UF Explore Magazine | Fall 2021

FALL 2021

Flower Power Carinata Provides Fuel & Feed

Fall 2021, Vol. 26, No.3

Extracts Research briefs

5 The Science of Reading

Flower Power

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A common mustard plant holds potential as a sustainable fuel and alternative crop

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CSI: Alzheimer's

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About the cover: The carinata plant can provide biofuel for airplanes and feed for livestock while providing Southern farmers with a winter cash crop.

Cover Photo and this page by Cristina Carrizosa

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Dozens of UF researchers are investigating Alzheimer’s from multiple directions

The Flamingo Literacy Matrix puts researchdriven reading help into the hands of teachers

UF and the National Science Foundation

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Building Blocks

The Conversation

From ancient times to the space age, concrete has staying power

Poison ivy can work itchy evil on your skin

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Kent Fuchs President David Norton Vice President for Research Board of Trustees Mori Hosseini, Chair David Bloom David L. Brandon Cooper Brown ‌Richard P. Cole Christopher T. Corr James W. Heavener Daniel T. O’Keefe Thomas G. Kuntz Rahul Patel Marsha D. Powers Fred S. Ridley Anita G. Zucker Explore is published by UF Research. Opinions expressed do not reflect the official views of the university. Use of trade names implies no endorsement by the University of Florida. © 2021 University of Florida. explore.research.ufl.edu Editor: Joseph M. Kays joekays@ufl.edu Art Director: Katherine Kinsley-Momberger Design and Illustration: Katherine Kinsley-Momberger Ivan J. Ramos Writers: Joseph Kays Cindy Spence Michelle Koidin Jaffee Copy Editor: Bruce Mastron Printing: RR Donnelly, Orlando Member of the University Research Magazine Association www.urma.org

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What Top 5 Looks Like

John Jernigan

I

David Norton Vice President for Research

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n September, the University of Florida achieved its long-sought goal of being recognized as one of the top five public universities in the nation by U.S. News & World Report.

This historic achievement did not occur overnight, but was, in fact, built on years, even decades, of focused effort by our faculty, staff, students, alumni and university leadership, pushing toward a common goal of making UF better tomorrow than it was yesterday. Similarly, our breakthroughs in research may appear to come suddenly, but are built on years of effort by researchers who are committed to addressing unanswered questions.

This issue of Explore contains four feature stories that personify UF’s commitment to making a difference by uncovering new understanding in areas of importance, including instances in which partnering with state offices, federal agencies, industry, and philanthropy are key to yielding the best path forward.

In efforts to improve health, UF medical researchers are tackling perhaps the most difficult neurological challenge of our generation, namely Alzheimer’s disease. They are searching for treatments and, perhaps, a cure for this dreaded ailment that already ravages more than half a million Floridians and is expected to impact many more over the next decade. In this work, UF scientists and doctors are leveraging support from the National Institutes of Health with millions more from private donors, like the Fixel family, whose generous and visionary gifts have helped to establish UF as a world leader in neuromedicine.

In agriculture, scientists from UF’s Institute of Food and Agricultural Sciences are leading a consortium of universities and industry to explore the potential of carinata, a humble mustard plant whose seeds can be converted into jet fuel and livestock feed.

At the Herbert Wertheim College of Engineering, researchers are working to make concrete – the essential element of construction worldwide – more durable and more sustainable.

And through the College of Education, teachers are getting new tools and techniques to help young children to read. UF education researchers are also developing a plan to implement a multimillion dollar program funded by the Florida Legislature to put a new book each month in the hands of students from kindergarten to fifth grade who are reading below grade level.

These are just a few of the many thousands of projects that are under way every day on the University of Florida campus and at sites throughout the state. This is what Top 5 looks like on the ground, where UF’s unparalleled faculty pursue all manner of research and scholarship to advance knowledge and train the next generation of leaders.

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UF Health, Scripps Florida Join Forces Integration creates research synergies he University of Florida and California-based Scripps Research have signed a definitive agreement to welcome the Florida branch of the science powerhouse into the research arm of UF’s academic health center — a step aimed at accelerating the translation of basic scientific discoveries into clinical advances that benefit human health in the state and beyond.

The integration is intended to celebrate and strengthen ongoing research at Scripps Florida, which has a stellar global reputation, while leveraging opportunities to explore avenues of mutual interest and providing Scripps with a strong clinical partner. The goal? To build on the excellent scientific work taking place to more expediently unlock clinical advances that improve outcomes for patients in the state and around the world, officials from both organizations said.

“We are excited to work collaboratively with our colleagues at Scripps to rapidly take discoveries made at the bench to the bedside, where they can have the most benefit to humanity,” said Dr. David R. Nelson, senior vice president for health affairs at UF and president of UF Health.

“We are looking forward to cultivating a culture of innovation that will extend from the outstanding science already underway.”

As part of the agreement, Scripps will transfer all assets associated with the 30-acre Scripps Florida campus in Jupiter, situated within Palm Beach County’s innovation corridor — property, buildings, equipment and adjacent 70-acre tract — to the University of Florida.

The campus, one of the top National Institutes of Health-supported research centers in the state, includes more than 40 faculty-led laboratories supported by a 500-member team dedicated to understanding an array of illnesses and seeking to generate effective treatments.

In addition, UF and UF Health have committed to work with Scripps Florida leadership to immediately invest in the new entity by hiring additional faculty; these

new recruits will come on board within the next five years and will complement the existing talented pool of scientists there, possibly expanding efforts in the artificial intelligence domain by hiring faculty focused on areas such as data science and AI. Other natural areas of collaboration with colleagues in other parts of UF Health potentially include cancer, drug discovery, immunology and infectious disease, neuroscience (including Alzheimer’s and other aging-related diseases, as well as autism), HIV/AIDS, and structural biology and molecular medicine.

“Florida supported us in establishing a world-class institute, and Scripps Florida together with UF, as part of the greater Florida research and education community, will have a tremendous impact on scientific research and human health,” said Peter Schultz, president and chief executive officer of Scripps Research.

Scripps Florida researchers are regularly heralded for their pioneering discoveries that have led to hundreds of patents and numerous spinoff companies. They are behind a robust research profile, with nearly $50 million in NIH funding and over $67 million in total research funding, which includes industry support.

As part of the arrangement, a site director and local leadership council will be appointed for the entity, which will be organized and operated independently and report to Nelson. Scripps scientists will join the UF faculty and also will retain an additional Scripps title.

“This integration between the University of Florida and Scripps Florida will create unprecedented collaboration among some of the world’s most brilliant and talented minds to address the biggest biomedical challenges we face today,” said Mori Hosseini, UF Board of Trustees chair. “Not only will this produce

enormous scientific and health-related advancements for the entire world, it also will lead to tremendous economic development and further elevated national and global stature for the state of Florida.

“We are exceptionally grateful for the efforts of Herbert Wertheim, who helped bring this tremendous opportunity to Scripps and the university,” Hosseini added. Wertheim is a member of the Scripps Research Board of Directors, a UF alumnus, founding chair of UF’s Herbert Wertheim College of Engineering and a longtime supporter of UF. UF President Kent Fuchs said the stage is set for the new entity to be a significant force for progress and for the door to open to new scientific and tech collaborations with others, including other State University System institutions such as Florida Atlantic and Florida International universities.

“With our deep faculty benches at UF, UF Health and Scripps — along with our combined resources and impressive research capacity — I fully expect we will see absolutely remarkable discoveries in the years to come that will benefit the state, the nation and the world,” Fuchs said.

Melanie Ross

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Antivirals Arsenal

Research targets genes that help viruses replicate multidisciplinary team of researchers at the University of Florida is making progress in the search for druggable targets to develop treatments against COVID-19. This summer, the team reported identifying 53 novel genes and pathways that could become targets for antiviral therapies for COVID-19 plus a broad array of coronaviruses.

The UF investigators used CRISPR gene editing techniques to search for genes and molecular pathways that aid coronavirus infections in people. Team members include Stephanie Karst (UF College of Medicine/Emerging Pathogens Institute), Chris Vulpe (UF College of Veterinary Medicine) and Michael Norris (UF College of Liberal Arts and Sciences/ Emerging Pathogens Institute).

Principal investigator Norris, a UF molecular biologist and bioengineer, says that identifying antiviral therapeutics is critical due to the increasing impact of new genetic variants in the pandemic.

“We need every possible weapon against this virus,” says Norris.

Antivirals work by blocking or slowing a virus’s ability to make more of itself inside a host. This can lessen the symptoms or length of an infection. The discovery of broad-spectrum antiviral targets would be useful against emerging variants of SARS-CoV-2, the virus that causes COVID-19, and other kinds of coronaviruses.

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Antivirals have been overlooked in the rush to vaccinate populations, but they are equally needed. Some people can’t receive vaccines and may remain vulnerable to infection. And even those who are vaccinated may find themselves up against new variants that erode the vaccine’s efficacy.

Antivirals could help in both situations.

They may also help relieve the burden of disease and slow transmission in regions with little or no access to COVID-19 vaccines.

The research team cultured cells that were experimentally infected with two different types of coronaviruses: SARSCoV-2 and OC43. The first produces COVID-19 while the second produces a relatively mild and seasonally circulating common cold.

They included OC43 to zero in on targets that span coronaviruses, which indicates that these could be broadspectrum druggable targets. The appeal of a broad-spectrum target is that it could be used to develop effective therapies against future coronaviruses that have not yet emerged but could be even more devastating than SARS-CoV-2.

The team used a gene-editing technique known as CRISPR to rapidly screen through all host genes. The goal was to identify the key genes that promote coronavirus infections in mammals. This pinpointed cellular pathways that the virus uses to copy itself inside human

cells. Inhibiting or silencing specific genes of interest allowed the team to confirm the role played by these pathways in viral growth during COVID-19 and common cold infections.

“Identification of these pathways is key to designing new drugs or identifying existing inhibitors for the treatment or prevention of coronaviral infections,” Norris says. “Our work demonstrates that existing drugs can inhibit SARS-CoV-2 replication and the production of infectious particles in human lung cells.”

The UF team found several host genes important for both SARS-CoV-2 and OC43 infections. These could be considered candidates for broad-spectrum therapies against human coronaviruses.

Three genes — CDK4, EDC4 and XRN1 — were found to play important roles in promoting replication pathways for the two coronaviruses. If drugs could safely target them and inhibit their role, it would limit the coronavirus’ ability to replicate and spread within a host; in essence, controlling the infection and the symptoms it produces.

Three additional genes were identified as possibly supporting viral propagation from the host cell. GNPTAB, GNPTG and NAGPA were found to be involved in encoding for proteins which the researchers speculate may promote the release of virions — the replicated progeny of a virus — from an infected cell.

Engineering Inventiveness Materials and computer engineers inducted into Florida Inventors Hall of Fame

Targeting these factors could lead to the development of a drug that prevents infected cells from releasing more coronaviruses. This effect might buy the immune system time to mount a more effective defense, while shortening the length and severity of an infection.

The team identified 21 additional genes previously reported in other CRISPR screening studies, which validates the technique and strength of their findings. They also evaluated several existing antiviral compounds which target the identified host genes in their search for candidate antiviral agents. Several compounds diminished coronavirus replication in cell culture experiments, including a cell cycle inhibitor known as ABE. “This compound and other candidate drugs which target the host capacity to support coronavirus replication hold great promise as a novel class of antiviral agents,” says principal investigator Vulpe.

“Of course, additional work to validate these findings and demonstrate efficacy in more complex models, such as a mouse model, and ultimately in people, are necessary.”

DeLene Beeland

Rajiv Singh

Susann Keohane

University of Florida professor emeritus in materials science and engineering who developed an innovative computer chip manufacturing process, and an alumnus in electrical and computer engineering who is a leader at IBM in the application of artificial intelligence to aging issues, are among the 2021 inductees to the Florida Inventors Hall of Fame.

During his 30 years at UF, Rajiv Singh became a world leader in the semiconductor processing field. Singh is one of the original developers of pulsed laser deposition and the inventor of chemical mechanical polishing for advanced electronic materials used in smart phones, electric vehicles, 5G communications and more. He holds 26 U.S. patents.

Sinmat, the company Singh co-founded in 2000 to commercialize his discoveries, was acquired in 2020 by Entegris, a global leader in advanced materials and process solutions for the semiconductor and other high-tech industries. He now serves as a vice president at Entegris.

Susann Keohane is IBM Watson Health Innovation Leader for Healthy Aging and Longevity and Emerging AI Product. She is an IBM Master Inventor and holds a series of seminal patents in autonomous vehicles. Her groundbreaking

advances in artificial intelligence, machine learning and the Internet of Things are transforming technology for people with disabilities and the aging population by applying advanced analytics and machine learning techniques to model activities of daily living and generating new insights that significantly improve quality of life.

She holds 137 U.S. patents.

“We take great pride in seeing our Gator Engineers receive this esteemed honor. Rajiv Singh gifted the world with materials enhancement for electronics and communications that businesses and citizens cannot live without today,” said Cammy R. Abernathy, dean of the Herbert Wertheim College of Engineering. “Through her seminal inventions in AI and smart technology, Susann Keohane promises that we will be working more efficiently tomorrow. Both Rajiv and Susann truly exemplify the spirit of innovation that is the hallmark of the New Engineer."

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AI Workforce Diversity

UF, FAMU will recruit, train underrepresented students unding for student fellowships is included in a new $1.4 million, threeyear National Science Foundation grant that faculty from the University of Florida and Florida A&M University (FAMU) will use to train a diverse workforce for potential careers in artificial intelligence.

The UF Institute of Food and Agricultural Sciences and FAMU — a historically Black university and UF’s land-grant partner — will collaborate to recruit and retain traditionally underrepresented students in AI-related education and research.

In the first year, faculty members from UF and FAMU will use $736,000 to fund faculty and 250 undergraduate student fellowships. Each student will receive $5,000 per year and the fellowships are potentially renewable for multiple years.

Although the fellowships are earmarked for students at UF and FAMU, more fellowship funds have been budgeted for FAMU students to help alleviate financial barriers to the courses.

Bryan Kolaczkowski, a UF/IFAS associate professor of microbiology and cell science, will lead the project. He sees the potential to leverage AI to bring huge advantages to society. But he wants the AI workforce to be inclusive so it can benefit all.

“AI is expected to impact all fields in the agricultural and life sciences in the future,” Kolaczkowski said. “Students engaged in AI are expected to be competitive in traditional agricultural and life sciences roles, including biomedical sciences. In addition to increasing competitiveness in traditional jobs, AI is expected to create massive new job opportunities in data science, process management, diagnostics and similar areas. Experience in AI will help students be competitive for these new types of careers in agricultural and life sciences.”

To educate a diverse, next-generation AI workforce, this project will develop a curriculum in which students from outside traditional computer-science fields can learn AI-related concepts and skills and 8 Fall 2021

Aavudai Anandhi Swamy, FAMU

Satyanarayan Dev, FAMU

Bryan Kolaczkowski, UF/IFAS

“In addition to increasing competitiveness in traditional jobs, AI is expected to create massive new job opportunities in data science, process management, diagnostics and similar areas.”

— Bryan Kolaczkowski how AI can address critical, emerging problems in their field.

A diverse AI-enabled workforce means that a variety of interests, backgrounds, experiences, socioeconomic status, races, ethnicities, genders and technical abilities are all present during the development, deployment and evaluation of AI systems, he said.

“We think the best way to achieve this is to make sure that everyone has a ‘seat at the table’ of AI, ” Kolaczkowski said.

This semester, for the first time, Kolaczkowski is teaching AI for agricultural and life sciences. As more courses are made available, most students will learn online, from anywhere in the world. But students will transition to an undergraduate research course, and much of that will be in-person, either at UF/IFAS or at FAMU, Kolaczkowski said.

“This approach of integrating ‘AI across the curriculum’ is expected to enable all interested students to graduate equipped to engage AI in their chosen discipline fairly and equitably. Every graduate should at least understand what AI can do,” Kolaczkowski said.

By leveraging UF’s partnership with NVIDIA, this project provides unprecedented student access to HiPerGator AI, one of the most advanced AI-focused computational resources in the world.

“By partnering with UF, students and faculty at FAMU are gaining unprecedented access to training and highperformance computing resources, which will help to increase the competitiveness of students from FAMU engaged in this program,” Kolaczkowski said. “Additionally, a strategic partnership between UF and FAMU provides avenues to engage diverse undergraduates in AI-related education and research, including fields such as agriculture, natural resources, business, engineering and health-related fields.”

Aavudai Anandhi Swamy, an associate professor of biological systems engineering at FAMU, added: “Diversity is important to us. Our program in the past 30 years has succeeded in increasing the pool of African Americans and other minorities in agricultural and biological engineering nationally, and many hold key positions in both the public and private sector.”

Satyanarayan Dev, also an associate professor of biological systems engineering at FAMU said: “We want to make sure that when an AI system makes a decision, it will be able to make an accurate one without any bias. This grant helps us make a step forward in this right direction.”

Brad Buck

Amber Lizard

Digital scans clarify new species

“From the moment we uploaded the first CT scan, everyone was brainstorming what it could be,” said Daza, assistant professor of biological sciences at Sam Houston State University. “In the end, a closer look and our analyses help us clarify its position.”

Researchers began analyzing the unusual lizard in 2019, the year before a separate team published a paper misidentifying a similar fossil as the smallest avian dinosaur ever found. The two species likely represent a previously unknown group of scaled reptiles.

Major clues that the mystery animal was a lizard included the presence of scales; teeth attached directly to its jawbone, rather than nestled in sockets, as dinosaur teeth were; lizardlike eye structures and shoulder bones; and a hockey stick-shaped skull bone that is universally shared among scaled reptiles, also known as squamates.

Natalie van Hoose

Edward Stanley

n international research team has described a new species of Oculudentavis, providing further evidence that the animal first identified as a hummingbirdsized dinosaur was actually a lizard.

The new species, named Oculudentavis naga in honor of the Naga people of Myanmar and India, is represented by a partial skeleton that includes a complete skull, exquisitely preserved in amber with visible scales and soft tissue. The specimen is in the same genus as Oculudentavis khaungraae, whose original description as the smallest known bird, published by a different group of researchers, was retracted last year. The two fossils were found in the same area and are about 99 million years old.

Researchers published their findings in Current Biology.

The team, led by Arnau Bolet of Barcelona’s Institut Català de Paleontologia Miquel Crusafont, used CT scans to separate, analyze and compare each bone in the two species digitally, uncovering a number of physical characteristics that earmark the small animals as lizards.

Oculudentavis is so strange, however, it was difficult to categorize without close examination of its features, Bolet said.

Herpetologist Juan Diego Daza examined the small, unusual skull, preserved with a short portion of the spine and shoulder bones. He, too, was confused by its odd array of features: Could it be some kind of pterodactyl or possibly an ancient relative of monitor lizards?

The team also determined both species’ skulls had deformed during preservation.

Oculudentavis khaungraae’s snout was squeezed into a narrower, more beaklike profile while Oculudentavis naga’s braincase — the part of the skull that encloses the brain — was compressed. The distortions highlighted birdlike features in one skull and lizardlike features in the other, said study co-author Edward Stanley, director of the Florida Museum of Natural History’s Digital Discovery and Dissemination Laboratory.

“Imagine taking a lizard and pinching its nose into a triangular shape,” Stanley said. “It would look a lot more like a bird.”

The majority of the study was conducted with CT data created at the Australian Centre for Neutron Scattering and the High-Resolution X-ray Computed Tomography Facility at the University of Texas at Austin. Oculudentavis naga is now available digitally to anyone with Internet access, which allows the team’s findings to be reassessed and opens up the possibility of new discoveries, Stanley said.

While Myanmar’s amber deposits are a treasure trove of fossil lizards found nowhere else in the world, Daza said the consensus among paleontologists is that acquiring Burmese amber ethically has become increasingly difficult, especially after the military seized control in February. The specimen was acquired following the ethical guidelines for the use of Burmese amber set forth by the Society for Vertebrate Paleontology.

CT scan of Oculudentavis naga

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Gut Feeling

AI helps identify bacteria linked to blood pressure and depression o solve the elusive medical mystery of why many adults have both high blood pressure and depression, University of Florida Health researchers took a long, in-depth look at one suspected culprit: gut bacteria.

The gut microbiome affects physiology and molecular events throughout the body, including parts of the brain that control blood pressure and depression, newly published findings show.

The gut’s role in the two prevalent, chronic conditions was first explained by a trio of UF Health researchers in September 2019. Now, using a branch of artificial intelligence known as machine learning, the researchers have zeroed in on the specific bacteria suspected of causing depression coupled with high blood pressure.

It’s a crucial step toward the long-term goal of improving health management and developing novel treatments based on the analysis and manipulation of gut bacteria, the researchers said. The two conditions are sometimes so intertwined it has also led them to coin a new phrase: depressive hypertension. The findings were published recently in the American Heart Journal.

High blood pressure and depression are interrelated in many people, yet unlinked in others. Cardiologists and psychiatrists don’t know why. That can make diagnosis and treatment challenging, said Bruce R. Stevens, a professor of physiology and functional genomics in the UF College of Medicine, and the study's lead author.

Stevens and his colleagues used a novel machine learning approach to develop a much more sophisticated DNA analysis of gut bacteria. Mohan K. Raizada, a 10 Fall 2021

co-author of the study and a distinguished professor emeritus of physiology and functional genomics in the College of Medicine, suspected that people with depression and hypertension would have unique gut microbiomes. To establish their findings, the researchers focused on four groups of people — those with high blood pressure and depression, those who only had high blood pressure, those who only had depression, and healthy people.

Stevens deployed machine learning to make sense of myriad data points about the patients and their gut bacteria. The computer analysis filtered out statistically

irrelevant “noise” and distilled the data into a coherent picture. Without machine learning, Stevens said the mind-boggling mountain of raw data would have been incomprehensible to the human brain.

“Because the patients have unique gut microbes, we knew we could use machine learning to identify them. The computer could distinguish the patients’ health conditions based on their personal microbiome,” Stevens said.

What emerged was a clear view of the unique gut bacteria in different patients: A trio of dominant bacteria were found in people with depression. Five other bacteria were prevalent in those with high blood pressure and five different dominant strains were noted in people with depression and hypertension. The

healthy patients in the study had yet another combination of four dominant bacteria.

Raizada and Carl J. Pepine, a co-author of the study and a professor in the UF College of Medicine’s department of medicine, said gut microbe analysis and manipulation holds significant promise for treating depression, hypertension or both.

For cardiologists and psychiatrists, analyzing gut bacteria may prove to be a reliable shortcut to finding the most effective therapies or recommendations for improving lifestyles.

A gut bacteria analysis could someday be used to quickly predict which patients will respond to particular medications in the manner of personalized medicine, Raizada said. Pepine added, “It would certainly take us forward from the approach where we try a drug to lower blood pressure or treat depression and then wait weeks or months for a possible response.”

While much more research is needed to develop new gut-based therapies, Stevens says this much holds true: The human body is actually a “meta-organism” — a complex, intertwined system of trillions of human and bacterial cells. Likewise, the gastrointestinal tract is a novel target for preventing, diagnosing and treating hypertension, depression or both.

“This is not just about the gut, the heart or the brain alone,” Stevens said.

“Depressive-hypertension is a threedimensional symphony of these three organs.”

Doug Bennett

Fighting Bias

Grant seeks to prevent implicit bias, racial disparities in clinical research

From left: Della V. Mosley, Crystal Johnson-Mann and Azra Bihorac

team of all-female physicians and scientists is leveraging personal experiences with underrepresentation in medicine to begin identifying a solution toward implicit bias in clinical research.

Azra Bihorac, Crystal Johnson-Mann and Della V. Mosley received an inaugural grant from UF Research in conjunction with the UF Office of the Chief Diversity Officer to advance and catalyze sustainable efforts toward racial justice, diversity, equity and inclusion at the University of Florida.

After all, when it comes to clinical research, representation can mean the difference between life and death.

Intuitively, clinical trials for new therapies in areas that disproportionately affect Black patients should include Black participants at a comparable proportion of enrollment. However, the data reflects otherwise.

For example: obesity, diabetes, hypertension, stroke, heart and kidney (ODSH2K) disease affect more than 50 million Americans. For Black Americans, these diseases occur even more frequently — and with worse outcomes. In fact, they account for 40% of all deaths.

“This is a population whose risk of developing kidney failure and being on dialysis is three-fold,” said Johnson-Mann, an assistant professor of surgery and the

only Black female surgeon at UF. “And at the same time, they’re less likely to receive a kidney transplant.”

But among 102,416 participants in 11 trials for a diabetes medication that prevents kidney failure, only 4% were Black.

The issue, like others rooted in health inequities, is systemic. So, Bihorac, Johnson-Mann and Mosley, are starting small — if you can call addressing racial equity in clinical trials at one of the largest research universities in the country small.

“One of the first steps to achieving racial equity in clinical trials at UF is an assessment of racial diversity among those who participate in trials and those who work with them,” said Bihorac, a professor

of medicine, surgery, and anesthesiology in the UF College of Medicine.

The three investigators intend to identify barriers to inclusive trial recruitment and participation at UF and develop a training intervention to reduce the impact of racial bias and discrimination among clinical researchers.

“Our collective expertise in clinical research, nephrology, obesity, surgery, racial justice and psychology lends us a complementary set of skills to address this issue comprehensively,” said Della V. Mosley, an assistant professor of counseling psychology. “Most importantly, we want to approach this systemic issue from a critical yet compassionate perspective.”

Each of the researchers’ backgrounds uniquely shape their approach to the issue.

Bihorac is a survivor of Bosnian genocide as a religious minority and was a refugee in Turkey and the United States. Mosley is an established scholar of Black psychology, racism, and antiracism interventions.

Johnson-Mann is nationally involved in advocacy for Black female physicians, and is all too familiar with the number of patients who are overwhelmingly affected

by ODSH2K diseases due to obesity.

“Lack of racial and gender diversity amongst principal investigators and those responsible for trial recruitment can deter gender and diversity among participants,” Johnson-Mann said. “It starts at the top.”

Implicit bias can be influenced by forces outside our awareness and control.

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Aquatic Invaders

Tool helps assess risk of invasive species

Jeff Hill

global risk-assessment tool shows 33 nonnative aquatic species worldwide pose a “very high risk” of becoming invasive in current and future climate conditions.

“These species readily establish, spread and have severe impacts across several regions of the world,” said Jeff Hill, a UF/ IFAS professor of fisheries and aquatics and a lead author on a new study that

used the risk-assessment tool. “The threat posed by invasive species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems.”

That’s why Hill worked with scientists across the globe to develop the Aquatic Species Invasiveness Screening Kit. Scientists, including Hill, used the kit to assess the risk of such invasions. Once established outside its native range, an invasive species can cause environmental, social or human health impacts, Hill said.

Here are a few invasive species and their potential impacts in Florida, as outlined by Hill: • Redear Slider, Trachemys scripta elegans. This turtle breeds with the native turtle known as the Yellowbelly Slider.

• Cane Toad, Rhinella marina. This large toad consumes smaller amphibians

Microgravity Mission UF plants fly on Virgin Galactic mission hile most of the attention during the July 11 launch of Virgin Galactic’s Unity spaceship was on billionaire company founder Richard Branson, University of Florida researchers Anna-Lisa Paul and Rob Ferl were focused on some other passengers – three small tubes of experimental plants.

The UF project, funded by NASA’s Flight Opportunities Program, was the only science experiment on the mission.

The experiment was meant to study the impact the transition to and from zero gravity has on gene expression in cells, and, more broadly, to develop protocols for “human-tended” suborbital flights.

“Although changes in gene expression are well characterized between orbital space (like the International Space Station) and on Earth, no science has yet been done to capture changes in gene 12 Fall 2021

expression during the transition to and from sustained microgravity,” said Paul.

“This was a first-of-its-kind experiment that will reveal new insights into how terrestrial organisms perceive the transition into the novel environment of space.”

Paul and Ferl, both professors of horticultural sciences, have been working for more than two decades to understand plant gene expression in microgravity, but most of their experiments have been done by astronauts in space. As Paul puts it, on rocket launches the astronauts and their payloads are just “strapped in for the ride.”

But new platforms, like Virgin Galactic’s space plane, offer scientists the opportunity to have astronauts conduct research throughout the transition to and from space. To achieve this goal, the researchers had to develop systems that could be easily implemented during the brief

periods of microgravity.

Fortunately, Ferl and Paul have spent years fine-tuning experimental tubes called Kennedy Space Center Fixation Tubes, or KFTs, that quickly mix test materials (a model plant called Arabidopsis thaliana) and a fixative, while keeping both components isolated from the surrounding environment.

On the Virgin Galactic flight, astronaut Sirisha Bandla had three KFTs in a customized pouch attached to the leg of her flight suit. She activated one prior to reaching space, one as soon as the vehicle reached its maximum altitude and the crew became weightless, and one at the end of the period of weightlessness as the vehicle began its descent and gravity returned. On the ground, Paul and Ferl received telemetry from the flight that allowed them to activate identical control

and competes with natives for food. It also secretes toxins dangerous to pets and wildlife.

• Amazon Sailfin Catfish, Pterygoplichthys pardalis (pictured). This armored catfish digs burrows for spawning. In doing so, it exacerbates erosion in natural waters and in stormwater ponds.

Hill helped lead a newly published study in the journal Science of the Total Environment that shows the risks of invasion by hundreds of species in the six inhabited continents.

For the study, 195 scientists used the Aquatic Species Invasives Kit (AS-ISK) to examine 819 species.

Their goal is to inform policy makers, those making day-to-day management decisions and other stakeholders about global threats to aquatic ecosystems, said Hill, a faculty member at the UF/ IFAS Tropical Aquaculture Laboratory in

Ruskin. Agencies and businesses across the word use the decision-support tool to help sustain aquaculture, the aquarium trade and fisheries management by identifying potentially invasive species before they establish and cause negative effects.

AS-ISK uses a scoring system. The higher the score, the higher the risk of a species becoming invasive. To get the most out of the tool, scientists calculate a score to differentiate between medium and high risk — normally non-invasive vs. potentially invasive. Researchers studied risk thresholds for species in various climates. Those factors provide a basis for scientists to interpret invasion thresholds.

Though helpful, the risk assessments are not meant to be comprehensive, Hill said. Each screen consists of 49 questions for basic assessment and six more questions about climate change.

Through their analyses, researchers

provided global thresholds so natural resource managers can now assign species as “low,” “medium” or “high” risk under current and future climate conditions, Hill said.

If the assessment is “high-risk,” responses are to determine which species: • Require an immediate, rapid management action such as eradication or control to avoid or mitigate negative impacts.

• Need a full risk assessment.

• Meet criteria for additional regulation in vulnerable areas.

The risk-screening tool used in this study is a generalized version of the Fish Invasiveness Screening Kit developed by the UF/IFAS Tropical Aquaculture Laboratory and the Centre for Environment, Fisheries and Aquaculture Sciences.

Researchers use it as an international tool for nonnative freshwater fish.

Brad Buck

tubes at the same times as the flight tubes were activated.

“The successful use of KFTs enables a wide range of biological experiments in suborbital space, as any biology that can fit inside the KFTs can be sampled at any phases of flight chosen, in real time, by the scientist astronaut,” Ferl said.

Paul and Ferl retrieved the KFTs shortly after the spaceship landed and brought them back to their lab in Gainesville for further study.

“In the future, astronauts may go back and forth between Earth, the Moon and Mars and orbiting platforms like the International Space Station and the Gateway outpost orbiting the Moon,” Ferl says.

“Understanding the changes that occur in cells during these missions will be important to maintaining their health.”

Joe Kays

Astronaut Sirisha Bandla (far right) activates a KFT at maximum altitude.

Explore 13

Flower Power A common mustard plant holds potential as a sustainable fuel and alternative crop

By Cindy Spence

14 Fall 2021

A

gronomist David Wright sees a future where jet fuel comes from a field of yellow flowers.

The flowers top the stalks of Brassica carinata, a variety of mustard whose seeds produce oil that can easily be converted into jet and diesel fuels that are nearly identical to their petroleum counterparts.

In 10 years of working with carinata at the University of Florida’s North Florida Research and Education Center in Quincy, Wright and his colleagues say they’ve discovered that jet and diesel fuels are only one benefit of the humble

mustard. At each stage in the growth cycle, carinata offers benefits to farmers, says Sheeja George, research project manager.

“Carinata fits for the Southeast in the winter when farmers grow nothing else, and it gives them an opportunity to build carbon in the soil and an opportunity to produce a high-protein meal that can be used to feed chickens and cows,” George says, “all on top of harvesting the seeds for oil for biofuel.”

In recognition of carinata’s potential, the USDA’s National Institute of Food and Agriculture awarded $15 million in

2017 to a public/private partnership led

by UF called SPARC, the Southeast Partnership for Advanced Renewables from Carinata.

George says 2022 will be a key year for SPARC, as varieties with higher yields and improved genetic traits are being field tested with the ultimate goal of giving growers a chance to make money from their fields year-round.

An offhand comment in 2010 led to the eventual creation of the $15 million SPARC project. Wright and George and their colleagues were working on a project with camelina, another oilseed, and a

E xplore 15

Tyler Jones

In field trials at the North Florida Research and Education Center in Quincy, researchers David Wright and Ian Small have discovered multiple benefits to growing carinata as a winter cover crop.

biofuels industry representative happened to show up at a field day.

“They were doing all this research,” recalls chemical engineer Ed Coppola, who had driven to Quincy from Panama City, where he works with the Better Fuels Group at Applied Research Associates. “I asked them if they had ever considered carinata?”

Unlike some other oilseed crops, the pods of carinata don't shatter when harvested, so there is little to no loss of the seeds, which are larger than those of other oilseed crops.

16 Fall 2021

Wright recalls his reply: “What’s carinata?”

Coppola filled them in, and the academic team and the industry team have been working together ever since.

As Wright learned more about carinata, he was intrigued enough to seek seed funding through the dean’s office in the Institute of Food and Agricultural Sciences. The seed funding allowed the team to plant several acres of carinata at the research center in Quincy and get acquainted with the emerging crop.

George and her colleagues explored best management practices, diseases, pests, appropriate herbicides and growth habits.

“This was an absolutely new crop,” George says. “We quickly saw that it had great promise. We had worked with other oil seeds, but in comparison, carinata seemed so much more promising in terms of yield and vigor.”

As carinata kept surpassing expectations, the trials extended to the West Florida Research and Education Center in Jay, the North Florida Research and

“We have to be sure the crop is profitable to growers in the winter and does not interfere with cotton, soybean, corn and peanuts … otherwise, growers will not accept it.” ­— David Wright Education Center-Suwannee Valley in Live Oak and to the Plant Science Research and Education Unit in Citra.

The Florida Department of Agriculture and Consumer Services took note with a $1.1 million grant, and then NIFA put out a call for bioenergy related agricultural projects.

Carinata was a perfect fit for a public/ private partnership.

Coppola and the UF researchers were already sold. Nuseed, a global seed company that owns the carinata germplasm, heads up plant breeding and crop improvement efforts. Nine universities in

Tyler Jones

the southeast also signed up and the collaborative venture pulled in the $15 million grant. As the group expanded to the Carolinas, Georgia, Alabama and Mississippi, they had to find ways to make the crop a fit in different soils and climates. Even in balmy Florida, climate can be a challenge.

“We have moderate winters, but we still have a winter,” George says. “Those occasional times when we freeze, this crop didn’t do well.”

Rick Bennett, a plant breeder with Nuseed who has worked with carinata since 2012, says cold tolerance will be a key to broadening the range for growing carinata throughout the south.

Versatile Seeds Wright has spent much of four-plus decades of research looking for the right winter cover crop for North Florida. Most farmland, he says, is left to the weeds in the winter, with less than 25 percent planted with a winter cover crop, a missed opportunity for much-needed farm income.

Crop cycles in North Florida. Adding carinata as a winter cover crop can be beneficial to farmers.

In the summer, Florida farmers focus on tried-and-true crops that pay the bills.

Carinata is only grown in the winter, when cropland is fallow, so it does not displace the summer crops. The situation creates a win-win for farmers.

“We have to be sure the crop is profitable to growers in the winter and does not interfere with cotton, soybean, corn and peanuts,” Wright says. “Otherwise, growers will not accept it.”

Carinata has a long growing season — November to May — so the timeline is tight. It must be planted right after summer crops are harvested and harvested quickly before the next summer planting season.

During their work with carinata, the team found it is best to rotate carinata in a field every three years. Corn and cotton leave nitrogen in the soil. Carinata removes it at the rate of roughly 50 pounds of nitrogen per acre and keeps it from leaching into groundwater or running off into streams. Carinata leaves the soil richer, creating a better growing

environment when summer crops take their turn.

Bennett says Nuseed is also working on shortening the maturity cycle for carinata.

“Rotation is important. We need a maturity cycle that is appropriate for growing carinata in the winter, so it’s not pushing into soybeans or peanuts or whatever is next in the rotation. So early maturity is an important trait,” Bennett says.

Breeding for higher yielding varieties with higher oil content is important, too, Bennett says.

Carinata does better than other oil seeds in heat and drought conditions.

When harvested, carinata pods generally don’t shatter — a problem with other oil seeds — so there is little to no loss of its seeds, which are larger than those of other oilseed crops. Carinata plants are larger as well, three to four times larger than camelina, creating more biomass.

Only half of the carinata seed is oil, but the other half is not wasted. The meal created after the oil is extracted from the seeds is roughly 45 percent protein,

E xplore 17

“There’s an opportunity here to be part of a movement, literally, in renewable energy, with sustainable aviation fuel and sustainable products from this crop. The renewable energy industry is booming.”

— Sheeja George

18 Fall 2021

making it ideal for beef cattle and other livestock.

Early reactions from growers were a mixed bag, George says, but their feedback has been valuable in directing research.

The latest research has revolved around new genetics to make carinata more coldtolerant and easier to manage.

“There’s a lot of new genetics we can use to replace some of the existing genetics.

We want to make it fit for them so that it doesn’t interfere with their regular cropping systems,” George says. “We are still adding to our toolbox.”

Carinata seeds have about 40 to 45% oil, roughly in the same ballpark as peanuts, sesame, sunflower seeds, walnuts, palm seeds and coconut.

The difference between carinata and these other oil-producing all-stars is that carinata is not edible, and that makes it a winner, hands-down, as a biofuel.

Growth in biofuels has created a shortage of land for food crops in some areas of the world, creating a sometimes contentious food vs. fuel debate in biofuel circles. About 33% of the U.S. corn crop,

Complete Solution

for example, is used to make ethanol.

Some critics have said that using corn for fuel drives up food prices and takes corn out of production as food or a source of livestock feed.

Sidestepping that debate will require oil from non-food crops. Like carinata.

George says the renewable energy industry partners in SPARC understand that food crops are not sustainable as biofuel because they are needed for food.

Food-grade oils are also more expensive, but since carinata’s oil is high in a fatty acid known as erucic acid, it’s considered inedible.

“The industry does not want a crop that competes with a food crop or that would displace another crop already in the landscape,” George says.

Carinata, she says, is a purpose-grown crop, and that purpose is fuel. The byproduct, the meal left after oil extraction, creates a second income stream for growers.

“There’s a big demand out there for these kinds of feedstocks, and we want to connect that demand to our farmers,” George says.

Depending on who you ask, the world will run out of oil by the end of this century. Even if more oil is discovered or new technologies extend its usage, oil is a finite resource.

Carinata packs all the potential of petroleum crude oil into a seed, making it a viable renewable alternative to petroleum, George says. For military and aviation uses, sustainable aviation fuel has long been a goal, with the military hoping to switch to biofuels by 2025.

Commercial aviation, too, has had success with jet fuel derived from carinata.

Qantas and United Airlines have both flown passenger jets with the biofuel, which George describes as a drop-in fuel that requires no retrofitting of jet engines.

Chemically, George says, carinata and petroleum share the same profile. A chromatogram of petroleum jet fuel vs. jet fuel from carinata produced with a process jointly developed by Chevron Lummus Global and Applied Research Associates look the same, George says.

The reduction in carbon emissions from carinata is estimated to be 60-80% compared to regular jet fuel, and Bennett says the timing could not be better for carinata research with the Paris Climate Accords and many government mandates to reduce greenhouse gas emissions.

“I just think the timing is fantastic.

The need is there, the demand is crazy, and thanks to the University of Florida

team and the SPARC program, we’re at a really good point to be able to step in and meet that need.”

George agrees, and says as non-food, industrial oilseed crops go, her money is on carinata.

“There’s an opportunity here to be part of a movement, literally, in renewable energy, with sustainable aviation fuel and sustainable products from this crop,” George says. “The renewable energy industry is booming.”

After working with carinata for more than a decade, George says carinata has passed enough tests to convince her of its merits. It makes sense as a biofuel, it makes sense as a crop and it makes sense for the environment.

“Carinata is a complete solution that just works,” George says.

And swaying fields of yellow flowers make for better scenery than oil wells any day.

David Wright Professor of Agronomy SPARC Project Director North Florida Research and Education Center wright@ufl.edu Sheeja George SPARC Project Manager North Florida Research and Education Center sheejageorge@ufl.edu Related Website: Southeast Partnership for Advanced Renewables from Carinata https://sparc-cap.org

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Louis Brems

20 Fall 2021

CSI:Alzheimer’s Dozens of UF researchers are investigating Alzheimer’s from multiple directions

Louis Brems

By Michelle Koidin Jaffee

Stefan Prokop

G

rowing up in the foothills of the Bavarian Alps, Stefan Prokop imagined he would follow in the footsteps of his father, a homicide detective. Prokop’s interest in analyzing evidence and solving mysteries led him to forensic pathology and, during medical school, into the lab of a prominent researcher in Alzheimer’s disease.

“From day one, I was just fascinated by the specific question of Alzheimer’s disease,” he says. “I just walked in and said, ‘That’s what I want to do.’”

Twenty years later, Prokop stands beneath fluorescent lights in a UF Health lab, a donated brain on the stainless-steel table before him and four medical residents leaning in to see. Now director of the UF Neuromedicine Human Brain and Tissue Bank, Prokop describes telltale signs of Alzheimer’s, such as shrinkage in the frontal lobe and other regions, as he dissects the brain.

A leader in the field of neuropathology, Prokop is among dozens of investigators at the University of Florida hunting for the keys to Alzheimer’s disease, a progressively disabling disorder that afflicts more than 6 million Americans over age 65. That number is projected to grow to 12.7 million by 2050, according to the Alzheimer’s Association. In Florida alone, about 580,000 people currently live with Alzheimer’s, and in just the next five years that number is expected to grow to 720,000.

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A lzheimer’s

disease by the numbers

6 million Americans over age 65 That number is projected to grow to

Louis Brems

12.7 million by 2050, according to the Alzheimer’s Association. In Florida alone, about 580,000 people currently live with Alzheimer’s, and in just the next five years that number is expected to grow to 720,000.

Prokop prepares samples for analysis.

Prokop is particularly focused on the two main Alzheimer’s-related brain changes: a protein called beta-amyloid that clumps into plaques between neurons and a protein called tau that abnormally accumulates inside neurons to form tangled threads known as neurofibrillary tangles.

22 Fall 2021

People with Alzheimer’s slowly lose the ability to handle daily tasks. Beyond memory loss and confusion, they have increasing difficulty with navigation, grocery shopping, bill paying, self-care such as dressing and bathing, motivation, balance and, in late stages, walking and swallowing.

Current treatment options are limited.

Some people see temporary improvement in cognitive function and memory using medications, but these do not stop the disease from progressing. The cost in unpaid dementia caregiving by family and friends was valued by the Alzheimer’s Association at $256.7 billion in 2020.

Examining brain segments under a microscope, Prokop seeks to understand which of the molecular and cellular changes related to Alzheimer’s that he sees are a cause of the disease — and which could be a result of it. He is particularly focused on the two main Alzheimer’srelated brain changes: a protein called beta-amyloid that clumps into plaques between neurons and a protein called tau that abnormally accumulates inside neurons to form tangled threads known as neurofibrillary tangles.

Prokop, who was recruited from the University of Pennsylvania in 2019 as the first Fixel Scholar of the new Norman Fixel Institute for Neurological Diseases at UF Health, is investigating how these plaques and tangles interact and damage the brain.

Like a good detective, he is coming at it from multiple directions.

Under a new National Institutes of Health grant, he and UF neuroscientists Todd Golde and Yona Levites are exploring a large number of proteins believed to accumulate alongside amyloid — looking simultaneously at their role in donated human brains and mouse models to reveal any possible correlation with severity of Alzheimer’s symptoms. Early data suggest many of these could be key players in Alzheimer’s disease and potential new targets for intervention.

Prokop is also collaborating with UF neurogeneticist Matt Farrer to sequence the genomes of donated brains. This could help identify protective gene variants, for example in a person who had significant Alzheimer’s pathology at autopsy but never had dementia in life.

To Prokop, one way to better understand Alzheimer’s is to examine brains from diverse racial backgrounds, as most published research on the disease involves white people of European ancestry. In his role as leader of the neuropathology core of the 1Florida Alzheimer’s Disease Research Center — a UF-led consortium of top research institutions known as the 1Florida ADRC — he is working to spread the word and encourage people of diverse racial backgrounds to make arrangements for future brain donation.

“In the end, we want to treat the population,” Prokop says. “We don’t want to treat one subgroup of the population, so what we hope to gain from our research is better insight: Are these genetically diverse

“I’m optimistic that we’re going to get there, but it’s going to take some time.

It’s not going to be necessarily a linear path with one success after another.”

Jesse S. Jones

Jesse S. Jones

— Todd Golde

Yona Levites

Todd Golde

populations similar, or have we studied one type of Alzheimer’s disease that occurs in Caucasians, and is the disease different?”

The 1Florida ADRC, funded by the National Institute on Aging, enrolls research participants with and without memory disorders and tracks them for years to reveal factors that influence progression rates, using blood samples, cognitive testing and state-of-the-art brain imaging. Some enrollees also participate in clinical trials to test potential new medicines.

One focus that distinguishes the 1Florida ADRC from 32 other such Alzheimer’s Disease Research Centers in the country is that over 60% of participants are Hispanic.

“We’re hoping to make a major contribution to understanding Alzheimer’s disease by understanding how it impacts diverse populations differently,” says Golde, director of UF’s McKnight Brain Institute and principal investigator of the 1Florida ADRC, which is a collaboration of over 40 researchers from UF, Mount Sinai Medical Center in Miami Beach, the University of Miami, Florida Atlantic University and Florida International University.

The clinical arm of the 1Florida ADRC is tracking up to 600 study participants, who are undergoing testing in a five-year, $15 million project.

Artificial intelligence will be used to combine all the data — behavioral, clinical, biological and advanced neuroimaging biomarkers — to predict future development of Alzheimer’s, says UF neuroscientist David Vaillancourt, who leads the biomarker core for the study. The data will be available to Alzheimer’s researchers nationwide.

The focus on diversity extends to those who study the disease. Valerie Joers and Karina Alviña are the first two scholars selected for the new “AlzSTARS” program, which recruits and trains junior investigators from diverse racial, ethnic and gender backgrounds, as well as from diverse locations and research interests.

Humbled, but Optimistic Golde, an internationally known expert in the scientific understanding of Alzheimer’s, describes the field’s 30-year pursuit as “humbling.” Initial excitement over the first discoveries of

Alzheimer’s-related brain changes led to many trials of therapies that, despite sound scientific basis, have failed to alter the course of the disease. But with incremental successes in the lab, recent increases in federal and state funding, the passion of up-and-coming young researchers and knowledge gained from past failures, he sees a future in which Alzheimer’s can be both treated and prevented.

“I’m optimistic that we’re going to get there, but it’s going to take some time,” he says. “It’s not going to be necessarily a linear path with one success after another. But we have learned enough from our failures that we’re going to have new approaches.”

One place where those new approaches are evident is at UF’s Center for Translational Research in Neurodegenerative Disease, where neuroscientists are creating new tools, like unique mouse models.

“At UF, we have some of the best basic science modelers, who have devised mouse models that are widely used throughout the world,” says Steven T. DeKosky, a renowned neurologist honored in 2020 with the Alzheimer’s Association’s Henry E xplore 23

“In general, the field thinks that amyloid comes first and then tau is downstream of that …

But there’s also another school of thought that tau may come first and interact with amyloid in that manner.”

Louis Brems

Louis Brems

Louis Brems

— Jada Lewis

David Borchelt

Wisniewski Lifetime Achievement Award.

“These models are yielding new insights into one of the big unanswered questions: How does beta-amyloid talk to tau?” Golde adds. “Current thinking is that amyloid pathology precedes tau in neurodegeneration and nobody understands the link, but we think that these novel mouse models are beginning to more faithfully reproduce that crosstalk and may give us insights.”

UF neuroscientist Jada Lewis, in collaboration with investigators at the University of Minnesota and Harvard, has developed mice that express human tau that can be turned on and off like a light switch using the antibiotic doxycycline.

This model has been cited in over 1,300 research papers, according to the database Web of Science.

“Mouse models are yet another tool in the arsenal of fighting against Alzheimer’s disease,” says Lewis, deputy director of the McKnight Brain Institute. “We exhaust

24 Fall 2021

every possibility we can through cell models, because it preserves animal use and it’s quicker and often cheaper. But there are some things you can’t model in cell culture or on the computer, and that’s the actual interaction between tau and amyloid pathologies and resultant behavioral problems.”

With funding from the National Institute on Aging and the National Institute of Neurological Disorders and Stroke, Lewis is working with fellow UF neuroscientist David Borchelt to produce new strains of mice that model the amyloid and tau pathologies characteristic of human Alzheimer’s disease. Their newest models should significantly reduce the number of mice that researchers have to use in many of these complex studies, Lewis says.

“In general, the field thinks that

amyloid comes first and then tau is downstream of that,” Lewis says. “But there’s also another school of thought that tau may come first and interact with amyloid in that manner.”

Pinpointing the timing could be instrumental in developing new treatments that interrupt the disease.

Lewis and Borchelt are investigating what happens when tau pathology is turned on first and, conversely, what happens when amyloid pathology is turned on first. They seek to answer the question: How does the timing affect the formation of global amyloid pathology often seen in Alzheimer’s disease patients?

“We know there’s a connection between the amyloid pathology and the tau pathology,” says Borchelt. “If you have amyloid, tau pathology seems to be worse — more severe or perhaps in different locations.

What we’re trying to understand is the connection between those two.”

In addition to modeling, Lewis’ other main focus is on training the next generation of researchers who will take on the complexity of Alzheimer’s and related dementias. She and two other UF scientists lead an NIH program to train postdoctoral fellows in clinical and translational research in Alzheimer’s disease.

“The more people we get looking at

“The high-fat, high-fructose diet made everything worse. It accelerated the whole timeline, which suggests that yes, having chronic inflammation in a setting where you are genetically predisposed is a bad thing.”

Louis Brems

­— Malú Gámez Tansey

cleared from neurons.

“We believe that could be a result of aging, sluggish or nonfunctional immune cells,” says Tansey, co-director of the Center for Translational Research in Neurodegenerative Disease. “The vacuum cleaners of the brain, the vacuum cleanHealthy Brain Diseased Brain ers of your organs that keep the house tidy, become it in different directions,” she says, “the less competent as you get older.” better we’ll be able to describe the disease Meaning, she says, amyloid buildup and attack the disease.” could be a consequence, rather than a cause, of Alzheimer’s.

Tansey believes Alzheimer’s and other Beyond Amyloid and Tau dementias are influenced by both genetAmong those looking at Alzheimer’s ics and environment, including variables from a different perspective is Malú such as diet, physical exercise, quality Gámez Tansey, a prominent neuroscientist and quantity of sleep, and exposure to recruited to UF from Emory University pesticides and pathogens. “We know that in 2019 through the founding gift for the a small percentage of cases for Alzheimer’s Norman Fixel Institute. and related dementias are strictly genetic Tansey’s research focuses on the roles — maybe 5 to 10%,” she says. of inflammation and the immune system In one line of research in her lab, a in the development and progression of high-fat, high-sugar diet resulted in an neurodegenerative diseases, including acceleration of amyloid buildup and Alzheimer’s. As humans age, she explains, immune dysfunction in mice genetically our immune systems are less efficient and engineered for Alzheimer’s pathology. more vulnerable to potential exposures, “The high-fat, high-fructose diet made leading in some cases to chronic inflammaeverything worse,” Tansey says. “It acceltion as toxic proteins accumulate and aren’t erated the whole timeline, which suggests

that yes, having chronic inflammation in a setting where you are genetically predisposed is a bad thing.”

Her lab then tested an experimental drug on mice on a high-fat, highfructose diet or a control diet. The drug, XPro1595, is designed to reduce neuroinflammation. By selectively inhibiting an inflammation-causing protein called soluble tumor necrosis factor, or soluble TNF, in the gut and brain, the drug “was able to reverse some of those changes in the stool microbiome,” she says, referring to changes in bacteria and other microorganisms of the gut. “We thought this was super interesting and may be important.”

It is a critical step showing that some immune system-targeted interventions have the potential to mitigate inflammation and prevent worsening, even when genetic predisposition increases risk, Tansey says.

XPro1595, or pegipanermin, was co-invented by Tansey before coming to UF, and it has been tested in a small, early clinical trial in Australia led by the biotech company INmune Bio, for which Tansey is a consultant. She also owns stock in INmune Bio. The trial was partially funded by a “Part the Cloud” award from the Alzheimer’s Association. In the trial, the drug lowered brain inflammation, decreased nerve cell death and improved synaptic function. The trial did not evaluate cognition. The next step will be a double-blind, multisite Phase 2 trial to determine if control of neuroinflammation could have an impact on cognition.

E xplore 25

“Ten to 15% of people who die with Alzheimer’s disease changes in their brain never developed dementia … So how did they escape the cognitive effects of that pathology?”

Superagers

cal record, such as no history of stroke or diagnosis of dementia and living independently, among other factors.

The team then ran an algorithm to tally such patients in the UF Health-based OneFlorida+ Data Trust, a repository holding millions of anonymous electronic medical records.

With de-identified medical record information, researchers may identify a cohort of patients who meet certain criteria, but they are not able to identify any specific individual. Then, under a process regulated by the UF Privacy Office and UF Institutional Review Board, which 26 Fall 2021

— Glenn Smith

Louis Brems

To better understand why some people get Alzheimer’s disease, Glenn Smith and Steve Anton are studying those who manage to avoid it.

The two clinical psychology researchers are co-principal investigators of the “Over 90 Study,” which examines those who have remained cognitively healthy, despite in some cases having a genetic predisposition for Alzheimer’s.

The hope is that by revealing the secrets of so-called “superagers,” researchers can learn how to prevent Alzheimer’s in others.

“Ten to 15% of people who die with Alzheimer’s disease changes in their brain never developed dementia,” Smith says.

“So how did they escape the cognitive effects of that pathology?”

To launch the Over 90 Study, a team of 10 UF Health experts worked together to determine a definition for successful aging that could be assessed from a medi-

protects the rights of human research subjects, postcards were sent to potential study participants in Alachua County, and over 200 people responded and participated in a telephone screening, mental status test and saliva test for genetics.

That first stage of the study aimed to demonstrate that medical records could be used to create a large enough study set, and the results were encouraging. “We’ve successfully enrolled over 100 older individuals at this point, and we’re continuing to recruit,” Anton says.

Smith and Anton have collaborated with Farrer, the neurogeneticist, who has completely sequenced the whole genomes of the first 20 participants to see what is revealed. They’re also recruiting a second group of 85- to 90-year-olds using the same criteria.

The next step is to work with partners at other institutions to design a large-scale, multisite trial that would enroll 5,000 successful agers from across the country, including over 2,000 individuals who identify as African-American or Hispanic.

“What we’re trying to figure out,” Smith says, “is are there both genetic and lifestyle factors that protect people against cognitive decline? So, we first need to figure out who are the people who avoided it. And then we could envision, in

addition to collecting biological samples and looking for genetics, subsequently doing interviews to try and map out what aspects of physical activity and social engagement might distinguish these people. What things did they avoid?”

One thing is known for certain.

“People over age 90 are rare,” Smith says, “and people over 90 who have aged successfully are rarer still.”

Which is why the Over 90 Study has one final goal: to determine if there are specific activities — cognitive, physical or otherwise — that could help these superagers stay that way.

Stefan Prokop, M.D. Director, UF Neuromedicine Human Brain and Tissue Bank sprokop@ufl.edu Todd Golde, M.D., Ph.D. Director, Evelyn F. and William L. McKnight Brain Institute tgolde@ufl.edu David Borchelt, Ph.D. Professor of Neuroscience drb1@ufl.edu Malú Gámez Tansey, Ph.D. Co-Director, Center for Translational Research in Neurodegenerative Disease mgtansey@ufl.edu Glenn Smith, Ph.D. Professor of Clinical and Health Psychology glennsmith@phhp.ufl.edu Jada Lewis, Ph.D. Deputy Director, McKnight Brain Institute jada.lewis@ufl.edu Yona Levites, Ph.D. Research Associate Professor of Neuroscience levites.yona@ufl.edu

BrainCheck

UF leading movement to check for cognitive impairment before surgery

By Michelle Koidin Jaffee

Catherine Price

Jesse S. Jones

t’s routine for patients with certain heart conditions to have their cardiac function checked before surgery for a non-heartrelated issue, such as a knee operation. But it’s not routine for certain patients who are at risk of cognitive complications to have a presurgery brain check.

UF neuropsychologist Catherine Price wants to change that.

In 2017, Price founded a first-of-its-kind clinic at UF Health Shands Hospital that provides presurgery screening for adults over age 65 to detect any form of cognitive impairment, from mild impairment to more severe forms such as Alzheimer’s disease or other dementias. Four years later, more than 1,000 patients a year go through screening at the clinic, called the Perioperative Cognitive Anesthesia Network.

Although adults over 65 commonly undergo surgery for urgent medical reasons as well as quality-of-life ones like joint replacement, there is a lack of evidence-based, perioperative medical care in older adults with cognitive impairment, Price says.

It’s estimated that 20% of seniors preparing for surgery have preexisting signs of neurocognitive disorders, research by Price and others shows, and such underlying conditions elevate the risk of complications like delirium. Delirium is an acute state of confusion and disrupted attention that is associated with longer hospital stays.

“We need to identify vulnerable people before surgery,” she says. “There needs to be a change in the way clinicians adjust patient care based on brain profiles.

People with neurodegenerative disease risk factors and diagnoses require special consideration when it comes to anesthesia and surgery procedure choices.”

The Perioperative Cognitive Anesthesia Network team includes anesthesiologists, neuroscientists, neurologists, surgeons,

Jesse S. Jones

I

Kristin Hamlet

biomedical engineers and experts in artificial intelligence, and it has clinical, research and training goals.

Funded by the National Institutes of Health, it is considered a model nationwide, says UF anesthesiologist Patrick Tighe, co-director of the program.

“Now, if you go to the anesthesiology national meetings, presurgical cognition is a hot topic,” Tighe says. At a pre-pandemic American Society of Anesthesiologists general assembly, he says, Price’s work was held up as “the idealized example so far of how to do presurgical cognitive assessments.”

Under the program, cognitive assessment begins with drawing an analog clock using a high-tech pen equipped with a tiny camera that captures images 80 times per second. The image is analyzed by neuropsychologists to determine if further cognitive testing and neuroimaging scans are needed.

The clinic, also led by neuropsychologist Kristin Hamlet, then produces a report to inform anesthesiologists, surgeons, geriatricians and primary care doctors about a patient’s cognitive status and provides personalized recommendations, such as use of a special monitor that assesses the depth of sedation during surgery or adjusting the dosage of certain drugs used for sedation or nausea.

Patrick Tighe

Under ongoing research, the clock drawing is also run through an artificial intelligence algorithm as a tool to make a prediction of cognitive outcomes, Tighe says.

A next important step, says Price, is a large, multisite study using artificial intelligence to analyze medical records to predict outcomes for people with preexisting dementia who undergo surgery.

Catherine Price, Ph.D. Director, Perioperative Cognitive Anesthesia Network cep23@phhp.ufl.edu Patrick Tighe, M.D., M.S. Co-director, Perioperative Cognitive Anesthesia Network ptighe@anest.ufl.edu Kristin Hamlet, Ph.D. Clinical Assistant Professor of Psychology kmoffett@phhp.ufl.edu

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John Jernigan

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28 Fall 2021

s ck

Blo

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he earliest known use of concrete is a floor that dates back to Galilee, circa 7000 BCE, still sound when unearthed in 2007. After thousands of years as the go-to building material, it might seem like science surely could come up with something better, perhaps a material that doesn’t crack or crumble when used in columns or sidewalks.

E xplore 29

The Anatomy of Concrete make the world’s favorite building material stronger, more durable and more sustainable.

+ Portland Cement (limestone, sand, and clay)

+ Water

CONCRETE

Sand and gravel

And science can, says University of Florida civil engineering researcher Christopher Ferraro.

The problem is that many materials that are stronger or more durable than concrete don’t provide clues that something is wrong. The cracks in concrete are a signal, Ferraro says, one that can save lives.

“Concrete will show signs of distress.

It’ll start cracking and start spalling,” says Ferraro, an assistant professor who directs the Concrete Materials Research Laboratory in UF’s Herbert Wertheim College of Engineering. “It’s a sign to pay attention, it’s time for maintenance.”

Concrete made the news when the Champlain Towers South collapsed in Surfside, Florida, in June, with attention 30 Fall 2021

=

Aging Well

focused on the condition of the concrete and rebar construction, which was showing signs of wear. Concrete will stay in the news as the massive federal infrastructure spending plan takes shape, with much of the outlay going to structures that will be made of concrete.

The climate crisis, too, focuses attention on concrete, which is a contributor to greenhouse gas emissions. Still, Ferraro says, the United States today has a pretty good track record compared to other industrializing countries. China, for instance, used as much concrete between 2011 and 2013 as the United States did in the whole 20th century.

And while it’s not likely that any other material will displace concrete any time soon, the science of concrete seeks to

Ferraro points out that many of the failures that are attributed to concrete aren’t because of concrete at all, but concrete’s nearconstant companion: steel.

As a professional engineer and frequent expert witness on all matters concrete from New York to Florida, Ferraro says he has seen his share of concrete, and 95 percent of all repairs to reinforced concrete structures are due to degradation of the steel encased within.

When steel corrodes, two things happen.

First the iron turns into iron oxide. Then, the iron oxide expands, up to seven times its original measurement. The expansion pushes against the concrete, which results in spalling, or cracking. When you see cracks in reinforced concrete, Ferraro says, it’s often attributed to the expanding steel underneath.

“Concrete lasts a long time,” Ferraro says. “What fails is the steel.”

Concrete and steel are used together to provide two kinds of strength. Concrete handles the compressive load, the weight of a structure. The steel takes care of the tensile load and allows for some flexibility. The combination of concrete and steel provide structural strength that’s hard to beat.

The ingredients in the recipe for concrete are among the most common raw materials on Earth, Ferraro says. Cement is made of limestone, sand and clay. Concrete is made of cement, plus sand and gravel and water. That makes cement — Portland cement, in particular — a key focus of research.

John Jernigan

In Ferraro’s lab in the Engineering School of Sustainable Infrastructure and Environment, research focuses on nondestructive testing, uses of alternative binders and aggregates, infrastructure condition, and virtual testing and modeling of the concrete microstructure.

Traditionally, Portland cement is combined with a pozzolan, a material that has binding properties when combined with water. One of the most effective and common pozzolans is fly ash, which is a byproduct of coal-burning power plants.

Coal fly ash also has the added benefit of recapturing a waste product of burning coal. Instead of releasing fly ash into the air or landfilling it, it is used to make concrete, and the addition of fly ash makes concrete more durable. As coal burning decreases, however, alternatives to fly ash will be in demand.

Some alternative pozzolans are crushed recycled glass and different types of clay.

Sugar bagasse, a waste product of sugar cane farming, also is being studied thanks to South Florida’s large sugar cane crop.

Ferraro is looking for alternative pozzolans that are structurally adequate, abundant, readily available and cost effective.

“We know that Portland cement on its own is less durable without fly ash, so we are looking for substitutes,” Ferraro says.

Concrete is porous, and one thing fly ash does really well, Ferraro says, is protect the steel encased within the concrete from chlorides that seep through the concrete layer. Pylons of coastal bridges, for example, sit in a chloride-rich environment of salt water.

“Fly ash gives us a long timeline on the initiation of corrosion and therefore extends the life cycle of the concrete,” Ferraro says.

Concrete can do a good job of protecting the steel rebar within, as in this sample from the Miami Marine Stadium, showing pristine rebar encased in the concrete despite the stadium's long-term exposure to salt water.

A Salty Environment While structures in Florida are protected from the freeze/thaw cycles farther north, and Florida bridges are spared the application of salt for snow removal, Florida faces other challenges, Ferraro says.

“We do have the world’s biggest corrosion laboratory called the Florida Keys,” Ferraro says. “So we do have to design our structures in a more robust manner for this high-chloride environment. And we do.”

But a salty, seaside environment does not automatically shorten a structure’s life span. Ferraro inspected the Miami Marine Stadium after Hurricane Andrew in 1990 and was surprised by what he found.

“I was amazed at how pristine the steel was, the rebar underneath the concrete,” Ferraro says, plucking a sample from the stadium from the specimens that line his office window ledge. The stadium, he says, was solid before the hurricane hit.

As a veteran of hundreds of structural inspections, Ferraro says he has seen poor construction practices that have scared him and poor maintenance practices that have been nerve-wracking. The condition of a structure, for the most part, is dependent on its age, how well it was constructed and how well it was maintained. Usually, he says, structures are

constructed pretty well, so that leaves age and maintenance as the two main factors in structural performance.

“Personally, I’ve seen a lot of concrete in Miami, and a lot of it’s in really good shape,” says Ferraro, who is working with another engineering professor to assess inspection reporting and building conditions in South Florida for the Florida Building Commission, a part of the Department of Business and Professional Regulation.

Ferraro snags another sample off his window ledge and holds it next to the sample from the marine stadium.

The rebar in the stadium sample is like chrome, gleaming. The other sample is rusty and brown.

Pointing to the stadium sample, he says, “This is Portland cement, nothing special, no amazing admixtures, and it’s literally sitting right on the water for as long as I’ve been alive. I was impressed with the wonderful nature of the concrete there.

“So it’s not necessarily the concrete,” Ferraro says. “Concrete can last a very, very, very, very long time.”

E xplore 31

As fly ash sources diminish and the Earth’s supply of materials to make cement dwindles, other sources of those minerals and metals are being investigated.

“There have been talks about how to harness a meteorite or asteroid to grab the minerals from within,” Ferraro says.

“We’re a ways from it, but part of my job is to look at science fiction and not make it science fiction anymore.”

Until we can grab a meteor and start extraterrestrial mining, we’re stuck with finding ways to make the materials on Earth more sustainable and more durable.

Concrete is a climate change issue because it is a point source producer of carbon dioxide. Limestone is a key component for Portland cement, and when limestone is heated in a kiln, up to 3000 F, the limestone decarbonates into calcium oxide and carbon dioxide.

Both the fuel used to heat cement and the release of carbon dioxide are climate change issues.

About 25 to 33 percent of all industrially produced CO2 comes from the concrete industry, Ferraro says. That seems like a huge number until you consider that concrete is the number one building construction material in the world, not only each year, but historically since its invention.

“It’s still relatively green when you consider that we use as much as we have and have produced as little CO2 as we have,” Ferraro says.

If Portland cement can be amended with other ingredients, the emissions can be reduced.

“Every time we can reduce the amount of Portland cement that goes into a Portland cement concrete mixture, we can do that,” Ferraro says.

The United States is responsible for 2% to 4% of all Portland cement production worldwide, while China is responsible for about 55%.

32 Fall 2021

John Jernigan

Materials and Meteorites

Concrete and steel are used together to provide two kinds of strength. Concrete handles the compressive load, the weight of a structure. The steel takes care of the tensile load and allows for some flexibility.

“The majority of all cement produced in the world happens in one place,” says Ferraro, who also collaborates with colleagues in China, Canada, Colombia and elsewhere on sustainability research.

“We all know we’re going to have to become much more sustainable if this species is going to be able to persist on this planet,” Ferraro says. “And a lot of us are working to make that happen.”

Infrastructure Backbone One thing that boosts the sustainability of concrete is its durability. Once a structure is built, generally it lasts a long time, Ferraro notes.

That’s one reason concrete is the backbone of the world’s infrastructure, including the largest concrete structure in the world, the Three Gorges Dam in China.

Closer to home, concrete and infrastructure get a report card every year.

The infrastructure grades issued annually by the American Society of Civil Engineers sometimes paint a dim picture of the condition of U.S. infrastructure.

The 2021 report card says: • A water main breaks every two minutes • 43% of roadways are in poor or

mediocre condition • 42% of bridges are at least 50 years

old, and 7.5% are structurally deficient

A boost in infrastructure spending, however, could change that, and concrete structures — roads, runways, sidewalks, bridges, levees, seawalls, dams, drainage systems — will mean more concrete.

Although concrete is estimated to be responsible for 8% of global emissions, the structures built with concrete often last half a century or more.

Ferraro says the U.S. compares better to other countries than the ASCE grades might indicate, with a few exceptions.

China, Japan and much of Europe have embarked on a rebuilding boom that makes portions of those countries more modern than the U.S. One of the research thrusts for Ferraro’s lab is testing concrete. How do you test something that could last 50 years and still retire on time?

“There are a number of proxy tests that give us a good indication of the durability of the aggregates we use with concrete,” Ferraro says. “But some tests can last two years, and you don’t want to wait two years for results if you want to build a bridge next month.

“We have to be able to do rapid testing to determine whether something will last for many years.”

Part of the lab’s focus is inventing new tests — “and arguing over the old tests” — and giving them the highest scrutiny, Ferraro says.

“I think AI will have a key role in the next few years in helping us really define some of the microstructural aspects that maybe we haven’t been able to look at in the same way.”

— Christopher Ferraro

In addition to traditional computer modeling, Ferraro is checking the robustness of models that use artificial intelligence and working with colleagues to develop virtual computer modeling. The training datasets to develop reliable algorithms have to be very robust, but with concrete’s long history, plenty of data are available.

“AI takes data and kind of black boxes it for us,” Ferraro says. “I think AI will have a key role in the next few years in helping us really define some of the microstructural aspects that maybe we haven’t been able to look at in the same way.

“We’re starting to ask those kinds of questions,” Ferraro says.

New developments in materials, testing and sustainability can’t come soon enough, and Ferraro says he and his colleagues stay busy.

“A breakthrough would have huge impact,” Ferraro says, “because there’s so much concrete out there.”

Christopher C. Ferraro Assistant Professor of Civil and Coastal Engineering ferraro@ce.ufl.edu

John Jernigan

Concrete Materials Research Laboratory https://concrete.essie.ufl.edu

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John Jernigan

The Science of Reading The Flamingo Literacy Matrix puts research-driven reading help into the hands of teachers

By Cindy Spence

34 Fall 2021

S

hauna Quirk has a degree in Spanish and arrived at a career in teaching by roundabout means.

So a few years ago, when she found herself facing a room full of kindergartners eager to learn to read, she also came face to face with a realization.

“There was a lot I didn’t know,” Quirk says.

That year, 2017, the University of Florida’s Lastinger Center for Learning was piloting a new literacy program called the Flamingo Literacy Matrix. Figuring she had a lot to gain, Quirk signed up.

And her toolbox grew.

“Almost right away, I found I could apply the lessons I was learning in the Flamingo Literacy Matrix in my

classroom,” says Quirk, who teaches at Glen Springs Elementary in Alachua County.

Professor Paige Pullen, the researcher behind the matrix, says she often hears from teachers like Quirk when she attends professional development workshops to talk about the Flamingo Literacy Matrix.

“I’ll ask teachers, ‘How many of you felt when you first graduated that you were prepared to teach reading?’” Pullen says. “No one raises their hand.”

With the Flamingo Literacy Matrix, teachers can get a major boost in their skills. In 2019-2020, 9% of teachers who signed up demonstrated mastery of literacy content on a pre-test. After they

finished, 98% demonstrated mastery on a post-test.

Pullen says her desire to use research to help teachers comes from her own experience. Between her master’s and doctoral programs at the UF College of Education, Pullen taught elementary school for 12 years. When she was asked to work with struggling readers, she realized she was not prepared.

“At that time, children were learning to read in spite of me, not because of me,” says Pullen, the chief academic officer of the Lastinger Center.

She began her Ph.D. research and a deep dive into the science of reading and discovered ways to demystify the process of teaching children to read.

E xplore 35

Reading Wars

“If you can't read, you are not going to be successful in math and social studies and science or any other content area. Reading holds the key and opens the door to knowledge in every other field.”

— Paige Pullen Children with phonological awareness can use the sounds of language to learn how to decode printed text. They can use phonemes, the smallest unit of sound, to understand the relationship between letters and the sounds they make. As they gain fluency, they can segment longer words and match and blend sounds to decode words.

Phonological awareness and reading gains go hand in hand.

Reading is particularly important now, as parents and teachers work to offset pandemic-related learning losses. Pullen

notes that this year, only 54 percent of third graders are reading on grade level, compared to 58 percent in 2019, before the pandemic.

The spotlight is on third grade because it is a transition stage, Pullen says. After third grade, students transition from learning to read to reading to learn, making it a skill that lays the foundation for all other learning. Pullen says struggling to read can have lifelong consequences: higher high school dropout rates, lower earnings and greater rates of incarceration.

– Flamingo Literacy Matrix –

5 Keys

1 ss lo

3

2

ne

no

36 Fall 2021

Paige Pullen

Pho

Since the 1980s, educators have debated the merits of reading programs, with whole language approaches on one end of the spectrum and phonics-based approaches on the other.

Whole language approaches emphasize putting books in children’s hands and teaching them to read by recognizing words in text and using other clues, such as pictures.

While access to books is still important, over the last 30 years, the science of reading has shown educators that helping children learn to read requires a systematic approach that recognizes key components: • Phonological awareness, or recognition of individual sounds in words • Decoding, or sounding out unfamiliar words • Fluency, the ability to read with speed and accuracy • Vocabulary • Comprehension For each area, the Flamingo Literacy Matrix provides strategies to assess and instruct a child as well as strategies on how to intervene when a child struggles.

The program is online, so accessible from anywhere. The program meets the requirements for the Florida reading endorsement, and South Carolina recently adopted it as part of the state’s Read to Succeed program. Other states are interested as well.

The matrix also allows teachers to upload a video of their teaching practices and get feedback.

“Can they translate the research into practice?” Pullen asks. “We’re teaching them the research, the evidence-based practices, behind how to teach reading.”

While the matrix boosts teacher knowledge, it also achieves the ultimate goal of helping students. Students whose teachers completed the matrix saw: • A 65% improvement in phonological awareness.

• An 86% improvement in their decoding skills.

• A half-year boost in reading growth.

gic al Awar

e

Fluency

De

coding

Pullen and her colleagues at the Lastinger Center took on another challenge this fall after the Florida Legislature passed a $200 million program called the New Worlds Reading Initiative, which was championed by House Speaker Chris Sprowls.

"We cannot overstate the profound impact teaching a child to read will have on their future success," Sprowls said.

"Not only do we open them up to new worlds and ideas, we give them the tools to expand their imagination, foster their curiosity and ultimately chart their own destiny.”

The Lastinger Center was asked to administer the program, which will put a new book each month in the hands of students from kindergarten to fifth grade who are reading below grade level. To complement the books, Pullen says the professional development resources in the Flamingo Literacy Matrix will be adapted to make modules that are easy for parents to use.

Short videos will demonstrate strategies parents can use at home to help support the development of foundational skills that go into reading.

“We'll actually be able to implement similar strategies from the literacy matrix, but designed for parents to implement at home, and these services will be delivered with the books,” Pullen says. “This will increase the opportunity for parents and children to read together while providing foundational skills.”

By combining teacher development, access to books and parental support, the goal would be improved outcomes for students on third grade reading and beyond.

John Jernigan

Book a Month

Shauna Quirk

“For struggling readers, we know that we have to go beyond the school day,” Pullen says.

“If you can’t read, you are not going to be successful in math and social studies

and science or any other content area,” Pullen says. “Reading holds the key and opens the door to knowledge in every other field.”

5 4

“Almost right away, I found I could apply the lessons I was learning in the Flamingo Literacy Matrix in my classroom.”

— Shauna Quirk

Vo

prehensio

n

C

om

cabular y E xplore 37

Words on a Page

Another example Pullen uses is Urdu (see graphic), an alphabetic language that immediately puts the viewer in the position of being a non-reader.

“Suddenly, you realize the complexities of learning how to read,” Pullen says.

“You have to understand the symbols.

You have to understand the sounds the symbols make. You have to understand how to put those sounds together. You have to understand where one word begins and another word ends. You have to understand directionality, where do you even start reading.”

Pullen says it takes explicit systematic instruction to pull all the subskills together to learn to read. The sound

system of language — where words begin and end, the sounds of letters and what the letters sound like when combined with others, and that the sounds go together to make words — is only part of the puzzle.

Readers need to understand the structure of language and how language works as they build their knowledge of grammar and vocabulary and learn to discern meaning from text.

“When we think of how all these processes have to work together, we suddenly realize how complex learning to read is,” Pullen says. “We’re not going to be able to just give a child a book and expect that they will figure it out.”

John Jernigan

For readers who struggle, words on a page are a frightening puzzle, one they lack the skills to figure out. There are clues, to be sure, like pictures on a page, but guessing a word is different than knowing it. And as school progresses, the pictures on the page become less and less common.

Pullen uses a slide in her professional development presentations that shows a phrase in other languages to demonstrate how alien text can look to a struggling reader: Tha leughadh na obair iom-fhillte a dh ‘ fheumas ioma-fho-sgilean a thoirt a-steach.

Feumar na fo-sgilean sin a chuir an sàs le ìre àrd de fèin-ghluasad agus mionaideachd.

That’s Scottish Gaelic for: Reading is a complex task that requires the integration of multiple subskills. These subskills must be implemented with a high degree of accuracy and automaticity.

Students like Ayanna Hornilla have improved their reading skills using the Flamingo Literacy Matrix in Shauna Quirk's class.

38 Fall 2021

The Toolbox In her path to teaching, Quirk was a veteran of multiple teacher training seminars and kept a cheat sheet handy for the professional jargon she often encountered.

Decoding the bureaucratic lingo, she said, was half the battle in getting trained.

“For me, there was a lot of technical jargon thrown about in professional development, and they expected you to just know it,” Quirk says. “I’d spend a lot of time writing down terms to look up later.”

By contrast, the Flamingo Literacy Matrix was easy and immediately usable.

No decoding necessary.

“The literacy matrix didn’t assume you knew it all but also didn’t dumb it down.

I think I knew I had absorbed it when I was walking home with my daughters and I remember stopping and saying, ‘Holy cow, I understand this well enough that I just explained it to my daughters.’’’

Pullen says she learned to teach reading in the 1980s using a whole language approach, so she is enthusiastic about sharing the science of reading in training the teachers of today. Raising children to be readers requires raising proficient readers, she says.

“Think about what we love and choose to do in our free time,” Pullen says. “If you’re not good at something, you’re not going to choose it. Part of the love of reading comes when we find success.”

Quirk recalls the change in her skills and the skills of her students in her 2017 kindergarten class. The literacy matrix, she says, became second nature for her, something she used every day, and it allowed her kindergartners to enter first grade with a solid foundation.

“Curriculum comes and goes,” Quirk says. “This will age well.”

Related Website: Lastinger Center's Flamingo Literacy Matrix https://lastinger.center.ufl.edu/literacy/literacy-matrix/ New Worlds Reading Initiative https://newworldsreading.com

John Jernigan

Paige Pullen Chief Academic Officer, Lastinger Center for Learning ppullen@coe.ufl.edu

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UF and the National Science Foundation The National Science Foundation is one of the University of Florida’s largest funding agencies, providing over $63 million annually to support more than 450 projects in fields as diverse as physics and natural history, education and cybersecurity. UF President Kent Fuchs is one of the 25 members of the National Science Board, who are appointed by the President to advise on NSF policy and on science to Congress and the Executive Branch.

iDigBio UF is home to iDigBio, a project to digitize natural history collections nationwide, making them available online to researchers, educators and community scientists around the world.

For the past decade, iDigBio, based at the Florida Museum of Natural History at the University of Florida, has led the push to digitize the estimated 1 billion biological specimens held in U.S. museums. These online records of animals, plants and other organisms serve as a searchable archive of life and help researchers identify species in danger of extinction, track the spread of invaders, study how climate change is reshaping ecosystems and possibly predict the next pandemic.

Thanks to iDigBio’s coordination, training and communitybuilding efforts, about 40% of specimens in U.S. collections are now represented in the program’s portal, comprising one of the largest virtual collections of Earth’s biodiversity and contributing to more than 2,000 studies so far.

One of iDigBio’s biggest achievements has been assembling a growing network of more than 300 museums and academic institutions and training their collections staff on how to fold digitization practices into standard curation protocols. As new digitization techniques emerge, such as 3D imaging and CT scanning, iDigBio has evolved in step.

40 Fall 2021

NHERI

LIGO

Engineers at UF’s Powell Family Structure and Materials Laboratory have designed one of the world’s most advanced wind hazard facilities to model the way extreme winds interact with man-made infrastructure.

The laboratory combines eight large fans with 319 individually controlled fans to more accurately replicate extreme wind phenomena beyond the eight-fan array. The bulk of the technology was created in-house using 3D printers.

The wind flows over 1,100 individually controlled elements that represent terrain around a building or other test subject.

Operators can quickly change the orientation and height of the elements, collectively referred to as the terraformer, to provide fine control over the turbulence close to the floor where the test subject is placed.

The laboratory is a national hub for experimental research making homes and businesses safer in hurricanes and tornadoes.

The lab is among seven labs in the nation with the designation of “Experimental Facilities” under NSF's National Hazards Engineering Research Infrastructure (NHERI) program and is one of the two dedicated to studying extreme wind events.

The facility attracts NSF-funded researchers from throughout the nation who are working on wind engineering projects and are part of a network of scientists who study different aspects of natural hazards. It provides undergraduate students, graduate students and faculty members access to one of the largest and most diverse suites of wind engineering experimental research infrastructure in the world.

UF researchers who helped confirm Einstein’s theory of gravitational waves in 2015 have observed a new type of black hole that challenges prior understanding of how the mysterious cosmic objects are formed across the universe.

The discovery identified an intermediate mass black hole, solving a riddle about a gap between the previously known categories of black holes: smaller black holes known as stellar mass black holes, and the largest black holes known as supermassive black holes.

Researchers observed the black hole using twin detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) and the Virgo gravitational-wave detector in Italy. These detectors are calibrated to sense tiny changes of distances on Earth that are then interpreted through algorithms to make sense of the cosmic communication.

In the six years since the LIGO project discovered gravitational waves, scientists across the world have fine-tuned instruments measuring these gravitational waves to find new phenomenon in space. The gravitational waves help reveal what happens in the universe and can tell us about how black holes are formed.

UF scientists invented and developed the algorithm, called coherent WaveBurst, that detected the first and so far only intermediate mass black hole.

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Poison ivy can work itchy evil on your skin

By Arthur Samia and Marjorie Montanez-Wiscovich

A

patient recently came in to our dermatology clinic with a rash and a story similar to so many others. He had been out camping with friends a few days earlier and helped carry some logs to stoke the fire. Little did he know he was going to pay for lending a helping hand. A couple of days later, red patches appeared on his forearms and chest, which soon began to itch miserably and form water blisters.

If you have ever spent any time outdoors — in the woods, working in the yard, even at the edges of a playground — maybe you’ve experienced something similar after encountering poison ivy. It’s not easy to forget.

Irritant Encounters

It’s a myth that the fluid from inside a blister can spread the rash.

Poison ivy is found everywhere in the continental U.S., mostly in Eastern and Midwestern states. Unfortunately for us humans, it is a hardy plant that can grow under many different conditions.

Its favorite places are in wooded areas, gardens and roadsides with partial shade or full sunlight.

And despite being a nuisance to people, poison ivy is an important member of the ecosystem. Its leaves, stems and berries are food for animals, and its vines can be shelter for small animals like toads and mice, even helping them climb trees. Climate change is turning out to benefit poison ivy, allowing for larger and more irritating plants.

You can usually spot poison ivy by its infamous three dull or glossy green leaves coming off a red stem. Sometimes there are flowers or fruits coming off the end of a branch.

Despite its name, poison ivy is not poisonous. It carries an oily sap on its leaves and stems called urushiol, which is irritating to most people’s skin. In fact, 85% to 90% of people are allergic to poison ivy’s urushiol to some degree, while the rest lack sensitivity

to this oil. You can occasionally see the urushiol oil as black spots on poison ivy leaves. Urushiol is what gives poison oak and poison sumac their evil power, too.

Touching poison ivy directly is obviously a bad idea. You can even get into trouble by touching clothing, pets or anything else that has brushed against the plant and picked up some of the urushiol. If a contaminated object isn’t cleaned, the urushiol will remain lying in wait – it can still cause a rash after hours, days or even years. Another danger is smoke from burning poison ivy, which can also affect your skin, as well as your nose, mouth, windpipe and lungs if you breathe it in.

42 Fall 2021

Oil to Rash Poison ivy’s rash can come in many forms, from small, red bumps to blisters or red patches. Whichever way it shows up, it is almost always mindbogglingly itchy.

When you get “poisoned,” you won’t know right away. It can take anywhere from four hours to 10 days for the rash to appear,

depending on how much urushiol gets on your skin, how sensitive you are to it and how many times you have been exposed to poison ivy previously.

Between exposure and itchy anguish, your body goes through a complex identification and reaction process. When the oil gets into your skin, your immune system’s sensor cells recognize urushiol as foreign to your body. These sensor cells then call in protector cells to the area, warning them of the invasion. The protector cells defend your body against the intruder by attacking the urushiol in the skin. Unfortunately, some of your body’s normal skin cells are casualties of this war, which is what leads to the itchiness and swelling of a poison ivy rash.

Your protector cells will then sit near the skin for many years and stand guard for urushiol if it ever shows up again. If it does, they remember having encountered this bad guy before, and their response is often faster and more powerful than the first time.

This rash is a type of allergic contact dermatitis – in the same family as the rashes some people get from wearing jewelry or metal belt buckles or from using certain fragrances or cosmetics.

Damage Done The saying “leaves of three; leave them be” highlights the best strategy to prevent poison ivy: avoidance. But if you do happen to come into contact with poison ivy, the first step should always be to remove and wash any clothing that has touched the plant.

Gently but thoroughly wash your skin immediately with soap and water. It can also help to clean under your fingernails and cut your nails short to prevent the urushiol from spreading if you scratch your skin.

Allergic contact dermatitis from poison ivy almost always results in a rash that usually lasts two to three weeks before it completely goes away.

It will eventually clear up on its own, but you can try some overthe-counter and home remedies to keep the itchiness and spread of the rash at bay. The blisters that form are not infected and do not normally require antibiotics. If you scratch though — and it can be very hard to resist — open skin can get infected.

To reduce itchiness, cool, wet compresses can help, as can a soak in a cool bath with baking soda or oatmeal bath products.

Calamine lotions or creams containing menthol can also cut the itch a bit. Over-the-counter cortisone cream or ointment can be used for the first several days after contact with poison ivy to quiet down your body’s reaction and keep the rash from getting severe. Taking antihistamines like diphenhydramine at night can slightly reduce itchiness and it has the benefit of helping you sleep better.

Seeing your doctor usually is not necessary for a poison ivy rash unless it spreads over large areas, becomes infected, lasts more than three weeks or is a rare extreme case that affects your breathing.

The best offense is a good defense. When you’re in the great outdoors, be careful what you touch and, when in doubt, if it has leaves of three, leave them be.

Arthur Samia Postdoctoral Research Fellow in Dermatology, University of Florida asamia@ufl.edu Marjorie Montanez-Wiscovich Clinical Assistant Professor of Dermatology, University of Florida m.montanez@ufl.edu

To read more articles by UF faculty, visit https://theconversation.com/institutions/university-of-florida-1392

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John Jernigan

The Flow

of Innovation More than 150 innovators and entrepreneurs gathered recently to unveil a new mural in the lobby of UF Innovate| Accelerate at The Hub. “The Flow of Innovation” depicts technologies and products birthed from UF inventions on 96 panels in the 42-foot-tall installation that is the centerpiece of The Hub. It includes discoveries made at UF that have had positive, global impacts.

From the top of the mural, perhaps the most famous UF invention and first UF technology transfer deal, Gatorade, flows over other UF innovations in engineering, medicine, and agriculture.

“This mural is intended to highlight the University of Florida’s work from Gatorade to the present day that is making the world better,” said Jim O’Connell, assistant vice president of UF commercialization and the director of UF Innovate|Tech Licensing. “We hoped to capture the past, present and future in our depiction of technologies and the products startups have created based on them. I think we achieved that.”

Katherine Kinsley-Momberger, art director of UF Research, is the artist behind the beautiful illustration. Kinsley-Momberger was also the artist of the previous mural centerpiece in the same location.

“I am honored to have been a part of this project — for the second time — collaborating with my colleagues at UF Research and UF Innovate. I hope that the mural will be enjoyed by those who work in The Hub and Gainesville’s Innovation District for many years to come,” said Kinsley-Momberger, who has worked at UF for over 20 years.

The unveiling was part of UF Innovate’s annual Standing Innovation event. Ophthalmology Professor and Eminent Scholar William Hauswirth was named Innovator of the Year for his decades of work to develop gene therapies to treat genetic forms of blindness and other diseases. Seven other researchers were recognized for their work.

To learn more, visit https://innovate.research.ufl.edu