Science-Watching: Proton-Coupled Energy Transfer/Omicron Spike Function

[from Science, First Release Notification for July 21]

Proton-Coupled Energy Transfer in Molecular Triads

Abstract

A photochemical mechanism was experimentally discovered and denoted proton-coupled energy transfer (PCEnT). A series of anthracenephenolpyridine triads formed the local excited anthracene state after light excitation at ca. 400 nm, which led to fluorescence around 550 nm from the phenolpyridine unit. Direct excitation of phenolpyridine would have required light around 330 nm, but the coupled proton transfer within the phenolpyridine unit lowered its excited state energy so that it could accept excitation energy from anthracene. Singlet-singlet energy transfer thus occurred despite the lack of spectral overlap between the anthracene fluorescence and the phenolpyridine absorption. Moreover, theoretical calculations indicated negligible charge transfer between the anthracene and phenolpyridine units. PCEnT was suggested as an elementary reaction of possible relevance to biological systems and future photonic devices.

Access the full paper [via institutional access or paid download].

Omicron Spike Function and Neutralizing Activity Elicited by a Comprehensive Panel of Vaccines

Abstract

The SARS-CoV-2 Omicron variant of concern comprises several sublineages with BA.2 and BA.2.12.1 having replaced the previously dominant BA.1, and BA.4 and BA.5 increasing in prevalence worldwide. We show that the large number of Omicron sublineage spike mutations lead to enhanced ACE2 binding, reduced fusogenicity, and severe dampening of plasma neutralizing activity elicited by infection or seven clinical vaccines relative to the ancestral virus. Administration of a homologous or heterologous booster based on the Wuhan-Hu-1 spike sequence markedly increased neutralizing antibody titers and breadth against BA.1, BA.2, BA.2.12.1, and BA.4/5 across all vaccines evaluated. Our data suggest that although Omicron sublineages evade polyclonal neutralizing antibody responses elicited by primary vaccine series, vaccine boosters may provide sufficient protection against Omicron-induced severe disease.

Read the full paper. [Archived PDF]

“2022 Monkeypox Outbreak: Situational Awareness” with Syra Madad [Zoom]

[from Harvard Kennedy School’s Belfer Center, part of Harvard University]

Thursday, July 21, 2:30-4:00 PM EDT

RSVP (Required)

The 2022 Monkeypox outbreak continues to expand with case counts mounting in many countries. This seminar will cover where we are in the global fight against monkeypox, where we may be headed as a nation, and what we need to do right now to mitigate the growing threat of monkeypox. Join Belfer Fellow Dr. Syra Madad in conversation with Kai Kupferschmidt, Dr. Krutika Kuppalli, Dr. Anne Rimoin, Dr. Boghuma Kabisen Titanji, and Dr. Jay K. Varma.

About the Speakers

Dr. Anne Rimoin is a Professor of Epidemiology at the UCLA Fielding School of Public Health. She is the Gordon-Levin Endowed Chair in Infectious Diseases and Public Health. Dr. Rimoin is the director of the Center for Global and Immigrant Health and is an internationally recognized expert on emerging infections, global health, surveillance systems, and vaccination.

Rimoin has been working in the DRC since 2002, where she founded the UCLA-DRC Health Research and Training Program to train U.S. and Congolese epidemiologists to conduct high-impact infectious disease research in low-resource, logistically-complex settings.

Dr. Rimoin’s research focuses on emerging and vaccine-preventable diseases. It has led to fundamental understandings of the epidemiology of human monkeypox in post-eradication of smallpox, long-term immunity to Ebola virus in survivors and durability of immune response to Ebola virus vaccine in health workers in DRC. Her current research portfolio includes studies of COVID-19, Ebola, Marburg, Monkeypox and vaccine-preventable diseases of childhood.

Boghuma Kabisen Titanji (MD, MSc., DTM&H, PhD) is a Cameroonian born physician-scientist and Assistant Professor of Medicine at Emory University in Atlanta. She obtained her MD from the University of Yaoundé I in Cameroon and worked for two years after graduation as a medical officer, before pursuing post-graduate research training in London, United Kingdom. As an awardee of the prestigious Commonwealth Scholarship program, she obtained a Masters Degree in Tropical Medicine and International Health from the London School of Hygiene and Tropical Medicine, a diploma in Tropical Medicine and Hygiene from the Royal College of Physicians and a Ph.D. in Virology from University College London. Dr. Titanji joined Emory University School of Medicine in 2016 where she completed a residency in Internal Medicine, on the ABIM research pathway and a fellowship Infectious Diseases. She has three parallel career interests: translational and clinical research in HIV and emerging virus infections, science communication, and global health. Her clinical focus is general infectious diseases and people with HIV. Her current research focuses on chronic inflammation as a mediator of cardiovascular disease in people with HIV. She is passionate about leveraging translational research to improve the care of people with HIV, global health equity and using science to influence health policy through science communication and advocacy.

Jay K. Varma, MD is a Professor of Population Health Sciences and Director of the Cornell Center for Pandemic Prevention and Response at Weill Cornell Medicine. Dr. Varma is an expert on the prevention and control of diseases, having led epidemic responses, developed global and national policies, and led large-scale programs that have saved hundreds of thousands of lives in China, Southeast Asia, Africa, and the United States. After graduating magna cum laude with highest honors from Harvard, Dr. Varma completed medical school, internal medicine residency, and chief residency at the University of California, San Diego School of Medicine. From 2001-2021, he worked for the U.S. Centers for Disease Control and Prevention with postings in Atlanta, Thailand, China, Ethiopia, and New York City. From April 2020 – May 2021, he served as the principal scientific spokesperson and lead for New York City’s COVID-19 response. Dr. Varma has authored 143 scientific manuscripts, 13 essays, and one book.

Kai Kupferschmidt is a science journalist based in Berlin, Germany. He is a contributing correspondent for Science where he often covers infectious diseases. Kai received a diploma in molecular biomedicine from the University of Bonn, Germany and later visited the Berlin Journalism School. He has won several awards for his work, including the Journalism Prize of the German AIDS Foundation. Together with two colleagues he runs a podcast on global health called Pandemia [German]. He has also written two books, one about infectious diseases and one about the science of the color blue.

Krutika Kuppalli, MD, FIDSA is a Medical Officer for Emerging Zoonotic Diseases and Clinical Management in the Health Emergencies Program at the World Health Organization where she currently supports activities for the Monkeypox outbreak and COVID-19 pandemic. She completed her Internal Medicine residency and Infectious Diseases fellowship at Emory University, a Post-Doctoral Fellowship in Global Public Health at the University of California, San Diego and the Emerging Leader in Biosecurity Fellowship at the Johns Hopkins Center for Health Security. Dr. Kuppalli currently serves on the American Society of Tropical Medicine and Hygiene (ASTMH) Trainee Committee and is the Chair of the Infectious Diseases Society of America (IDSA) Global Health Committee.

Dr. Kuppalli was previously awarded the NIH Fogarty International Clinical Research Fellowship and conducted research in Southern India to understand barriers to care and how emerging infections impacted persons living with HIV/AIDS. She was the medical director of a large Ebola Treatment Unit in Sierra Leone during the 2014 West Africa Ebola outbreak, helped lead the development and implementation of pandemic response preparedness activities in resource limited settings, and has consulted on the development of therapeutics for emerging pathogens. Her clinical and research interests focus on health systems strengthening in resource limited settings, research and clinical care for emerging infections, outbreak preparedness and response, and policy. She has worked in numerous countries including Ethiopia, India, Sierra Leone, Uganda, and Haiti.

During the COVID-19 pandemic Dr. Kuppalli served as a consultant for the San Francisco Department of Health and helped develop and operationalize a field hospital. She served as an expert witness to the U.S. Congress, Financial Services Committee Task Force on Artificial Intelligence (AI) about how digital technologies may be leveraged for exposure notification and contact tracing to improve the pandemic response. She also collaborated with the Brennan Center for Justice to develop guidelines to inform “Healthy in-person Voting” in advance of the 2020 U.S. election and testified before the U.S. House Select Subcommittee regarding these recommendations. Prior to her position at WHO, she was the medical lead for COVID-19 vaccine rollout at the Medical University of South Carolina (MUSC) and helped coordinate vaccine education events for the staff and community and oversaw the reporting of adverse vaccine events.

Since joining WHO in August 2021, Dr. Kuppalli has been part of the WHO headquarters incident management team (IMST) for COVID-19, the clinical characterization and management working group for COVID-19, the COVID-19 therapeutics steering committee, and is the technical focal point for the post COVID-19 condition (Long COVID) steering committee. She is a member of the secretariat on the scientific advisory group on the origins of emerging and re-emerging infectious diseases (SAGO) which was convened by the Director General to understand and investigate the origins of SARS-CoV-2 and other novel pathogens. More recently since the development of the multi-country monkeypox outbreak she has been part of the IMST at WHO as one of the clinical management focal points. In this capacity she was part of the WHO core group that helped write the recently published Clinical Management and Infection Prevention and Control guidelines for Monkeypox and advising on the clinical endpoints for the global CORE therapeutics protocol.

Dr. Kuppalli is recognized as a scientific expert in global health, biosecurity and outbreak response. She was recognized by NPR Source of The Week early in the pandemic as an expert to follow and named to Elemental’s 50 Experts to Trust in a Pandemic. She has been a frequent contributor to numerous domestic and international media outlets including The New York Times, NPR, Reuters, The Washington Post, Vox, Stat News, San Francisco Chronicle, Forbes, NBC Bay Area, BBC News.

Climate-Watching: A Collision of Economics and History: In Pennsylvania, the Debate over Climate Is a Bitter One

The state has both a long history of environmental action and a longstanding dependence on fossil fuels.

[from Inside Climate News, by David Shribman, July 17, 2022]

This is a state where natural gas production reached a record 7.1 trillion cubic feet in 2020, the most of any state outside Texas and more than the energy supplied by the state’s nuclear power plants. It’s a state that has 49 underground gas storage sites, more than any other in the nation.  Its coal production ranks behind only Wyoming and West Virginia, and only Wyoming and Texas export more total energy to other parts of the country.

This is also a state where voters will select a new governor and a new senator in November. No state has more vital elections this year; no state has a more complicated and more contentious political culture; and no state provides a better test case for environmental issues and for the future of the climate-change debate.

Welcome to Pennsylvania.

Don’t pack a sweater: the average temperature in the state has risen by 2.8 degrees Fahrenheit since the first Earth Day, in 1970, a bigger increase than the national average.

Don’t breathe deeply: the state’s two major cities, Philadelphia and Pittsburgh, are among the nation’s worst 25 metropolitan areas for annual particulate air pollution

And don’t fail to note the irony—of a state whose economy and lifestyle are unusually dependent on fossil fuels but whose history is unusually rich in the love of nature and the protection of the environment. It is this collision of economics and history that makes environmental issues so emotional, the debate so bitter, the outcome so vital.

Pennsylvania was the home of John J. Audubon, who cultivated in Americans a love of bird life; Rachel Carson, whose clarion call about the environment jolted the country and shook the Kennedy administration; John Chapman, known to school children nationwide as Johnny Appleseed; J. Horace McFarland, a photographer and conservationist celebrated as the Father of the National Park Service; Harold L. Ickes, the pathfinding Secretary of the Interior during the Franklin D. Roosevelt years who shored up perhaps the least effective and most corrupt arm of government while elevating the standards and practices of the National Park Service; and Jerome Rodale, the publisher whose books gave voice to the ethos of sustainable agriculture. And it was the adopted home of William Penn, the founder of the colony that would bear his name and the author of a conservation edict requiring that 20 percent of the land in the Province of Pennsylvania be preserved as wooded. It is no surprise that Pennsylvania was one of the first states to adopt an Environmental Bill of Rights.

But Pennsylvania also was the setting for environmental milestones of an entirely different type. In Donora, a 1948 smog episode killed 20 people and saddled some 40 percent of the town’s population with respiratory disease. A third of a century later, the partial meltdown of Unit 2 of the Three Mile Island nuclear plant in Dauphin County spewed radioactivity into the Harrisburg area. 

The state has had multiple mine disasters and the subsequent contamination of nearby fields and streams. As early as 1883, the explorer and adventure travel writer Willard Glazer wrote that Pittsburgh’s industry was “rendered possible by the coal which abounds in measureless quantity in the immediate neighborhood of the city”—and which contributed to the poisoning of many of the area’s waterways and the despoiling of the air. As late as 1940, 81 percent of the city’s dwellings burned coal. The emissions from the steel mills that helped the country win two world wars and build a robust mass-consumer economy only added to the environmental distress.

This duality is part of, defines all of, Pennsylvania’s natural and political history.  It is embedded in the origin story of Pennsylvania and reinforced in contemporary history. In the WPA Guide to Pennsylvania, the writers of the New Deal-era product of the Federal Writers Project spoke in 1940 of how the main plant of the Pittsburgh Plate Glass Company in Ford City, Pennsylvania, “extends for a mile along Third Avenue in a series of long squat units composed of red brick,” and how the state’s Red Hills were exceeded only in Belgium as “the finest farm section in the world.” Precisely three-quarters of a century ago, in his classic 1947 book, Inside U.S.A., the journalist John Gunther wrote, “To a degree the story of Pennsylvania is the story of iron, coal, and steel. Yet of its 26 million acres, almost half is forest!”

A state known for producing metals and fouling the air is also a state known for hunting grouse, pheasant, deer and bear. A state teeming with factory workers is a state loaded with farmers. A state with two major power centers, Philadelphia and Pittsburgh, is a state where elections often are decided in the agricultural “T” between the two. A state known for building belching steel plants is also a state where, this spring, the owners of Fallingwater, the Frank Lloyd Wright masterpiece, announced that they would install solar panels on the iconic house to offset the power used at the site on Bear Run in Fayette County. And when it comes to environmental issues, Pennsylvania is a state where manufacturing and banking interests have enormous influence in the stately Capitol in Harrisburg, and also a state full of climate activists determined to hold industry in check and battle climate change.

“It is particularly difficult in Pennsylvania to come to any agreement on environmental issues because coal and natural gas have countervailing pressure against attempts to deal with climate change,” said Joel A. Tarr, a Carnegie Mellon University historian who studies the effect of technology on the urban environment. “When you tell people that we have a problem with air quality here, their response is that it used to be much worse. This is a place where we won’t have a water-quality solution until we have a cholera epidemic and we won’t address climate change until we have a major catastrophe that brings it home to Pennsylvania.”

Not that there haven’t been efforts. “A generalized good always takes a back seat to a specific interest,” Gov. Tom Wolf, a Democrat, told me in an interview for this article. “We all benefit from a healthy environment, but there are specific interests that are specifically harmed if we do the right thing. Those specific interests have a lot of power in places like Harrisburg.”

The frequent result of these countervailing impulses and competing interests: paralysis on environmental matters, even as the latest United Nations report, published in April, warned that the world was on a path to a rate of global warming more than double the 2.7-degrees Fahrenheit set as the preferred global goal in 2015 in Paris.

U.N. Secretary General António Guterres warned that the result would be “unprecedented heatwaves, terrifying storms, widespread water shortages and the extinction of a million species of plants and animals,” adding, “This is not fiction or exaggeration. It is what science tells us will result from our current energy policies.”

 A City (and State) in Crisis

As man proceeds toward his announced goal of the conquest of nature, he has written a depressing record of destruction, directed not only against the earth he inhabits but against the life that shares it with him.

Rachel Carson, in Silent Spring

In many ways, Pittsburgh—once smoky, still gritty, now proud of its “eds-and-meds” economy, its edgy youth culture and yeasty locavore restaurant scene—stands as a symbol of Pennsylvania’s environmental and climate crisis.

In the past half century, the city’s average temperature has risen by 2.8 degrees, according to figures compiled by Climate Central—a jarring result for a city where the local political grandees like to emphasize how the area has moved beyond its heavy-manufacturing past. Even with the dramatic decline in the steel industry, Pittsburgh remains the 10th worst city in the country in terms of the presence of short-term particulate matter, and the Breathe Meter indicator that monitors the area’s air has found that 88.5 percent of metro areas in the country have cleaner air. Moreover, a study by Community Partners in Asthma Care found that the rate of asthma in Pittsburgh-area school children is nearly three times the national average.

For generations, no essay on the environment of Pennsylvania was complete without citing Charles Dickens’ characterization of mid-19th century Pittsburgh as “hell with the lid lifted,” or Lincoln Steffens’ complaint about the city’s “smoky gloom” and the “volcanic light upon the cloud of mist and smoke” that appeared with the periodic opening of the blast furnaces. When my wife and I bought a house in Pittsburgh two decades ago—when almost the entire steel industry had closed down in the area—we paid thousands of dollars to have a century’s worth of soot blasted from the brick facade.

All of that before the word “fracking” was introduced into the lexicon of the Pennsylvania debate.

“There is gas in the ground and people have been taking it out of the ground since before I was governor,” Wolf said in the interview. “If I could snap my fingers, we would go completely to wind and solar. I haven’t figured out how to do this. The job is to manage the transition to that energy future.”

Republicans in recent years have sought to deregulate the natural gas industry, expand drilling, ease stipulations for gas permits, open state parklands for energy extraction and open new opportunities for gas pipelines, having the state subsidize them.

“These things were not always Republican goals,” said David Hess, who was secretary of the Pennsylvania Department of Environmental Protection under Republican Governors Tom Ridge and Mark Schweiker. “Republicans once had environmental issues as a pretty high priority. Only recently have Republicans changed their approach. This issue is no longer bipartisan, and that applies especially to climate change. But the only way we can break the loop we are on is to do something different, and yet industry and their Republican allies want more and more. Putting all the stuff in the air from fossil fuels cannot be good, especially when we have clean alternatives.”

And yet the Keystone State has not been entirely a conscientious objector to environmental initiatives.

At a time when there was so much soot in the air that Pittsburgh kept its street lights on all day long and businessmen were forced to change their soiled shirts after returning from a walk to a lunch appointment, Mayor David Lawrence undertook a dramatic anti-smoke campaign in 1946 that greatly improved the air quality in the city. “I am convinced that our people want clean air,” the mayor said in his first inaugural address. “There is no other single thing which will so dramatically improve the appearance, the health, the pride, the spirit of the city.”

Lawrence was not alone. “The advocates of the Pittsburgh Renaissance conceived of decreased pollution as a means of assisting the transition of the city from a heavy-industry to a service economy by improving, modernizing, and reconstructing its central business district,” Stefano Laconi, who teaches the history of the Americas at the University of Florence, wrote in a 1999 essay in the journal Pennsylvania History. He argued that the initiative provided Lawrence “not only with the foundation of a public-private partnership but also with the basis of a bipartisan political coalition with local Republican moguls like Richard King Mellon.”

Years later, Republican Gov. Ridge, with Democratic support, began his administration with an initiative to clean up and redevelop brownfield sites. At the same time, the legislature won national attention by reorganizing the state’s approach to these issues, creating separate departments of Environmental Protection, which concentrates on protecting the air, water and land from pollution, and Conservation and Natural Resources, focused on state parks and state forests.

“At the beginning of my administration, I issued a challenge to Pennsylvania to become a national leader in finding new ways to protect our environment while promoting economic progress, to provide for the needs of the present without compromising the ability for future generations to meet needs of their own, and to think in terms of sustainability, with both the economy and our environment,” Ridge told me.  

The governor was fond of quoting the adage, “We do not inherit the earth from our ancestors; we borrow it from our children.” As governor, he said that,“I would often remind myself that the air we breathe and the water we drink should never be taken for granted.”

Much to be Done and an Election That Matters

The fact that a man is to vote forces him to think.

Jonathan Chapman, known as Johnny Appleseed

Ordinarily, the multi-interest collision of jobs and climate, energy and environment, might be top-shelf issues in a state that ranks second only to Texas in energy production and that had the largest increase in natural-gas production in the last decade. But that collision is a side show rather than the main event.

“All of these candidates need to speak up and tell us what they would do about the energy situation and the climate crisis that is growing more critical by the minute,” said Larry Schweiger, a former president of the National Wildlife Federation, PennFuture and the Western Pennsylvania Conservancy. “It is very frustrating to see candidates for governor and the Senate not making an effort to say how they would address these urgent issues. Both parties are guilty of  this, and it is a big omission and a big problem.”

Now Democratic Attorney General Josh Shapiro and Republican state Sen. Douglas Mastriano are facing off for governor and Democratic Lt. Gov. John Fetterman and Republican celebrity doctor Mehmet Oz are fighting for the U.S. Senate seat being relinquished by GOP Sen. Patrick Toomey

The four will face questions about their commitment to climate change with new urgency—and new stakes. And the pressure may well come from a newly critical group of voters: young people.

A Harris Poll survey conducted with 4-H found just fewer than half of teenagers believe political and global leaders are taking meaningful action to protect the environment. There is reason to believe that the top tier of teenagers, eligible to vote, and their older brothers and sisters will be motivated and perhaps mobilized by these issues.

“There’s no question that environmental issues are far more critical for younger voters,” said Steven Farnsworth, the political scientist who is director of University of Mary Washington’s Center for Leadership and Media Studies in Virginia. “This has been going on since the first Earth Day. It has to do with the fact that younger people are going to be on this planet longer than older people.”

The approach that these four nominees bring to these matters is important. “It’s not about issues, it’s about values,” said John Della Volpe, director of polling at Harvard Kennedy School of Government’s Institute of Politics and the author of the newly published How Gen Z is Channeling Their Fear and Passion to Save America. “And the degree to which candidates can connect climate change into values, and display that they are thinking about the future, they could affect the turnout of young people and how they do vote.”

There is much to be done. Pennsylvania ranks 19th among the states in the rate of growth for wind power, according to the PennEnvironment Research and Policy Center, and 23rd among the states in the rate of growth for solar power. The potential is great; if solar units were placed on the roofs of Pennsylvania’s big-box stores, for example, the result could be the annual production of more than 3,000 gigawatt-hours of clean electricity. There are bills in the legislature to require the state’s suppliers of electricity to generate nearly a third of their energy from renewable sources by 2030 and to put the state on a course to having 100 percent of its energy needs provided by wind and solar energy and other sources by the middle of the century.

Much of the emphasis will be on the state level, which is why the gubernatorial race between Shapiro, the Democratic attorney general, and GOP state Sen. Mastriano is so critical.

Shapiro speaks easily about clean energy, says he believes that more electric-vehicle infrastructure investments must be made, and pledges strict monitoring of the state’s utility companies. But he has broken with Gov. Wolf over whether the state should join the Regional Greenhouse Gas Initiative, known as RGGI, which puts a price and descending cap on carbon emissions. With an eye toward the power of the state’s building trades, he believes RGGI will be ineffective and will cause hardship among the state’s energy workers and companies.

As the state’s Democratic Senate candidate, Lt. Gov. Fetterman speaks of the climate issue as an “existential crisis” and argues that the jobs-versus-environment calculus represents a false choice. “We still need to make stuff in this country, you know?” A onetime advocate of a moratorium on new fracking sites, he now sees a rationale for a limited, perhaps temporary, expansion. “I have been steadfastly talking about how important it is that we retain the manufacturing jobs and the energy jobs in Pennsylvania that currently provide our energy security,” he said at a debate at Carnegie Mellon University, but added, “We also must acknowledge and recognize that we have to trend …. away from these.”

The Republican candidates in these two high-profile races take substantially different positions from their Democratic rivals. Oz, the Senate candidate, has abandoned his onetime advocacy of strict environmental regulation and calls for the “freedom to frack.” Mastriano, the Republican gubernatorial nominee, has argued that Wolf’s RGGI plan would “do far more harm than good” and this spring he submitted legislation to ban the federal government from regulating coal and gas extraction in Pennsylvania and to exempt the state’s industrial plants from the federal wastewater and air pollution rules. “We’re going to open up our energy sector like you’ve never seen,” Mastriano said at his victory celebration after he won the GOP primary.

A Monumental Figure

Unless we practice conservation, those who come after us will have to pay the price of misery, degradation, and failure for the progress and prosperity of our day.

Gifford Pinchot

If there is one symbol of the tensions, perspectives, history and impulses of Pennsylvania in environmental matters it is not the gentle Audubon, who nurtured a love of birds in the heart and mind of the nation, nor the hard-faced leaders of power plants and coal mines. It is not the passionate Carson nor the resolute lobbyists who besiege the legislative chambers in Harrisburg. All are part of the Keystone State culture, but none of them personifies the colliding interests in this vital and emotional area of political conflict.

Only one person does, and that is Gifford Pinchot.

Today, Pinchot is largely a forgotten figure, overshadowed as a conservationist by John Muir, eclipsed as a visionary by Theodore Roosevelt. Today, Gaylord Nelson, the late senator from Wisconsin and the founder of Earth Day, is regarded as the political magus of the conservation movement, a title once plausibly claimed by Pinchot. Today the world regards Wangari Maath, the Kenyan activist who founded the Green Belt Movement and won the 2004 Nobel Peace Prize, as the most celebrated troubadour and warrior for the environment.

All these titles once belonged to Pinchot, a monumental figure who was the 28th governor of the Commonwealth of Pennsylvania. He served two terms in the Capitol and lived in a family home named Grey Towers, just outside the tourist town of Milford, Pennsylvania. The home is now a National Historic Site and home to the Pinchot Institute for Conservation, dedicated to fashioning innovative responses to conservation and environmental challenges.

Pinchot, who died in 1946, went to his grave with a green-plated resume: First chief of the U.S. Forest Service. Chief of the U.S. Division of Forestry. Head of the Pennsylvania forestry division. At one time, the term “Pinchotism” was derided in Congress by business interests the way “Reaganomics” was criticized by early 1980s Democrats—until Pinchotism, like Reagonomics, was redeemed in the public eye.

And yet Pinchot does not wear an unblemished hero’s halo in history. Until recent damaging disclosures, that belonged to his chief rival, John Muir, his one-time ally and patron, though the shine on Muir was darkened in 2020, when Michael Brune, executive director of the Sierra Club that Muir helped found in 1892, cited him for having “made derogatory comments about Black people and Indigenous peoples that drew on deeply harmful racist stereotypes, though his views evolved later in his life.”

But in the long-ago conflict between Muir and Pinchot that spanned the period 1908 to 1913 and spilled over into later years is a story that captures the conflict at the heart of the environmental issue in the nation—and in Pinchot’s home state.

In the perspective of today, Pinchot had an ability, in the phrasing of his biographer, Char Miller, “to maintain what might seem like contradictory impulses—the desire to live simultaneously and within nature, to exult in its splendors while exploring its resources.” But in his titanic clash with Muir, Pinchot was cast as the bête noire of the movement he plausibly could claim to have helped create.

Muir was all about preservation and Pinchot was about wise or multiple uses of the land,” Douglas Brinkley, the Rice University historian who wrote about the PinchotMuir conflict in his 2010 The Wilderness Warrior, said in an interview. “The dispute was over what was conservation. Muir became a folk hero through the long shadow of the Sierra Club but Pinchot never had a legacy organization group.”

The venue of the clash was the Hetch Hetchy Valley in Yosemite National Park, but its implications extended nationwide and the forces at play continue to collide in Pennsylvania. Pinchot, a close advisor and friend to Theodore Roosevelt, was caught in the vise created by the moral passion of conservationists and the physical thirst of Californians. San Francisco wanted water, early environmentalists worshiped wilderness. There was no middle ground, though Pinchot was caught in the middle of the struggle.

It was, as the Library of Congress would characterize it a century later, “a division between those committed to preserving the wilderness and those more interested in efficient management of its use.” The two combatants had conflicting profiles: Pinchot was an insider, Muir was an outsider. Thus Muir claimed the moral high ground as the protector of the outdoors. The battle between the two men had its origins in Muir’s evolution to a view that, as Miller characterized it in his monumental 2001 Gifford Pinchot and the Making of Modern Environmentalism, “the practice of forestry and the preservation of wilderness were incompatible, a tentative conclusion that would harden into conviction in the first years of the new century.” The result was temporarily to place Pinchot, politically if not emotionally—and supremely awkwardly—in the same camp as his traditional opponents, business executives with a lust for land and lucre.

Pinchot saw this issue as a struggle between “the extreme desirability of preserving the Hetch Hetchy in its original beauty” against the legitimate water needs of San Francisco and other communities in the Bay area. Muir, in a letter to Pinchot, said the proposal to flood the valley to provide water for “the dear people” was “full of graft,” later characterizing it as a moral outrage and a mortal threat to wilderness values. It was a classic confrontation between a master of the political world and a mystic of the natural world.

The struggle wore on for years. Later Pinchot would tell a congressional hearing that “injury to Hetch Hetchy by substituting a lake for the present swampy shore of the valley…is altogether unimportant when compared with the benefits to be derived from its use from a reservoir.”

In the end, Hetch Hetchy was flooded and, though Pinchot remained prominent in conservation circles—he was advising Franklin Delano Roosevelt on these matters as they related to the future United Nations as late as the World War II years—his reputation was no longer unsullied.

The crosswinds of the Hetch Hetchy controversy—the issues it raised, the passions it ignited, the arguments it prompted—now blow as a gale through Pinchot’s home state. They are the prevailing winds of Pennsylvania.

A Step in the Right Direction

A true conservationist is a man who knows that the world is not given by his fathers, but borrowed from his children.

John J. Audubon

Coal once accounted for 60 percent of all electricity generated in Pennsylvania, a rate that has declined by more than half; today only a handful of large grid-connected coal-fired electric plants operate in the state. That represents a steep decline, though Homer City Generation said this spring that it would not follow through with tentative plans to deactivate its units in Indiana County. “This decreasing dependence on these sorts of plants shows we are going in the right direction in reducing climate-changing emissions from coal-fired plants,” said Hess, the former GOP environmental commissioner. “But it is mostly because of the competition between natural gas and coal. The problem is that we are now getting down to the point in the power sector that we can’t get additional big emission reductions. There aren’t more plants to close to give us those reductions. So we have to adopt other kinds of strategies.”

Pennsylvania has more than 86,000 miles of streams, more than any state in the lower 48. The miles of these waterways that can support brook trout are dwindling, in part because of climate change and in part because the invasion of the hemlock wooly adelgid insect has infected the shoreline hemlock trees that otherwise would provide shade for the streams.

This is only the latest incarnation of the centuries-long decline in the health of the state’s waterways. In the 18th century, the British army captain Harry Gordon pronounced the site of the confluence of Pittsburgh’s three rivers as “the most healthy, the most pleasant, the most commodious, the most fertile spot of Earth known to European people.” A century later, another British observer said that in Pittsburgh, “Man befouled the streams, bedraggled their banks, ripped up the cliffs, hacked down the trees, and dumped refuse in their stead.”

But the environmental crisis is not confined to western Pennsylvania. To take a random reading of air pollution in the state, Pennsylvania’s worst air quality on April 5 was in Mechanicsburg, outside Harrisburg, in the center of the state, followed by New Bloomfield, 23 miles away, according to IQ Air real-time figures. At the same time, Wilkes-Barre, with an average increased temperature of 3.3 degrees since 1970, substantially beats the average national rate of 2.6 degrees. So does State College, at an increase of 3 degrees.

Over the decades, the emphasis has changed from “conservation” to “stopping climate change,” with the threat of neighborhood contamination (the late 1970s), acid rain (the early 1980s), and the ozone hole (the mid 1980s) joined by global warming, a term introduced into the scientific and then the political lexicon when James Hansen, a NASA atmospheric expert warned a Congressional committee in 1988 that he and a set of climate modelers believed they could “confidently state that major greenhouse climate changes are a certainty.” He told the lawmakers that “the global warming predicted in the next 20 years will make the Earth warmer than it has been in the past 100,000 years.”

Opposition from an Unusual Coalition

To contemplate nature, magnificently garbed as it is in this country, is to restore peace to the mind, even if it does make one realize how small and petty and futile the human individual really is.

Harold Ickes

Many of the political tensions in Pennsylvania were visible in the debate that began last year—and became even more bitter this year—over RGGI. Gov. Wolf made becoming a part of the alliance of 10 New England and Middle Atlantic states—and, as a result reducing Pennsylvania’s greenhouse gas emissions by as many as 227 million tons by 2030—one of the top priorities of his final year in office.

The result was opposition by an unusual coalition of Republicans and labor unions, who argued that the governor’s plan would reduce jobs in the state.

“The ‘jobs-versus-environment’ framework is almost always part of these debates,” said Christopher Borick, a political scientist at Muhlenberg College in Allentown. “Environmental laws are for the public good—to protect the health and well being of individuals—so it is hard to argue against that. So what do you use as your argument? Jobs. It is sometimes a false choice, and often the environmentally sensitive approach can be a good economic choice. But politically, it is very powerful argument even if the reality isn’t the case.”

Last December, the Republican-controlled legislature passed a resolution that would halt the governor’s effort to join RGGI. The governor then exercised his veto, citing technicalities in the resolution and arguing that joining the group “is a vital step for Pennsylvania to reduce carbon emissions and achieve our climate goals.” When a stay issued by the Commonwealth Court expired in late April, the Wolf administration went ahead and published the regulation, and in less than a day the odd-couple coalition of coal unions and coal companies went to court to fight the order, which required operators of power plants fired by coal and natural gas to buy allowances for every ton of carbon dioxide they emitted.

“I want to give $150 million a year to a board headed by organized labor,” the governor, referring to a trust fund to aid individuals displaced by the transition to sustainable energy sources, told Inside Climate News as the controversy raged. “What don’t they like about this?”

In a separate interview, state Sen. Wayne Fontana, the chairman of the chamber’s Democratic Caucus and a member of the Game and Fisheries Committee, described the resistance mounted by Republicans in the legislature as “a wedge to use against the Democratic gubernatorial candidate in the fall.” He said the state has taken substantial steps to address environmental threats, arguing, “We have done a lot with lead in the water, we have beaten up air and water polluters.”

A Lack of Urgency

And so we live in a time when change comes rapidly—a time when much of that change is, at least for long periods, irrevocable. This is what makes our own task so urgent. It is not often that a generation is challenged, as we today are challenged. For what we fail to do—what we let go by default, can perhaps never be done.

Rachel Carson, accepting the Audubon Medal of the National Audubon Society in 1963

Now the challenge is global warming, which dwarfs the threat from 19th century industrial pollution and 20th century acid rain.

This past year did not have a silent spring when it came to the climate change issue. Indeed, the reports were more dire, the warnings more urgent, the lack of substantial attention more dangerous. The world, and Pennsylvania, face dramatic alternative outcomes from their actions or inaction. One choice might redound to cities underwater or lower energy consumption as a result of the creation of, in the characterization of the Intergovernmental Panel on Climate Change, of  “compact, walkable cities.” Another might be a continued reliance on private, gasoline-powered automobiles, trucks and buses or the “electrification of transport in combination with low-emission energy sources, and enhanced carbon uptake and storage using nature.”

The April report of the IPCC, the United Nations group that assesses science in relation to global warming, was sobering if not chilling. The bottom line: Net emissions are continuing to rise. “It’s now or never, if we want to limit global warming to 1.5°C [2.7°F] without immediate and deep emissions reductions across all sectors,” said Jim Skea, co-chair of the working group that produced the latest report, “it will be impossible.”

That will require what the IPCC working group co-chair Priyadarshi Shukla described as “the right policies, infrastructure and technology…to enable changes to our lifestyles and behavior.” And it will require a combination of policies and planning.

“We are opposed to long-term planning here in Pennsylvania,” said Professor Tarr of Carnegie Mellon University. “We react to crises, and we do so inadequately. People here generally have no sense of urgency about these kinds of issues.”

David Shribman served as editor of the Pittsburgh Post-Gazette for 16 years and won a Pulitzer Prize for his reporting on American political culture as Washington bureau chief of The Boston Globe. He now writes a nationally syndicated column, contributes a separate column to The Globe and Mail in Canada, and teaches American politics at both McGill University’s Max Bell School of Public Policy and Carnegie Mellon University.

Science-Watching: Forecasting New Diseases in Low-Data Settings Using Transfer Learning

[from London Mathematical Laboratory]

by Kirstin Roster, Colm Connaughton & Francisco A. Rodrigues

Abstract

Recent infectious disease outbreaks, such as the COVID-19 pandemic and the Zika epidemic in Brazil, have demonstrated both the importance and difficulty of accurately forecasting novel infectious diseases. When new diseases first emerge, we have little knowledge of the transmission process, the level and duration of immunity to reinfection, or other parameters required to build realistic epidemiological models. Time series forecasts and machine learning, while less reliant on assumptions about the disease, require large amounts of data that are also not available in early stages of an outbreak. In this study, we examine how knowledge of related diseases can help make predictions of new diseases in data-scarce environments using transfer learning. We implement both an empirical and a synthetic approach. Using data from Brazil, we compare how well different machine learning models transfer knowledge between two different dataset pairs: case counts of (i) dengue and Zika, and (ii) influenza and COVID-19. In the synthetic analysis, we generate data with an SIR model using different transmission and recovery rates, and then compare the effectiveness of different transfer learning methods. We find that transfer learning offers the potential to improve predictions, even beyond a model based on data from the target disease, though the appropriate source disease must be chosen carefully. While imperfect, these models offer an additional input for decision makers for pandemic response.

Introduction

Epidemic models can be divided into two broad categories: data-driven models aim to fit an epidemic curve to past data in order to make predictions about the future; mechanistic models simulate scenarios based on different underlying assumptions, such as varying contact rates or vaccine effectiveness. Both model types aid in the public health response: forecasts serve as an early warning system of an outbreak in the near future, while mechanistic models help us better understand the causes of spread and potential remedial interventions to prevent further infections. Many different data-driven and mechanistic models were proposed during the early stages of the COVID-19 pandemic and informed decision-making with varying levels of success. This range of predictive performance underscores both the difficulty and importance of epidemic forecasting, especially early in an outbreak. Yet the COVID-19 pandemic also led to unprecedented levels of data-sharing and collaboration across disciplines, so that several novel approaches to epidemic forecasting continue to be explored, including models that incorporate machine learning and real-time big data data streams. In addition to the COVID-19 pandemic, recent infectious disease outbreaks include Zika virus in Brazil in 2015, Ebola virus in West Africa in 2014–16, Middle East respiratory syndrome (MERS) in 2012, and coronavirus associated with severe acute respiratory syndrome (SARS-CoV) in 2003. This trajectory suggests that further improvements to epidemic forecasting will be important for global public health. Exploring the value of new methodologies can help broaden the modeler’s toolkit to prepare for the next outbreak. In this study, we consider the role of transfer learning for pandemic response.

Transfer learning refers to a collection of techniques that apply knowledge from one prediction problem to solve another, often using machine learning and with many recent applications in domains such as computer vision and natural language processing. Transfer learning leverages a model trained to execute a particular task in a particular domain, in order to perform a different task or extrapolate to a different domain. This allows the model to learn the new task with less data than would normally be required, and is therefore well-suited to data-scarce prediction problems. The underlying idea is that skills developed in one task, for example the features that are relevant to recognize human faces in images, may be useful in other situations, such as classification of emotions from facial expressions. Similarly, there may be shared features in the patterns of observed cases among similar diseases.

The value of transfer learning for the study of infectious diseases is relatively under-explored. The majority of existing studies on diseases remain in the domain of computer vision and leverage pre-trained neural networks to make diagnoses from medical images, such as retinal diseases, dental diseases, or COVID-19. Coelho and colleagues (2020) explore the potential of transfer learning for disease forecasts. They train a Long Short-Term Memory (LSTM) neural network on dengue fever time series and make forecasts directly for two other mosquito-borne diseases, Zika and Chikungunya, in two Brazilian cities. Even without any data on the two target diseases, their model achieves high prediction accuracy four weeks ahead. Gautam (2021) uses COVID-19 data from Italy and the USA to build an LSTM transfer model that predicts COVID-19 cases in countries that experienced a later pandemic onset.

These studies provide empirical evidence that transfer learning may be a valuable tool for epidemic forecasting in low-data situations, though research is still limited. In this study, we aim to contribute to this empirical literature not only by comparing different types of knowledge transfer and forecasting algorithms, but also by considering two different pairs of endemic and novel diseases observed in Brazilian cities, specifically (i) dengue and Zika, and (ii) influenza and COVID-19. With an additional analysis on simulated time series, we hope to provide theoretical guidance on the selection of appropriate disease pairs, by better understanding how different characteristics of the source and target diseases affect the viability of transfer learning.

Zika and COVID-19 are two recent examples of novel emerging diseases. Brazil experienced a Zika epidemic in 2015–16 and the WHO declared a public health emergency of global concern in February 2016. Zika is caused by an arbovirus spread primarily by mosquitoes, though other transmission methods, including congenital and sexual have also been observed. Zika belongs to the family of viral hemorrhagic fevers and symptoms of infection share some commonalities with other mosquito-borne arboviruses, such as yellow fever, dengue fever, or chikungunya. Illness tends to be asymptomatic or mild but can lead to complications, including microcephaly and other brain defects in the case of congenital transmission.

Given the similarity of the pathogen and primary transmission route, dengue fever is an appropriate choice of source disease for Zika forecasting. Not only does the shared mosquito vector result in similar seasonal patterns of annual outbreaks, but consistent, geographically and temporally granular data on dengue cases is available publicly via the open data initiative of the Brazilian government.

COVID-19 is an acute respiratory infection caused by the novel coronavirus SARS-CoV-2, which was first detected in Wuhan, China, in 2019. It is transmitted directly between humans via airborne respiratory droplets and particles. Symptoms range from mild to severe and may affect the respiratory tract and central nervous system. Several variants of the virus have emerged, which differ in their severity, transmissibility, and level of immune evasion.

Influenza is also a contagious respiratory disease that is spread primarily via respiratory droplets. Infection with the influenza virus also follows patterns of human contact and seasonality. There are two types of influenza (A and B) and new strains of each type emerge regularly. Given the similarity in transmission routes and to a lesser extent in clinical manifestations, influenza is chosen as the source disease for knowledge transfer to model COVID-19.

For each of these disease pairs, we collect time series data from Brazilian cities. Data on the target disease from half the cities is retained for testing. To ensure comparability, the test set is the same for all models. Using this empirical data, as well as the simulated time series, we implement the following transfer models to make predictions.

  • Random forest: First, we implement a random forest model which was recently found to capture well the time series characteristics of dengue in Brazil. We use this model to make predictions for Zika without re-training. We also train a random forest model on influenza data to make predictions for COVID-19. This is a direct transfer method, where models are trained only on data from the source disease.
  • Random forest with TrAdaBoost: We then incorporate data from the target disease (i.e., Zika and COVID-19) using the TrAdaBoost algorithm together with the random forest model. This is an instance-based transfer learning method, which selects relevant examples from the source disease to improve predictions on the target disease.
  • Neural network: The second machine learning algorithm we deploy is a feed-forward neural network, which is first trained on data of the endemic disease (dengue/influenza) and applied directly to forecast the new disease.
  • Neural network with re-training and fine-tuning: We then retrain only the last layer of the neural network using data from the new disease and make predictions on the test set. Finally, we fine-tune all the layers’ parameters using a small learning rate and low number of epochs. These models are examples of parameter-based transfer methods, since they leverage the weights generated by the source disease model to accelerate and improve learning in the target disease model.
  • Aspirational baseline: We compare these transfer methods to a model trained only on the target disease (Zika/COVID-19) without any data on the source disease. Specifically, we use half the cities in the target dataset for training and the other half for testing. This gives a benchmark of the performance in a large-data scenario, which would occur after a longer period of disease surveillance.

The remainder of this paper is organized as follows. The models are described in more technical detail in Section 2. Section 3 shows the results of the synthetic and empirical predictions. Finally, Section 4 discusses practical implications of the analyses.

Access the full paper [via institutional access or paid download].

Nature Portfolio Collection: Nature Mental Health

[from Nature]

To mark the upcoming launch of Nature Mental Health, and to showcase the potential breadth and scope of the journal, the editors present a collection of recent and representative mental health-themed articles from across the Nature portfolio.

In this Nature portfolio collection:

Read the full collection [some articles require a subscription].

Coronavirus Update: Fall Boosters Could Have Bits of Omicron

[from ScienceNews Coronavirus Update, by Erin Garcia de Jesús]

For all the coronavirus variants that have thrown pandemic curve balls—including alpha, beta, gamma, deltaCOVID-19 vaccines have stayed the same. That could change this fall.

Yesterday, an advisory committee to the U.S. Food and Drug Administration met to discuss whether vaccine developers should update their jabs to include a portion of the omicron variant—the version of the coronavirus that currently dominates the globe. The verdict: The omicron variant is different enough that it’s time to change the vaccines. Exactly how is up in the air; the FDA still has to weigh in and decide what versions of the coronavirus will be in the shot.

“This doesn’t mean that we are saying that there will be boosters recommended for everyone in the fall,” Amanda Cohn, chief medical officer for vaccine policy at the U.S. Centers for Disease Control and Prevention said at the June 28 advisory meeting. “But my belief is that this gives us the right vaccine for preparation for boosters in the fall.”

The decision to update COVID-19 vaccines didn’t come out of nowhere. In the two-plus years that the coronavirus has been spreading around the world, it has had a few “updates” of its own—mutating some of its proteins that allow the virus to more effectively infect our cells or hide from our immune systems.

Vaccine developers had previously crafted vaccines to tackle the beta variant that was first identified in South Africa in late 2020. Those were scrapped after studies showed that current vaccines remained effective.

The current vaccines gave our immune systems the tools to recognize variants such as beta and alpha, which each had a handful of changes from the original SARS-CoV-2 virus that sparked the pandemic. But the omicron variant is a slipperier foe. Lots more viral mutations combined with our own waning immunity mean that omicron can gain a foothold in the body. And vaccine protection isn’t as good as it once was at fending off COVID-19 symptoms.

The shots still largely protect people from developing severe symptoms, but there has been an uptick in hospitalizations and deaths among older age groups, Heather Scobie, deputy team lead of the CDC’s Surveillance and Analytics Epidemiology Task Force said at the meeting. And while it’s impossible to predict the future, we could be in for a tough fall and winter, epidemiologist Justin Lessler of the University of North Carolina at Chapel Hill said at the meeting. From March 2022 to March 2023, simulations project that deaths from COVID-19 in the United States might number in the tens to hundreds of thousands.

A switch to omicron-containing jabs may give people an extra layer of protection for the upcoming winter. PfizerBioNTech presented data at the meeting showing that updated versions of its mRNA shot gave clinical trial participants a boost of antibodies that recognize omicron. One version included omicron alone, while the other is a twofer, or bivalent, jab that mixes the original formulation with omicron. Moderna’s bivalent shot boosted antibodies too. Novavax, which developed a protein-based vaccine that the FDA is still mulling whether to authorize for emergency use, doesn’t have an omicron-based vaccine yet, though the company said its original shot gives people broad protection, generating antibodies that probably will recognize omicron.

Pfizer and Moderna both updated their vaccines using a version of omicron called BA.1, which was the dominant variant in the United States in December and January. But BA.1 has siblings and has already been outcompeted by some of them.

Since omicron first appeared late last year, “we’ve seen a relatively troubling, rapid evolution of SARS-CoV-2,” Peter Marks, director of the FDA’s Center for Biologics Evaluation and Research in Silver Spring, Maryland, said at the advisory meeting.

Now, omicron subvariants BA.2, BA.2.12.1, BA.4 and BA.5 are the dominant versions in the United States and other countries. The CDC estimates that roughly half of new U.S. infections the week ending June 25 were caused by either BA.4 or BA.5. By the time the fall rolls around, yet another new version of omicron—or a different variant entirely—may join their ranks. The big question is which of these subvariants to include in the vaccines to give people the best protection possible.

BA.1, the version already in the updated vaccines, may be the right choice, virologist Kanta Subbarao said at the FDA meeting. An advisory committee to the World Health Organization, which Subbarao chairs, recommended on June 17 that vaccines may need to be tweaked to include omicron, likely BA.1. “We’re not trying to match [what variants] may circulate,” Subbarao said. Instead, the goal is to make sure that the immune system is as prepared as possible to recognize a wide variety of variants, not just specific ones. The hope is that the broader the immune response, the better our bodies will be at fighting the virus off even as it evolves.

The variant that is farthest removed from the original virus is probably the best candidate to accomplish that goal, said Subbarao, who is director of the WHO’s Collaborating Center for Reference and Research on Influenza at the Doherty Institute in Melbourne, Australia. Computational analyses of how antibodies recognize different versions of the coronavirus suggest that BA.1 is probably the original coronavirus variant’s most distant sibling, she said.

Some members of the FDA advisory committee disagreed with choosing BA.1, instead saying that they’d prefer vaccines that include a portion of BA.4 or BA.5. With BA.1 largely gone, it may be better to follow the proverbial hockey puck where it’s going rather than where it’s been, said Bruce Gellin, chief of Global Public Health Strategy with the Rockefeller Foundation in Washington, D.C. Plus, BA.4 and BA.5 are also vastly different from the original variant. Both BA.4 and BA.5 have identical spike proteins, which the virus uses to break into cells and the vaccines use to teach our bodies to recognize an infection. So when it comes to making vaccines, the two are somewhat interchangeable.

There are some real-world data suggesting that current vaccines offer the least amount of protection from BA.4 and BA.5 compared with other omicron subvariants, Marks said. Pfizer also presented data showing results from a test in mice of a bivalent jab with the original coronavirus strain plus BA.4/BA.5. The shot sparked a broad immune response that boosted antibodies against four omicron subvariants. It’s unclear what that means for people.

Not everyone on the FDA advisory committee agreed that an update now is necessary—two members voted against it. Pediatrician Henry Bernstein of Zucker School of Medicine at Hofstra/Northwell in Uniondale, N.Y., noted that the current vaccines are still effective against severe disease and that there aren’t enough data to show that any changes would boost vaccine effectiveness. Pediatric infectious disease specialist Paul Offit of Children’s Hospital of Philadelphia said that he agrees that vaccines should help people broaden their immune responses, but he’s not yet convinced omicron is the right variant for it.

Plenty of other open questions remain too. The FDA could authorize either a vaccine that contains omicron alone or a bivalent shot, although some data hinted that a bivalent dose might spark immunity that could be more durable. Pfizer and Moderna tested their updated shots in adults. It’s unclear what the results mean for kids. Also unknown is whether people who have never been vaccinated against COVID-19 could eventually start with such an omicron-based vaccine instead of the original two doses.

Maybe researchers will get some answers before boosters start in the fall. But health agencies need to make decisions now so vaccine developers have a chance to make the shots in the first place. Unfortunately, we’re always lagging behind the virus, said pediatrician Hayley Gans of Stanford University. “We can’t always wait for the data to catch up.”

New Ultrathin Capacitor Could Enable Energy-Efficient Microchips

Scientists turn century-old material into a thin film for next-gen memory and logic devices

[from Berkeley Lab, by Rachel Berkowitz]

Electron microscope images show the precise atom-by-atom structure of a barium titanate (BaTiO3) thin film sandwiched between layers of strontium ruthenate (SrRuO3) metal to make a tiny capacitor. (Credit: Lane Martin/Berkeley Lab)

The silicon-based computer chips that power our modern devices require vast amounts of energy to operate. Despite ever-improving computing efficiency, information technology is projected to consume around 25% of all primary energy produced by 2030. Researchers in the microelectronics and materials sciences communities are seeking ways to sustainably manage the global need for computing power.

The holy grail for reducing this digital demand is to develop microelectronics that operate at much lower voltages, which would require less energy and is a primary goal of efforts to move beyond today’s state-of-the-art CMOS (complementary metaloxide semiconductor) devices.

Non-silicon materials with enticing properties for memory and logic devices exist; but their common bulk form still requires large voltages to manipulate, making them incompatible with modern electronics. Designing thin-film alternatives that not only perform well at low operating voltages but can also be packed into microelectronic devices remains a challenge.

Now, a team of researchers at Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley have identified one energy-efficient route—by synthesizing a thin-layer version of a well-known material whose properties are exactly what’s needed for next-generation devices.

First discovered more than 80 years ago, barium titanate (BaTiO3) found use in various capacitors for electronic circuits, ultrasonic generators, transducers, and even sonar.

Crystals of the material respond quickly to a small electric field, flip-flopping the orientation of the charged atoms that make up the material in a reversible but permanent manner even if the applied field is removed. This provides a way to switch between the proverbial “0” and “1” states in logic and memory storage devices—but still requires voltages larger than 1,000 millivolts (mV) for doing so.

Seeking to harness these properties for use in microchips, the Berkeley Lab-led team developed a pathway for creating films of BaTiO3 just 25 nanometers thin—less than a thousandth of a human hair’s width—whose orientation of charged atoms, or polarization, switches as quickly and efficiently as in the bulk version.

“We’ve known about BaTiO3 for the better part of a century and we’ve known how to make thin films of this material for over 40 years. But until now, nobody could make a film that could get close to the structure or performance that could be achieved in bulk,” said Lane Martin, a faculty scientist in the Materials Sciences Division (MSD) at Berkeley Lab and professor of materials science and engineering at UC Berkeley who led the work.

Historically, synthesis attempts have resulted in films that contain higher concentrations of “defects”—points where the structure differs from an idealized version of the material—as compared to bulk versions. Such a high concentration of defects negatively impacts the performance of thin films. Martin and colleagues developed an approach to growing the films that limits those defects. The findings were published in the journal Nature Materials.

To understand what it takes to produce the best, low-defect BaTiO3 thin films, the researchers turned to a process called pulsed-laser deposition. Firing a powerful beam of an ultraviolet laser light onto a ceramic target of BaTiO3 causes the material to transform into a plasma, which then transmits atoms from the target onto a surface to grow the film. “It’s a versatile tool where we can tweak a lot of knobs in the film’s growth and see which are most important for controlling the properties,” said Martin.

Martin and his colleagues showed that their method could achieve precise control over the deposited film’s structure, chemistry, thickness, and interfaces with metal electrodes. By chopping each deposited sample in half and looking at its structure atom by atom using tools at the National Center for Electron Microscopy at Berkeley Lab’s Molecular Foundry, the researchers revealed a version that precisely mimicked an extremely thin slice of the bulk.

“It’s fun to think that we can take these classic materials that we thought we knew everything about, and flip them on their head with new approaches to making and characterizing them,” said Martin.

Finally, by placing a film of BaTiO3 in between two metal layers, Martin and his team created tiny capacitors—the electronic components that rapidly store and release energy in a circuit. Applying voltages of 100 mV or less and measuring the current that emerges showed that the film’s polarization switched within two billionths of a second and could potentially be faster—competitive with what it takes for today’s computers to access memory or perform calculations.

The work follows the bigger goal of creating materials with small switching voltages, and examining how interfaces with the metal components necessary for devices impact such materials. “This is a good early victory in our pursuit of low-power electronics that go beyond what is possible with silicon-based electronics today,” said Martin.

“Unlike our new devices, the capacitors used in chips today don’t hold their data unless you keep applying a voltage,” said Martin. And current technologies generally work at 500 to 600 mV, while a thin film version could work at 50 to 100 mV or less. Together, these measurements demonstrate a successful optimization of voltage and polarization robustness—which tend to be a trade-off, especially in thin materials.

Next, the team plans to shrink the material down even thinner to make it compatible with real devices in computers and study how it behaves at those tiny dimensions. At the same time, they will work with collaborators at companies such as Intel Corp. to test the feasibility in first-generation electronic devices. “If you could make each logic operation in a computer a million times more efficient, think how much energy you save. That’s why we’re doing this,” said Martin.

This research was supported by the U.S. Department of Energy (DOE) Office of Science. The Molecular Foundry is a DOE Office of Science user facility at Berkeley Lab.

Science-Watching: Nature webinar

Cryo-EM and artificial intelligence: A marriage made in cell extracts

Date: Thursday, June 16, 2022

Reserve your seat

This webcast has been produced on behalf of Nature’s sponsor who retains sole responsibility for content. About this content.

About this webcast

Deep insights into how cellular proteins interact have been out of reach, especially in a native context. In this webcast, Dr. Panagiotis Kastritis of Martin Luther University Halle-Wittenberg will describe how analysis of endogenous cell extracts with cryo-EM and artificial intelligence methods can provide integrated biological analysis of protein communities in a closer-to-native setting.

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Science-Watching: High-Energy Physics (CERN Courier – May/June 2022)

[from CERN Courier – May/June 2022, by Matthew Chalmers, editor]

As the LHC beams prepare to set new records in brightness and energy, the Courier takes an in-depth look at the Run 3 physics prospects in searches, precision measurements, flavor and heavy-ion physics. Together with a diverse fixed-target program, the LHC experiments are forging new research directions, while recent developments advance the feasibility study for a possible Future Circular Collider.

Also in the issue: a massive surprise from CDF, intriguing results at Moriond, luminosity versus energy, the CERN Neutrino Platform, International Linear Collider, and much more.

Read the May/June 2022 issue [archived PDF].

Climatology-Watching: Tyndall Centre for Climate Change Research

[from Tyndall Centre for Climate Change Research]

UK’s climate change readiness has made ‘significant progress’

by Renee Karunungan on May 4, 2022

There is significant progress in the UK for reporting and implementing climate change adaptation, according to a new study led by Tyndall UEA’s Katie Jenkins. Katie has created an Adaptation Inventory of adaptation actions happening based on official records of adaptation projects being implemented by both public and private sector, accompanied by  a systematic review of the peer-reviewed literature of adaptation case studies.

Adapting to climate change means taking action to prepare for and adjust to current and predicted effects of climate change. Adaptation plays an important role in managing past, present and future climate risk and impacts. However, there is an “adaptation gap” where the distance between existing adaptation efforts versus adaptation needs is widening, according to the United Nations Environment Programme’s Adaptation Gap Report. Tracking national adaptation plans is deemed critical to support future decision-making and drive future actions.

Studies of adaptation consider the UK at the forefront of adaptation planning, setting an early example with the Climate Change Act 2008 which contains a five-year cycle of adaptation planning, published as the UK Climate Change Risk Assessment. Evidence from the UK Climate Change Committee shows that adaptation action has failed to keep pace with increasing climate risks. 

According to the Committee’s assessment, adaptation planning for 2C and 4C global warming is not happening, and that the gap between future risks and planned adaptation has widened, delivering the minimum level of resilience.

Katie’s new Adaptation Inventory provides insight on what is currently being implemented, which helps policymakers and practitioners learn from existing knowledge and practical case studies.

“The Adaptation Inventory provides a consistent and easily searchable database which will continue to evolve. It can provide evidence on the specific types of adaptation implemented on the ground as well as provide more detailed insight into the specific examples of action being implemented. This has the potential to help and inform UK-based decision-making,” Katie said.

The Adaptation Inventory identifies and documents current and planned adaptation in the UK, and how it is being implemented through adaptation actions, the sectors where adaptation is occurring, and where the gaps remain. There were 360 adaptation actions identified in the Inventory, comprising 134 adaptation types. Out of these 360 adaptation actions, 80% have already been implemented.

The private sector accounts for 74% of the actions with water companies dominating. Regulatory frameworks, standards, and reporting requirements are key drivers required by water companies by the Regulator. For example, water companies are already required to plan their resilience to drought.

The most common types of adaptation actions are flood protection (12%), leakage reduction (4%), water metering (3%), property level flood protection (3%), operational improvements (3%), and back-up generators (3%). Most actions were categorized as structural and physical interventions. Other interventions were categorized as technological and ecosystem based. 

An example of a structural adaptation action is raising boat landings to address higher tides because of rising sea levels. For an example of technology, London Transport has installed air cooling units and mechanical chillers at two key busy tube stations to address heat stress. An ecosystem-based example  introduces barley straw to reservoirs to control blue green algae, more common with warmer summers.

The Adaptation Inventory also looks at the types of climate hazards being addressed. It found that 76% of the actions were in response to drought, 26% for extreme rainfall, 13% for flooding, and 11% for higher temperatures. One example of adaptation for drought is rainwater recovery using storage facilities available on the site, reducing the demand for fresh water during drought. For alleviating flooding, a water company is using afforestation. The London Underground has doubled the capacity of ventilation shafts on the Victoria line, which provide more air flow on hot days.