April 27, 2017
Growing up in small-town Central Alabama, Justin Smith was drawn to Legos and science fiction books and films, like Star Wars and Star Trek — things that allowed him to imagine futuristic realities. He’s still building works inspired by his love of science fiction, but they’re very real. For the past year, the University of Florida doctoral student and colleagues have been developing software using artificial intelligence, specifically a neural network, that can be taught and even learn on its own. The developers hope the new software will lead to faster, cheaper and more accurate testing of treatments and potential cures for diseases and viruses, like diabetes and HIV. “I wanted to make a difference in the way medicine is developed, ” said Smith, who studies at UF’s chemistry department and recently introduced the software in a study. “With this software, drug companies can identify a target protein, like those that drive the HIV virus, and test binding molecules to proteins that can stop the protein from working, essentially stopping the disease in its tracks.” The software is called ANAKIN-ME (Accurate NeurAl networK engINe for Molecular Energies) or Ani for short. And describing Ani as “fast” is an understatement. In order to bind a molecule to a protein, researchers need to understand the molecule’s energy. Smith taught the neural network to calculate energies and forces in molecules hundreds of thousands of times faster than the previous most accurate method — and much more accurately than the quickest methods that currently exist. The combination of speed, accuracy and low cost will allow researchers to run experiments that were previously impossible, said Smith’s mentor Adrian Roitberg, a UF chemistry professor and study co-author. “Drugs that used to take decades to test can be tested in months,” said Roitberg, who emphasized the software’s accuracy. Justin Smith (right) and Adrian Roitberg discuss the new method. The software might also help engineers and manufacturers develop materials like solar cells and plastics. The network is useful when building things, as it can identify the right materials and take away much of the trial and error, Roitberg said. The problem with some previous methods is that they were not adapted to the way molecules move and bend, while others that were adapted to movement failed to work in complex chemical environments. So, Smith took a different approach. “The idea was to design a method that works the same way they teach cars to drive. You don’t teach a car to drive down a straight road and then expect it to take corners, for instance, “ said Smith, a UF Foundation graduate fellowship recipient. “Because molecules move, I realized we needed to design a way to teach the neural network that things are not rigid.” The speed at which Ani computes might allow researchers to test huge numbers of possible molecule and protein connections, or study big, complex molecules. Though it’s already advanced, Ani is still learning. It knows organic chemistry, but eventually the network might be able to train itself to perform even more accurately. And as for the reason Ani’s creators named it after a Star Wars character, Roitberg said, “In those movies, computers were solving problems long before words like artificial intelligence or machine learning existed. So it’s a shout out to science fiction and the way it spurred interest in computers solving real-world problems.” Olexandr Isayev with the University of North Carolina at Chapel Hill co-authored the study.
April 26, 2017
The U.S. Defense Department is looking for ways to speed up cognitive skills training — the types of skills useful for specialists such as linguists, intelligence analysts and cryptographers — and is awarding University of Florida engineers and neuroscientists up to $8.4 million over the next four years to investigate how to do that by applying electrical stimulation to peripheral nerves as a means of strengthening neuronal connections in the brain. Two neuroengineering experts in UF’s Herbert Wertheim College of Engineering are among eight team leaders across the country receiving awards announced Wednesday under the Targeted Neuroplasticity Training program of the Defense Advanced Research Projects Agency, or DARPA. The program’s goal is to develop safe and effective enhanced training regimens that accelerate the acquisition of cognitive skills while reducing the cost and time of the DoD’s extensive training program. A large percentage of the work involves fundamental research to decipher the neural mechanisms that underlie the influence of nerve stimulation on brain plasticity. Under an award of up to $4.2 million, Kevin J. Otto, Ph.D., will lead a team of neuroscientists from the Evelyn F. and William L. McKnight Brain Institute of the University of Florida and the Malcom Randall VA Medical Center to identify which neural pathways in the brain are activated by vagal nerve stimulation. The team will conduct behavioral studies in rodents to determine the impact of vagal nerve stimulation on perception, executive function, decision-making and spatial navigation. This could potentially lead to an expansion of the use of vagal nerve stimulation, a therapy currently applied to prevent seizures in patients with epilepsy and to treat depression and chronic pain. “There are clinical applications, but very little understanding of why it works,” said Jennifer L. Bizon, a professor of neuroscience at UF and an investigator on Otto’s team. “We are going to do the systematic science to understand how this stimulation actually drives brain circuits and, ultimately, how to maximize the use of this approach to enhance cognition.” The research funded by the DARPA awards will test the mechanisms by which peripheral nerve modulations make learning faster and more efficient. For military analysts on the job, “One hypothetical example would be target detection,” said co-investigator Barry Setlow, Ph.D., a professor of psychiatry at UF. “So for people who spend hours a day looking for things of interest on a screen, if by stimulating their vagus nerve at just the right time you can help them realize performance improvements more quickly, then they become better attuned to the fine details of images.” The technology has the potential to help Defense Department personnel advance through training more quickly, yet effectively. “Currently, they could spend 50 years of their careers, 80 hours a week, just doing training and still wouldn’t be qualified to do every single thing,” said Otto, an associate professor in the J. Crayton Pruitt Family Department of Biomedical Engineering. “So they’re always interested in increasing mechanisms of learning and memory.” Otto said if investigators can gain a more complete understanding of how targeted neuroplasticity works, they may be able to figure out how to optimize learning while avoiding potential side effects, such as blood pressure manipulation, heart rate changes and perceived visceral pain. In a second UF effort, and with an additional $4.2 million award, Karim Oweiss, Ph.D., a professor of electrical and computer engineering, biomedical engineering and neuroscience, will study the mechanisms by which cranial nerve stimulation can affect brain activity. His lab will use advanced optical imaging that will produce extremely high-resolution images of brain dynamics to map the functional circuitry in areas of the brain responsible for executive function. Additionally, optogenetic interrogation, a technique to drive specific brain cells to fire or go silent in response to targeted illumination, will be used to study the causal involvement of these areas in learning cue salience and working memory formation in rodents trained on auditory discrimination and decision making tasks. Oweiss will collaborate with Qi Wang, an assistant professor at Columbia University. Wang’s lab will focus on the noradrenergic pathway — a neuromodulator widely responsible for brain attention and arousal — and the extent to which it is engaged when rodents learn a tactile discrimination task. Oweiss’ project seeks to demonstrate the effects of vagal nerve stimulation on cognitive-skill learning and the brain activity supporting those skills, as well as to optimize the stimulation parameters and training protocols for long-term retention of those skills. “We want to see if it’s possible to promote targeted changes in specific brain circuits to accelerate this process by stimulating the vagus nerve, which sends close to 80 percent of its output back to the brain,” Oweiss said. “So if one knows that ‘brain area A’ talks to ‘brain area B’ when learning a new language, can we develop training protocols that promote the exchange between these two areas while leaving other areas unaltered? Then the person will learn at a faster rate and retain the skills for much longer.” The implications of both projects reach beyond accelerated learning speeds. “If we identify specific ways that neural pathways change as a person learns, then if a person loses brain function, we could potentially rewire disconnected brain areas and personalize neural rehabilitation,” said Oweiss. “This technology could be used to restore quality of life much quicker if brain function has been compromised.”
April 24, 2017
A mathematical model of cholera transmission in Haiti following the 2010 earthquake suggests that current approaches to cholera control and elimination, which focus primarily on improving sanitation, are not likely to solve the problem. However, eradication of cholera is possible with use of oral cholera vaccine. “We need to focus on routine vaccination in areas that are at risk of cholera transmission in Haiti,” said Ira Longini, a professor in the College of Public Health and Health Professions and the College of Medicine’s department of biostatistics. Longini is the senior author of the report. Previous cholera elimination strategies have emphasized the need for infrastructure improvements; the authors, however, suggest that this approach has led to few if any changes in Haiti’s water and sanitation infrastructure. According to the authors, resources should be allocated toward administering oral cholera vaccines, or OCVs, in order to end transmission over the next few years. Longini stressed the need for urgency, citing climatic instability as a factor that could increase disease occurrence. “We need to start now,” he said. “We don’t know when the next disaster is coming – the next hurricane or the next earthquake – that could cause another big jump in transmission. We know it is going to happen. We just don’t know when.” The study relied on data from the Ouest Department of Haiti, a region that includes Haiti’s capital of Port-au-Prince and the surrounding area. It suggests, however, that several vaccination strategies have the potential to end cholera transmission throughout Haiti before 2023 – the deadline established by Haiti’s Ministry of Public Health and Population in 2013 to eliminate cholera from the country. The article, titled “Controlling cholera in the Ouest Department of Haiti using oral vaccines,” was published online in April 2017 in PLOS Neglected Tropical Diseases. The vaccine would not need to be 100 percent effective in order to eliminate cholera transmission. In fact, the study’s mass vaccination projections assume that vaccine effectiveness will only be 60 percent – a level surpassed by Shanchol, one the two OCVs prequalified by the World Health Organization, in previous studies. The WHO manages a stockpile of several million doses of OCVs. Since more than 1 billion people live in regions at risk of cholera, however, campaigns relying on WHO resources will likely have to begin with targeted vaccination instead of mass vaccination. Longini is currently developing models that will identify where vaccination campaigns should be targeted to be most effective. “Transmission occurs along river systems and in areas with poor sanitation,” Longini said. “UF researchers have been tracking where cholera transmission occurs since the beginning of the epidemic, so we know where to look for transmission. Now we just need national and international leaders and health policy officials to place a strong emphasis on administering these vaccines to the population.”
April 20, 2017
All over the University of Florida campus, researchers grapple with how to meet the world’s ever-increasing need for access to clean, fresh water. For a group that convened at the College of Journalism and Communications in November 2015, however, the challenge was how to convey water issues to the public. At “Covering Water in a Changing World,” a McCormick Specialized Reporting Institute, journalists from print, digital and broadcast outlets around the country gathered to learn from UF scientists, visiting experts and communications professors, including Ann Christiano, UF’s Karel Endowed Chair for Public Interest Communications, and author Cynthia Barnett, UF’s Environmental Journalist in Residence, who organized the institute. Over a year later, the lessons from the event continue to inform participants’ coverage, with stories in outlets such as National Public Radio, Bloomberg BNA and the Christian Science Monitor, tapping into the insight they gained on topics like algae blooms, public utilities and extreme weather. Paddling on the Ichetucknee River with scientists, participants saw the links between groundwater and surface water firsthand. “It's helped me research many stories since,” said Texas-based freelancer Lana Straub, whose story on groundwater pollution aired on the Texas Standard, a group of 20 stations around the state. Straub also worked with reporters she met at the institute to apply for a Spotlight Investigative Journalism Fellowship focusing on water infrastructure. She didn’t win this time, but she’s hoping to gather a team of institute alumni to apply again.
April 19, 2017
Commencement 2017 Information Jordan Kooiman has a special appreciation for the veterans and active duty military personnel he has worked with during his clinical internships as part of the University of Florida doctor of physical therapy program. “They work hard, they’re resilient and they don’t know how to take it easy,” he said. “They’re in therapy several hours a day kicking butt. They want to keep pushing themselves, and that’s so fun to work with.” It also helps that Kooiman has a unique rapport and understanding of these patients. A U.S. Navy veteran, Kooiman has undergone his own physical therapy to heal from injuries he experienced while in service, including those he received from a roadside bomb. Jordan Kooiman, 3rd from right. “As veterans we can be a little testy sometimes, especially with people who don’t understand our experiences,” Kooiman joked. “But if they meet someone like me who has been deployed, they may think, ‘This guy knows what I’ve been through and maybe I’ll give him a little more information or listen better to what he’s saying.’” Kooiman, a Wisconsin native who graduates this month from the department of physical therapy in the College of Public Health and Health Professions, joined the Navy in 2007 and did two tours in Iraq as part of a riverine squadron charged with maritime security and disrupting enemy forces along the Euphrates and Shatt al-Arab rivers and Lake Tharthar. His unit also worked with other branches of the armed forces to provide support, intelligence, surveillance and reconnaissance, and transportation of ground troops. During his second tour in 2010, his unit was on its way back to base in Nasiriyah after training Iraqi police on waterborne operations when the vehicle Kooiman was in was struck by an improvised explosive device. Fortunately, no one was severely injured. But for Kooiman, the blast exacerbated a decade of back and neck injuries accumulated through contact sports and the physical demands of deployment and training, including running for miles with heavy weights or riding out rough waters. During his rehabilitation, Kooiman was impressed by his physical therapists and fellow veterans and military personnel, many of whom who had very serious injuries, such as amputations and traumatic brain injuries. “When I went through it myself, I saw the broadness of physical therapy and all the conditions it treats, such as neuromuscular, skeletal, balance and traumatic brain injury,” Kooiman said. “I realized how physical therapy could address all of that in veterans, a population that can have a lot of different health issues.” Two of Kooiman’s four clinical internships have placed him with these patients. At James A. Haley Veterans’ Hospital in Tampa, he worked with patients with traumatic brain injury in the polytrauma center. He was accepted for an internship at Walter Reed National Military Medical Center in Bethesda, Maryland, where he treated patients in the outpatient orthopedic unit. Following graduation, Kooiman expects he will have the opportunity to work with several veterans and military personnel at his new position at a sports medicine facility in Chesapeake, Virginia, which is close to several naval bases. As a student, Kooiman has demonstrated confidence, the ability to put challenging situations into perspective and sound clinical reasoning, said Kevin Lulofs-MacPherson, a clinical lecturer and the assistant director of clinical education in the department of physical therapy. “I personally believe Jordan’s confidence comes from knowing exactly what is on the line in clinical practice and his ability to rapidly assess and adapt to the situation -- hallmark behaviors of someone with a background of active military service who has experience in situations with much higher stakes,” he said. Commencement 2017 Information
WEEKLY NEWS: April 13, 2017