IU scientists to participate in Ask Me Anything session on Reddit

On Dec. 7, three IU scientists will invite the public to “Ask Me Anything.”

Hui-Chen Lu, Yousuf Ali and Hunter Allen will participate in a Q-and-A session from 1 to 2 p.m. EST on r/Science, the science message board of Reddit.

Yu and colleagues will participate in PLOS Science Wednesdays AMA Series on Dec. 7.

Lu and colleagues will participate in PLOS Science Wednesdays AMA Series on Dec. 7.

The massively popular social media platform, which hosts daily Ask Me Anything sessions, or “AMAs,” regularly attracts an audience of over 10,000 people to these online events.

The session is organized by the online peer reviewed journal PLOS as part of the PLOS Science Wednesdays AMA Series.

Earlier this year, Lu and colleagues published a paper in PLOS reporting evidence that the enzyme NMNAT2 appears to exert a protective effect on memory.

The study is significant since the research could affect how scientists understand the mechanisms behind a range of neurodegenerative diseases known as “proteinopathies,” which include Alzheimer’s, Parkinson’s and Huntington’s diseases, as well as amyotrophic lateral sclerosis, also known as ALS or Lou Gehrig’s disease.

These diseases are called as proteinopathies because they occur when proteins “misfold,” causing them to grow “sticky” and clump up in the brain. These clumps of proteins are often referred to as “plaques,” or “tangles.”

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Virtual liver model could help reduce overdose risk from acetaminophen, other drugs

Biocomplexity Institute researchers at IU Bloomington create computer simulation to analyze drug absorption at the cellular to whole-body level

Researchers at Indiana University’s Biocomplexity Institute have developed a virtual model of the human liver to better understand how the organ metabolizes acetaminophen, a common non-prescription painkiller and fever-reducer used in over-the-counter drugs such as Tylenol.

The study, reported in the peer-reviewed online journal PLOS ONE, suggests that virtual tissues models could play an important role in modern pharmacokinetics, the branch of pharmacology concerned with the movement of drugs within the body.

“This image shows an overview of the multi-scale computer model for drug metabolism. The images on the left show the three biological scales in the model – the whole-body level, the liver organ level and the cellular level.”

An overview of the multi-scale computer model for drug metabolism. The images on the left show the three biological scales in the model: the whole-body level, the organ level and the cellular level.

Specifically, the study employs “virtual tissue” technology developed at the institute to model the distribution of drugs in the human body at multiple scales — time and location in the body — an ability that could help contribute to more personalized prescription guidelines that reduce the risk of overdose.

Acetaminophen metabolism is significant because poisoning from a liver metabolite of acetaminophen is the leading cause of acute liver failure in the United States, resulting in over 33,000 hospital admissions and 500 deaths each year. Acute liver failure can lead to death since the liver is the primary organ responsible for the metabolism and clearance of toxins, including drugs, from the body.

“Although this model of acetaminophen toxicity isn’t currently directed at developing interventions to accidental overdoses, it suggests a surprisingly large degree of difference in sensitivity to the drug across large populations,” said James Sluka, a research scientist at the Biocomplexity Institute, who is a co-lead author on the paper. “According to our model, as many as one in a thousand people may be unusually sensitive to the drug’s toxicity.”

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IU informatics researcher earns three federal patents to strengthen user control in the ‘app economy’

“The future is apps” is a phrase commonly uttered by technology experts. Anyone who has ever struggled to find the right app at the right time might not share that opinion, however.


Sameer Patil

Sameer Patil‘s efforts to strike at the heart of this modern dilemma — and also strengthen user privacy in the “app economy” — was recently recognized by the U.S. Patent and Trademark Office, which has issued three patents to the assistant professor in the IU School of Informatics and Computing for his efforts on app search and discovery.

The work that led to the patents was conducted in 2014 at Quixey, a Mountain View, California-based company that aims to connect people with apps. A research scientist at Finland’s Helsinki Institute for Information Technology at the time, Patil spent four weeks during the summer of 2014 as a consultant at Quixey. He jokingly calls the job his “summer vacation” that year.

“The two major U.S. players in app search — Google’s Play Store and the Apple App Store — need improvement on two major fronts: relevance and accuracy, and search,” said Patil, who joined IU in August. “There currently isn’t a good way to sort or filter or find apps, and both services are overly focused on precise queries. If you don’t know an app happens to be called ‘Yelp,’ for example, you might not be able to find it. A search for ‘app for finding places to eat’ doesn’t cut it.”

His work at Quixey, which involved designing and conducting focus groups with users to understand their practices and preferences regarding finding and using mobile apps, generated insight that resulted in eight patent applications, three of which have been granted within the past couple of months. The common thread connecting the patents is their focus on protecting individual privacy while also opening up the convenience of social app search to a wider audience.

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Philosopher Dennett to lecture at IU Bloomington

Post by IU News and Media Specialist Steve Hinnefeld who normally writes for the Policy Briefings blog:

Daniel Dennett has been called “one of our most important living philosophers,” a “Darwinian fundamentalist” and quite a few other things, positive and negative. As Julian Baggini observed in a profile for the Guardian, big thinkers make big targets, and they don’t come much bigger than Dennett.

Dan C. Dennett

Daniel C. Dennett | Tufts University

Expect thought-provoking analysis and lively discussion this week when Dennett presents two lectures at IU Bloomington as the inaugural event in the Department of Philosophy distinguished speaker series.

Dennett will speak Nov. 10 on “From Bacteria to Bach and Back: The Evolution of Minds” and Nov. 11 on “A Magician’s View of Consciousness.” Both lectures will be from 4 to 6 p.m. in Whittenberger Auditorium of the Indiana Memorial Union. They are free and open to the public.

“For almost five decades now, Daniel Dennett has been a powerful and influential advocate for explaining minds and behavior in scientific terms,” said Gary Ebbs, professor and chair of the philosophy department. “He draws on results from biology, psychology and neuroscience to demystify the mind.  His writings and lectures weave together vivid, thought-provoking examples, informed expositions of scientific results and high-level clarifications of key concepts and experiences of our mental life.”

Dennett is co-director of the Center for Cognitive Studies at Tufts University, where he is also University Professor and Austin B. Fletcher Professor of Philosophy. He is the author of “Breaking the Spell,” “Freedom Evolves”, “Darwin’s Dangerous Idea” and other books. He co-edited “The Mind’s I,” published in 1981, with IU College of Arts and Sciences Distinguished Professor Douglas Hofstadter.

His most recent books include “Intuition Pumps and Other Tools for Thinking” and “Caught in the Pulpit: Leaving Belief Behind.” His latest, “From Bacteria to Bach and Back,” is in press. His TED Talks, including “The Illusion of Consciousness” and “Dangerous Memes,” have been viewed millions of times.

The author of over 400 scholarly articles, Dennett has received two Guggenheim Fellowships, a Fulbright Fellowship and a Fellowship at the Center for Advanced Studies in Behavioral Science. He was elected to the American Academy of Arts and Sciences in 1987. He was an Indiana University William T. Patten Lecturer in 2006.

For more on Dennett and his IU lectures, see Hussain Ather’s article in the Indiana Daily Student.

Robots invade and volcanos erupt on campus at third annual Science Fest

Post by IU Newsroom intern Sheila Raghavendran

On Saturday, Oct. 22, IU was overrun with robots.

These robots — machines such as PARO, the therapeutic robotic seal — were on site for holding and petting as part of the School of Informatics and Computing’s activities at the IU Bloomington College of Arts and Sciences’ third annual Science Fest.

Parents and youngsters examine rocks during Science Fest outside Owen Hall on Saturday, Oct. 22, 2016.

Parents and children explore rocks outside Owen Hall at IU’s third annual Science Fest.

Many science departments in the college, including chemistry, astronomy, physics and psychological and brain sciences, also hosted activities for students and the general public.

When Science Fest started in 2014, it was the first time these departments and other groups were brought together to hold an event to share science with the public all on one day, according to Tina Gilliland, outreach liaison for the College of Arts and Sciences’ Office of Science Outreach.

This year there were 15 departments and groups holding activities — the highest number Science Fest has seen.

Along with PARO, Science Fest also offered a station for people to try their hand at designing 3D models with the help of Matt Francisco, a visiting lecturer at the School of Informatics and Computing, and his students.

“The kids learn that they need to provide us with enough information to create a 3D model,” Francisco said. “They’re often very good at drawing one perspective, but it’s not enough information to do 3D modeling, so I have my assistants, who are getting them to do at least two views.”

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IU physicist played early role in history of Nobel Prize-winning theory

A physicist at Indiana University played an important role in the history of the work of two scientists honored by today’s Nobel Prize in Physics.

The winners of the 2016 Nobel Prize in Physics are David J. Thouless, Michael Kosterlitz and F. Duncan M. Haldane, who were recognized Oct. 4 for theoretical discoveries of topological phase transitions and topological phases of matter.

Jorge V. José

Jorge V. José

Topology is a branch of mathematics that describes objects with special geometric properties. Thouless and Kosterlitz’s ideas were first described in 1971 as a novel phase transition of topological objects called vortices under the name Berezinskii-Kosterlitz-Thouless Theory.

A professor of physics in the IU Bloomington College of Arts and Sciences’ Department of Physics, Jorge V. José led theoretical work in the late 1970s that helped spur wider scientific acceptance of BKT theory, which has since been used to advance mathematical methods to study unusual phases of matter such as those found in superconductors, superfluids and ultra-thin magnetic films.

More recently, in recognition for this role in the early history of the theory, José was selected to edit a 40th anniversary book on the subject whose first chapter is authored by Thouless and Kosterlitz.

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IU study reveals rats have greater episodic memory than previously thought

Anyone who has ever spotted a familiar face at a party but been unable to place where or when they last met that person knows the difference between episodic memory and familiarity.

Familiarity is mere recognition. Episodic memory is the ability to recall a memory’s context — to remember where and when you saw that familiar face. It’s also the difference between sputtering your way through a reintroduction or smoothly referring back to details about the last time you talked to your acquaintance.

A rat in the center of eight spices. IU scientists used over 30 spices in two mazes with different circular patterns on the floor to gauge rat’s ability to remember information in specific contexts.

A rat in the center of eight spices. IU scientists used over 00 spices in two circular “arenas” with different black-and-white patterns on the floor to gauge rat’s ability to remember information in specific contexts.

Although it’s easy to grasp the difference in these types of memory in ourselves, it’s not easy to know how animals see the world. Do their memories also take context into account?

A new study by Indiana University researchers that appears online today in the journal Current Biology suggests that rats exhibit much stronger episodic memory than previously thought. It is the first study to show that these animals can remember more than 30 events in context.

The lead author on the study is Danielle Panoz-Brown, a graduate student in the lab of Jonathon Crystal, a professor in the IU Department of Psychological and Brain Sciences, who is also an author on the paper.

“Most work shows that rats, and other animals, remember one, two or perhaps three events,” Crystal said. “This new work shows that rats remember many events — over 30 — and are likely able to remember many more using episodic memory.”

He added that the existence of episodic memory in lower animals has implications for research on human diseases that affect memory, including Alzheimer’s, Parkinson’s and Huntington’s diseases, since the majority of research on the brain — and the drugs used to treat memory diseases and dementia — start out based on insights into how the brain works in rats.

So, if a pharmaceutical company creates an Alzheimer’s drug to target memory based on research into one type of memory — the part of the brain responsible for finding missing objects, for example — but doesn’t also have data on the type of memory that helps individuals remember the important people, places and things in their life, it runs the risk of producing a product that helps a person remember where they put the car keys, but not how they met their spouse.

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IU part of $1 million grant from NSF to create country’s first big data “spoke” focused on neuroscience

“The field of neuroscience is transforming,” wrote IU neuroscientist Franco Pestilli in a commentary published last year in the journal Nature Scientific Data. “Brain data from people and institutions around the world are being openly shared — moving from office desks and personal storage devices to institutionally supported cloud systems and public repositories.”

This process of openly sharing brain data — a part of the larger movement toward “open science” — is ushering in the era of “big data neuroscience.”

An environmental portrait of Franco Pestilli.

IU neuroscientist Franco Pestilli is principal investigator on the NSF grant funding the Neuroscience Spoke of the Midwest Big Data Hub.

And now, as part of the team named recipient on a $1 million grant, IU will play a role on the forefront of this era by contributing to the establishment of the Neuroscience Spoke in the Midwest Big Data Hub. The principal investigator on the award is Pestilli, an assistant professor in the IU Bloomington College of Arts and Sciences’ Department of Psychological and Brain Sciences.

The award — a part of a major new initiative from the National Science Foundation and White House to “create a national ecosystem for Big Data and Data Science” — is a symbol of IU’s progression toward leadership in the field of both neuroscience and big data science. It is also part of $11 million in federal grants announced today to advance research and create infrastructure designed to ensure data acquired by publicly funded basic research is effectively shared and used.

“This award will help put IU on the map as a leader in the big data neuroscience,” Pestilli said. “We will contribute to moving neuroscience research beyond a cottage industry model, where independent labs generate data that remains unshared, by establishing a regional and national network of professionals and scientists who are proficient in data science and who possess the assets necessary to share data, software and computing resources that contribute to the impact of the scientific enterprise and the reproducibility of results.”

Pestilli’s co-investigators on the Neuroscience Spoke are Olaf Sporns, IU Distinguished Professor in Psychological and Brain Sciences, and Andrew Saykin, Raymond C. Beeler Professor of Radiology and Imaging Sciences at the IU School of Medicine.

The term “spoke” refers to IU’s position as part of the Midwest Big Data Hub, one of four regional “hubs” across the country funded under the NSF’s Big Data Hub program. The award makes IU part of the only spoke in the United States focused on neuroscience.

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IU graduate students share passion for science and conversation with ‘ScIU’

A committed team of graduate students from across the sciences at IU are banding together to provide a glimpse inside the world of Bloomington’s research labs through a new effort that seeks inform, entertain and spark conversations about science.

ScIU: Conversations in Science,” which officially launches Aug. 22, is a new blog that seeks to foster discussion and awareness about science across the university and the community.

ScIU students

Among the writers and editors of ScIU are Lana Ruck, Ed Basom, Nichole Nagoette, Victoria Kohout, Noah Zarr, Daniel Bullock and Benjamin Draper (left to right, back row) and Maria Tiongco, Amrita Bhattacharya, Josey Topolski, Mark Juers, Anna Jessee, Clara Boothby and Fabio Mendes (left to right, front row). Photo by Mike Jackson.

“We’re taking the time to do this because we love the discovery, the questions and the excitement of science – of trying to work and understand, and to build upon the knowledge of those who came before us,” said Briana K. Whitaker, a graduate student in the IU College of Arts and Sciences’ Department of Biology and a member of the blog’s editorial team. “With ScIU, we’re hoping to foster conversations between scientists and non-scientists and to start a dialogue about IU science that helps connect different people on and around campus.”

The graduate student editors and writers at ScIU represent a wide swath of science departments at IU Bloomington, all of whom have been collaborating on the project since last spring. Together, they’ve brainstormed topics, discussed the challenges of science writing and worked to raise excitement about the blog among their peers and research mentors.

The project was originally proposed and remains supported by the IU Bloomington College of Arts and Sciences’ Research Office and Office of Science Outreach, whose mission includes the promotion of diversity, awareness and accessibility of science to everyone.

“This project is all about public engagement with the sciences and focusing a two-way dialogue that not only communicates IU’s cutting-edge research to the public but is responsive to the public about what they need from science to make informed decisions in their lives,” said Jo Anne Tracy, director of the Office of Science Outreach and assistant dean for research in the College of Arts and Sciences.

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IU physicist presents new evidence about nature of the third mass state in neutrinos

A year and a day after delivering the first results from a multi-million-dollar detector built to shed light on the nature of neutrinos, IU physicist Mark Messier announced the project had produced new evidence about the nature of the “third mass state” of these mysterious subatomic particles.

An illustration of the three neutrino mass states and the three flavors that make them up (electron, muon and tau), as they were previously though to mix. NOvA’s new result shows that the third mass state may not have equal amounts of muon (yellow jellybeans) and tau (blue jellybeans) flavors. Image by Fermilab/Sandbox Studios.

The results were presented at the 2016 International Conference of High-Energy Physics in Chicago.

“Neutrinos are always surprising us,” said Messier, who is co-spokesperson for the NOvA experiment, the project that generated the results. “This result is a fresh look into one of the major unknowns in neutrino physics.”

A $278 million international collaboration of nearly 230 scientists and engineers from 41 institutions across the globe, the NOvA experiment is headquartered at the U.S. Department of Energy’s Fermi National Accelerator Laboratory

Neutrinos have previously been detected in three types, called flavors – muon, tau and electron. They also exist in three mass states, but those states don’t necessarily correspond directly to the three flavors.

The results of the experiment announced Aug. 8 suggest that one of the three neutrino mass states might not include equal parts of muon and tau flavor, as previously thought. Scientists refer to this as “non-maximal mixing,” and NOvA’s result is the first hint that this may be the case for the third mass state.

“In physics, symmetries are often important clues about what’s going on behind the scenes,” Messier said. “In this case we’ve seen a symmetry break, and exactly how and in which direction can tell us more about how neutrinos relate to each other and the other fundamental particles.”

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