Healthy plant-based diets better for the environment than less healthy plant-based diets

Peer-Reviewed Publication

HARVARD T.H. CHAN SCHOOL OF PUBLIC HEALTH

Boston, MA— Healthier plant-based dietary patterns were associated with better environmental health, while less healthy plant-based dietary patterns, which are higher in foods like refined grains and sugar-sweetened beverages, required more cropland and fertilizer, according to a new study led by researchers at Harvard T.H. Chan School of Health and Brigham and Women’s Hospital. The findings also showed that red and processed meat had the highest environmental impact out of all food groups in participants’ diets, producing the greatest share of greenhouse gas emissions and requiring the most irrigation water, cropland, and fertilizer. 

“The differences between plant-based diets was surprising because they’re often portrayed as universally healthy and good for the environment, but it's more nuanced than that,” said Aviva Musicus, postdoctoral research fellow in the Department of Nutrition at Harvard Chan School and corresponding author of the study. “To be clear, we’re not asserting that less healthy plant-based diets are worse for the environment than animal-based diets. However, our findings show that plant-based diets can have different health and environmental impacts.” 

The study, which is one of the first to look simultaneously at the health and environmental impacts of various plant-based diets, was published in the November 2022 edition of The Lancet Planetary Health.

Previous research has documented that different types of plant-based diets have various health effects. For example, plant-based diets higher in whole grains, fruits, vegetables, nuts, legumes, vegetable oils, and tea/coffee are associated with reduced chronic disease risk, while plant-based diets high in fruit juices, sugar-sweetened beverages, refined grains, potatoes, and sweets/desserts are associated with an increased risk of chronic disease. Yet little research has been conducted to determine the environmental impacts, such as greenhouse gas emissions, use of high-quality cropland, nitrogen from fertilizer, and irrigation water, of these dietary approaches. 

Using data from the Nurses’ Health Study II, the researchers analyzed the food intakes of more than 65,000 qualifying participants, and examined their diets’ associations with health outcomes, including relative risks of cardiovascular disease, and with environmental impacts. To differentiate plant-based dietary patterns, the researchers characterized participants’ diets using various dietary indices, including the Healthy and Unhealthy Plant-based Diet Indices. Higher scores on the unhealthy plant-based diet index indicated higher consumption of refined grains, sugary drinks, fruit juice, potatoes, and sweets/desserts; while higher scores on the healthy plant-based diet index indicated higher consumption of vegetables, fruits, whole grains, nuts, legumes, vegetable oils, and tea/coffee.  

Participants who consumed healthy plant-based diets had lower cardiovascular disease risk, and those diets had lower greenhouse gas emissions and use of cropland, irrigation water, and nitrogenous fertilizer than diets that were higher in unhealthy plant-based and animal-based foods. Participants who ate unhealthy plant-based diets experienced a higher risk of cardiovascular disease, and their diets required more cropland and fertilizer than diets that were higher in healthy plant-based and animal foods. The findings also reinforced earlier studies showing that diets higher in animal-based foods, especially red and processed meat, have greater adverse environmental impacts than plant-based diets.  

“Because human health ultimately depends upon planetary health, future U.S. dietary guidelines should include nuanced consideration of environmental sustainability and recognize that not all plant-based diets confer the same health and environmental benefits,” said Daniel Wang, assistant professor in the Department of Nutrition at Harvard Chan School, the Channing Division of Network Medicine at Brigham and Women’s Hospital and Harvard Medical School and co-author of the study. 

This study was supported by the National Institutes of Health (NIH grants U01 CA176726, UM1 CA186107, HL35464, and 2T32CA057711).  

“Health and environmental impacts of plant-rich dietary patterns: A U.S. prospective cohort study,” Aviva A. Musicus, Dong D. Wang, Marie Janiszewski, Gidon Eshel, Stacy A. Blondin,  Walter Willett, Meir J. Stampfer, The Lancet Planetary Health, online November 2022, doi:10.1016/S2542-5196(22)00243-1. 

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Harvard T.H. Chan School of Public Health brings together dedicated experts from many disciplines to educate new generations of global health leaders and produce powerful ideas that improve the lives and health of people everywhere. As a community of leading scientists, educators, and students, we work together to take innovative ideas from the laboratory to people’s lives—not only making scientific breakthroughs, but also working to change individual behaviors, public policies, and health care practices. Each year, more than 400 faculty members at Harvard Chan School teach 1,000-plus full-time students from around the world and train thousands more through online and executive education courses. Founded in 1913 as the Harvard-MIT School of Health Officers, the School is recognized as America’s oldest professional training program in public health. 

Brigham and Women’s Hospital is a founding member of Mass General Brigham and a teaching affiliate of Harvard Medical School. With nearly 1,000 inpatient beds, approximately 50,000 inpatient stays, and over 2.6 million outpatient encounters annually, clinicians across the Brigham provide compassionate, high-quality care in virtually every medical and surgical specialty to patients locally, regionally, nationally and around the world. An international leader in basic, clinical, and translational research, Brigham and Women’s Hospital has nearly 5,000 scientists, including physician-investigators, renowned biomedical researchers and faculty supported by nearly $750 million in funding. The Brigham’s medical preeminence and service to the community dates to 1832, with the opening of the Boston Lying In, one of the nation's first maternity hospitals designed to care for women unable to afford in-home medical care. Its merger with the Free Hospital for Women resulted in the Boston Hospital for Women in 1966. In 1980, the Boston Hospital for Women, the Peter Bent Brigham Hospital and the Robert Breck Brigham Hospital officially merged to become Brigham and Women’s Hospital. With nearly 21,000 employees across the Brigham family – including the Brigham and Women’s Physicians Organization and Brigham and Women’s Faulkner Hospital – that rich history is the foundation for our commitment to providing superb care for some of the most complex cases, pursuing breakthroughs in biomedical research, training the next generation of health care providers, and serving the local and global community. 

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JOURNAL

The Lancet Planetary Health

DOI

10.1016/S2542-5196(22)00243-1 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Health and environmental impacts of plant-rich dietary patterns: A U.S. prospective cohort study

ARTICLE PUBLICATION DATE

10-Nov-2022

Heat or eat? Prepayment users consume less fruit and vegetables, study finds

Peer-Reviewed Publication

UNIVERSITY OF EAST ANGLIA

People using prepayment energy meters consume less fruit and vegetables compared to those using alternative payment methods, according to new research.

The study, by academics at the Universities of East Anglia (UEA) and Reading in the UK, and the University of Macedonia in Greece, explores the role of prepayment meters in the ‘heat-or-eat’ dilemma, a trade-off typically between paying for food or heating.

Households with prepaid meters typically pay more for their energy and the researchers found a strong link between this and lower consumption of fruit and vegetables – on average almost three fewer portions a week compared to those using alternative payment methods, such as direct debit.

The difference in consumption is roughly split between one fewer fruit and two fewer vegetables. The results, published in the journal Social Science & Medicine, suggest targeted support for prepayment users may have beneficial effects on people’s fruit and vegetable consumption patterns, and that this could be more effective in protecting women’s health in particular.

Drawing on a sample of more than 24,800 people living in Great Britain, the analysis further reveals that prepayment meter users are not only less likely to meet the World Health Organisation's recommended ‘5-a-day’, but also more likely to use food banks, which often do not provide fruit and vegetables because of the cost and perishable nature of the goods, as well as demand, with households relying on cold boxes and kettle boxes that either do not need cooking or only need hot water from a kettle. 

The researchers say the heat-or-eat dilemma has resurfaced during the ongoing energy price crisis and warn it has the potential to worsen diet quality among the UK population if expenditure on healthy food is traded-off for energy consumption.

The study’s lead author Dr Andrew Burlinson, Lecturer in Energy Economics at UEA’s Norwich Business School, explained that while the link between prepayment meters and consumption of fruit and vegetables might seem obvious, there has been little research into it with regards to the different payment methods.

“Most importantly, our findings show that prepayment meters play a role in lower levels of fruit and vegetable consumption among potentially more vulnerable households,” said Dr Burlinson. 

“Short-term support is necessary but not sufficient to protect households from future energy price shocks. The UK government should develop strategies that could make a lasting difference to households.

“For example, a new social tariff could eliminate the prepaid meter price premium, bringing prices in-line with direct debit customers – paid for in the short-term by a windfall tax on oil and gas companies and general taxation in the longer-term.”

According to the National Food Strategy only a quarter of the UK population meets the recommended consumption of fruit and vegetables - an important source of dietary fibre, minerals, and vitamins - despite the lower associated risk of morbidity and mortality.

To help address this, the study makes four key policy recommendations, including allocating financial support to prepayment meter users via channels likely to increase fruit and vegetable consumption. For example, public health initiatives, such as the Healthy Start Scheme or Best Start Foods, may be expanded to include vulnerable prepayment meter users. 

Targeted support measures are necessary as they may increase healthy food choices, in particular fruit and vegetables, for those more vulnerable; this may be viewed as a preventable measure from a public health perspective as healthier food has the potential to reduce cardiovascular disease, cancer, and premature mortality risks.

“Over the medium and long term, governments should scale up the installation of energy efficiency and low-carbon technologies in the residential sector, including insulation and solar panels,” said Dr Apostolos Davillas, co-author, from the University of Macedonia.

Co-author of the study, Dr Cherry Law at the University of Reading added: “Policy instruments aimed at reducing energy demand, whilst ensuring energy services are affordable, may not only help vulnerable households, including prepayment meter users, achieve adequate levels of energy.

“They could also increase their resilience to future energy price volatility, reduce carbon emissions, and have the potential to improve the quality of diets and population health as a result.”

Commenting in light of the research, national fuel poverty charity National Energy Action (NEA) warned that not addressing the issues as soon as possible will result in “continued and unnecessary hardship”.

Peter Smith, Director of Policy and Advocacy at NEA, said: “With energy bills already at record highs, prepayment meter customers face the starkest choices over the coming months. Hundreds of thousands of people are likely to ration their use or stop topping up simply because they cannot afford to.

“Most worryingly, this new research shows for the first time that prepayment users are increasingly unable to feed the meter at the same time as feeding themselves or their families. We know children face some of the most severe consequences, too many will be going hungry and cold as the winter months approach. 

“The UK government must urgently prioritise and deepen support for low income and vulnerable households this winter and beyond. We particularly need to reduce the number of legacy prepayment meters which prohibit support reaching people more easily and standing charges which grow daily, irrespective of whether any energy is being used.

“Ultimately, we need to put an end to the shocking energy waste in our leaky homes which has made us much more exposed to this energy crisis.” 

‘Pay (for it) as you go: Prepaid energy meters and the heat-or-eat dilemma’, Andrew Burlinson, Apostolos Davillas and Cherry Law, is published in Social Science & Medicine.

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JOURNAL

Social Science & Medicine

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Pay (for it) as you go: Prepaid energy meters and the heat-or-eat dilemma

ARTICLE PUBLICATION DATE

11-Nov-2022

GREENWASHING

Biofuel on the road to energy, cost savings

Peer-Reviewed Publication

DOE/ARGONNE NATIONAL LABORATORY

Argonne collaborates with U.S. laboratories on research to identify promising biofuels for different engine types.

Biofuel is closer to becoming a cost-competitive, climate-friendly solution for slashing carbon emissions in cars and trucks, according to two new studies.

The U.S. Department of Energy’s (DOE) Argonne National Laboratory  collaborated with the DOE’s National Renewable Energy Laboratory (NREL), Pacific Northwest National Laboratory (PNNL) and Idaho National Laboratory (INL) on the research. Results showed that biofuel combined with advanced engine design can reduce greenhouse gas (GHG) emissions by roughly 60% while improving fuel efficiency or reducing tailpipe emissions.

Argonne energy system analyst Pahola Thathiana Benavides,  NREL process engineer Andrew W. Bartling and PNNL engineer Steven Phillips were lead analysts for the two studies published in ACS Sustainable Chemistry & Engineering.

“The idea is to develop new biofuels blended with conventional fuels to improve engine performance. This means a gasoline car or truck could go further on the same amount of fuel or a diesel vehicle could meet more stringent emissions standards.” — Troy Hawkins, Argonne’s group manager, Fuels and Products Group

Biofuel has significant advantages over petroleum gasoline. But the engines themselves are also critical to energy efficiency. Designing low-carbon fuels and engines to work together can maximize energy use and vehicle performance.

“We are at the intersection of new innovations in both engines and biofuel,” said Troy Hawkins, Argonne’s group manager, fuels and products group, an author on both ACS Sustainable Chemistry & Engineering studies. ​“Our goal was to develop new biofuels blended with conventional fuels to improve engine performance. This means a gasoline-powered car or truck could go further on the same amount of fuel. Or a diesel vehicle could meet more stringent emissions standards.”

In both studies, Argonne scientists worked with other national labs to identify promising fuels for different engine types. Researchers considered cost, environmental impact and potential for expanding to commercial markets.

The research is supported by the Co-Optimization of Fuels & Engines (Co-Optima) initiative jointly led by DOE’s Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office and Vehicle Technologies Office.

Argonne is part of Co-Optima’s consortium of nine national laboratories and over 20 university and industrial partners. The consortium studies how simultaneous innovations in fuel and engines can boost fuel economy and vehicle performance while reducing emissions.

Scientists and experts at every DOE laboratory played an important role in each phase of the research, Hawkins said.

“This research is a really good example of how laboratories can work together to help the DOE accomplish its mission,” Hawkins said.

Finding biofuel pathways

Co-Optima’s research builds on the goal to identify and understand bioblendstocks, or biofuel. Biofuel is produced from biomass — organic materials including plants, agricultural waste and wet waste. Biofuel can be blended with conventional fuel to reduce emissions and improve fuel and engine performance.

Collaborating with Co-Optima fuel experts, researchers used a screening process to develop a list of biofuels for their research, Benavides said.

Argonne scientists developed the list of biofuels working with experts including PNNL technical team manager and Co-Optima Leadership Team member Daniel Gaspar, NREL senior scientist Gina Fioroni, NREL senior research fellow Robert McCormick, and Anthe George, senior manager at DOE’s Sandia National Laboratories (SNL).

“We worked with other experts to use specific criteria to narrow many biofuel candidates down to a short list for our research. This list was developed based on the required properties and the engine’s combustion mode,” Benavides said.

Converting biomass to biofuel is a complex process involving variables in feedstock, conversion technologies and fuel types. It is especially challenging finding biofuel pathways that also meet economic, technology and energy goals.

One study was co-first-authored by Benavides. The team assessed 12 biofuel production pathways for optimizing multimode internal combustion engines. Multimode engines can deliver greater efficiency and cost savings by using different methods of ignition, combustion and/or fuel-preparation, depending on driving demands.

Researchers used renewable biomass feedstock found in forestry byproducts such as wood waste and agricultural byproducts such as corn stover. They used conversion technologies including either fermentation, catalysis under high heat and pressure, or a combination of both.

“We found that not only can seven biofuels be produced cost-competitively, but that these seven are varied in terms of feedstock used and conversion technology,” Bartling said. ​“This means that biorefineries can be more flexible in choosing where and how to build their facilities.”

NREL and PNNL researchers did a techno-economic assessment of the biofuel production pathways, analyzing cost and technology performance.

“Our findings showed that many of the biofuels are competitive with the current cost of petroleum fuel,” Phillips said.

Researchers also analyzed environmental impact. A life cycle analysis of the pathways using Argonne’s GREET® (Greenhouse Gases, Regulated Emissions, and Energy used in Technologies) model showed impressive results. Ten biofuels have the potential to reduce GHG emissions by 60% compared to petroleum gasoline. The list includes alcohols, furan mixtures and olefins.

Biofuel promising for diesel engines

The second study was co-first-authored by Bartling. Researchers analyzed 25 pathways for producing biofuel optimized to improve combustion for mixing-controlled compression ignition engines. These are a type of diesel engine mainly used for freight transportation.

To develop biofuel production pathways, researchers used feedstocks ranging from plant materials such as wood chips or corn stover, to oils from soybean and cuphea, to wet wastes and recycled grease. They used conversion technologies including fermentation, gasification, and hydrothermal liquefaction.

“The diverse set of biomass resources available in the U.S. has great potential to replace a portion of fuels and chemicals that now come from petroleum,” said Damon Hartley, INL’s Operations Research and Analysis Group lead. ​“However, one of the largest barriers is the wide variability in quality in the raw materials. This can have a large impact on how the material performs in conversion.”

As with the first study, most of the technologies performed well. Most of the biofuels were cost-competitive with current gas prices.

In terms of environmental impact, GHG emissions were reduced more than 60% in 12 of the 25 pathways, according to the GREET life cycle analysis.

“We evaluated the life cycle GHG emissions for each mixing-controlled compression ignition engine pathway. This included not only the tailpipe emissions but also upstream emissions resulting from biomass cultivation, feedstock transportation, biofuel production and biofuel distribution,” Hawkins said.

Creating a biofuel playbook

Researchers did not intend to produce a definitive list of biofuels, Benavides said. Instead, the studies offer a guide for stakeholders on selecting biofuel pathways that best meet their needs.

“We provide researchers and industry guidance on assessing biofuels based on a number of complex variables,” Benavides said. ​“The life cycle and techno-economic analysis is important in guiding stakeholders as early as possible. We can’t tell stakeholders what choices to make. But these tools can point them in the right direction from the beginning.”

While many of these biofuel pathways could potentially be cost-competitive, it is too soon to lock in prices in a constantly fluctuating gas market. ​“The challenge is providing cost-competitive prices in the long term,” Hawkins said.

While these biofuel production pathways target cars and diesel trucks, Argonne researchers are also studying the potential for using these pathways in hard-to-electrify sectors like aviation and maritime industries. The goal is to bring biofuel to market across a range of industries as quickly as possible.

“DOE is constantly working on sustainable solutions for decarbonizing the transportation sector. Biofuel is a big piece of that,” Hawkins said. ​“We will continue to expand on Co-Optima’s important work.”

Along with Argonne, ORNL, NREL, PNNL, INL, and SNL, other U.S DOE national labs in the Co-Optima Initiative are Los Alamos, Lawrence Berkeley, and Lawrence Livermore national laboratories.

ACS Sustainable Chemistry & Engineering research authors:

“Identification of key drivers of cost and environmental impact for biomass-derived fuel for advanced multimode engines based on techno-economic and life cycle analysis”: Pahola Thathiana Benavides, Argonne, Andrew W. Bartling, NREL, Steven D. Phillips, PNNL, Troy R. Hawkins, Argonne, Avantika Singh, NREL, George G. Zaimes, Argonne, Matthew Wiatrowski, NREL, Kylee Harris, NREL, Pralhad H. Burli, INL, Damon Hartley, INL, Teresa Alleman, NREL, Gina Fioroni, NREL, Daniel Gaspar, PNNL.

“Environmental, economic, and scalability considerations of selected bio-derived blendstocks for mixing-controlled compression ignition engines”: Andrew W. Bartling, NREL, Pahola Thathiana Benavides, Argonne, Steven D. Phillips, PNL, Troy Hawkins, Argonne, Avantika Singh, NREL, Matthew Wiatrowski, NREL, Eric C. D. Tan, NREL, Christopher Kinchin, NREL, Longwen Ou, Argonne, Hao Cai, Argonne, Mary Biddy, NREL, Ling Tao, NREL, Andrew Young, NREL, Kathleen Brown, NREL, Shuyun Li, PNNL, Yunhua Zhu, PNNL, Lesley J. Snowden-Swan, PNNL, Chirag R. Mevawala, PNNL, Daniel J. Gaspar, PNNL.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://​ener​gy​.gov/​s​c​ience.

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JOURNAL

ACS Sustainable Chemistry & Engineering

DOI

10.1021/acssuschemeng.2c00944 

ARTICLE TITLE

Identification of Key Drivers of Cost and Environmental Impact for Biomass-Derived Fuel for Advanced Multimode Engines Based on Techno-Economic and Life Cycle Analysis

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PETA science group celebrates 10 years of advancing animal-free toxicity testing

Reports and Proceedings

PEOPLE FOR THE ETHICAL TREATMENT OF ANIMALS (PETA)

Washington — With its spotlight on non-animal tests, PETA Science Consortium International e.V. has helped transform toxicity testing and the definition of good science. Its 25 scientists located in Belgium, France, Germany, India, the U.K., and the U.S. are now celebrating a decade of success in collaborating with government agencies and corporations to replace animals in toxicity tests and in the funding and development of cutting-edge, animal-free methods.

Today, the group released a report showcasing its impact in advancing the field of non-animal toxicity testing. (NOTE: PLEASE LINK THIS AT "REPORT" https://www.thepsci.eu/wp-content/uploads/2022/11/PETA-Science-Consortium-International-10-Year-Report.pdf)

The Science Consortium was established to modernize toxicity testing globally, as regulatory agencies around the world require the testing of chemicals, pharmaceutical drugs, pesticides, and other substances to assess their potential to harm humans, wildlife, or the environment. Millions of animals are used each year in these tests, many of which are decades old. In its first decade, the Science Consortium has spared countless animals painful, deadly tests.

“Now more than ever, harnessing the power of modern science and technology allows us to make accurate predictions about the potential of substances to cause adverse effects, keeping our friends, family, and world safer,” says Science Consortium President Dr. Amy Clippinger. “We are grateful for the fruitful partnerships we have made over the past 10 years and look forward to many more years of advancing reliable and relevant animal-free science.”

The report features successful collaborations with government, industry, method developers, academics, and nongovernmental organizations on precedent-setting projects. For example, funding from the group helped create a first-of-its-kind, three-dimensional model that can study the effects of chemicals on the deepest part of the human lung. 

The Science Consortium also funded a project that led to the creation of fully human-derived antibodies capable of blocking the toxin that causes diphtheria to replace the existing diphtheria treatment that’s produced using horses. Another project involved collaborating with the U.S. Environmental Protection Agency on research that resulted in a policy preventing hundreds of birds each year from being used in tests that have produced duplicative information.

For more information, please visit ThePSCI.eu.

Argonne scientists promote FAIR standards for managing artificial intelligence models

Peer-Reviewed Publication

DOE/ARGONNE NATIONAL LABORATORY

 

IMAGE: SCIENTIFIC VISUALIZATION OF BRAGG DIFFRACTION PEAKS IN A 15X15 PIXEL PATCH OF AN UNDEFORMED BI-CRYSTAL GOLD SAMPLE. THE HEIGHT DENOTES PHOTON COUNTS. THIS DATA WAS ACQUIRED AT THE ADVANCED PHOTON SOURCE AND PROCESSED AT THE THETAGPU SUPERCOMPUTER. view more 

CREDIT: (IMAGE BY ARGONNE NATIONAL LABORATORY/ELIU HUERTA.)

New data standards created for AI models.

Aspiring bakers are frequently called upon to adapt award-winning recipes based on differing kitchen setups. Someone might use an eggbeater instead of a stand mixer to make prize-winning chocolate chip cookies, for instance.

Being able to reproduce a recipe in different situations and with varying setups is critical for both talented chefs and computational scientists, the latter of whom are faced with a similar problem of adapting and reproducing their own ​“recipes” when trying to validate and work with new AI models. These models have applications in scientific fields ranging from climate analysis to brain research.

“When we talk about data, we have a practical understanding of the digital assets we deal with,” said Eliu Huerta, scientist and lead for Translational AI at the U.S. Department of Energy’s (DOE) Argonne National Laboratory. ​“With an AI model, it’s a little less clear; are we talking about data structured in a smart way, or is it computing, or software, or a mix?”

In a new study, Huerta and his colleagues have articulated a new set of standards for managing AI models. Adapted from recent research on automated data management, these standards are called FAIR, which stands for findable, accessible, interoperable and reusable.

“By making AI models FAIR, we no longer have to build each system from the ground up each time,” said Argonne computational scientist Ben Blaiszik. ​“It becomes easier to reuse concepts from different groups, helping to create cross-pollination across teams.”

According to Huerta, the fact that many AI models are currently not FAIR poses a challenge to scientific discovery. ​“For many studies that have been done to date, it is difficult to gain access to and reproduce the AI models that are referenced in the literature,” he said. ​“By creating and sharing FAIR AI models, we can reduce the amount of duplication of effort and share best practices for how to use these models to enable great science.”

To meet the needs of a diverse community of users, Huerta and his colleagues combined a unique suite of data management and high performance computing platforms to establish a FAIR protocol and quantify the ​“FAIR-ness” of AI models. The researchers paired FAIR data published at an online repository called the Materials Data Facility, with FAIR AI models published at another online repository called the Data and Learning Hub for Science, as well as with AI and supercomputing resources at the Argonne Leadership Computing Facility (ALCF). In this way, the researchers were able to create a computational framework that could help bridge various hardware and software, creating AI models that could be run similarly across platforms and that would yield reproducible results. The ALCF is a DOE Office of Science user facility.

Two keys to creating this framework are platforms called funcX and Globus, which allow researchers to access high performance computing resources straight from their laptops. ​“FuncX and Globus can help transcend the differences in hardware architectures,” said co-author Ian Foster, director of Argonne’s Data Science and Learning division. ​“If someone is using one computing architecture and someone else is using another, we now have a way of speaking a common AI language. It’s a big part of making AI more interoperable.”

In the study, the researchers used an example dataset of an AI model that used diffraction data from Argonne’s Advanced Photon Source, also a DOE Office of Science user facility. To perform the computations, the team used the ALCF AI Testbed’s SambaNova system and the Theta supercomputer’s NVIDIA GPUs (graphics processing units).

“We’re excited to see the FAIR productivity benefits from model and data sharing to provide more researchers with access to high performance computing resources,” said Marc Hamilton, NVIDIA vice president for Solutions Architecture and Engineering. ​“Together we’re supporting the expanding universe of high performance computing that’s combining experimental data and instrument operation at the edge with AI to increase the pace of scientific discovery.”

“SambaNova is excited to partner with researchers at Argonne National Laboratory to pursue innovation at the interface of AI and emergent hardware architectures,” added Jennifer Glore, vice president for Customer Engineering at SambaNova Systems. ​“AI will have a significant role in the future of scientific computing, and the development of FAIR principles for AI models along with novel tools will empower researchers to enable autonomous discovery at scale. We’re looking forward to continued collaboration and development at the ALCF AI Testbed.”

A paper based on the study, ​“FAIR principles for AI models, with a practical application for accelerated high energy diffraction microscopy,” appeared in Nature Scientific Data on Nov. 10, 2022.

In addition to Huerta, other authors of the study include Argonne’s Nikil Ravi, Pranshu Chaturvedi, Zhengchun Liu, Ryan Chard, Aristana Scourtas, K.J. Schmidt, Kyle Chard, Ben Blaiszik and Ian Foster.

The research was funded by DOE’s Office of Advanced Scientific Computing Research, the National Institutes of Standards and Technology, the National Science Foundation and Laboratory Directed Research and Development grants.

The Argonne Leadership Computing Facility provides supercomputing capabilities to the scientific and engineering community to advance fundamental discovery and understanding in a broad range of disciplines. Supported by the U.S. Department of Energy’s (DOE’s) Office of Science, Advanced Scientific Computing Research (ASCR) program, the ALCF is one of two DOE Leadership Computing Facilities in the nation dedicated to open science.

About the Advanced Photon Source

The U. S. Department of Energy Office of Science’s Advanced Photon Source (APS) at Argonne National Laboratory is one of the world’s most productive X-ray light source facilities. The APS provides high-brightness X-ray beams to a diverse community of researchers in materials science, chemistry, condensed matter physics, the life and environmental sciences, and applied research. These X-rays are ideally suited for explorations of materials and biological structures; elemental distribution; chemical, magnetic, electronic states; and a wide range of technologically important engineering systems from batteries to fuel injector sprays, all of which are the foundations of our nation’s economic, technological, and physical well-being. Each year, more than 5,000 researchers use the APS to produce over 2,000 publications detailing impactful discoveries, and solve more vital biological protein structures than users of any other X-ray light source research facility. APS scientists and engineers innovate technology that is at the heart of advancing accelerator and light-source operations. This includes the insertion devices that produce extreme-brightness X-rays prized by researchers, lenses that focus the X-rays down to a few nanometers, instrumentation that maximizes the way the X-rays interact with samples being studied, and software that gathers and manages the massive quantity of data resulting from discovery research at the APS.

This research used resources of the Advanced Photon Source, a U.S. DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://​ener​gy​.gov/​s​c​ience.

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JOURNAL

Scientific Data

DOI

10.1038/nature14539 

METHOD OF RESEARCH

News article

ARTICLE TITLE

FAIR principles for AI models with a practical application for accelerated high energy diffraction microscopy

ARTICLE PUBLICATION DATE

10-Nov-2022

Video surveillance, now for viruses

Watch a virus in the moments right before it attacks.

Peer-Reviewed Publication

DUKE UNIVERSITY

DURHAM, N.C. -- When Courtney “CJ” Johnson pulls up footage from her Ph.D. dissertation, it’s like she’s watching an attempted break-in on a home security camera.

The intruder cases its target without setting a foot inside, looking for a point of entry. But this intruder is not your typical burglar. It’s a virus.

Filmed over two and a half minutes by pinpointing its location 1,000 times a second, the footage shows a tiny virus particle, thousands of times smaller than a grain of sand, as it lurches and bobs among tightly packed human intestinal cells.

For a fleeting moment, the virus makes contact with a cell and skims along its surface but doesn’t stick before bounding off again. If this were an actual home break-in, Johnson says, “this would be the part where the burglar has not broken the window yet.”

Johnson is part of a Duke University team led by assistant chemistry professor Kevin Welsher. Together with Welsher’s postdoctoral associate Jack Exell and colleagues, they have come up with a way to capture real-time 3D footage of viruses as they approach their cellular targets.

We inhale, ingest and take in millions of viruses every day. Most of them are harmless, but some of them -- such as the viruses that cause the flu or COVID-19 -- can make us sick.

Infection starts when a virus binds to and enters a cell, where it hijacks the cellular machinery to make copies of itself.  But before it can break in, a virus has to reach the cell first, Johnson said.

That often means getting through the protective layer of cells and mucus that line the airways and the gut -- one of the body’s first lines of defense against infection.

The researchers wanted to understand how viruses breach these frontline defenses. “How do viruses navigate these complex barriers?” Welsher said. But these critical early moments before infection begins have long been difficult if not impossible to watch with existing microscopy methods, he added.

Part of the reason is that viruses move two to three orders of magnitude faster in the unconfined space outside the cell, compared with its crowded interior. To make things even trickier from an imaging perspective, viruses are hundreds of times smaller than the cells they infect.

“That's why this is such a hard problem to study,” Johnson said. Under the microscope, “it's like you're trying to take a picture of a person standing in front of a skyscraper. You can’t get the whole skyscraper and see the details of the person in front of it with one picture.”

So the team developed a new method called 3D Tracking and Imaging Microscopy (3D-TrIm), which essentially combines two microscopes in one. The first microscope “locks on” to the fast-moving virus, sweeping a laser around the virus tens of thousands of times per second to calculate and update its position. As the virus bounces and tumbles around in the soupy exterior of the cell, the microscope stage continuously adjusts to keep it in focus.

While the first microscope tracks the virus, the second microscope takes 3D images of the surrounding cells. The combined effect, Welsher said, is akin to navigating with Google Maps: it not only shows your current location as you drive, it also shows the terrain, landmarks and the overall lay of the land, but in 3D.

“Sometimes when I present this work people ask, ‘is this a video game or a simulation?’” said Johnson, now a postdoctoral associate at the Howard Hughes Medical Institute Janelia Research Campus. “No, this is something that came from a real microscope.”

With their method the researchers can’t just, say, watch a healthy person breathe in virus particles from an infected person’s cough or sneeze. For one, they have to attach a special fluorescent label to a virus before they can track it -- what the microscope follows is the movement of the glowing spot. And currently they can only track a virus for a few minutes at a time before it goes dim.

“The biggest challenge for us now is to produce brighter viruses,” Exell said.

But Welsher said he hopes the technique will make it possible to follow viruses in action beyond the coverslip, and in more realistic tissue-like environments where infections first take hold.

“This is the real promise of this method,” Welsher said. “We think that's something we have the possibility to do now.”

This work appeared online Nov. 10 in the journal Nature Methods.

This research was supported by a grant from the National Institutes of Health (R35GM124868).

CITATION: "Capturing the Start Point of the Virus-Cell Interaction With High-Speed 3D Single-Virus Tracking," Courtney Johnson, Jack Exell, Yuxin Lin, Jonathan Aguilar, and Kevin D. Welsher. Nature Methods, Nov. 10, 2022. DOI: 10.1038/s41592-022-01672-3

 

 

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JOURNAL

Nature Methods

DOI

10.1038/s41592-022-01672-3 

METHOD OF RESEARCH

Imaging analysis

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Capturing the Start Point of the Virus-Cell Interaction With High-Speed 3D Single-Virus Tracking

ARTICLE PUBLICATION DATE

10-Nov-2022

Economic interests cloud hazardous chemicals reductions

Peer-Reviewed Publication

UNIVERSITY OF GOTHENBURG

The regulation of hazardous chemicals in Europe has been shaped by economic interests, according to a study published in Nature Communications. The researchers, from the University of Gothenburg and Chalmers University of Technology, find that regulators focus on chemicals of secondary importance leading to lesser than anticipated hazard reductions.

“We show that the most important factor in whether a substance is subjected to binding limitations and conditions is whether it is being produced in, or imported into, the European Economic Area. The regulators are less likely to list a substance as hazardous in the Candidate List of substances of very high concern if it affects the economic interests of European firms”, says Jessica Coria, Associate Professor in Economics.

Estimates by the European Environment Agency suggest that 62 percent of the volume of chemicals consumed in Europe in 2016 were hazardous to human health, with the potential to cause a broad range of diseases. 

In the European Union, the REACH regulation (Registration, Evaluation, Authorization, and Restriction of Chemicals) has the explicit aim of ensuring a high level of protection for human health and the environment. Through the Authorization program, the manufacture and use of substances of very high concern, which may have serious effects on human health and the environment, can be subjected to binding limitations and conditions, including complete prohibitions.

The route to authorization starts with the listing of substances on the Candidate List, where member states or the European Chemical Agency propose substances for inclusion. Chemicals included on the list undergo then a prioritization process to be included on the Authorization List.

In their study in Nature Communications, researchers Jessica Coria, Erik Kristiansson, and Mikael Gustavsson, at the University of Gothenburg and Chalmers University of Technology, investigate the relative importance of toxicological properties, economic motivations, and available scientific knowledge as drivers of inclusion on the Candidate List.

Naturally, they find that hazard reduction and available scientific evidence about the effects of the chemicals are important drivers. However, the evidence in the published paper suggests that regulators have listed chemicals of secondary importance leading to lesser than anticipated hazard reductions, either because production and imports had already ceased before the listing, or because the compound has never been produced or imported into the European Economic Area at all.

“Our study includes all chemicals in REACH and clearly shows that economic factors influence what chemicals are included on the Candidate List”, says Mikael Gustavsson.

“Even if it is not surprising that economic interests affect the selection of chemicals, the relative importance of current production or importing of the substance in the European Economic Area is somewhat surprising and calls into question the actual effect of the Candidate List in removing substances of very high concern from the market”, Erik Kristiansson adds.

The results of the study suggest that low-hanging fruit has been picked first and that it may well become increasingly difficult over time to agree on chemicals of very high concern for which there is little political opposition due to a lack of local production.

“This might require a fundamental redesign of the process to ensure that hazardousness becomes the most important driver of inclusion on the Candidate List and that hazardous chemicals produced or imported in the EEA are listed even if they affect the economic interests of European firms”, Jessica Coria says.

Read the full study in Nature Communications: https://doi.org/10.1038/s41467-022-34492-2  

Contact Information:

• Jessica Coria, Associate Professor in Economics at the School of Business, Economics and Law at the University of Gothenburg, Sweden. Corresponding Author. Email: jessica.coria@economics.gu.se, phone: +46 31-786 48 67
• Mikael Gustavsson, PhD, Department of Economics, University of Gothenburg, Sweden; and Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Sweden. Email: mikael.gustavsson@chalmers.se
• Erik Kristiansson, Professor, Department of Mathematical Sciences, Chalmers University of Technology/University of Gothenburg, Sweden. E-mail: erik.kristiansson@chalmers.se, phone: +46 31-772 35 21

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JOURNAL

Nature Communications

DOI

10.1038/s41467-022-34492-2 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Economic interests cloud hazard reductions in the European regulation of substances of very high concern

ARTICLE PUBLICATION DATE

10-Nov-2022