NIMBioS

Predictive Modeling of the COVID-19 outbreak in Knox County

Posted on August 5, 2020 by Jennifer Spar

Coronavirus is capturing headlines around the world, and infectious disease experts are relying on data and mathematical models to help curb its spread.

NIMBioS Associate Director and UT Mathematics Professor Suzanne Lenhart, three former UT math PhD students and UT Epidemiology Professor Agricola Odoi have been working on modeling COVID-19 in Knox County using the cumulative number of cases and deaths.

The former UT math PhD students are Dr. Ibrahim Halil Aslan, Dr. Mahir Demir, and Dr. Michael Morgan Wise. Along with Lenhart they are collaborating authors of the Coronavirus-19 Outbreak Response Experts (CORE-19) at the University of Tennessee, Knoxville. Odoi is a member of the CORE-19 steering committee.

Their findings use modeling techniques and COVID-19 data from the Knox County Health department to forecast outbreak dynamics 3 months into the future. It also investigates the efficacy of social distancing policy, forecasting additional peaks for the outbreak if social distancing mandates are relaxed.

This collaborative group is now working on modeling the effects of some UT students returning to live on campus and interacting with UT and Knox County communities.

To view their models and read more, http://core19.utk.edu/policy-briefs

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2020 SRE Students Selected

Posted on May 8, 2020 by Greg Wiggins

NIMBioS is pleased to announce the 16 undergraduate student participants selected for its highly competitive 2020 Summer Research Experience (SRE) program. Participants were selected from a pool of more than 100 applicants from across the U.S. Due to COVID-19 travel and distancing guidelines, this year’s program will be a first, in that it will be conducted remotely and will run for four weeks, from June 1– 30, 2020.

Participants will work in teams with NIMBioS postdocs and UT faculty on five research projects at the interface of mathematics and biology.

2020 SRE participants and their assigned team projects are as follows:

Laurinne Balstad (Mathematics, Biology, Saint Olaf College), Jackie Folmar (Ecology & Evolutionary Biology, Yale Univ.), and Abigail Sallee (Biochemistry and Cellular & Molecular Biology, Univ. of Tennessee, Knoxville) will collaborate on a project developing an individual-based model to explain the co-evolutionary dynamics of quorum sensing and biofilms.

Matthew Clark (Computer Science, Mathematics, Fisk Univ.), Chelsea Seggern (Kinesiology, Univ. of Tennessee, Knoxville), and Anna Thomas (Mathematics, Computer Science, Lehigh Univ.) will be working on agent-based simulations of Caenorhabditis elegans.

Charlotte Beckford (Mathematics, Fordham Univ.), Elliott Smith (Ecology & Evolutionary Biology, Univ. of Michigan), and Amy Tian (Biology, Public Policy, Univ. of Chicago) will team up to investigate the influence of climate change velocity on future species distributions.

Umang Joshi (Biology, Computer Science, Xavier Univ.), Michael Lin (Biophysics, Johns Hopkins Univ.), and Stephanie Westaway (Physics, Mathematics, Samford Univ.) will work on a project modeling the effects of pathogenic bacteria on phytoplankton community mortality.

Spencer Catron (Mathematics, Physics, Univ. of Tennessee, Knoxville), Sarah Roth (Ecology & Evolutionary Biology, Univ. of Tennessee, Knoxville), Savannah Rumley (Biochemistry, Molecular Biology, Fisk Univ.), and Francesca Zumpano (Mathematics, Statistics, College of New Jersey) will work to model the individual and population effects of elevated incubation temperatures of sea turtles.

To read more about the NIMBioS SRE program, visit https://legacy.nimbios.org/sre/sre2020.

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SRE Students Publish in Population Ecology

Posted on March 25, 2020 by Catherine Crawley

2017 SRE students (from L) Sharee Brewer, Kimberly Dautel, Alan Liang and Brian Lerch strike a bird pose apropos of their team project studying mating patterns in birds’ evolution.

Celebration is in order for a group of students from the 2017 Summer Research Experiences (SRE ) for Undergraduates Program whose research has been published this month in Population Ecology.

The paper, “Space, density and extra‐pair matings have opposing impacts on male and female reproductive success,” analyzed the role of spatial configuration on the reproductive success of territorial species. The study found that sexual conflict between male and female breeders emerged when considering the effects of space on territorial breeders. The findings could have important implications for conservation and the role of mating dynamics in fragmented breeding habitats.

The paper’s lead author is Brian A. Lerch, who at the time of the SRE was a student at Case Western Reserve University. He is now completing a Ph.D. in biology at the University of North Carolina, Chapel Hill.

The other SRE authors are Kimberly A. Dautel, Sharee Brewer, and Alan Liang.

Dautel is completing a Ph.D. in mathematical modeling at the Rochester Institute of Technology (RIT).

Brewer is completing a Doctor of Veterinary Medicine degree at the University of Tennessee College of Veterinary Medicine.

Liang is a student in computer science at Cornell University.

SRE mentors and co-authors on the paper are former NIMBioS postdoctoral fellows Nourridine Siewe and Sarah Flanagan. Siewe is currently a postdoctoral research associate in computer science at the University of British Columbia and in the fall will join the faculty at RIT’s School of Mathematical Sciences. Flanagan is a Lecturer in the School of Biological Sciences at the University of Canterbury, New Zealand.

Congratulations, team!

The paper can be found here.

Citation: Lerch BA, Dautel KA, Brewer S, Liang A, Siewe N, Flanagan S. 2020. Space, density and extra‐pair matings have opposing impacts on male and female reproductive success. Population Ecology.

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Partnering for Success with Minority Serving Institutes: The Story of Fisk

Posted on March 17, 2020 by Catherine Crawley

A recent gathering at Fisk University with Sanjukta Hota (center, in red) and Suzanne Lenhart (to Hota’s left)

“The pursuit of knowledge and understanding is enriched by an environment in which people of diverse backgrounds learn together and from each other, and participate in free and genuine exchanges of views.” (University of Tennessee Diversity Action Plan)

Since its beginnings in 2008, NIMBioS has fostered strong collaborations in areas of research, science and education with several Minority Serving Institutions (MSIs). In signed joint agreements, the primary goal has been to cultivate a more diverse group of researchers capable of conducting research at the math/biology interface.

One of the most productive partnerships has been with Fisk University. From the beginning, the NIMBioS Education and Outreach team has worked closely with Sanjukta Hota, an associate professor of mathematics at Fisk University.

Hota’s research focuses on developing mathematical models on human respiratory dynamics, artificial ventilation, HIV control and other optimization models.

The collaboration with Fisk has involved helping write successful grant proposals, co-authoring research articles, as well as supporting NIMBioS postdoctoral visits to Fisk classrooms and supporting Fisk students in the NIMBioS Summer Research Experience for undergraduates program and the NIMBioS Undergraduate Research Conference at the Interface of Biology and Mathematics.

Dr. Folashade Agusto (right), then a NIMBioS Postdoctoral Fellow, visits Dr. Hota and Fisk University students to present her model of avian influenza. December 2010. Agusto is now an assistant professor of ecology & evolutionary biology at The University of Kansas.

Ashish Gauli (far left) was a student in the 2015 Summer Research Experiences program. Gauli along with his SRE teammates Nathan Wikle (center) and Ryan Yan (far right) developed an award-winning interactive website to help track invasive species using global shipping routes.

The collaboration has reinvigorated the STEM disciplines at Fisk and created new opportunities.

“Partnering with NIMBioS has been extremely beneficial to the STEM faculty and students of Fisk University. It has enabled a number of Fisk faculty to engage in research in various bio-mathematical topics and has provided excellent opportunities for many of our students to participate in research conferences, seminars and internship programs,” Hota said.

“The informal and friendly research atmosphere at NIMBioS and the valuable research advice and suggestions provided by Dr. Suzanne Lenhart, Dr. Lou Gross and other research personnel associated with NIMBioS are of great inspiration to Fisk students and faculty,” Hota added.

One of the new STEM avenues is the establishment of a new interdisciplinary program on biomathematics and bionformatics, which Hota directs. Hota is Principal Investigator on the funding from the National Science Foundation that supports the development of the new program.

NIMBioS Associate Director for Education and Outreach Suzanne Lenhart has been an external advisor to the new program.

“Dr. Lenhart’s input and constructive suggestions in all our committee meetings and seminars has been very helpful in making our program successful,” Hota said.

Other joint agreements at NIMBioS have been signed with California State University-San Marcos, Howard University, Tennessee State University, and University of Texas-El Paso.

Posted in Education/Outreach, MSIs | Comments Off

Filling the Research Gap: Mathematics of Gun Violence

Posted on January 29, 2020 by Catherine Crawley

NIMBioS/DySoC Investigative Workshop on the Mathematics of Gun Violence, May 1-3, 2019

Coronavirus is capturing headlines around the world, and infectious disease experts are relying on data and mathematical models to help to curb its spread.

Another public health menace capturing news headlines would also benefit from data and mathematical models: the scourge of gun violence.

The NIMBioS/DySoC Investigative Workshop on the Mathematics of Gun Violence, held in May 2019, helped to fill the research void, and activities from the workshop were recently described in an article, “The Mathematics Underlying Gun Violence” in the January/February 2020 newsletter of the Society for Industrial and Applied Mathematics (SIAM).

The three-day interdisciplinary workshop brought together 29 scholars from a variety of quantitative fields including mathematics (computer science, statistics, and informatics), social science areas (geography, psychology, and criminology), and biological disciplines (behavior, medicine, and ecology). The workshop included presentations from participants, a poster session to indicate the diversity of methods currently being used in the field, and breakout groups on topics chosen with input from the participants.

The article summarized the existing literature presented at the workshop and identified some promising ideas that emerged from the workshop, spanning stakeholder collaboration, evidence-based interventions, effects of rare events, epidemiological criminology, theoretical models, technology, spatiotemporal characteristics, and network models.

The article also highlighted the need for more cross-disciplinary and interdisciplinary collaboration, better evaluation techniques, improved data, and increased funding support.

Posted in DySoC, interdisciplinary, Investigative Workshops, publication, Workshop | Comments Off

Undergraduate Research Wins Award

Posted on November 13, 2019 by Catherine Crawley

Abby Williams presents award winning SRE poster.

A team of undergraduate researchers from the NIMBioS 2019 Research Experiences for Undergraduate (REU) program received a best poster award this month at the 15th annual Regional Mathematics and Statistics Conference at the University of North Carolina, Greensboro.

Abby Williams, a junior in mathematics at Salem College, presented the poster at the conference.

“Impact of Climate Change on the Distribution of Buzz Pollinators” presents research that Williams and her REU team conducted at NIMBioS. The research uses ecological niche modeling to predict the potential habitat suitability for 16 different bee species native to North America that buzz pollinates tomatoes, based on preserved specimen data and climate scenarios of varying carbon emissions. The main map on the poster depicts the change in habitat suitability that should occur by the year 2050 under a high emissions scenario. These regions of habitat loss were compared to areas that are currently known to produce a substantial amount of tomatoes. The research found that high production areas, such as around Indiana and Ohio, are predicted to lose significant habitat suitability for buzz pollinators, which would in turn negatively impact tomato crop yield.

Other group members on the REU project were Ellie Lochner, a math student at the University of Wisconsin, and Brandyn Ruiz, a statistics and applied math student at Arizona State University. Mentors were NIMBioS postdoc Luis Carrasco; Mona Papeş, who directs the Spatial Analysis Lab at NIMBioS and is an assistant professor in the Department of Ecology & Evolutionary Biology at UT; and NIMBioS Education & Outreach Coordinator Greg Wiggins.

The NIMBioS REU program helped Williams really hone her research skills and interests.

“I really enjoyed learning about ecological niche modeling and how to use R and ArcGIS. I use R almost every day now,” she said.

For Williams, meeting different people from diverse backgrounds was the best part of the REU program.

“The connections and friends that I made last summer introduced me to a world of possibilities, and I cannot wait to explore what that world has to offer,” she said.

Congratulations Team!

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Girls Dig STEM at NIMBioS

Posted on November 12, 2019 by Catherine Crawley

Suzanne Lenhart (center) leads a building triangles exercise.

Virginia Dale from Oak Ridge National Laboratory

Fifty middle school girls dug deep into science-technology-engineering-and-math at NIMBioS on Saturday with the Expanding Your Horizons Network STEM Activity Day.

The event was organized by Suzanne Lenhart and Greg Wiggins at NIMBioS, in consultation with Judith Iriate-Gross from Middle Tennessee State University.

Women faculty and staff from the University of Tennessee led hands-on activities, from “Squishing Specimens for Science” to “Powering VOLt City.” They were Virginia Dale from Oak Ridge National Laboratory, Jessica Budke and Liz Derryberry from Ecology and Evolutionary Biology, Anne Skutnik from Electrical Engineering and Computer Science, Audra Hinson from Microbiology, and Lenhart, Joan Lind, and Marie Jameson from Mathematics.

The Expanding Your Horizons Network promotes the continuing development in mathematics and science of all people, with particular emphasis on the needs of women and girls.

The day was co-sponsored by the Knoxville Branch of the American Association of University Women (AAUW).

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Networking? New Software Studies the Ecological Kind

Posted on September 23, 2019 by Catherine Crawley

Meeting 4 of the Ecological Network Dynamics Working Group: (L to R) Front: Mathilde Besson, Cecilia Diaz Castelazo, Mathias Pires, Laura Burkle, Jimmy O’Donnell; Rear: Justin Yeakel, Marcus Aloizio Martinez de Aguiar, David Hembry, Erica Newman, Ulrich Mueller.

The activities of the Ecological Network Dynamics Working Group, which concluded this year, have culminated in a new R software package, now available, for analyzing the properties of large-scale ecological networks.

EcoNetGen constructs and samples networks with predetermined topologies including network size and structure. The networks can represent communities varying in size and types of interactions. The software gives its users the ability to simulate the complete underlying structure of a network and compare it to the size and structure of a sampled network.

Working Group members co-authored a paper, recently published in PeerJ, detailing use of the software package.

In “Revealing biases in the sampling of ecological interaction networks,” the study simulates large networks of species interactions and then subsamples from the simulations to simulate field sampling. The study is able then “to determine what biases exist in our study of network structure, and what aspects of real ecological networks slip through the cracks in empirical studies,” writes co-author David Hembry.

Several recommendations are made for empirical field ecologists to use in their projects that aim to characterize large species interaction networks.

The Working Group, which met four times at NIMBioS since June 2015, included field biologists, theoreticians and computational biologists. Co-organizers were David Hembry (Ecology and Evolutionary Biology, Univ. of Arizona); Dominique Gravel (Biology, Univ. de Sherbrooke, Quebec, Canada); Paulo Guimaraes Jr. (Ecology, Univ. of Sao Paulo (USP), Brazil); and James O’Donnell (School of Marine and Environmental Affairs, Univ. of Washington, Seattle).

Citation: de Aguiar et al. 2019. Revealing biases in the sampling of ecological interaction networks. PeerJ. DOI: 10.7717/peerj.7566

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Top of Class: Quantitative Bioscience at UT

Posted on September 16, 2019 by Catherine Crawley

As a service to the university, NIMBioS has unveiled a new Quantitative Bioscience website showcasing the multiple routes to success for graduate education in quantitative bioscience at the University of Tennessee.

With 20 different research areas to explore, UT has become a world-leader in quantitative bioscience disciplines. The website highlights each of these areas.

The site describes in detail the various pathways for developing a graduate program in quantitative bioscience and includes options within the Division of Biology, Department of Mathematics, UT-ORNL Graduate School of Genome Science and Technology, Tickle College of Engineering, Bredesen Center for Interdisciplinary Research and Graduate Education and UT’s Institute of Agriculture.

UT has a long history as one of the world’s largest collections of faculty in quantitative bioscience, located in a variety of departments and research labs across campus. The site includes a list of 60 UT faculty who are associated with quantitative bioscience research.

To provide evidence of the success of quantitative bioscience education at UT, another page showcases student success stories, with a listing of the PhD students who have obtained their degrees under the mentorship of faculty affiliated with quantitative bioscience, along with their position following graduation, whether in academia, government or industry.

Convergence research across mathematics, statistics, computational and data science is building new frameworks and novel ways for problem solving in the life sciences. Over the past decade, NIMBioS has fostered these efforts to develop cutting-edge, cross-disciplinary collaborative connections that address the vast array of challenging questions at the interface of the quantitative and life sciences.

For more information, visit www.nimbios.org/qb. A brochure is also available.

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Saving Amphibians, One Tadpole at a Time

Posted on September 10, 2019 by Catherine Crawley

A collaboration with former NIMBioS postdocs Angela Peace and Suzanne O’Regan, along with UT’s Matt Gray, has culminated in a new study in Ecological Modeling that investigates the dynamics of a highly virulent ranavirus and helps to illustrate its threat to biodiversity in North America.

Globally emerging pathogens that affect amphibians, reptiles and fish, ranaviruses have caused catastrophic die-offs of thousands of larval wood frogs. In some cases, population projection models suggest that ranaviruses can cause outright amphibian extinction.

Using a highly virulent chimeric ranavirus recently discovered at a bullfrog farm in southern Georgia, the researchers combined experiments and disease modeling to examine the potential consequences of the ranavirus on wood frog tadpoles.

The disease models included multiple transmission pathways—direct contact, environmental transmission via pathogens in the water, and transmission via feeding on dead individuals. A novel modeling approach, the study also incorporated multiple host infection stages and analyzed effects as the disease progressed, which appeared to strengthen the models’ predictions.

The model simulations predicted 100% mortality of a wood frog tadpole population in two weeks.

The authors recommend that surveillance for the pathogen occur at a minimum in the river watershed, and that disease management strategies should be prioritize spatial containment of the pathogen.

All transmission pathways in the study had high invasion potential and so targeting only one transmission pathway is unlikely to be effective, the authors wrote.

Citation: Peace A et al. 2019. A highly invasive chimeric ranavirus can decimate tadpole populations rapidly through multiple transmission pathways. Ecological Modelling 410: 108777.

Posted in ecology, publication, research, viruses, Wildlife | Comments Off