Tuesday, August 03, 2021

New report: State of the science on western wildfires, forests and climate change

UNIVERSITY OF WASHINGTON

2021 Cedar Creek fire — IMAGE: THE CEDAR CREEK FIRE BURNS IN WASHINGTON STATE'S METHOW VALLEY IN LATE JULY 2021. LUCKY JIM BLUFF, NEAR MAZAMA, IS SEEN BEHIND. view more
CREDIT: JESSICA KELLEY

Exceptionally hot and dry weather this summer has fueled dozens of wildfires across the western U.S., spewing smoke across the country and threatening to register yet another record-breaking year. More than a century of fire exclusion has created dense forests packed with excess trees and brush that ignite and spread fires quickly under increasingly warm and dry conditions.

Scientists largely agree that reducing these fuels is needed to make our forests and surrounding communities more resilient to wildfires and climate change. But policy and action have not kept pace with the problem and suppressing fires is still the norm, even as megafires become more common and destructive.

Seeing the urgent need for change, a team of scientists from leading research universities, conservation organizations and government laboratories across the West has produced a synthesis of the scientific literature that clearly lays out the established science and strength of evidence on climate change, wildfire and forest management for seasonally dry forests. The goal is to give land managers and others across the West access to a unified resource that summarizes the best-available science so they can make decisions about how to manage their landscapes.

“Based on our extensive review of the literature and the weight of the evidence, the science of adaptive management is strong and justifies a range of time- and research-tested approaches to adapt forests to climate change and wildfires,” said co-lead author Susan Prichard, a research scientist in the University of Washington’s School of Environmental and Forest Sciences.

These approaches include some thinning of dense forests in fire-excluded areas, prescribed burning, reducing fuels on the ground, allowing some wildfires to burn in backcountry settings under favorable fuel and weather conditions, and revitalizing Indigenous fire stewardship practices. The findings were published Aug. 2 as an invited three-paper feature in the journal Ecological Applications.

The authors studied and reviewed over 1,000 published papers to synthesize more than a century of research and observations across a wide geographic range of western North American forests. The analysis didn’t include rainforests in the Pacific Northwest or other wet forests where thinning and prescribed burning wouldn’t be advised.

“The substantial changes associated with more than a century of fire exclusion jeopardize forest diversity and keystone processes as well as numerous other social and ecological values including quantity and quality of water, stability of carbon stores, air quality, and culturally important resources and food security,” said co-lead author and UW researcher Keala Hagmann.

This ambitious set of articles was inspired by the reality that under current forest and wildfire management, massive wildfires and drought are now by far the dominant change agents of western North American forests. There is an urgent need to apply ecologically and scientifically credible approaches to forest and fire management at a pace and scale that matches the scope of the problem, the authors say.

Part of the solution involves addressing ongoing confusion over how to rectify the effects of more than a century of fire exclusion as the climate continues to warm. Land managers and policymakers recognize that the number and size of severe fires are rapidly increasing with climate change, but agreement and funding to support climate and wildfire adaptation are lagging.

To that end, these papers review the strength of the science on the benefits of adapting fire-excluded forests to a rapidly warming climate. The authors address 10 common questions, including whether management is needed after a wildfire, or whether fuel treatments (thinning, prescribed burning) work under extreme fire weather. They also discuss the need to integrate western fire science with traditional ecological knowledge and Indigenous fire uses that managed western landscapes for thousands of years.

Although climate change brings with it many uncertainties, the evidence supporting intentional forest adaptation is strong and broad based. The authors clearly demonstrate that lingering uncertainties about the future should no longer paralyze actions that can be taken today to adapt forests and communities to a warming climate and more fire.

“This collection represents a blending of scientific voices across the entire disciplinary domain,” said co-lead author Paul Hessburg, a research ecologist with the U.S. Forest Service and affiliate professor at the UW. “After reviewing the evidence, it is clear that the changes to forest conditions and fire regimes across the West are significant. The opportunity ahead is to adapt forests to rapidly changing climatic and wildfire regimes using a wide range of available, time-tested management tools.”

Co-authors on this special report are from University of Arizona, University of British Columbia, University of California, Berkeley, University of California, Merced, University of Idaho, University of Montana, University of New Mexico, Northern Arizona University, Oregon State University, The Pennsylvania State University, Utah State University, U.S. Forest Service research stations (Pacific Northwest, Pacific Southwest, Rocky Mountain), U.S. Forest Service, Pacific Southwest Region, Washington State Department of Natural Resources, California Department of Forestry and Fire Protection, U.S. Fish and Wildlife Service, U.S. Geological Survey, The Nature Conservancy, R.W. Gray Consulting, Rocky Mountain Tree-Ring Research and Spatial Informatics Group.

John Marshall Photography

For more information, contact Prichard at sprich@uw.edu, Hagmann at hokulea@uw.edu and Hessburg at paul.hessburg@usda.gov. (Note: Prichard is unavailable for interviews the week of Aug. 2)

Download images: https://drive.google.com/drive/folders/1Z9mepOBBWQSFwaRZky5rM9piDAytW7yy?usp=sharing (If link doesn’t work, copy and paste into a browser)

JOURNAL

Ecological Applications

DOI

10.1002/eap.2432

METHOD OF RESEARCH

Literature review

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Special feature: Climate change and western wildfires (3 related papers)

ARTICLE PUBLICATION DATE

2-Aug-2021

Researchers use AI to unlock the secrets of ancient texts

Peer-Reviewed Publication

UNIVERSITY OF NOTRE DAME

The Abbey Library of St. Gall in Switzerland is home to approximately 160,000 volumes of literary and historical manuscripts dating back to the eighth century — all of which are written by hand, on parchment, in languages rarely spoken in modern times.

To preserve these historical accounts of humanity, such texts, numbering in the millions, have been kept safely stored away in libraries and monasteries all over the world. A significant portion of these collections are available to the general public through digital imagery, but experts say there is an extraordinary amount of material that has never been read — a treasure trove of insight into the world’s history hidden within.

Now, researchers at University of Notre Dame are developing an artificial neural network to read complex ancient handwriting based on human perception to improve capabilities of deep learning transcription.

“We’re dealing with historical documents written in styles that have long fallen out of fashion, going back many centuries, and in languages like Latin, which are rarely ever used anymore,” said Walter Scheirer, the Dennis O. Doughty Collegiate Associate Professor in the Department of Computer Science and Engineering at Notre Dame. “You can get beautiful photos of these materials, but what we’ve set out to do is automate transcription in a way that mimics the perception of the page through the eyes of the expert reader and provides a quick, searchable reading of the text.”

In research published in the Institute of Electrical and Electronics Engineers journal Transactions on Pattern Analysis and Machine Intelligence, Scheirer outlines how his team combined traditional methods of machine learning with visual psychophysics — a method of measuring the connections between physical stimuli and mental phenomena, such as the amount of time it takes for an expert reader to recognize a specific character, gauge the quality of the handwriting or identify the use of certain abbreviations.

Scheirer’s team studied digitized Latin manuscripts that were written by scribes in the Cloister of St. Gall in the ninth century. Readers entered their manual transcriptions into a specially designed software interface. The team then measured reaction times during transcription for an understanding of which words, characters and passages were easy or difficult. Scheirer explained that including that kind of data created a network more consistent with human behavior, reduced errors and provided a more accurate, more realistic reading of the text.

“It’s a strategy not typically used in machine learning,” Scheirer said. “We’re labeling the data through these psychophysical measurements, which comes directly from psychological studies of perception — by taking behavioral measurements. We then inform the network of common difficulties in the perception of these characters and can make corrections based on those measurements.”

Using deep learning to transcribe ancient texts is something of great interest to scholars in the humanities.

“There’s a difference between just taking the photos and reading them, and having a program to provide a searchable reading,” said Hildegund Müller, associate professor in the Department of Classics at Notre Dame. “If you consider the texts used in this study — ninth-century manuscripts — that’s an early stage of the Middle Ages. It’s a long time before the printing press. That’s a time when an enormous amount of manuscripts was produced. There is all sorts of information hidden in these manuscripts — unidentified texts that nobody has seen before.”

Scheirer said challenges remain. His team is working on improving accuracy of transcriptions, especially in the case of damaged or incomplete documents, as well as how to account for illustrations or other aspects of a page that could be confusing to the network.

However, the team was able to adjust the program to transcribe Ethiopian texts, adapting it to a language with a completely different set of characters — a first step toward developing a program with the capability to transcribe and translate information for users.

“In the literary field, it could be really helpful. Every good literary work is surrounded by a vast amount of historical documents, but where it’s really going to be useful is in historical archival research,” said Müller. “There is a great need to advance the digital humanities. When you talk about the Middle Ages and early modern times, if you want to understand the details and consequences of historical events, you have to look through the written material, and these texts are the only thing we have. The problem may be even greater outside the Western world. Think of languages that are disappearing in cultures that are under threat. We must first of all preserve these works, make them accessible and, at some point, incorporate translations to make them a part of cultural processes that are still underway — and we are racing against time.”

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JOURNAL

IEEE Transactions on Pattern Analysis and Machine Intelligence

Researchers envision better health interventions for men who have sex with men

Peer-Reviewed Publication

VIRGINIA COMMONWEALTH UNIVERSITY

While much of the health research around men who have sex with men (MSM) involves HIV, these communities are at increased risk for other health problems including certain types of cancer, substance use and mental health issues. A new scoping review by VCU School of Medicine and Massey Cancer Center researchers finds that a specific type of data collection methodology called ecological momentary assessment (EMA), alongside of or as an intervention itself, could be particularly effective in supporting these populations.

EMA is a research method that repeatedly samples subjects in their natural environment to better understand their experiences over a period of time. It has the potential to create a rich dataset allowing researchers and clinicians to identify behavioral trends and contributing factors. This contrasts with other types of health behavior research that rely on retrospective feedback given directly to researchers or clinicians at a single point in time. EMAs minimize recall bias and can improve engagement among participants.

A scoping review provides an overview of available research evidence relative to a specific subject matter.

The authors first identified an initial set of 129 studies in their preliminary search, of which 15 met their eligibility criteria for the scoping review. The eligible studies included a total of 952 participants, with the smallest sample size being 12 and the largest being 120. They found that EMA methodology is both feasible and acceptable at high rates among MSM, especially when examining psychological and behavioral outcomes such as negative or positive affect, risky sexual behavior and substance use.

“Ecological momentary assessment is a relatively novel approach to health behavior research, so I wanted to see what had been done, what were the best practices and what gaps existed in the research in order to inform future studies as well as behavioral and therapeutic interventions for MSM and other populations,” says Viktor Clark, M.S., lead author on the study and doctoral student in the Department of Health Behavior and Policy at VCU School of Medicine. “We found strong support for EMAs, but we also found many of the study designs to be lacking best practices and a tendency for the research to focus on stigmatized behaviors such as substance abuse and unprotected sex.”

Clark conceived of the scoping review while taking a research methodology class led by Sunny Jung Kim, Ph.D., assistant professor in the Department of Health Behavior and Policy at VCU School of Medicine and Harrison Scholar and member of the Cancer Prevention and Control research program at VCU Massey Cancer Center. Kim’s class covered experience-sampling methods, including EMAs, and Clark felt they could be uniquely applied to benefit MSM, a collection of populations they had previously studied.

“EMAs have traditionally used methods such as written diaries and phone calls to sample participants over a period of time. 85 percent of Americans now own a smart phone, so there is great potential for EMAs to evolve with advances in technology,” says Kim. “Short, micro surveys delivered through text messages or apps have the ability to collect extensive longitudinal data over time to better understand patterns and changes in behavior. They even have the potential to help health care professionals predict and intervene to prevent negative health outcomes in a variety of populations.”

The review evaluated the different studies based on the Center for Disease Control’s compendium of evidence-based interventions and best practices for HIV prevention. Most studies did not meet the full criteria for best standards defined by the CDC’s recommendations. Kim and Clark stress the importance of developing evidence-based best practices for designing future EMAs, especially when delivered via smartphone or computer as there are unique challenges and opportunities associated with these platforms.

“I hope to continue this line of research into my Ph.D. dissertation. I have submitted a grant application to fund a study to test a conceptual model for interactions between health care providers and gender-and sexual-minority patients to identify points where EMA methodology could add further depth to findings,” says Clark. “The goal is to make the patient-provider relationship better with communication and technology in order to improve things like medicine adherence and overall health outcomes.”

Kim has also submitted a grant application to fund an EMA-based intervention study for cancer survivors. She plans to conduct research to identify factors, barriers and themes related to pain management and quality of life, and then use that information to design and deliver a technology-based intervention that distills scientific evidence into easy-to-understand messages that help support patient care.

Both authors stress the importance of an open science framework in which methods and results can be widely shared. Their article is publicly available on the Journal of Medical Internet Research’s website.

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About VCU Massey Cancer Center
VCU Massey Cancer Center is working toward a future without cancer – one discovery, one successful therapy and one life saved at a time. Among the top 4 percent of cancer centers in the country to be designated by the National Cancer Institute to lead and shape America’s cancer research efforts, Massey is dedicated to saving and improving lives by discovering, developing, delivering and teaching effective means to prevent, detect and treat cancer and to making those advancements equally available to all. Massey is leading the nation in establishing a 21st-Century model of equity for cancer research and care, in which the community is informing and partnering with Massey on its research to best address the cancer burden and disparities of those the cancer center serves. Massey conducts cancer research spanning basic, translational, clinical and population sciences; offers state-of-the-art cancer therapies and clinical trials, including a network that brings trials to communities statewide; provides oncology education, teaching and training; and promotes cancer prevention. At Massey, subspecialized oncology experts collaborate in multidisciplinary teams to provide award-winning, comprehensive cancer care at multiple sites throughout Virginia. Visit Massey online at masseycancercenter.org or call 877-4-MASSEY for more information.

JOURNAL

Journal of Medical Internet Research

DOI

10.2196/27751

METHOD OF RESEARCH

Systematic review

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Ecological Momentary Assessment and mHealth Interventions Among Men Who Have Sex With Men: Scoping Review

Social and spatial networks influence HIV and hepatitis transmission in people who inject drugs

Understanding social and spatial networks in the transmission of HIV and hepatitis C among people who inject drugs could identify hubs for more efficient and timely intervention

Peer-Reviewed Publication

ELIFE

The risk of HIV or hepatitis C in people who inject drugs is influenced as much by their social interactions and the venues where they inject as other risk factors, according to a study published today in eLife.

The findings could help direct public health efforts to locations where HIV and hepatitis is most frequently transmitted, allowing more efficient use of harm reduction services and more quickly interrupting disease transmission.

India has one of the highest burdens of HIV and hepatitis C resulting from injection drug use. Efforts to stop the spread of these diseases are hindered by a suboptimal understanding of the role social networks can play in the spread of infectious diseases, especially in a population which includes many people who are without homes and hard to reach.

Social interactions can be used to interrupt disease transmission and can be useful for combating epidemics among populations that are linked by a common behaviour – in this case, injecting drugs – according to the authors. However, developing network-based interventions in this population is challenging because the network structure is often unknown or poorly understood, particularly indirect networks (as in ‘friend-of-a-friend’ connections).

To address this, the authors set out to understand the structure of the social connections (injection partners) and spatial connections (places where people inject) of those who inject drugs in New Delhi, India. They started by recruiting an initial group of 10 people who inject drugs, who then provided the names of injecting partners. They were asked to recruit these contacts into the study. These recruits were, in turn, asked to do the same. The study was set up so that none of the contacts were duplicated, but if a person was referred by more than one contact, they were then interconnected to each of the named contacts. The result was a network of direct and indirect connections between 2,512 people who injected drugs, mostly men and aged 26 years on average, covering a total of 181 venues across a 20km radius.

The team then offered testing for HIV and hepatitis C to the participants, with appropriate referrals to care when applicable, and asked them to complete surveys to provide additional information on factors such as education level, homelessness, injection frequency, type of drug injected, sexual activity and syringe-sharing.

At the start of the study, 37% were HIV-positive and 65% had antibodies to hepatitis C, with 80% of these people having an active infection. Most were unaware they had hepatitis C. Of those living with HIV, 65% were directly connected with one other HIV-positive person. Of those with an active hepatitis C infection, 74% were directly connected with at least one other person who had an active infection.

The strongest determinant of testing positive for HIV or hepatitis C was injecting at the most popular injection venue – this increased the odds of infection by 50%. Even if an individual did not personally inject at that site, their odds of infection increased if one of their injection partners did. For each person separating a given individual with the most popular location, the likelihood of having HIV or hepatitis C reduced by 14%. Similarly, for each person separating a given individual from a person testing positive for HIV or hepatitis C, the likelihood of having HIV and hepatitis C decreased by 13%.

The findings show that HIV and hepatitis C infection is not only associated with individual risk factors such as age, education or injection frequency, but also direct and indirect social and spatial network connections – even after accounting for individual-level characteristics. The study has led to a better understanding of the network structure of people who inject drugs in New Delhi and highlighted the role of indirect connections and space on disease burden. The authors say it also urges a rethink of ‘networks’ to incorporate indirect network connections and spaces when thinking about interventions to interrupt disease transmission.

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This study was supported by the National Institute on Drug Abuse, part of the National Institutes of Health, under award numbers R01DA041736, DP2DA040244, R01DA041034, K24DA035684.

Media contact

Emily Packer, Media Relations Manager

eLife

e.packer@elifesciences.org

+44 (0)1223 855373

About eLife

eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We aim to publish work of the highest standards and importance in all areas of biology and medicine, including Epidemiology and Global Health, and Medicine, while exploring creative new ways to improve how research is assessed and published. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Epidemiology and Global Health research published in eLife, visit https://elifesciences.org/subjects/epidemiology-global-health.

And for the latest in Medicine, see https://elifesciences.org/subjects/medicine.

DOI

10.7554/eLife.69174

ARTICLE TITLE

Role of direct and indirect social and spatial ties in the diffusion of HIV and HCV among people who inject drugs: A cross-sectional community-based network analysis in New Delhi, India

ARTICLE PUBLICATION DATE

2-Aug-2021

'Virtual nature' experiences reduce stress in prisons

Peer-Reviewed Publication

UNIVERSITY OF UTAH

Nature imagery in prison — IMAGE: A PROJECTOR SHOWS NATURE IMAGERY ON THE WALL OF A PRISON. view more
CREDIT: BENJ DRUMMOND

Before you read any more, find a picture of a natural setting or play a sound of a natural habitat. Here’s a YouTube video with both, if you need it. A few minutes should be enough.

You’ve just had a “virtual nature experience.” How do you feel? If you felt less stress, you’re not alone. The experience might even feel like it transports you to a different place.

For people who are in jails or prisons, experiencing nature virtually is usually their only option. A new study from University of Utah researchers finds that exposure to nature imagery or nature sounds decreased physiological signs of stress in the incarcerated, and spurred their interest in learning more about the habitats they experienced. The researchers also found that, in general, people didn’t strongly prefer visual to auditory nature experiences.

The findings from the study, published in Ecopsychology, could be put to use to benefit the physical and mental health of the incarcerated, says Nalini Nadkarni of the School of Biological Sciences.

“Findings from this study provide also help us understand how providing nature or nature imagery might be beneficial for other nature-deprived populations,” she says.

Virtual nature

For nearly 20 years, Nadkarni has been bringing science and nature into prisons, to people who have little to no contact with what she and her colleagues call the “the non-built green and blue parts of our world.” In multiple facilities at multiple levels of the correctional system, she’s found people that are curious and eager to learn all they can about the natural world.

One of her efforts, at the Snake River Correctional Facility, is called the “Blue Room,” a room in a maximum security facility where people in solitary confinement are able to watch videos showing natural environments. Previous work showed that the people who watched the videos reported more positive moods and committed fewer violent infractions. The Blue Room was even named one of 2014’s top 25 innovations by Time magazine.

For the new study, Nadkarni and her colleagues including Sara Yeo, associate professor in the College of Humanities and James Ruff, associate instructor in the School of Biological Sciences, met with 71 men in medium or minimum security blocks in the Salt Lake County Jail. After a survey about their opinions on science and nature, the participants viewed and listened to three-minute segments of video and audio of four different nature habitats: forests, mountains, oceans and streams. The researchers call these sessions “virtual nature experiences.”

The researchers monitored the participants’ stress level throughout with two measures: salivary cortisol, which responds to changes in stress within minutes, and galvanic skin response, which measures unconscious changes in skin electrical properties related to emotional states.

The participants reported feeling less stressed after the virtual nature experiences, and the physiological measurements backed that up. Nature exposure measurably decreased their stress.

Audio/visual

The researchers had expected that the sights of nature would produce a stronger stress-reducing effect than the sounds, but found that that wasn’t always the case. “We learned that both visual and auditory stimuli evoked positive responses,” Nadkarni says, “but that these responses were mixed – some of the respondents articulated a stronger preference and exhibited stronger physiological responses to auditory versus visual responses.”

The researchers also noted that videos produced a more variable response overall than audio, meaning that different video habitats produced different stress-relieving responses, whereas responses to different audio habitats were largely constant. When asked to rate the different segments, the participants rated highest the videos of streams and lakes, videos of ocean and beaches and sounds of streams, followed by videos of mountains.

Eager to learn

At the end of the experiment, the researchers asked participants how interested they might be in taking a biology or ecology course to learn more about the habitats they’d seen and heard. Overall, they were more interested in learning about nature after the experience. Yeo, who studies science communication, says this result is encouraging, as people who are incarcerated not only have limited access to nature but may have had limited exposure to science before their incarceration.

“And so it’s really hopeful to think that one can see these changes even among groups that are not necessarily selecting science, or that we maybe don’t think of as having an affinity for science,” she says. “It’s still important for us to try to share experiences with science, even in places where we normally wouldn’t.”

Ruff adds that helping people in prisons reduce their stress may help them later successfully re-enter society.

“Decreasing their stress while incarcerated,” he says, “through low cost-methods like exposure to nature imagery, could allow them to better focus on their educational, mental health and job training needs leading to better outcomes. What this study does is begin to fine-tune what aspects of nature imagery optimally reduces stress.”

Nadkarni hopes the results can be applied to people in other institutional or nature-deprived environments, such as residential treatment center, senior assisted living centers, or even windowless cubicles for office workers.

“Our work leads to future studies of the effects of virtual nature in such habitats,” she says.

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Find the full study here.

Other co-authors on this study included Tierney M. Thys of the California Academy of Sciences, Allison Anholt of the University of Newfoundland, and Jeff Treviño of California State University, Monterey Bay.

The Prison Education Project

This isn’t the only effort by the U to improve the lives of incarcerated people in Utah. The U’s Prison Education Project works to advance educational equity in prisons. Inspired by a 2016 Honors College course and directed by Educational Leadership and Policy associate professor Erin Castro, the project launched at Draper prison in 2017. Project researchers participated in a recent study to survey the educational opportunities available in prisons and examined the barriers to accessing higher education while in prison, including facility rules against online classes and completing paperwork for financial aid. The project is working to develop a comprehensive state-wide strategy to prison higher education that will expand access and pathways to completion. Learn more about the Prison Education Project here.

JOURNAL

Ecopsychology

DOI

10.1089/eco.2020.0043

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Providing Virtual Nature Experiences to Incarcerated Men Reduces Stress and Increases Interest in the Environment

ARTICLE PUBLICATION DATE

9-Jun-2021

MRIs on crop roots open new doors for agriculture

Scientists examine plant roots to make improvements, enhance water-use efficiency

Grant and Award Announcement

TEXAS A&M AGRILIFE COMMUNICATIONS

A team of scientists led by Texas A&M AgriLife is taking a page from the medical imaging world and using MRI to examine crop roots in a quest to develop crops with stronger and deeper root systems.

Nithya Rajan, Ph.D., stands with the low-field MRI rhizotron in the greenhouse at Texas A&M University. (Texas A&M AgriLife photo by Laura McKenzie)

The team from Texas A&M AgriLife Research, Harvard Medical School, ABQMR Inc. and Soil Health Institute developed a novel MRI-based root phenotyping system to nondestructively acquire high-resolution images of plant roots growing in soil and established the Texas A&M Roots Lab to further develop this technology as a new tool for assessing crop root traits.

The “Field-Deployable Magnetic Resonance Imaging Rhizotron for Modeling and Enhancing Root Growth and Biogeochemical Function” is a part of the Rhizosphere Observations Optimizing Terrestrial Sequestration, ROOTS, program funded through U.S. Department of Energy’s Advanced Research Projects Agency-Energy program.

Nithya Rajan, Ph.D., AgriLife Research crop physiologist/agroecologist in the College of Agriculture and Life Sciences Department of Soil and Crop Sciences, Bryan-College Station, is leading this multidisciplinary project team.

“We are applying this technology to see if we can sense roots growing in agricultural soils and characterize them,” she said. “To date, imaging roots in soil has been challenging because the soil is complex, with solids, moisture and roots. We just want to image the roots.”

We need to develop crop root systems that store more carbon in soil. In addition, deeper root systems can take up more water from soil profiles, increasing crop drought resilience.
John Mullet, Ph.D., biochemist and Perry L. Adkisson Chair in Agricultural Biology in the Department of Biochemistry and Biophysics

From concept to applications, in sorghum and beyond

The project was initially funded for three years with a $4.6 million grant. The second phase of funding was approved this year at $4.4 million.

Will Wheeler, post-doctoral researcher with Texas A&M AgriLife Research, is lowering sorghum plants into the MRI rhizotron for root imaging. Steve Altobelli from ABQMR is on the right. (Texas A&M AgriLife photo by Nithya Rajan)

“In the first phase, we developed the proof of concept and initial prototypes, and in the second phase we developed a low-field MRI rhizotron for high throughput imaging and applications in a wide variety of crops in addition to energy sorghum,” Rajan said.

Also on the team with AgriLife Research are Bill Rooney, Ph.D., sorghum breeder and Borlaug-Monsanto Chair for Plant Breeding and International Crop Improvement in the Department of Soil and Crop Sciences, and John Mullet, Ph.D., biochemist and Perry L. Adkisson Chair in Agricultural Biology in the Department of Biochemistry and Biophysics.

Rooney and Mullet are using the MRI system to advance bioenergy sorghum genetics. Brock Weers, Ph.D., and Will Wheeler, Ph.D., are support scientists working with the AgriLife Research team.

“We need to develop crop root systems that store more carbon in soil,” Mullet said. “In addition, deeper root systems can take up more water from soil profiles, increasing crop drought resilience.”

From a crop improvement perspective, Rooney added, this technology is essential to effectively screen crop germplasm for specific genotypes with enhanced root systems.

Getting to the root of the matter, without disturbing the soil

A 3D Image of the sorghum root system generated using the low-field MRI rhizotron. (Photo provided by ABQMR Inc.)

Using MRI allows researchers to gather root images without damaging plants, unlike traditional methods such as trenching, soil coring and root excavation, Rajan said.

The AgriLife Research team is working with ABQMR Inc., a group of MRI scientists in Albuquerque, New Mexico, who are involved in designing and building the system.

“With low magnetic fields, MRI can be used to image roots in natural soils,” said Hilary Fabich, Ph.D., president of ABQMR. “The low magnetic fields also mean there is less of a safety risk working with the sensor in an agricultural setting.”

Using “machine learning” to see through the noise

Matt Rosen, Ph.D., is the co-principal investigator of the project. He is director of the Low-field MRI and Hyperpolarized Media Laboratory and co-director of the Center for Machine Learning at the Martinos Center for Biomedical Imaging at Harvard. Rosen and his team bring their experience with both low-field MRI physics and state-of-the-art artificial intelligence techniques to the project.

MRI 3D seGmentation and Analysis for Root Description — MIDGARD — software rendering of MRI sorghum root image. (Image provided by Bragi Sveinsson)

The Rosen lab pioneered the use of deep learning for processing MRI data. Neha Koonjoo, Ph.D., a postdoctoral fellow in the Rosen lab, has been leveraging the AUTOMAP — Automated TransfOrm by Manifold Approximation — deep learning-based image reconstruction approach to reduce the influence of environmental noise in root MRI images. Her approach was described in a recent research article.

Bragi Sveinsson, Ph.D., a postdoctoral fellow working with Rosen, developed the first prototype of a software named “MIDGARD” — MRI 3D seGmentation and Analysis for Root Description — for extracting quantitative root trait information from MRI images of roots.

The team plans to release MIDGARD as an open-source software after further testing.

“Using MIDGARD, we can extract quantitative root trait information, and this data will be used for selection of ideal plant characteristics,” Rosen said. “In the future, MIDGARD will also have the ability to three-dimensionally image soil water content, a key property that drives root growth and exploration.”

Technology to market

Technology-to-market activities of this project are led by Cristine Morgan, Ph.D., chief scientific officer of Soil Health Institute, Research Triangle Park, North Carolina, and principal investigator of the first phase of the project when she was at Texas A&M. To foster collaborations with industry partners, the Soil Health Institute established the company Intact Data Services.

“I am excited to translate this technology for phenotyping at scale, as well as the ability to use MRI to 3D-image soil water intact,” Morgan said.

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Media Inquiries to Laura Muntean, laura.muntean@ag.tamu.edu, 6012481891

Written by Kay Ledbetter, 806-547-0002, skledbetter@ag.tamu.edu

SwRI, UTSA collaborate on a novel process to produce low carbon fuels

Project will develop catalyst formulations to create cleaner, more cost-effective fuels

Grant and Award Announcement

SOUTHWEST RESEARCH INSTITUT

SAN ANTONIO — Aug. 3, 2021 — Southwest Research Institute and The University of Texas at San Antonio are collaborating to combine two catalytic processes into a single reactor, with the overall goal of recycling carbon from CO2 to produce low-cost hydrocarbon fuels. The work, led by Dr. Grant Seuser of SwRI’s Powertrain Engineering Division and Dr. Gary Jacobs of UTSA’s College of Engineering, is supported by a $125,000 grant from the Connecting through Research Partnerships (Connect) Program.

Greenhouse gas emissions are expected to increase by about 17% by 2040 as a result of increasing energy and transportation needs in the developing world.

“We’re facing a lack of renewable fuels and the technology to deliver cleaner power generation,” Seuser said. “We’re seeing a rise in battery-powered passenger vehicles, but the high power demands of the aviation, locomotive, shipping, and long-haul trucking industries will continue to require energy-dense hydrocarbons for the foreseeable future.”

Seuser and Jacobs propose using a process called carbon dioxide (CO2) hydrogenation to produce cleaner renewable liquid hydrocarbon fuels for transportation. To accomplish this, they plan to build a single reactor capable of performing two chemical processes in one step. The first will react hydrogen with CO2 to make carbon monoxide (CO) and the second will convert the CO and hydrogen, a blend known as synthesis gas or syngas, into liquid hydrocarbon fuel by a catalytic process known as Fischer-Tropsch synthesis.

“Fischer-Tropsch synthesis was discovered in Germany about a century ago and is still used in places like South Africa and Quatar to convert coal and natural gas into liquid hydrocarbon fuels. Plant capacities ranging from tens of thousands to hundreds of thousands of barrels of fuel per day. It will be an interesting challenge to integrate this catalytic technology into a process that uses CO2 in the feed,” Jacobs said.

Additionally, the process the SwRI-UTSA team is developing will be able to utilize CO2 captured at fossil fuel-fired power plants that would otherwise be sequestered underground or emitted into the atmosphere.

“Combining the functionality of these two catalytic processes, reverse water-gas shift and Fischer-Tropsch synthesis, into a single reactor would simplify the process and increase its economic viability,” Jacobs said.

The effort will also explore novel catalyst formations aimed at combining reverse water-gas shift and Fischer Tropsch synthesis functions, which Jacobs will create and characterize at UTSA. Seuser will use the catalysts in a SwRI reactor to assess their industrial viability.

“Reducing the complexity of converting CO2 into hydrocarbon fuels would have a big impact,” Seuser said. “Finding a way to produce low-carbon fuels and maintain our current energy infrastructure is critical to avoid further increases in Earth’s temperature.”

SwRI’s Executive Office and UTSA’s Office of the Vice President for Research, Economic Development, and Knowledge Enterprise sponsor the Connect program, which offers grant opportunities to enhance greater scientific collaboration between the two institutions.

For more information, visit https://www.swri.org/emissions/catalyst-formulation.

The graveyard never lies

New Study Shows which Countries have Underreported their COVID-19 Deaths and the Extent of their Deception

Peer-Reviewed Publication

THE HEBREW UNIVERSITY OF JERUSALEM

For the past year and a half, many of our decisions regarding whether it is safe to fly to country X or to vacation in country Y have been based a given country’s reported COVID-19 deaths. These stats give the public a sense of how successful—or unsuccessful—that country has been at containing the spread of the coronavirus and its variant offspring. However, not all countries have been playing fair. Several have underreported their numbers, either deliberately or due to faulty testing capacities.

Now, two young researchers, one from Israel and one from Germany, have teamed up to set the record straight. Instead of relying on countries’ published COVID-19 death rates, they created the World Mortality Dataset, the largest existing collection of overall mortality data, to uncover the true rate of COVID-19 deaths in more than 100 countries. They published their findings in eLife journal.

In any given period of time, a certain number of people die due to a variety of reasons: old age, illness, violence, traffic accidents and more. These deaths are commonly known as “expected deaths”. Researchers use this data to predict the number of expected deaths in coming months and years. However, pandemics, wars, natural and manmade disasters cause additional deaths, above and beyond the expected. These are known as “excess deaths”.

To calculate a given country’s true COVID-19 death toll, Ariel Karlinsky, a graduate student at Hebrew University of Jerusalem (HU)’s economics Department and Dmitry Kobak from Germany’s Tübingen University collected mortality data from 103 countries. “We gathered mortality data to answer a number of questions,” Karlinsky shared. “We wanted to find out whether the pandemic caused excess deaths in the countries we covered and, if so, to what extent.”

To do so, the team compared the number of overall “known deaths” during the COVID pandemic with the number of overall deaths from previous years. In this way, they were able to determine the likely number of excess deaths caused by the coronavirus pandemic. “Even though the number of excess deaths does not exactly equal the mortality rate from COVID-19 infections, for many countries it is the most objective indicator of their pandemic death toll,” Karlinsky explained.

For example, several Latin American countries, namely Bolivia, Ecuador, Mexico and Peru underreported their COVID-19 deaths, even though the number of excess deaths sustained during the pandemic period was over 50% higher than the number of expected deaths. According to Karlinsky and Kobak’s World Mortality Dataset, Bolivia’s true number of COVID deaths is likely 2.5 times higher than they reported—36,000 deaths instead of 15,000. In Ecuador, it’s 2.9 times higher—64,000 deaths instead of the 22,000 reported, while in Mexico, the figure is 2.1 times higher—471,000 instead of the 221,000 pandemic deaths that were reported.

However, Peru stood out from the bunch. They originally underreported their COVID-19 deaths—claiming only 69,000 deaths when in reality that figure was closer to 185,000. After an outcry by public health officials, Peru’s health ministry made amends. They audited all deaths during the pandemic period and resubmitted COVID-19 death stats to the World Health Organization that more accurately reflect the true number of excess deaths caused by the pandemic.

Meanwhile, other countries have obstinately continued to underreport their COVID-19 deaths. The true number of pandemic deaths sustained by Russia is likely 4 times higher than reported—551,000 deaths instead of 135,000. In Belarus that number is 14.5 times higher—5,700 deaths, instead of 392, and in Uzbekistan 29 times higher—21,500 deaths, instead of the 740 reported. Tajikistan wins the underreporting prize with a COVID-19 death rate that is whopping 100-times higher than reported—9,000 deaths, instead of 90.

The former Soviet Union is not alone in vastly underreporting its COVID-19 deaths. According to the Karlinsky-Kobak study, Nicaragua’s true number of pandemic deaths is 50 times higher than reported—7,000 coronavirus deaths instead of the 137 reported. However, it’s not all doom and gloom. Australia and New Zealand’s death rate during the pandemic was actually lower than previous periods. This is likely due to their virus-containment efforts, which included border closures, social distancing and mask-wearing which decreased their overall number of deaths during the pandemic period.

Among European nations, the team found that many countries faithfully reported their pandemic deaths. Per 100,000 people, the United Kingdom suffered 159 deaths, France 110, Switzerland 100. The Czech Republic suffered 320 pandemic deaths and Poland 310. Denmark and Norway were unique in that they experienced no excess mortality during the pandemic. The United States had 194 excess deaths per 100,000 persons.

“Our results present a comprehensive picture of the impact of COVID-19,” Kobak shared. “We hope these findings—and their methodology –will lead to a better understanding of the pandemic and highlight the importance of open-source and fast mortality reporting.”

In the Middle East, Israel’s excess deaths during the coronavirus pandemic were actually smaller than their reported figures—5,000 instead of 6,400, as reported. This is likely due to a decrease in the overall number of deaths from non-COVID 19 respiratory infections during the winter months. At 58 excess deaths per 100,000 persons, Israel fared better than its neighboring countries (which provided overall mortality data). Egypt’s excess deaths were 13 times higher than reported—196,000 instead of 15,000, Iran’s were 2.15 times higher—115,000 COVID-19 deaths instead of 54,000, and Lebanon’s figures were 1.23 times higher than reported—9,000 deaths instead of 7,300.

When analyzing the overall figures, Karlinsky shared his hope, “that our dataset will be a valuable asset for public health officials looking to assess the risks and benefits of a given pandemic-containment measure. Kobak and I are constantly expanding our dataset and will continue to track excess mortality around the world for the remainder of the COVID-19 pandemic”.

DOI

10.7554/eLife.69336

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset

ARTICLE PUBLICATION DATE

2-Aug-2021

Study tracks global death toll of COVID-19 pandemic

Using the World Mortality Dataset, the largest existing collection of mortality data, researchers have tracked the impact of COVID-19 across more than 100 countries.

Peer-Reviewed Publication

ELIFE

New insight on the death toll of the COVID-19 pandemic worldwide has been published in the open-access eLife journal.

Comparing the impact of COVID-19 between countries or during a given period of time is challenging because reported numbers of cases and deaths can be affected by testing capacity and reporting policy. The current study provides a more accurate picture of the effects of COVID-19 than using these numbers, and may improve our understanding of this and future pandemics.

In any given period of time, a certain number of people die due to many particular reasons, such as old age, illness, violence, traffic accidents and more. Researchers are able to predict the number of deaths from these causes over coming months or years, known as expected deaths, using the same information gathered from previous months and years. However, pandemics, conflicts, and natural and man-made disasters cause additional deaths above and beyond those expected, which are known as ‘excess deaths’.

“Measuring excess deaths allows us to quantify, monitor and track pandemics such as COVID-19 in a way that goes above testing and reporting capacity and policy,” says Ariel Karlinsky, a graduate student at the Hebrew University of Jerusalem in Israel, and co-author alongside research scientist Dmitry Kobak, from Tübingen University, Germany. “However, until now, there has been no global, frequently updated repository of mortality data across countries.”

To fill this gap, Karlinsky and Kobak collected weekly, monthly or quarterly mortality data from 103 countries and territories, which they have made openly available as the World Mortality Dataset. They then used the data to work out the number of excess deaths in each country during the COVID-19 pandemic.

“We used our data to answer a number of questions,” Karlinsky explains. “Specifically, we wanted to find out whether the pandemic caused excess deaths in the countries we covered and, if so, to what extent. We were also curious to see whether the numbers of excess deaths were matched across countries.”

Their analyses showed that, in several of the countries worst affected by COVID-19 – namely Peru, Ecuador, Bolivia and Mexico – excess deaths were more than 50% above the expected annual mortality rate, or above 400 excess deaths per 100,000 people as in Peru, Bulgaria, North Macedonia and Serbia. At the same time, in countries such as Australia and New Zealand, mortality during the pandemic was below the usual level, which the authors suggest is likely due to social distancing measures reducing the number of deaths caused by other infections besides COVID-19.

Furthermore, the researchers found that while many countries have been reporting their COVID-19 death rates accurately, some including Nicaragua, Belarus, Egypt and Uzbekistan have underreported these numbers by more than 10 times.

“Together, our results present a comprehensive picture of the impact of COVID-19, which we hope will contribute to better understanding of the pandemic and assessing the success of different mitigation strategies,” Kobak concludes. “The work also highlights the importance of open and rapid mortality reporting for monitoring the effects of COVID-19. We hope that our dataset will provide a valuable resource to help other investigators answer their own questions about the pandemic. We are constantly expanding our dataset and will continue to track excess mortality around the world.”

Media contacts

Emily Packer, Media Relations Manager

eLife

e.packer@elifesciences.org

+44 (0)1223 855373

Tali Aronsky, International Media Director

The Hebrew University of Jerusalem

taliaron@savion.huji.ac.il

+972-55-666-4371

About eLife

eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We aim to publish work of the highest standards and importance in all areas of biology and medicine, including Epidemiology and Global Health, while exploring creative new ways to improve how research is assessed and published. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Epidemiology and Global Health research published in eLife, visit https://elifesciences.org/subjects/epidemiology-global-health.

About Hebrew University

The Hebrew University of Jerusalem (HU) is Israel's leading academic and research institution, serving 24,000 students from 80 countries. Founded in 1918 by visionaries including Albert Einstein and Sigmund Freud, HU is ranked among the world's 100 leading universities. To date, HU faculty and alumni have won eight Nobel Prizes, one Fields Medal and one Abel Prize. For more information, visit http://new.huji.ac.il/en.

About the University of Tübingen

Innovative. Interdisciplinary. International. These have been our guiding principles in research and teaching since our founding in 1477. Tübingen’s success in the German government’s Excellence programs since 2012 have placed it among the most outstanding universities in Germany. The University is also well-placed in international higher education rankings.

More than 4,500 scientists and academics work at the University of Tübingen. We invest more than 200 million euros annually in a wide variety of research projects. As a comprehensive research university, Tübingen has solid foundations in the Sciences and Life Sciences as well as in the Humanities and Social Sciences. We have special strength due to our close collaboration with many non-university research institutions in our region and with notable universities around the world.

With more than 200 subjects on offer, the University of Tübingen gives prospective students a wide range of choices. A sharp focus on research is a major drawcard for Master’s students and doctoral candidates. The University not only trains our future experts and leaders; it is living up to its responsibility for the world of tomorrow.

DOI

10.7554/eLife.69336

METHOD OF RESEARCH

Data/statistical analysis

ARTICLE TITLE

Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset