise or food?
Recreating the brain of the extinct Tasmanian tiger

Tuesday, May 1, 2018

Emory chemistry receives $7.5 million to lead fuel cell research

"A deeper understanding of electrochemical processes is important in the quest for more efficient, renewable forms of energy," says Emory physical chemist Tim Lian, shown in his lab. Photo by Stephen Nowland, Emory Photo/Video.

By Carol Clark

The U.S. Department of Defense awarded $7.5 million to Tianquan (Tim) Lian, professor of physical chemistry at Emory University, to lead an investigation of electrochemical processes underlying fuel-cell technology. The award comes through the DoD’s highly competitive Multidisciplinary University Research Initiative, or MURI. The program funds teams of investigators from more than one discipline to accelerate the research process.

“A deeper understanding of electrochemical processes is important in the quest for more efficient, renewable forms of energy,” Lian says. His lab develops sum-frequency generation spectroscopy to selectively probe reactions on the surface of an electrode. The technique can provide insights into the fundamental steps involved in energy generation, conversion and storage technologies — ranging from solar cells, to fuel cells and batteries.

Fuel cell electric vehicles use a fuel cell instead of a battery — or in combination with a battery — to generate electricity for power. While they have lower emissions and higher fuel-efficiency than internal-combustion engines, fuel cell vehicles are currently limited to lighter fuels, such as hydrogen.

The Air Force Office of Scientific Research accepted the MURI proposal from Lian, principal investigator of the project, and his colleagues from five other universities, including Yale, Cornell, Massachusetts Institute of Technology, the University of Pennsylvania and the University of Southern California. Together, the researchers encompass the disciplines of advanced spectroscopy, electrochemical mass spectroscopy and electrochemical theory to model, test and interpret reactions.

“Bringing together experimentalists and theorists with different backgrounds gives us the expertise to tackle more challenging problems,” Lian says.

The concept of fuel cells was first demonstrated in 1801, while the invention of the first working fuel cell occurred in 1842, when William Grove showed that an electrochemical reaction between hydrogen and oxygen could produce an electric current. NASA later developed fuel cell applications for the space program.

“Electrochemistry goes way back in science, and has many important applications, but our understanding of it remains largely empirical,” Lian says. “The Air Force wants to make a concerted effort to advance the field by boosting our understanding of electrochemical processes at the molecular and atomic level.”

The research team will develop software for electrochemical platforms as an experimental tool to gather data at the microscopic scale of processes such as the current-voltage curve generated in an electrochemical cell. The team will also develop theoretical tools to interpret the data. They will apply these experimental and theoretical tools to study fuel-cell technologies that use methanol and ethanol directly as fuels. These fuels are more energy dense than hydrogen, giving them the potential to greatly improve the range of fuel-cell vehicles, although their use in fuel-cell technology currently suffers from poorly understood side reactions that occur on electrode surfaces.

The software and theoretical tools that Lian’s team develops will be open source, allowing researchers in other labs to use it to simulate their own electrochemical experiments as well as interpret their data.

Providing these tools to the broader electrochemical industry will support widespread efforts for innovation and discovery, Lian says. “We hope to make a lasting impact in the field, opening doors to do things with electrochemistry that are currently out of reach.”

Over the past 30 years, DoD’s MURI program has brought significant new capabilities to U.S. military forces and opened up new lines of research. Notable examples include foundations in the fabrication of nanoscale and microscale structures by the processes of self-assembled materials and microcontact printing, the integration of vision algorithms with sensors to create low-power, low-latency, compact adaptive vision systems, and advances in fully optical data control and switching.

Related:
Chemists find new way to do light-driven reactions

Monday, April 30, 2018

Physics of a glacial 'slushy' reveal granular forces on a massive scale

The ridge in the right center of the photo shows where icebergs have broken off from Jakobshavn Glacier and tumbled into the water to form a slushy ice mélange — the world's largest granular material. Photo by Ryan Cassotto.

By Carol Clark

The laws for how granular materials flow apply even at the giant, geophysical scale of icebergs piling up in the ocean at the outlet of a glacier, scientists have shown.

The Proceedings of the National Academy of Sciences (PNAS) published the findings, describing the dynamics of the clog of icebergs — known as an ice mélange — in front of Greenland’s Jakobshavn Glacier. The fast-moving glacier is considered a bellwether for the effects of climate change.

“We’ve connected microscopic theories for the mechanics of granular flowing with the world’s largest granular material — a glacial ice mélange,” says Justin Burton, a physicist at Emory University and lead author of the paper. “Our results could help researchers who are trying to understand the future evolution of the Greenland and Antarctica ice sheets. We’ve showed that an ice mélange could potentially have a large and measurable effect on the production of large icebergs by a glacier.”

The National Science Foundation funded the research, which brought together physicists who study the fundamental mechanics of granular materials in laboratories and glaciologists who spend their summers exploring polar ice sheets.

“Glaciologists generally deal with slow, steady deformation of glacial ice, which behaves like thick molasses — a viscous material creeping towards the sea,” says co-author Jason Amundson, a glaciologist at the University of Alaska Southeast, Juneau. “Ice mélange, on the other hand, is fundamentally a granular material — essentially a giant slushy — that is governed by different physics. We wanted to understand the behavior of ice mélange and its effects on glaciers.”



For thousands of years, the massive glaciers of Earth’s polar regions have remained relatively stable, the ice locked into mountainous shapes that ebbed in warmer months but gained back their bulk in winter. In recent decades, however, warmer temperatures have started rapidly thawing these frozen giants. It’s becoming more common for sheets of ice — some one kilometer tall — to shift, crack and tumble into the sea, splitting from their mother glaciers in an explosive process known as calving.

Jakobshavn Glacier is advancing as fast as 50 meters per day until it reaches the ocean edge, a point known as the glacier terminus. About 35 billion tons of icebergs calve off of Jakobshavn Glacier each year, spilling out into Greenland’s Ilulissat fjord, a rocky channel that is about five kilometers wide. The calving process creates a tumbling mix of icebergs which are slowly pushed through the fjord by the motion of the glacier. The ice mélange can extend hundreds of meters deep into the water but on the surface it resembles a lumpy field of snow which inhibits, but cannot stop, the motion of the glacier.

“An ice mélange is kind of like purgatory for icebergs, because they’ve broken off into the water but they haven’t yet made it out to open ocean,” Burton says.

While scientists have long studied how ice forms, breaks and flows within a glacier, no one had quantified the granular flow of an ice mélange. It was an irresistible challenge to Burton. His lab creates experimental models of glacial processes to try to quantify their physical forces. It also uses microscopic particles as a model to understand the fundamental mechanics of granular, amorphous materials, and the boundary between a free-flowing state and a rigid, jammed-up one.

“Granular material is everywhere, from the powders that make up pharmaceuticals to the sand, dirt and rocks that shape our Earth,” Burton says. And yet, he adds, the properties of these amorphous materials are not as well understood as those of liquids or crystals.

In addition to Amundson, Burton’s co-authors on the PNAS paper include glaciologist Ryan Cassotto — formerly with the University of New Hampshire and now with the University of Colorado Boulder — and physicists Chin-Chang Kuo and Michael Dennin, from the University of California, Irvine.

The researchers characterized both the flow and mechanical stress of the Jacobshavn ice mélange using field measurements, satellite data, lab experiments and numerical modeling. The results quantitatively describe the flow of the ice mélange as it jams and unjams during its journey through the fjord.

The paper also showed how the ice mélange can act as a “granular ice shelf” in its jammed state, buttressing even the largest icebergs calved into the ocean.

“We’ve shown that glaciologists modeling the behavior of ice shelves with ice mélanges should factor in the forces of those mélanges,” Burton says. “We’ve provided them with the quantitative tools to do so.”

Related:
The physics of a glacial earthquake
How lifeless particles can become 'life-like' by switching behaviors

Thursday, April 26, 2018

DNA analysis adds twists to ancient story of a Native American group

"I want to help Native American tribes to reclaim knowledge of their very ancient evolutionary histories — histories that have been largely wiped away because of colonialism," says Emory geneticist John Lindo. Photo by Kay Hinton, Emory Photo/Video.

By Carol Clark

The ancient genomes of the Tsimshian indigenous people left tell-tale markers on the trail of their past, revealing that at least 6,000 years ago their population size was on a slow but steady decline.

The American Journal of Human Genetics published the findings, which draw from the first population-level nuclear DNA analysis of a Native American group from ancient to modern times.

“The finding contradicts a popular notion,” says John Lindo, a geneticist in Emory University’s Department of Anthropology and first author on the paper. “There is this idea that after Native Americans came in through the Bering Strait that they were all expanding in population size until Europeans showed up. At least for this one population, we’ve shown that was not the case.”

A boon in next-generation DNA sequencing technology has opened the possibility to explore the evolutionary history of different populations. “Ancient nuclear DNA analysis is a relatively new field,” Lindo says. “Not until recently have we had methods to sequence an entire genome quickly and inexpensively.”

Nuclear DNA provides information on an individual’s lineages going back hundreds of thousands of years. Lindo is one of the few geneticists looking at ancient whole genomes of Native Americans. He is especially interested in understanding how the genomes of their different populations evolved over time.

“Their evolutionary histories are radically different,” Lindo says. “Over thousands of years, various Native American populations have adapted to living in every ecology throughout North and South America, from the Arctic to the Amazon. That’s about as an extreme as you can get for differences in environments.”

The Tsimshian people historically lived in longhouses in coastal British Columbia and southern Alaska where they harvested the abundant sea life. Lindo and his colleagues sequenced the genomes of 25 living Tsimshian people and 25 ancient individuals who lived in the same region between 6,000 and 500 years ago, and confirmed that they were a continuous population through time.

Members of the Tsimshian Native American tribe hold a tea party near Fort Simpson, British Columbia, in 1889. Image from the Library and Archives Canada.

In a previous paper, drawing from the same data set, they found a dramatic shift between the two time periods in a class of genes associated with the immune system, suggesting a strong evolutionary pressure on the population to adapt to pathogens. A demographic model indicated a crash in the Tsimshian population size of about 57 percent during the early-to-mid 19th century. That finding fitted with historical accounts for how smallpox, introduced by European colonization, devastated the Tsimshian population during two epidemics within that time-frame.

The current paper looked at broader genetic variations between the ancient and modern DNA. An analysis showed both how the variation declined slowly in the ancient population before the collapse, but has since recovered.

“After a population collapse, only a subset of the genetic diversity remains,” Lindo says. “We find a more nuanced story, that despite the population collapse, the genetic diversity of modern Tsimshian people varies significantly.”

Intermarriage with other Native American groups and non-native populations increased the genetic diversity of some of the modern-day Tsimshian people so that it is near the levels prior to their population collapse, the analysis showed.

“A population with relatively high genetic diversity has a greater potential to fight off pathogens and avoid recessive traits,” Lindo says. “It exemplifies the benefits of gene flow between populations, especially following catastrophic events such as the small pox epidemics that the Tsimshian endured.”

Senior authors on the paper are Michael DeGiorgio from Pennsylvania State University and Ripan Malhi from the University of Illinois. The paper’s coauthors include Tsimshian representatives Joycelynn Mitchell and Barbara Petzelt from the Metlakatla Treaty Office in Prince Rupert, Canada.

Malhi, a leader in forging trusting relationships between genetic researchers and indigenous people, was a mentor to Lindo, who earned his PhD at the University of Illinois at Champaign-Urbana.

Lindo is continuing that tradition of building trust and working closely with indigenous populations. His ancient DNA research at Emory integrates the approaches of ancient whole genomes, statistical modeling and functional methods.

One of his projects is focused on genetic fluctuations to help understand ancient adaptions in various Native American populations. He is currently working with 10 different tribes from throughout North America.

“Community engagement is essential when working with indigenous communities,” says Lindo, explaining that he first meets personally with a tribal community to talk about how a genetic study might add to their knowledge of their own history.

“I listen to their stories and how they are working to keep their cultures alive,” he says. “One elder from a southwestern tribe told me that his grandfather was taken away in the early 1900s because he was a shaman and Christianity was swelling through the area. Each tribe’s stories are different but they are all powerful, and sometimes difficult, stories to hear.”

Most ancient DNA analyses have come out of Europe, where more ancient DNA labs are based and cold temperatures have helped preserve specimens.

Lindo wants to bring some of the same insights that those of European ancestry are gaining about their past to Native Americans.

“I’d like to disentangle this idea that Native Americans are part of a singular race,” he says. “I want to help Native American tribes to reclaim knowledge of their very ancient evolutionary histories — histories that have been largely wiped away because of colonialism.”

Related:
Malawi yields oldest-known DNA from Africa

Thursday, April 5, 2018

Science Art Wonder: Students team with labs to bring research to life

Art by Emory senior Pamela Romero, Science.Art.Wonder. founder and president, portrays how aphids can develop wings in response to environmental changes. The DNA painted along the edges of the canvases is the same, except that different genes are switched on. Photo by Ann Watson, Emory Photo/Video

By Carol Clark

A small crowd gathers in Emory’s White Hall before the menacing sight: Large rubber worms arrayed on triangular red spikes. The jagged spikes, from a few inches to more than a foot tall, lean crazily in all directions. Some of the worms — suspended on near-invisible fishing line — appear to rise off the spikes, escaping to a circular mirror hanging from above.

“This is how evolution works!” says Ethan Mock, a sophomore majoring in ancient history, who created the sculpture, titled "The Crucible." He looks dapper in a leather vest and tweed cap and speaks with theatrical flair to the crowd. “The spikes represent the trials and tribulations of the worms’ struggles. Most are trapped in the spikes but a few climb out, not realizing that they are simply climbing into a new trial, a new test.”

The onlookers include a mix of college students, children and their parents, brought together by campus events during the recent Atlanta Science Festival. Joining the regular attractions of Physics Live! and Chemistry Carnival is the debut of an art exhibit by a new, student-run program called Science.Art.Wonder., or S.A.W. Just over 100 artists — most of them untrained college students — teamed with scientists from Emory and Georgia Tech to translate their research into art.

Ethan Mock and his art, "The Crucible"
Mock worked with the lab of Levi Morran, an assistant professor in Emory’s Department of Biology who studies co-evolutionary dynamics by experimenting with a host (a microscopic worm called C. elegans) and a parasite (a bright red species of bacteria called Serratia marcescens that is lethal to C. elegans upon consumption).

“This is so cool!” says Pareena Sharma, a first-year biochemistry major at Emory, as she snaps a photo of the sculpture. “It’s so relatable to me. I’ve been doing this same experiment since the first of the semester in Biology 142.”

Two young boys draw near the spikes. “Look up into the mirror,” Mock encourages them. “Now tell me what you see.”

“The same thing,” one of the boys replies.

“That’s right!” Mock says. “The process of evolution keeps repeating, going in a loop.”

Morran, arriving with his eight-year-old daughter, Maggie, is impressed. “You could see the light come on in those boys’ eyes,” he says. “They understood what Ethan is trying to convey. And it’s not an easy concept to grasp — the continual evolutionary struggle.”

Both artists and researchers engage with visitors as they peruse more than 140 works of art, set up on the Quad, in White Hall, the Math and Science Center and the Atwood Chemistry Center during the festival.

“This artwork gives you a snapshot of how much research is being done in Atlanta. I’m taken aback by how cutting edge and varied it is,” says Pamela Romero, president of S.A.W. The program is the brainchild of Romero, a senior majoring in neuroscience and behavioral biology and minoring in computer science.

Young visitors to the Emory campus peruse science-inspired art on the Quad. Photo by Ann Watson, Emory Photo/Video

The Emory S.A.W. contributions span labs across the University and beyond. The artists picked their mediums, from acrylic to watercolor and everything in between.

Emily Isaac, a first-year Emory student majoring in environmental sciences and theater, stands on the Quad next to a large watercolor she painted. “Art can help scientists make a point without using any scientific jargon,” she says.

She teamed with Robert Wallace from Georgia Tech’s Agricultural Technology Research Program. One of Wallace’s projects gave plots of farmland to women in India who had been victims of an acid attack. Isaac did a portrait of a woman with a scarred face. The woman’s head is partially wrapped in strips of bandages that Isaac painted to look like rows of newly sprouting plants. “I wanted to show hope, and how connecting with the environment can help people,” Isaac says.

This year’s 36 Emory S.A.W. artists are mainly undergraduates — many of them science majors — but they also include a few graduate students, faculty and staff members. Georgia Tech makes up the bulk of other contributing artists and researchers in this year’s S.A.W., although 10 independent artists also got involved, along with Georgia State University undergraduates and the Atlanta campus of SCAD.

“S.A.W. is collaborative, not only across disciplines and institutions, but also across students, faculty, staff and members of the Atlanta community,” Romero says. “We even have one international artist, from Puerto Rico.”

A painting by Georgia Tech student Bianca Guerrero portrays a virtual reality game used to measure players' perception of time as well as eye movement. The art is based on research by Georgia Tech psychologist Malia Crane. Photo by Ann Watson, Emory Photo/Video.

As long as she can remember, everyone thought Romero would become an artist, or maybe an architect. She began taking art classes at the age of three in her home town of Tegucigalpa, Honduras. She continued making and studying art, developing a surrealist style.

In ninth grade, however, a psychology course sparked a fascination for neurobiology. Romero took online classes and started reading up on subjects like optogenetics and deep-brain stimulation.

By the time she was accepted to Emory, she had decided to forge a career as a scientist. “A lot of people told me that if I chose neuroscience I would have to forsake art, because I would be a bad scientist if I tried to do both,” she recalls. “I was determined to prove them wrong.”

Romero sought out kindred spirits like Nicole Gerardo, associate professor of biology, who also grew up with twin passions for science and art. Gerardo once had students create artwork using microbes in her lab under the direction of Nancy Lowe — a former lab technician at Emory who went on to create a retreat center in North Carolina called AS.IF: Art and Science in the Field.

Gerardo later paired students with labs to create ceramic representations of research under the direction of Diane Kempler, who formerly taught visual arts at Emory.

“Art provides a way to reach people who may be intimidated by science,” Gerardo says. “And working with an artist lets scientists see their own work in a different way. That could lead to new scientific approaches.”

When Romero first joined forces with Gerardo it was simply to produce art for her lab, which focuses on evolutionary ecology. “We were test subjects for S.A.W.,” Romero says.

Emory senior Maureen Ascona, a neuroscience and behavioral biology major, discusses her art with visitors to the Quad. Ascona teamed with Helen Mayberg, from the Emory School of Medicine, who uses deep-brain stimulation to help patients with treatment-resistant depression. Photo by Ann Watson, Emory Photo/Video.

One of the pieces Romero created consists of triangular canvases that can be shifted into different positions. The acrylic painting depicts how aphids develop wings in the presence of predators, like ladybugs, or if food becomes scarce. “When Dr. Gerardo explains her work to people, she can move the canvases to show how the aphids change in response to their environment,” Romero says.

Romero wanted to give other students the chance to enter research labs and experiment with art.

“Pamela is an amazing woman, a force of nature,” says Gerardo, who is the faculty mentor for S.A.W. “What she has done with the support of her fellow students is incredible. I had envisioned maybe 20 pairings of scientists and artists. I’m still surprised by how big it became.”

Connections from across the University helped S.A.W. grow. Wei Wei Chen and John Wang, student leaders of Emory Arts Underground, provided the platform for Romero to launch S.A.W. and encouraged her to form a charter, bylaws and an executive team. That team includes Emory undergraduates Alex Nazzari (vice-president), Aila Jiang, Veronica Paltaraskaya, Anne Pizzini, Deborah Seong and John Wang, along with Georgia Tech students Olivia Cox, Siyan Li and Iris Liu.

The students’ efforts paid off with S.A.W.’s smash debut at the Atlanta Science Festival.

“One of my favorite parts was guiding artists through the process of disentangling the science, reassuring them that they could do it,” Romero says. “Many of them felt overwhelmed after first talking to a scientist. Some of them were first-year students who hadn’t even had introductory biology or chemistry.”

A piece by Alice Yang, a first-year Emory student majoring in neuroscience and behavioral biology who teamed with researchers of human genetics in the Emory 3q29 Project. Photo courtesy of S.A.W.

Exploring a lab through an art project allows students to develop a relationship with a researcher and often find a mentor, Romero says.

Alice Yang, a first-year Emory student majoring in neuroscience and behavioral biology, teamed with Jennifer Mulle, assistant professor at Rollins School of Public Health. Mulle is co-principal investigator of the Emory 3q29 Project, which seeks to understand a genetic deletion associated with an increased risk for schizophrenia.

“I’m so grateful for the experience,” Yang says of spending time with the 3q29 Project team. “I learned what it’s like to actually do science. And I caught their passion. People are just now realizing how genetics can be involved in mental illness. It’s a very new field.”

To create her art pieces, Yang ordered special scratch-off paper from her native China. “This paper’s easy to work with and it’s great for showing patterns and textures,” she says. She explains how she carefully cut slices from the black top layer of the paper to reveal the glowing, rainbow colors beneath. Her pictures portray the nanomapping of fluorescent-labeled alleles from the 3q29 lab while also paying tribute to Salvador Dali’s surrealism.

Even those who are not aspiring scientists can catch the science-art bug. Independent artist Aaron Artrip teamed with scientists Matthew Jackson and Dan Cook at Georgia Tech to demonstrate interaction with sound. A group of children buzzes around Artrip’s exhibit in White Hall. A piece of paper sprinkled with powdered black ink is taped to a wooden speaker, which is plugged into an electronic synthesizer. As Artrip taps a keyboard, the powder moves across the page, creating patterns.

“I’m making drawings with vibrations. Forcing sound through the ink causes it to move,” he explains.

“Would you like to try?” he asks a young girl watching him.

She doesn’t have to be asked twice.

A painting by Georgia Tech student Kate Bernart, "Connecting the Cycle," portrays Austin Ladshaw's research at Georgia Tech's School of Environmental Engineering on the nuclear fuel cycle and ways to prevent excessive accumulations of radioactive waste. Photo by Ann Watson, Emory Photo/Video

Ultimately, S.A.W. hopes to find ways to integrate its art-science model into grades K-12. “We would like to have artists and researchers go into K-12 classrooms to talk about the art and the research together,” Romero says.

She presented S.A.W. at the recent Georgia Tech STEAM Leadership Conference, which brought together educators and policymakers to explore new ways to teach science, technology, engineering, art and math, or STEAM. S.A.W. is now working to put together an anthology of its art into a booklet, to include descriptions of the science. The booklet will be aimed at high school students “to give them a glimpse of some of the possible fields available to them in college,” Romero says.

S.A.W. is also creating a web site where the art will be accessible in digital form, including videos of some of the interactive art pieces, along with other resources for K-12 teachers.

After graduating this spring, Romero plans to take a gap year, then go on to graduate school with the aim of becoming a professor with a research lab. “S.A.W. has an incredible executive team and I’m making sure that the program continues after I leave Emory,” she says. “I would also like to stay involved with it in some way.”

As she prepares for graduation, Romero is working on an art narrative piece funded by the Emory Center for Creativity and Arts. The work will combine acrylic painting and sculpture to represent the element Vanadium, discovered by Mexican mineralogist Andrews Manuel del Rio in 1801. A series of circular canvases will each represent an atom in Vanadium. Each canvas will also represent a country or group of countries in Latin America, on which Romero will depict the research of a scientist from that area.

“My main goal with this piece is to celebrate and encourage more Latin American science,” Romero says. She is calling the piece “Elementally Latino,” to describe how Latinos are an elemental, or basic, part of science and how they also embody an elemental force. “Latinos are such a passionate people that I can only adequately describe them as a force of nature,” she says.

Related:

The art and science of symbiosis
Frankenstein and robots rise up for Atlanta Science Festival

Wednesday, March 28, 2018

The Peeps experiments: A seasonal celebration of science

Why experiment on Peeps? "Because they're there!" says Emory chemist Douglas Mulford.

It’s that time of year again when Peepus Marshmalleous, commonly known as Peeps, pop up everywhere — even in an Emory University chemistry lab.

Emory's groundbreaking Peeps research began in 1999 when researchers Gary Falcon and James Zimming investigated the effects of smoking and alcohol on Peeps health and performed the medical miracle of separating quintuplet Peep siblings, conjoined at birth. You can read more here: peepresearch

Douglas Mulford, senior lecturer and director of undergraduate studies for the Department of Chemistry, continues the tradition by treating students every spring to a Peeps show. “Basically, it’s 45-minutes of every chemical thing that you can do to a Peeps,” Mulford explains. “It’s amazing what they can survive.” 

Watch a brief video summarizing the show, below. And check out Emory’s new Instagram account, Science Seen, for more quick, behind-the-scenes looks at science at Emory.

Physicists show why it's hard to clog a drain with soft particles

Emory sophomore Mia Morrell conducted the experiments with hydrogel balls. "You can learn a lot from them because they provide a simple model for physics, kind of like fruit flies do for biology," she says.

By Carol Clark

For decades, scientists have studied how groups of solid objects — everything from falling grains of sand to a rushing crowd of panicked people — can get stuck as they try to pass through a small opening. The classic result is known as “faster is slower.” When the objects flow out, if an arch of the objects forms across the opening, then a large pressure can stabilize the arch and cause a clog.

Now scientists have shown that when the objects are squishy instead of solid, the reverse is true. The journal Physical Review E published the findings by physicists at Emory University, demonstrating that when soft particles feel a larger pressure, they squish together and the arch breaks, and so clogging is less likely.

“We’ve quantified the clogging dynamics of soft objects for the first time and identified the parameters that seem to explain why it’s completely opposite physics to that of hard objects,” says Emory physics professor Eric Weeks, whose lab conducted the research. “One surprising result is that, while friction is often suspected to be important for arch formation, our particles are frictionless and yet still form arches.”

Questions about how clogs form have implications for everything from improving highway design and the flow of traffic to avoiding jam-ups of people fleeing a burning building.

The dynamics of soft objects that the Weeks lab investigated could give insights into biological processes such as the flow of cells, bacteria and other “squishy” particles through blood vessels.

“It’s new physics and yet it’s so simple,” Weeks says. “We used tools such as a basic physics formula from 1882 and some cheap hydrogel balls that we ordered from Amazon.”

"Hydrogels have interesting properties and that makes them fun to work with," says Mia Morrell, a member of the Weeks lab.

Weeks, who specializes in the study of soft condensed materials, became intrigued by the growing number of studies on how solid objects clog. It sounds counterintuitive — after a rush of solid particles through an opening forms an arch, greater pressure behind them solidifies that arch. But the process appears to work similarly to a keystone arch in architecture: The pressure from the weight of stones above presses the stones in the arch below more firmly together.

Weeks and his students decided to explore the process of soft-particle clogging. Graduate students Xia Hong and Meghan Kohne worked on experiments involving tiny oil droplets and then computer simulations.

Motivated by those preliminary results, Emory senior Haoran Wang (who graduated in 2017) conducted early experiments with the marble-sized, water-filled hydrogel balls. They are sometimes called plant balls since they are commonly used to hold up stems in flower vases. Wang built a two-dimensional, Plexiglas hopper that allowed gravity to pull the hydrogel balls down through two triangular wedges that could be adjusted in width to change the size of the opening between them.

Mia Morrell, a sophomore, continued the work when she joined the Weeks lab last year.

“I loved doing the hydrogel experiments because it’s really hands-on — not just sitting at a desk,” Morrell says, adding that the project also required her to learn how to become handy with a drill and a laser cutter.

The hydrogel balls start out as deflated polymer husks. They are left in a tray of water until they swell up into squishy, slippery, plastic spheres that feel almost like living tissue.

“Hydrogels have interesting properties and that makes them fun to work with,” Morrell says. “You can learn a lot from them because they provide a simple model for physics, kind of like fruit flies do for biology.”

Morrell loaded the hydrogels into the two-dimensional hopper. She tilted the hopper to vary the effects of gravity and checked to see if the particles would clog as they flowed through it. This process required her to reload the hopper more than 400 times to investigate different conditions.

The Hertzian force law, an 1882 formula by Heinrich Hertz, allowed the researchers to measure the displacement and compression force of individual hydrogel spheres and compare the hydrogel results with the oil droplet experiments and the computer simulations. The comparison showed that these different systems all have the same physical behavior, apparently universal to soft particles.

“We quantified the dynamics of soft particles in a two-dimensional environment under the influence of gravity and what happens when you present them with an obstacle,” Morrell says. “What we learned from this single system may have many broader applications.”

Related:
Physicists crack another piece of the glass puzzle
Crystal-liquid interface made visible for the first time

Sunday, March 25, 2018

Frankenstein at 200 sparks wonder and debate

Emory's Stuart A. Rose Manuscript, Archives and Rare Book Library holds an 1881 original edition of "Frankenstein" and an 1831 edition, above, with a depiction of the "creature" and a prologue by Mary Shelley.

It’s the 200th anniversary year of “Frankenstein, Or the Modern Prometheus,” an enduring novel at the nexus of major questions of our time. Emory faculty explore many of them in a newly published anthology, “Frankenstein: How a Monster Became an Icon, the Science and Enduring Allure of Mary Shelley’s Creation.”

“When you see a contemporary film about androids, like ‘Blade Runner 2049,’ you’re seeing the ‘Frankenstein’ story in a 21st-century guise,” says Sidney Perkowitz, Emory emeritus physicist and co-editor of the new anthology. “The androids are sleek and modern instead of the shambling, stitched-together creature in ‘Frankenstein,’ but they have the same questions swirling around them. Even as we’re on the verge of artificially generating life, we’re no closer to knowing whether we should.”

You can read more here.

Related:
Chemists boldly go in search of 'little green molecules'
Prometheus: Seeding wonder and science

Thursday, March 15, 2018

Biologists unravel another mystery of what makes DNA go 'loopy'

Interior of a cell showing the nucleus with the chromatin fiber (yellow) arranged in the three-dimensional space by loops formed by the CTCF protein (shown in pink). DNA is represented by thin blue lines on the chromatin. Graphic by Victor Corces. 

By Carol Clark

Scientists discovered another key to how DNA forms loops and wraps inside the cell nucleus — a precise method of “packing” that may affect gene expression.

The journal Science published the research by biologists at Emory University, showing that a process known as hemimethylation plays a role in looping DNA in a specific way. The researchers also demonstrated that hemimethylation is maintained deliberately — not through random mistakes as previously thought — and is passed down through human cell generations.

“In order for a protein called CTCF to make loops in the DNA, we discovered that it needs to have hemimethylated DNA close by,” says Emory biologist Victor Corces, whose lab did the research. “Nobody had previously seen that hemimethylated DNA has a function.”

Chenhuan Xu, a post-doctoral fellow in the Corces lab, developed experimental methods for DNA methylome mapping to conduct the research for the Science paper.

Chromatin is made up of CTCF and other proteins, along with DNA and RNA. One role of chromatin is to fold and package DNA into more compact shapes. Growing evidence suggests that this folding process is not just important to fit DNA into a cell nucleus — it also plays a role in whether genes are expressed normally or malfunction.

The Corces lab specializes in epigenetics: The study of heritable changes in gene function — including chromatin folding — that do not involve changes in the DNA sequence.

DNA methylation, for example, can modify the activity of DNA by adding methyl groups to both strands of the double helix at the site of particular base pairs. The process can be reversed through demethylation.

As cells divide they make a copy of their DNA. In order to do so, they have to untangle the two strands of DNA and split them apart. Each parental strand then replicates a daughter strand.

“When cells divide, it’s important that they keep the methylation the same for both strands,” Corces says, noting that altered patterns of methylation are associated with cancer and other diseases.

Hemimethylation involves the addition of a methyl group to one strand of the DNA helix but not the other. Some researchers observing hemimethylation have hypothesized that they were catching it right after cell division, before the cell had time to fully replicate to form a daughter strand. Another theory was that hemimethylation was the result of random mistakes in the methylation process.

The methods developed by Xu in the Corces lab allowed the researchers to observe hemimethylation on DNA in human cells in real-time before, during and after cell division. They also mapped it as the cells continued to replicate.

“If the parental DNA was hemimethylated, the daughter DNA was also hemimethylated at the same place in the genome,” Corces says. “The process is not random and it’s maintained from one cell generation to the next over weeks.”

The researchers found that hemimethlyation only occurs near the binding sites of CTCF — the main protein involved in organizing DNA into loops.

“If we got rid of the hemimethlyation, CTCF did not make loops,” Corces says. “Somehow, hemimethylation is allowing CTCF to make loops.”

And when CTCF makes a loop, it does so by binding ahead, going forward in the DNA sequence, they observed.

“Research suggests that some disorders are associated with CTCF binding — either mutations in the protein itself or with the DNA sequence where the protein binds,” Corces says. “It comes back to the story of how important these loops are to the three-dimensional organization of chromatin, and how that organization affects the gene expression.”

Related:
Small steps lead to big career
Teen scientists bloom in lab
Epigenetics zeroes in on nature vs. nurture

Monday, March 12, 2018

Biophysicists discover how small populations of bacteria survive treatment

"We showed that by tuning the growth and death rate of bacterial cells, you can clear small populations of even antibiotic-resistant bacteria using low antibiotic concentrations," says biophysicist Minsu Kim. His lab conducted experiments with E. coli bacteria (above).

By Carol Clark

Small populations of pathogenic bacteria may be harder to kill off than larger populations because they respond differently to antibiotics, a new study by Emory University finds.

The journal eLife published the research, showing that a population of bacteria containing 100 cells or less responds to antibiotics randomly — not homogeneously like a larger population.

“We’ve shown that there may be nothing special about bacterial cells that aren’t killed by drug therapy — they survive by random chance,” says senior author Minsu Kim, an assistant professor in the Department of Physics and a member of Emory’s Antibiotic Resistance Center.

“This randomness is a double-edged sword,” Kim adds. “On the surface, it makes it more difficult to predict a treatment outcome. But we found a way to manipulate this inherent randomness in a way that clears a small population of bacteria with 100 percent probability. By tuning the growth and death rate of bacterial cells, you can clear small populations of even antibiotic-resistant bacteria using low antibiotic concentrations.”

Jessica Coates, as a graduate student at Emory, and Bo Ryoung Park, a research associate in the Kim lab, are co-first authors of the paper. Additional authors are graduate student Emrah Simsek and post-doctoral fellows Dai Le and Waqas Chaudry.

The researchers developed a treatment model using a cocktail of two different classes of antibiotic drugs. They first demonstrated the effectiveness of the model in laboratory experiments on a small population of E. coli bacteria without antibiotic-drug resistance. In later experiments, they found that the model also worked on a small population of clinically-isolated antibiotic-resistant E. coli.

“We hope that our model can help in the development of more sophisticated antibiotic drug protocols — making them more effective at lower doses for some infections,” Kim says. “It’s important because if you treat a bacterial infection and fail to kill it entirely, that can contribute to antibiotic resistance.”

Antibiotic resistance is projected to lead to 300 million premature deaths annually and a global healthcare burden of $100 trillion by 2050, according to the 2014 Review on Antimicrobial Resistance. The epidemic is partly driven by the inability to reliably eradicate infections of antibiotic-susceptible bacteria.

For decades, it was thought that simply reducing the population size of the bacteria to a few hundred cells would be sufficient because the immune system of an infected person can clear out the remaining bacteria.

“More recently, it became clear that small populations of bacteria really matter in the course of an infection,” Kim says. “The infectious dose — the number of bacterial cells needed to initiate an infection — turned out to be a few or tens of cells for some species of bacteria and, for others, as low as one cell.”

It was not well understood, however, why treatment of bacteria with antibiotics sometimes worked and sometimes failed. Contributing factors may include variations in the immune responses of infected people and possible mutations of bacterial cells to become more virulent.

Kim suspected that something more fundamental was a factor. Research has shown unexpected treatment failure for antibiotic-susceptible infections even in a simple organism like the C. celegans worm, a common model for the study of bacterial virulence.

By focusing on small bacteria populations, the Emory team discovered how the dynamics were different from large ones. Antibiotics induce the concentrations of bacterial cells to fluctuate. When the growth rate topped the death rate by random chance, clearance of the bacteria failed.

The researchers used this knowledge to develop a low-dose cocktail drug therapy of two different kinds of antibiotics. They combined a bactericide (which kills bacteria) and a bacteriostat (which slows the growth of bacteria) to manipulate the random fluctuation in the number of cells and boost the probability of the cell death rate topping the growth rate.

Not all antibiotics fit the model and more research is needed to refine the method for applications in a clinical setting.

 “We showed that the successful treatment of a bacterial infection with antibiotics is even more complicated than we thought,” Kim says. “We hope this knowledge leads to new strategies to fight against infections caused by antibiotic-resistant bacteria.”

Related:
CDC funds Emory project to automate analysis of mixed strains of antibiotic-resistant bacteria
Brazilian peppertree packs power to knock out antibiotic-resistant bacteria

Mathematician works to improve artificial intelligence

Emory mathematician Lars Ruthotto is pioneering a new field that applies the logic of differential equations to refine the chaos of deep learning. (Emory Photo/Video)

By April Hunt
Emory Report

 If you’ve ever told Siri to call your friend Bob and she answers with, “Calling cops,” you’ve seen the instability of artificial intelligence (AI) in action.

Those mistakes are the limitation of the AI technology known as deep learning. They arise from the design of the deep neural network, as well as the network’s “training,” which applies mathematical optimization methods to massive amounts of data rather than hand-crafting rules to accomplish a specific task.

Emory mathematician Lars Ruthotto has dedicated his research to modeling and solving such 21st century problems with the innovative use of differential equations that date back to the late 1600s. The National Science Foundation has rewarded his efforts with a CAREER Award, its most prestigious honor for junior faculty.

Put simply, Ruthotto is pioneering a new field — combining applied math, engineering and computer science — that applies the logic of differential equations to refine the chaos of deep learning.

“Focusing on this research question can impact specific areas of deep learning now as well as emerging technology,” says Ruthotto, an assistant professor in mathematics and computer science. “It’s uncharted territory, and my students and I will be at the forefront exploring it.”

The award is recognition of the new knowledge Ruthotto and his students are creating in the emerging field and also a hint of what’s to come, says Vaidy Sunderam, chair of Emory's Department of Math and Computer Science.

 “This grant establishes Emory as a research and education pioneer in innovative methods for robust deep learning, a key technology in the coming AI decade,” Sunderam says.

Read more in Emory Report.

Related:
Emory team vies for best social bot via Amazon's Alexa Prize 
CDC funds Emory project to automate analysis of mixed strains of antibiotic-resistant bacteria

Wednesday, February 28, 2018

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

Faculty advisor Eugene Agichtein (far right) with the Mathematics and Computer Science Alexa Prize team (clockwise from top left): Ali Ahmadvand, Mingyang Sun, Jason Choi, Sergey Volokhin, Zihao Wang and Harshita Sahijwani. (Photo by Ann Borden, Emory Photo/Video)

By Carol Clark

“Alexa, when will you learn to chat with me like people I might meet at a party or a pub?”

“I couldn’t say.”

Alexa may be a popular talking bot, but she has not yet acquired the “social” skills to turn that query into a conversation.

A team of Emory students from the Department of Mathematics and Computer Science are trying to help her develop those skills sooner, rather than later. They are among eight university teams selected from around the world to create a social bot and compete for this year’s Alexa Prize. Amazon is sponsoring the $3.5 million university challenge in order to advance the conversational capabilities of bots such as Alexa — Amazon’s “personal assistant” software that responds to voice commands through a growing list of devices.

“Conversational AI is one of the most difficult problems in the field of artificial intelligence,” says Zihao Wang, a graduate student and the leader of the Emory team. “Human language is so rich. We use combinations of words to form different expressions and idioms. It’s difficult to represent them in computer language.”

Wang’s teammates include Ali Ahmadvand, Jason Choi, Harshita Sahijwani and Sergey Volokhin — all graduate students — and senior Mingyang Sun. The team’s faculty advisor is Eugene Agichtein, an associate professor of Mathematics and Computer Science.

Each of the university teams received a $250,000 research grant, Alexa-enabled devices, and other tools, data and support from Amazon. A $500,000 prize will be given next November to the team that creates the best social bot, while second- and third-place teams will receive $100,000 and $50,000.

Additionally, a $1 million research grant will be awarded to the winning team’s university if their social bot achieves the grand challenge — conversing coherently and engagingly with humans for 20 minutes with a user rating of 4.0 or higher.

“The contest is a wonderful way for students to get hands-on experience developing a social bot using state-of-the-art technology,” Agichtein says. “Their work will be tested out by millions of real-world consumers through Amazon. And Amazon provides support and training so they can get experience with data and computing environments that are usually only accessible to those within major corporations.”

Agichtein’s IR Lab is developing new techniques for intelligent information access, including Web search and automated question answering. Conversational search capabilities are a key emerging trend, he says.

He notes that his children love asking Alexa trivia questions or about music and sports. “It’s natural for them to talk to devices instead of having to type in a question because they’re growing up amid this technology,” Agichtein says. “And as time goes on, it’s clear that voice-based communication devices are going to keep improving and become more ubiquitous.”

Wang is a native of China who earned his master’s in civil engineering at Carnegie Mellon University. A robotics project sparked his interest in information retrieval powered by machine learning, leading him to Emory and Agichtein’s lab to work on his PhD.

“Machine learning is widely applied in the real world,” Wang says. “It’s changing peoples’ lives in every way.”

Autonomous vehicles, drones, online shopping mechanisms and robots designed to detect and remove dangerous objects are just a few examples of how machine learning is being applied.

 “The idea is to train an algorithm to ‘learn’ patterns embedded in data,” Wang explains.

While a machine learning algorithm to simulate natural, human conversation is a difficult challenge, Wang says it’s one well worth pursuing.

Possible healthcare uses for conversational social bots include providing companionship to isolated seniors, serving as therapeutic agents for people suffering from depression and conducting patient interviews to streamline admissions to a medical clinic.

Wang also led an Emory team in the inaugural Alexa contest last year, but the team did not make it to the finals. “We learned a lot from the experience,” he says.

The working title for the Emory social bot this year is IRIS, which stands for information retrieval and informative suggestion agent. “Our focus will be on the accuracy and usefulness of information that we provide to users,” Wang says. “And we will add conversational functionality to our design to make the responses as natural and engaging as possible.”

IRIS will incorporate “ideas from each member of the team,” he adds. “That’s one of the most fun things about the contest, is working as a team.”

Starting in May, the public can access competing bots to provide feedback and rate them by saying, “Alexa, lets chat,” to an Echo device, or to the Amazon mobile app. The bots will be randomly assigned and remain anonymous, so that people providing feedback cannot identify the university that generated them.

By August, Amazon will have used this feedback to winnow the contestants down to three finalists that will continue to get more consumer feedback until the winner is announced in November.

Other university teams competing this year include: Heriot-Watt University in Edinburgh, Scotland, Czech Technical University in Prague, Brigham Young University, UC Davis, KTH Royal Institute of Technology in Stockholm, Sweden, UC Santa Cruz, and Carnegie Mellon.

Related:
Raising IQ of web searches
Mouse trail leads to online shoppers

Monday, February 26, 2018

Ecosystems hanging by a thread

Emory disease ecologist Thomas Gillespie served on an international committee that developed best practice guidelines for health monitoring and disease control in great ape populations, part of a growing public education effort.

By Tony Rehagen
Emory Magazine

Thomas Gillespie’s parents and teachers always wanted him to go into medicine.

“Growing up in Rockford, Illinois, if you were smart and interested in biology, you were supposed to be a doctor,” he says.

Gillespie, meanwhile, was always more interested in primates. In seventh grade, he phoned animal psychologist Penny Patterson, famous for teaching the gorilla Koko how to use sign language, and interviewed the scientist about Koko’s diet while punching out notes on a typewriter. He was premed at the University of Illinois, but spent his internship at the Brookfield Zoo in Chicago, working in the “Tropic World” primate exhibit. His favorite undergrad course was biological anthropology, the study of biological and behavioral aspects of humans and nonhuman primates, looking at our closest relatives to better understand ourselves.

Gillespie eventually took a year off before graduate school to work with primate communities in the Peruvian Amazon. The apes finally won out — Gillespie would choose a doctorate in zoology over medical school.

But it wasn’t long before the two fields of study collided. While monitoring the group behavior of colobine monkeys in Africa, Gillespie observed that some of the animals were eating bark from the African cherry tree — not a typical food source for them. When he dug deeper, Gillespie learned that human doctors in the region used that same bark to treat parasites in their patients. The monkeys, he realized, were self-medicating.

“That discovery in these monkeys brought me back toward the health science side of biology,” says Gillespie.

Gillespie’s return to a medical approach to zoology came not a moment too soon—for the sake of the primates and maybe even all of humankind. As an associate professor in Emory’s Department of Environmental Sciences specializing in the disease ecology of primates, Gillespie and his team of researchers have helped uncover a crisis among our nearest taxonomic neighbors. According to an article coauthored by Gillespie and thirty other experts and published in the journal Science Advances, 75 percent of the world’s five-hundred-plus primate species are declining in population, and a whopping 60 percent face extinction, largely due to human encroachment.

Read more in Emory Magazine.

Related:
Experts warn of impending extinction of many of the world's primates
Chimpanzee studies highlight disease risks to all endangered wildlife

Thursday, February 22, 2018

Frankenstein and robots rise up for Atlanta Science Festival

Hair-raising, spine-tingling fun: A young visitor to the Emory campus during last year's Atlanta Science Festival experiences the thrill of static electricity.

By Carol Clark

From the lumbering, 200-year-old Frankenstein to sleek, modern-day robots, this year’s Atlanta Science Festival — set for March 9 to 24 — highlights creations that spark wonder and fun, giving glimpses of the past and the future.

The five-year-old festival expanded to more than two weeks, encompassing 120 events sponsored by 90 different partners at 70 venues across metro Atlanta, including many on the Emory campus. The festival culminates with a day-long “Exploration Expo” on Saturday, March 24, set in Piedmont Park.

“Rise Up, Robots!” kicks off the festival on the evening of Friday, March 9 at the Ferst Center, when three robots and their inventors will take the stage.

“We thought about how we could possibly top last year’s featured speaker, astronaut Mark Kelly — someone so inspirational to children and adults all over the planet,” says Meisa Salaita, co-director of the Atlanta Science Festival. “We finally realized that no human could match him, and we would have to resort to artificial intelligence.”

Heather Knight, professor of robotics at Oregon State University, will demonstrate the interactive quips of “Data,” the world’s first robotic comedian. Georgia Tech’s Gil Weinberg will jam with “Shimon,” a marimba playing robotic musician. And Stewart Coulter, from DEKA Research and Development, will show how a bionic arm named LUKE (Life Under Kinetic Evolution) changed an amputee’s life.

Tickets are required for the event, which starts at 7 pm. Door open early with an Interactive Robotic Petting Zoo, starting at 6 pm.

Frankenstein rises up on the Emory campus on Thursday, March 22. Three Atlanta playwrights will reanimate Mary Shelley’s creation, which turns 200 this year, in the context of scientific research ongoing at Emory. Following the short plays join ethicists, scientists and the playwrights to discuss the work over refreshments. The event, titled “Frankenstein Goes Back to the Lab,” begins at 5:30 pm in Emory’s Science Commons.

On Friday, March 23, from 3:30 to 7 pm, Emory will host “Chemistry Carnival,” where visitors can join scientists in carnival games like Peptide Jenga and Bacterial Telepathy, in the Atwood Chemistry Center. On the same day and time, the ever-popular “Physics Live!” will again feature giant soap bubbles and liquid nitrogen ice cream, among other treats in the Math and Science Center.

A new Emory event this year, “Science.Art.Wonder,” will run concurrently with the chemistry and physics events, on the Emory Quadrangle and in nearby buildings, including White Hall and the Atwood Chemistry Center. For the past year, the program has paired local artists and scientists to explore ideas of research through the visual arts. You can stroll through an exhibit of the resulting artwork and meet some of the artists and scientists involved in the project.

Adult fare is featured on Monday, March 19, including “The Science of ‘Motherese,’” an overview of early vocal development in infants at the Marcus Autism Center, and “CDC in the Scene,” which features CDC scientists sorting fact from fiction surrounding movies like “Outbreak,” in the Mathematics and Science Center.

On Tuesday, March 20, “Become an Archeologist” lets you in on secrets revealed by ancient skeletons and artifacts, while “Mock Climate Change Negotiation” turns you into an international policymaker for a day.

During “Unveiling the Internet,” on Wednesday, March 21, Emory computer scientists will give interactive lessons on everything from the workings of YouTube to Snapchat.

“STEM Gems: Giving Girls Role Models in STEM Careers,” on Saturday, March 10, is an interactive discussion where panelists offer advice and guidance specific to girls and young women intrigued by science, technology, engineering and math. “Women and Minorities in STEM: Surprises, Setbacks and Successes,” set for the evening of Thursday, March 22 at the Oxford campus, is a panel discussion with voices from a diverse set of scientific fields who will share their stories and take questions.

Click here for more details of Emory campus events, and events throughout the city featuring members of the Emory community.

Among the dozen Emory booths at “Exploration Expo” will be chemistry students running their non-Newtonian fluid dance pit. The Center for the Study of Human Health will explore the human gut microbiome in a booth called “Your Hundred Trillion Best Friends.” And the “Science.Art.Wonder” team will display art from the program and invite you to help create a mural.

The Atlanta Science Festival was founded by Emory, Georgia Tech and the Metro Atlanta Chamber and is a collaboration among diverse community partners and sponsors.