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Data Management in the Environmental Health Sciences Seminar Series, Sept 10 – Oct 8, 2021

July 20, 2021 By Curnick, Jacqueline A


Data Management in the Environmental Health Sciences Seminar Series

 

September 10, 2021 / 10:45 a.m. / View presentation slides

Ontologies 101: Standardize your data using ontologies

Nicole Vasilevsky, PhD, Research Assistant Professor and Lead Biocurator, The Translational and Integrative Science Center

Ontologies are powerful tools that are used for classifying information, organizing data, and creating connections between data that allow for enhanced information retrieval, filtering, and analysis. This talk will introduce the basic concepts of ontologies, with a focus on biomedical ontologies, and provide some examples of how ontologies are used in everyday life and disease diagnostics and discuss how you can contribute to ontologies and participate in the biomedical ontology community.

 

September 17, 2021 / 10:45 a.m. / View presentation slides 

Using ontologies and knowledge graphs to link multi-modal data across scales and disciplines

Anne Thessen, PhD Semantic Engineer, The Translational and Integrative Science Center

Biology is a very heterogeneous discipline that has benefitted from the reductionist empirical approaches that have spawned thousands of subdisciplines, from neurobiology to landscape ecology, each with its own data types and research cultures. While we have learned much by isolating and experimenting on individual components of natural systems, there is much to be gained from looking at systems more holistically, which requires data integration at an unprecedented scale. In addition, these holistic approaches require expertise and data from outside biology, such as geology, computer science, and economics to name a few. This talk will present methodologies for integrating multi-modal data across disciplines to enable large-scale, holistic studies of natural systems and discuss the team science aspects of this work in the context of the GenoPhenoEnvo and Biomedical Data Translator project.


September 24, 2021 / 10:45 a.m. 

Title US-EPA Chemicals Dashboard – An integrated data hub for environmental science

Antony Williams, PhD, Scientist at Center of Computational Toxicology and Exposure at US Environmental Protection Agency

Abstract: The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program utilizes computational and data-driven approaches that integrate chemistry, exposure and biological data to help characterize potential risks from chemical exposure. The National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences, including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. The CompTox Chemicals Dashboard website provides access to data associated with ~900,000 chemical substances. New data are added on an ongoing basis, including the registration of new and emerging chemicals, data extracted from the literature, chemicals studied in our labs, and data of interest to specific research projects at the EPA. Hazard and exposure data have been assembled from a large number of public databases and as a result the dashboard surfaces hundreds of thousands of data points. Other data includes experimental and predicted physicochemical property data, in vitro bioassay data and millions of chemical identifiers (names and CAS Registry Numbers) to facilitate searching. Other integrated modules include real-time physicochemical and toxicity endpoint prediction and an integrated search to PubMed. This presentation will provide an overview of the CompTox Chemicals Dashboard and how it has developed into an integrated data hub for environmental data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

 

October 1, 2021 / 10:45 a.m. 

Improving alternative method adoption through tools and resources to support community knowledge

Shannon Bell, PhD, Principal Data Scientist at Integrated Laboratory Systems, Inc. (ILS), Apex, North Carolina

Over the past decade, efforts ranging from publications to workshops to science policy have been directed at moving from traditional, animal-based toxicity testing towards new approach methodologies (NAMs) that do not require animals. Key barriers hindering adoption of NAMs are knowledge gaps, both in terms of technical information deficiencies as well as lack of confidence in the methodologies. Information, comprised of data and the context within which it is used, is constantly evolving, and is typically a focal point when considering knowledge gaps. Efforts using standardized terminologies and improving data FAIRness (data should be findable, accessible, interoperable, and reusable) aid in addressing information challenges. Improving acceptance of information and methods/tools generating the data are equally important and increasing access to resources that promote approachability and transparency can support confidence building in end-users. This can be done by creating user-friendly tools that provide an access point for diverse users to explore data and techniques. These user-friendly resources build comfort and context that aids in bridging the communication gap between naive users often “traditionally” trained in in vivo approaches and subject matter experts in the NAMs. This presentation will highlight the DNTP’s Integrated Chemical Environment and other freely available web resources to illustrate ways in which knowledge gaps for NAM adoption are being addressed. Three common questions will be addressed as part of an overarching user story: How do I identify and obtain data for my compound? How can I put this data into a relevant context? How do I interpret and apply the data? Structure similarity, read-across, and in vitro to in vivo extrapolation will be discussed as a series of user-stories highlighting efforts of web-based tools to promote NAM adoption by closing knowledge gaps.

 

October 8, 2021 / 10:45 a.m. 

Building a Better Tox Test: Reproducibility and Sampling Error in

Toxicology

Lyle Burgoon, PhD, Director, Center for Existential Threat Analysis and Leader, Bioinformatics and Computational Toxicology, Michigan State University

Most current computational toxicology predictive models require toxicology data from laboratory experiments. Although not always apparent, the predictions from these computational models can have significant ramifications. For instance, a combatant commander in the Army may require soldiers to put on MOPS gear (suits that protect soldiers from chemical exposures) during a battle based on toxicity predictions that use current environmental levels from sensors as inputs. The problem is that MOPS gear is difficult to move and fight in, thus making our soldiers easier targets. It also means that taxpayer money may be wasted on needless and unnecessary remediation of training grounds. I have noticed that the reproducibility of toxicology data that go into our computational models tend to suffer from being underpowered, exhibiting excessive sampling error, and lack the details required for reproducibility. In many cases, chemicals are being found toxic based only on p-values, which the American Statistical Association considers a very poor practice. In this talk, I will discuss and demonstrate the problems with sampling error and reproducibility that I am seeing both as a regulatory toxicologist and a military scientist. I will discuss how we can do better as a toxicology community, to improve our science, and the reproducibility of our studies. And I will demonstrate why these steps are necessary for ensuring the quality of our future computational toxicology models, and for safeguarding human health. There are real-world consequences when we fail to practice science well, and together, we can make a difference.

Filed Under: Events, Seminars

Winners Selected in Statewide Radon PSA Poster and Video Contests; EHSRC Participates

June 25, 2021 By Curnick, Jacqueline A

Each year in Iowa, the American Lung Association and the Iowa Department of Public Health, in partnership with the U.S. Environmental Protection Agency, Region 7 and the Iowa Radon Coalition host the annual statewide Iowa Radon Poster and Video Contests.

Iowa citizens ages 9-14 are invited to create a radon poster that will increase public awareness of radon gas and encourage others to test their homes. A committee will select the top five winning posters from throughout the entire state of Iowa to receive monetary prizes. The school that submits the most entries wins $200.

Concurrently, high school students are invited to submit entries to the Iowa Radon Video Contest, for which three top prizes are awarded.  As a member of the Iowa Radon Coalition, EHSRC Coordinator Nancy Wyland has participated in judging this event for the past three years in representation of the Center.

“The submissions are quite creative, and the students work hard on their entries,” Ms. Wyland offered.  It’s a great event that engages young adults in environmental awareness and the dangers of radon, which is particularly prevalent in Iowa.”

Radon is a colorless, odorless, tasteless, radioactive gas produced by the natural decay of uranium in the soil. Exposure to elevated radon levels increases the risk of developing lung cancer. Radon is the leading cause of lung cancer among non-smokers and is the number one cause of death in homes, surpassing falls, poisoning, fires, choking, and drowning. As all Iowa counties are considered at high risk, this contest provides an opportunity to educate Iowa youth and the general public. By participating in this activity, students learn about radon and how to reduce their risk of exposure.

Wyland added, “Our Center has a longstanding research interest in radon and its environmental health impacts, so we’re proud to participate in this educational activity through our membership in the Iowa Radon Coalition.”

Poster Contest Winners can be viewed here:  https://www.lung.org/local-content/ia/radon-poster

The Top Ten Video Contest Winners can be viewed here: https://youtube.com/playlist?list=PLsIpNVMVEwiiT0UM6ax1cHFBVWkAD65G2

The EHSRC has a longstanding history of radon research, including studies of residential radon in Iowa, research on outdoor concentrations, and testing of monitoring devices. Recently, EHSRC Member Bill Field and Co-PI Ka Kahe (Columbia University Health Sciences) received an NIH R01 titled, “Residential radon exposure and stroke risk: the REGARDS study.”  This project will examine the association between radon exposure and stroke risk and to investigate whether geographic variation of radon concentration is related to the distribution of stroke rate in the U.S.

Filed Under: Events, Video

Iowa Public Radio- Restoring Environmental Protections and the Race Against Climate Change

January 29, 2021 By Curnick, Jacqueline A

EHSRC Deputy Director Dr. Peter Thorne was a guest on the show River to River to discuss restoring environmental protections and the race against climate change. Listen to the interview here. 

Blurb from Iowa Public Radio:

“President Joe Biden has vowed to restore environmental protections that have been weakened, altered or rolled back by the Trump Administration over the past four years.

The new president has ordered a review of more than 100 rules and regulations on air, water, public lands, endangered species and climate change and legal experts say it could take two to three years, or even longer, to put many of the old rules back in place.

On this edition of River to River, host Ben Kieffer talks with environmental health scientist Peter Thorne to talk about stances the new administration is taking when it comes to environmental policy. Thorne chaired the Environmental Protection Agency’s Science Advisory Board from 2015 to 2017.”

Filed Under: News, Research

Dr. Ashutosh Mangalam received a Merit Award from the Department of Veteran Affairs

January 21, 2021 By Curnick, Jacqueline A

Dr. Ashutosh Mangalam, member of the EHSRC, received a four-year VA Merit Award entitled, “Effect of Gut Microbiome Dysbiosis in the Pathobiology of Multiple Sclerosis”. Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system and affects around one million people in the US. The proposed studies will build upon recent findings from Dr. Mangalam’s laboratory showing that patients with MS have gut dysbiosis (altered gut microbiome compared to healthy controls). This study will test the hypothesis that gut dysbiosis promotes MS through enrichment of pathobionts which leads to leaky gut syndrome in addition to depletion of Equol producing gut bacteria. The latter are an important class of gut bacteria responsible for metabolizing phytoestrogen into beneficial compounds. Dr. Mangalam will utilize samples from MS patients and healthy control as well as from animal models of MS, to determine the mechanism(s) through which gut microbiome plays a role in the pathobiology of MS. Dr. Deema Fattal, a neurologist at the Iowa City VA and Dr. Kai Wang, a biostatistician in the College of Public Health are the co-investigators participating in the study. The focus of Dr. Mangalam’s team is to better understand the role of the gut microbiome in MS with a long term goal of manipulating the gut microbiome as a treatment option for MS patients.
This notice was first published by the University of Iowa Department of Pathology.

Filed Under: Research, Research Awards

Lab tour video – Lehmler Lab

December 30, 2020 By Curnick, Jacqueline A

Phd Candidate Derek Simonsen explains the work that goes on in Dr. Hans Lehmler’s lab and the Exposure Science Facility. Watch it now!

 

 

Image from Lehmler Lab tour video.

Filed Under: Video

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