Changes in Earth’s orbit may have triggered ancient warming event

Peer-Reviewed Publication

PENN STATE

 

IMAGE: VICTORIA FORTIZ (RIGHT), THEN A GRADUATE STUDENT AT PENN STATE, AND JEAN SELF-TRAIL, A RESEARCH GEOLOGIST AT THE U.S. GEOLOGICAL SURVEY, WORK ON A CORE SAMPLE FROM THE HOWARDS TRACT SITE IN MARYLAND view more 

CREDIT: PENN STATE

UNIVERSITY PARK, Pa. — Changes in Earth’s orbit that favored hotter conditions may have helped trigger a rapid global warming event 56 million years ago that is considered an analogue for modern climate change, according to an international team of scientists.

“The Paleocene-Eocene Thermal Maximum is the closest thing we have in the geologic record to anything like what we’re experiencing now and may experience in the future with climate change,” said Lee Kump, professor of geosciences at Penn State. “There has been a lot of interest in better resolving that history, and our work addresses important questions about what triggered the event and the rate of carbon emissions.”

The scientists analyzed core samples from a well-preserved record of the PETM near the Maryland coast using astrochronology, a technique for dating sediments against orbital patterns that occur over tens to hundreds of thousands of years, known as Milankovitch cycles.

They found the shape of Earth’s orbit, or eccentricity, and the wobble in its rotation, or precession, favored hotter conditions at the onset of the PETM and that these orbital configurations together may have played a role in triggering the event. 

“An orbital trigger may have led to the carbon release that caused several degrees of global warming during the PETM as opposed to what’s a more popular interpretation at the moment that massive volcanism released the carbon and triggered the event,” said Kump, the John Leone Dean in the College of Earth and Mineral Sciences.

The findings, published in the journal Nature Communications, also indicated the onset of the PETM lasted about 6,000 years. Previous estimates have ranged from several years to tens of thousands of years. The timing is important to understand the rate at which carbon was released into the atmosphere, the scientists said.

“This study allows us to refine our carbon cycle models to better understand how the planet reacts to an injection of carbon over these timescales and to narrow down the possibilities for the source of the carbon that drove the PETM,” said Mingsong Li, assistant professor in the School of Earth and Space Sciences at Peking University and a former assistant research professor of geosciences at Penn State who is lead author on the study.

A 6,000-year onset, coupled with estimates that 10,000 gigatons of carbon were injected into the atmosphere as the greenhouse gases carbon dioxide or methane, indicates that about one and a half gigatons of carbon were released per year.

“Those rates are close to an order of magnitude slower than the rate of carbon emissions today, so that is cause for some concern,” Kump said. “We are now emitting carbon at a rate that’s 5 to 10 times higher than our estimates of emissions during this geological event that left an indelible imprint on the planet 56 million years ago.”

The scientists conducted a time series analysis of calcium content and magnetic susceptibility found in the cores, which are proxies for changes in orbital cycles, and used that information to estimate the pacing of the PETM.

Earth’s orbit varies in predictable, calculable ways due to gravitational interactions with the sun and other planets in the solar system. These changes impact how much sunlight reaches Earth and its geographic distribution and therefore influence the climate.

“The reason there’s an expression in the geologic record of these orbital changes is because they affect climate,” Kump said. “And that affects how productive marine and terrestrial organisms are, how much rainfall there is, how much erosion there is on the continents and therefore how much sediment is carried into the ocean environment.”

Erosion from the paleo Potomac and Susquehanna rivers, which at the onset of the PETM may have rivaled the discharge of the Amazon River, carried sediments to the ocean where they were deposited on the continental shelf. This formation, called the Marlboro Clay, is now inland and offers one of the best-preserved examples of the PETM.

“We can develop histories by coring down through the layers of sediment and extracting specific cycles that are creating this story, just like you could extract each note from a song,” Kump said. “Of course, some of records are distorted and there are gaps — but we can use the same types of statistical methods that are used in apps that can determine what song you are trying to sing. You can sing a song and if you forget half the words and skip a chorus, it will still be able to determine the song, and we can use that same approach to reconstruct these records.”

Timothy Bralower, professor of geosciences at Penn State, also contributed to this research.

Other contributors were James Zachos, distinguished professor at the University of California Santa Cruz; William Rush, a postdoctoral associate at Yale University and the Cooperative Institute for Research in Environmental Science at the University of Colorado Boulder; and Jean Self-Trail and Marci Robinson, research geologists at the Florence Bascom Geoscience Center, United States Geological Survey.

The National Key R&D Program of China and the Heising-Simons Foundation provided funding for this work.

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JOURNAL

Nature Communications

DOI

10.1038/s41467-022-33390-x 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Astrochronology of the Paleocene-Eocene Thermal Maximum on the Atlantic Coastal Plain

Scientists find new hints that dark matter could be made up of dark photons

These hypothetical new particles could well explain the observations made by Cosmic Origin Spectrograph on board the Hubble Space Telescope, a new study says.

Peer-Reviewed Publication

SCUOLA INTERNAZIONALE SUPERIORE DI STUDI AVANZATI

 

IMAGE: 2D PROJECTION OF THE COSMIC WEB AS OBTAINED FROM A SUPERCOMPUTER SIMULATION. view more 

CREDIT: DR EWALD PUCHWEIN AND THE SHERWOOD-RELICS COLLABORATION

Dark matter could be made up of ultralight dark photons that heated up our universe: this is a new scenario proposed in a study recently published in the scientific journal Physical Review Letters. This hypothesis, the authors say, is in excellent agreement with observations made by the Cosmic Origin Spectrograph (COS) on board the Hubble Space Telescope, which takes measurements of the “cosmic web”, the complex and tenuous network of filaments that fills the space between galaxies. The data collected by COS suggest that the cosmic intergalactic filaments are hotter than predictions from hydrodynamical simulations of the standard model of structure formation. “Since dark photons would be able to convert into low-frequency photons and heat up the cosmic structures,” the scientists explain “they could well explain the experimental information”. The study has been carried out by SISSA researchers in collaboration with researchers at Tel Aviv, Nottingham and New York Universities.

“Dark photons are good candidate for dark matter”

“Dark photons are hypothetical new particles that are the force carriers for a new force in the dark sector, much like how the photon is the force carrier for electromagnetism” the authors James S. Bolton (University of Notitngham), Andrea Caputo (CERN and Tel Aviv University), Hongwan Liu (New York University), and Matteo Viel (SISSA) explain. “Unlike the photon, however, they can have mass. In particular, the ultralight dark photon—with a mass as small as twenty orders of magnitude less than that of the electron—is a good candidate for dark matter”. Dark photons and regular photons are also expected to mix like the different types of neutrinos, allowing ultralight dark photon dark matter to convert into low-frequency photons. These photons will heat up the cosmic web but, unlike other heating mechanisms, based on astrophysical processes, such as star formation and galactic winds, this heating process is more diffuse and efficient also in regions that are not very dense.

The missing element

Matteo Viel explains: “Usually, cosmic filaments have been used to probe small scale properties of dark matter, while in this case we have used for the first time the low redshift intergalactic medium data as a calorimeter, to check whether all the heating processes we are aware of are sufficient to reproduce the data. We found that this is not the case: there is something missing, that we model as a contribution produced by the dark photon”.

The work identified the mass and mixing of the dark photon with the Standard Model photon required to reconcile the discrepancy between observations and simulation; this effort could drive further theoretical and observational investigations in order to explore the exciting possibility that the dark photon could constitute the dark matter.

 

 

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JOURNAL

Physical Review Letters

DOI

10.1103/PhysRevLett.129.21110 

ARTICLE TITLE

Comparison of Low-Redshift Lyman-α Forest Observations to Hydrodynamical Simulations with Dark Photon Dark Matter

An integrated, net-negative system captures carbon and produces ethylene

UIC engineers publish details in Energy & Environmental Science 

Peer-Reviewed Publication

UNIVERSITY OF ILLINOIS CHICAGO

 

IMAGE: UIC GRADUATE STUDENT ROHAN SARTAPE IN ASSISTANT PROFESSOR MEENESH SINGH’S LAB, WITH THE DEPARTMENT OF CHEMICAL ENGINEERING. view more 

CREDIT: JIM YOUNG/UIC ENGINEERING

Engineers at the University of Illinois Chicago have built a machine that captures carbon from flue gas and converts it to ethylene.  

The device integrates a carbon capture system with an ethylene conversation system for the first time. And, the system not only runs on electricity, but it also removes more carbon from the environment than it generates – making it what scientists call net-negative on carbon emissions. 

Among manufactured chemicals worldwide, ethylene ranks third for carbon emissions after ammonia and cement. Ethylene is used not only to create plastic products for the packaging, agricultural and automotive industries but also to produce chemicals used in antifreeze, medical sterilizers and vinyl siding for houses, for example.  

The system and the results of the UIC College of Engineering scientists’ experiments are published in an Energy & Environmental Science paper titled “Fully-Integrated Electrochemical System that Captures CO2 from Flue Gas to Produce Value-Added Chemicals at Ambient Conditions.” 

“This is the first demonstration of a net-negative, all-electric integrated system to capture carbon from pollutants and create a highly valuable resource,” said Meenesh Singh, UIC assistant professor in the department of chemical engineering. 

“There is an urgent need to develop efficient technologies for integrated carbon capture and conversion to sustainably produce net-negative fuels. Currently, integrated carbon capture and conversion systems are highly energy-intensive and work in a discontinuous cycle of carbon dioxide capture and reduction. Efficiently integrating carbon capture with the conversion system eliminates the need for transportation and storage, and thereby increasing its energy efficiency.” 

The integrated carbon capture and conversion system developed at UIC continuously captures carbon dioxide from flue gas to produce high-purity ethylene.  

“This is an important milestone in ethylene decarbonization,” Singh said.  

To capture carbon from the air or flue gas, Singh’s lab modified a standard artificial leaf system with inexpensive materials to include a water gradient — a dry side and a wet side — across an electrically charged membrane.  

On the dry side, an organic solvent attaches to available carbon dioxide to produce a concentration of bicarbonate, or baking soda, on the membrane. As bicarbonate builds, these negatively charged ions are pulled across the membrane toward a positively charged electrode in a water-based solution on the membrane’s wet side. The liquid solution dissolves the bicarbonate back into carbon dioxide, so it can be released and harnessed for CO2 conversion.  

The system uses a modular, stackable design that allows the system to be easily scaled up and down. 

To convert captured carbon dioxide to ethylene, Singh and his colleagues used a second system in which an electric current is passed through a cell. Half of the cell is filled with carbon dioxide captured from a carbon capture system, the other half with a water-based solution. An electrified catalyst draws charged hydrogen atoms from the water molecules into the other half of the unit separated by a membrane, where they combine with charged carbon atoms from the carbon dioxide molecules to form ethylene.  

The UIC researchers integrated the two systems by feeding the captured carbon dioxide solution to the carbon conversion system and recycling it back. The closed-loop recycling of solution ensures a constant supply of carbon dioxide from flue gas and its conversion to ethylene. 

To test their integrated system, the researchers implemented a 100-square-centimeters bipolar membrane electrodialysis unit to capture carbon dioxide from the flue gas and hydraulically connected it to the 1-square-centimeter electrolysis cell to produce ethylene.  

They were able to test the system continuously, 24 hours per day for seven days. The system was not only stable the entire time, it also captured carbon at a rate of 24 grams per day and produced ethylene at a rate of 188 milligrams per day. 

“In the journey to make ethylene production green, this is a potential breakthrough,” Singh said. “Our next step is to scale up the integrated carbon capture and conversion system to produce ethylene at higher rates — a rate of 1 kilogram per day and capture carbon at a rate higher than kilograms per day.” 

Co-authors of the study include Aditya Prajapati and Rohan Sartape of UIC, and Miguel Galante, Jiahan Xie, Samuel Leung, Ivan Bessa, Marcio Andrad, Robert Somich, Marcio Reboucas, Gus Hutras and Nathalia Diniz of Braskem. Research to develop this technology has received support from the U.S. Department of Energy (DE-SC-0022321) and Braskem. 

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JOURNAL

Energy & Environmental Science

DOI

10.1039/D2EE03396H 

METHOD OF RESEARCH

Experimental study

ARTICLE TITLE

Fully-integrated electrochemical system that captures CO2 from flue gas to produce value-added chemicals at ambient conditions

Illinois Tech joins Midwest semiconductor network to strengthen microelectronics industry

The partnership of 20 higher education institutions aims to develop innovative solutions in higher education to grow collective capacity and advance the U.S. microelectronics industry

Business Announcement

ILLINOIS INSTITUTE OF TECHNOLOGY

 

IMAGE: ILLINOIS INSTITUTE OF TECHNOLOGY (ILLINOIS TECH) HAS JOINED THE MIDWEST REGIONAL NETWORK TO ADDRESS NATIONAL NEEDS IN SEMICONDUCTOR AND MICROELECTRONICS. view more 

CREDIT: ILLINOIS INSTITUTE OF TECHNOLOGY

CHICAGO—Illinois Institute of Technology (Illinois Tech) has joined the Midwest Regional Network to Address National Needs in Semiconductor and Microelectronics—a partnership of 20 colleges and universities committed to developing innovative solutions in higher education to best support the onshoring of the advanced semiconductor and microelectronics industry.

“As the impacts of a global shortage of semiconductors reverberate throughout the supply chain, now is the time to collaborate on cutting-edge  technological advancements  in microelectronics,” said Illinois Tech provost Kenneth T. Christensen. “Chicago, Illinois and the Midwest share a deep reserve of talent and innovation, and this network of educational institutions is poised to make great contributions to the industry. Illinois Tech is at the forefront of engineering and industry-relevant research and education, and with our recent partnership with DMG MORI establishing a national center for advanced manufacturing, Illinois Tech is ready to help shape the semiconductor industry.”

The network began after a two-day workshop hosted by Ohio State University in April, and Illinois Tech joined in November. 

Partner institutions will leverage existing research, curricular and experiential learning assets, capabilities, and expertise within the region and grow the collective capacity to support the domestic growth of robust semiconductor and microelectronics innovation and supply chain ecosystems. 

“With our legacy of innovation in engineering  and computing and our proven record of  generating cutting-edge ideas, Illinois Tech is honored to help address the needs of the U.S. semiconductor industry and be a key contributor in this partnership,” said Illinois Tech president Raj Echambadi. “We look forward  to collaborating with such incredible institutions of higher learning throughout the Midwest to help make the United States a global leader in semiconductor production.”

Universities in Illinois, Ohio, Indiana, and Michigan comprise the Midwest Semiconductor Network, which is expected to grow further.

Integrated approach to local governments: a study on vertical collaboration

New study offers insights into the importance of vertical collaboration with the higher government for the sustainable functioning of municipalities

Peer-Reviewed Publication

DOSHISHA UNIVERSITY

One of the major hindrances to the functioning of local governments is the lack of sufficient funds. Therefore, fiscal efficiency is the foremost factor that determines the productivity of a local government.

In a new study published first on October 25, 2022, in the journal Public Administration Review, Prof. Yu Noda from the Faculty of Policy Studies at Doshisha University, Japan, examined waste management—a capital-intensive service—in the local municipal areas in Japan as an example of how “vertical” collaboration with higher governments can help local municipalities achieve efficiency in administrative functioning.

Fiscal efficiency in the local governments can be achieved through collaboration, which helps in mitigating risks and gaining benefits. Now traditionally, this collaboration has been fostered with other regional municipalities because of the already existing trust and cooperation engendered over time among such bodies. These are psychological factors that enable smooth functioning of the municipalities. Such a “horizontal” collaboration is fiscally sound because it reduces transaction costs.

Horizontal relationships in the form of contracted services also help to improve service quality. With the foundation of strong trust and ties across municipalities, contracted services ensure greater benefits. They enable a smooth, organic integration with low political costs. Although it dilutes autonomy of the local government to some extent in terms of managing services in the region, it can still hold the reins of regional governance by deciding the manner of integration with such services.

In addition to the horizontal collaborations, this study explains the importance of another aspect of this integration—a “vertical” collaboration with the higher governments. “Democracy is based on the autonomous policy-making of local governments, but for fiscal efficiency, the appropriate involvement of higher-level government is rather crucial. As taxpayers pay taxes to both basic and higher levels of government, we need to reassess and monitor the division of roles between them,” says Prof. Noda. This vertical collaboration was found to accrue more benefits for the municipalities. Even though the transaction costs were found to increase, the overall benefits arising out of this collaboration more than made up for the rise in transaction costs.

It was believed earlier that municipal cooperation alone would be sufficient to overcome fiscal problems. However, this study demonstrated that both vertical and horizontal relationships are required for the better functioning of local governments. The study also found that establishment of special district governments improved the efficiency of municipalities by enforcing fiscal distribution. But, collaborative benefits, including such efficiency, were higher when there were better horizontal ties within the regional government.

While the horizontal collaborations increased the municipal capacity to solve regional issues, vertical collaboration led to a more efficient and integrated approach. Horizontal collaborations can only help to a certain extent. When severe financial difficulties strike, help from the higher government becomes necessary. “In 5 or 10 years' time, municipalities may be facing more financial difficulties, and in such cases, not only inter-municipal cooperation, but also appropriate commitment from higher level governments such as prefectures and the national government could increase the financial efficiency of the municipalities,” explains Prof. Noda.

This study offers novel insights into the importance of establishing vertical relationships, an area that has thus far largely been ignored. This research will pave the way to a sounder-working ecosystem of local governments in the future through an integrated framework.

 

About Professor Yu Noda from Doshisha University, Japan
Dr. Yu Noda is a Professor at the Graduate School of Policy Science, Faculty of Policy Studies, Doshisha University, Japan. His research interests include citizen-government relations, citizen satisfaction, intermunicipal cooperation, and behavioral public administration. He is associated with the American Society for Public Administration, the Japanese Society for Public Administration any many other societies. He is the supervisor of Public Policy Studies Association, JAPAN and has been the Chairman of various other committees. He has been a recipient of Nippon Urban Management and Local Government Research Association Award, Fulbright scholarship etc. He has several publications under his name in his areas of research.

Funding information
This study was supported JSPS KAKENHI, Grant/Award Number: 19K01490

Media contact:
Organization for Research Initiatives & Development
Doshisha University
Kyotanabe, Kyoto 610-0394, JAPAN
E-mail：jt-ura@mail.doshisha.ac.jp

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JOURNAL

Public Administration

DOI

10.1111/puar.13569 

METHOD OF RESEARCH

Survey

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Intermunicipal cooperation, integration forms, and vertical and horizontal effects in Japan

New research finds that social group values are most readable in the way we write

Peer-Reviewed Publication

UNIVERSITY OF EXETER

Analysing the style of language used by social groups could offer insight into their values and principles that goes beyond what they publicly say about themselves. 

New research has found that the way in which groups communicate online reveals how the group views itself – and by looking at how group members write, it is possible to track how a group’s values change over time.

The work, conducted by psychologists at the Universities of Exeter, Bath and Lancaster, could offer social scientists a new method of studying group behaviour and social dynamics. It might also help authorities to address harmful behaviours such as the spreading of conspiracy theories or to better predict when groups are at risk of radicalisation or criminal behaviour. 

“The study of group dynamics often involves asking people to tell us about their group – for example, what does being an England football supporter mean to you?”

says Dr Alicia Cork from the University of Bath.

“The drawbacks of this, in simple terms, is that these questions can be quite ambiguous to answer, and it is tricky to articulate what particular group memberships may mean to a person. However, when you concentrate on the style of communication used by group members, you can access the overarching principles that guide the behaviour of those members.” 

The PhD research, funded by the Engineering and Physical Sciences Research Council, was conducted in three distinct stages. In the first, the academics tested whether similar groups communicated in similar ways. Based on five existing group types – vocational, political, religious/ethnic, relational, or stigmatised – they selected three communities on the online forum Reddit for each type. For example, for the relational type, they chose communities specific to fatherhood and motherhood, but also a more general one focused on relationships; for the political type, they selected a political party (Conservative), a social movement (Feminist) and a shared ideology (Libertarian); and for the stigmatised type, they selected a transgender community, one focused on alcohol abuse and one discussing homelessness.

After gathering one year’s worth of Reddit comments from the 15 online communities, the researchers ran the words through specialist software, which computed the writing style of each group. This took into account elements such as formality, or how emotive/reflective the language was. They then compared the groups’ writing styles to understand how similar or dissimilar they were. 

Plotting their relative positions on a graph, they found that groups clustered closely with their counterparts, suggesting that similar groups do in fact communicate in similar ways. The exception to this was the communities related to stigma, which showed greater variation in the way they communicated. 

In the second phase, the team sought to more closely map the way a group communicates with the explicit values that they hold. Analysing the posts against ten well-established values such as benevolence, security, conformity, power and achievement, they were able to build a picture of how the groups most likely described themselves. They then compared this to their relative clustering position.  

“The results indicated that our vocational identities such as entrepreneurs and white-collar salespeople expressed high levels of achievement but fairly little benevolence,”

said Dr Miriam Koschate-Reis, Associate Professor of Computational Social Psychology, from the Institute for Data Science and AI (IDSAI) at Exeter.

“Groups that expressed benevolence were consistent with the relational types – mothers, fathers, and those focused on relationships. Interestingly, we also found that while the political and religious/ethnic groups tended to espouse conformity, the latter tended to express greater benevolence in their language.” 

The final stage of the project investigated whether it was possible to use this linguistic technique to chart the evolution and development of a group’s collective self-understanding over time. Focusing upon the transgender identity, they analysed Reddit data going back to 2011, and found that it had migrated away from fellow stigmatised groups (communities discussing homelessness or alcohol abuse), towards those defined more by the theme of collective action, such as those in the political and religious/ethnic groups.  

“The changes we observe in the linguistic style of this transgender group appears to correspond with the gradual politicisation and de-stigmatisation of that group,”

said Prof Mark Levine, of the Department of Psychology at Lancaster.

“And this is consistent with what we know of the development of LGBTQ+ rights over that period.” 

The researchers say that this linguistic method could enable better identification of emerging political movements, such as those that start out as mutual support groups but then become radicalised. It also enables them to learn about groups that may wish to disguise their true nature such as criminal organisations hiding in plain sight on online forums. 

“Understanding what groups stand for is integral to a diverse array of social processes, ranging from understanding political conflicts to promoting public health behaviours,”

adds Prof Richard Everson, a Professor of Machine Learning at the University of Exeter.

“The results from these three studies provide compelling evidence that suggests that linguistic style can be used to understand the collective self-understanding of social groups.”  

Collective self-understanding: A linguistic style analysis of naturally occurring text data has been published in the journal Behavior Research Methods.  

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JOURNAL

Behavior Research Methods

DOI

10.3758/s13428-022-02027-8 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Collective self-understanding: A linguistic style analysis of naturally occurring text data

Novel 3D imaging model may show path to more water-efficient plants

Peer-Reviewed Publication

PENN STATE

 

IMAGE: A THREE-DIMENSIONAL IMAGE OF STOMATAL GUARD CELLS SEGMENTED BY 3D CELLNET. view more 

CREDIT: ORIGINAL MICROSCOPIC IMAGE COURTESY OF LABORATORY OF CHARLES T. ANDERSON. SEGMENTED IMAGE COURTESY OF JAMES Z. WANG RESEARCH GROUP / PENN STATE.

UNIVERSITY PARK, Pa. — A new computational pipeline for analyzing three-dimensional imaging data can help biologists more accurately and quickly see how the cells in a plant’s leaves respond to the environment and identify plants that more efficiently use water, according to researchers.

A team of computer scientists and biologists from Penn State developed a 3D imaging model to study how tiny structures called stomatal guard cells, which are involved in plant photosynthesis and transpiration, interact with neighboring cells when undergoing physical changes. The model is more efficient and accurate than existing methods of analyzing cellular geometry and mechanics, and the researchers found that the guard cells behaved in unexpected ways. The research will help biologists run experiments more efficiently and identify plants, including important agricultural crops, that can better adapt to a changing climate.

“Currently, it takes experts five to eight hours to manually label just the guard cells in a single 3D image set,” said Dolzodmaa Davaasuren, a doctoral candidate in Penn State’s College of Information Sciences and Technology who led development of the pipeline. “Our team wanted to automate processes so we could study more images.”

The researchers built and tested their pipeline using the model plant Arabidopsis thaliana, commonly known as thale cress. They used a specialized confocal microscope to take 3D images of guard cells on the leaves of the plant. Guard cells surround stomatal pores and regulate how much carbon dioxide and water vapor pass through the pores. The team collected images before and after ablating, or using a laser beam to poke holes in, neighboring cells that were touching guard cells to see how stomatal volume changed.

The scientists used the 3D U-Net segmentation model as a basis for their model, which they called 3D CellNet, and added an encoder that better preserves spatial information. They also added an attention module, which tells the model to focus on specific parts of the 3D image. In this case, they told the module to focus on the tiny guard cells. The researchers used just five manually labeled 3D images to train their model. Further image processing steps were taken in the pipeline to measure the shapes of the guard cells.

The team found that their new pipeline labeled images and measured cell volumes more quickly and accurately than trained cell biologists. They also found that 3D CellNet segmentation outperformed the base model on which it was built plus two additional 2D models. They reported their findings in the journal Patterns.

“From a computer science standpoint, this is the first time we’re able to use a machine trained with a limited number of labeled examples to achieve highly accurate 3D images in such a demanding situation,” said James Wang, distinguished professor of information sciences and technology and study co-author. “If you think about medical imaging, even though they have similar 3D issues, they don’t have the challenge of looking deeper in a sample where the imaging becomes fuzzier because of light scattering. The deeper you go, the more light scattering you get, and how much light scattering is not well defined. It’s a technical challenge that we must deal with, and our research is one of the first steps to successfully tackle the problem.”

Using this new pipeline to segment and measure cell volume after ablation, the team found that the guard cells responded to external stimuli differently than expected. The researchers thought that guard cell volume would increase and cause the pores to open if they decreased the pressure beside the guard cells by ablating the flanking neighboring cells, . Instead, the researchers observed little change. However, when they ablated the neighboring cells at the top and bottom of each guard cell pair that are thought to prevent stomatal complex lengthening, thus forcing the guard cells apart when they expand and opening the stomatal pore, they found that guard cell volume measurably increased.

“The neighboring cells impose mechanical constraints on the guard cells, but they’re doing it in a way that was completely unexpected and might be somewhat independent of the water status of those neighboring cells,” said Charles Anderson, associate professor of biology and study co-author. “We’d like to investigate this further to understand what’s happening at the biomechanical level that allows plants to respond to drought by effectively closing their stomata and keeping them closed.

"One of the most exciting aspects of the paper is that it really is a tour de force in terms of computer science — developing a new algorithm that outperforms existing algorithms for measuring the 3D volumes of cells — and that it immediately applies that advance to help answer the important biological question of how stomatal pores, which power photosynthesis and water transport in plants, really work.”

Tools like 3D CellNet can help biologists better understand how guard cells and stomata react to external stimuli, which is important for addressing food security concerns in the face of a growing global population and climate change, Anderson said.

Additional contributors include Yintong Chen, who graduated with a doctorate in molecular cellular and integrative biosciences from Penn State and is now a postdoctoral researcher at the Salk Institute for Biological Studies; Leila Jaafar, doctoral candidate in molecular cellular and integrative biosciences at Penn State; Rayna Marshall, who graduated with a bachelor’s degree from Penn State and is now a medical student at Drexel University College of Medicine; and Angelica Dunham, a current undergraduate researcher in Anderson’s laboratory.

The National Science Foundation supported this research.

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JOURNAL

Patterns

DOI

10.1016/j.patter.2022.100627 

ARTICLE TITLE

Automated 3D segmentation of guard cells enables volumetric analysis of stomatal biomechanics

Molecules found in mucus could prevent cholera infection

Harnessing these protective molecules may offer a new way to treat the disease, which spreads through contaminated water

Peer-Reviewed Publication

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

CAMBRIDGE, MA -- MIT researchers have identified molecules found in mucus that can block cholera infection by interfering with the genes that cause the microbe to switch into a harmful state.

These protective molecules, known as glycans, are a major constituent of mucins, the gel-forming polymers that make up mucus. The MIT team identified a specific type of glycan that can prevent Vibrio cholerae from producing the toxin that usually leads to severe diarrhea.

If these glycans could be delivered to the site of infection, they could help strengthen the mucus barrier and prevent cholera symptoms, which affect up to 4 million people per year. Because glycans disarm bacteria without killing them, they could be an attractive alternative to antibiotics, the researchers say.

“Unlike antibiotics, where you can evolve resistance pretty quickly, these glycans don’t actually kill the bacteria. They just seem to shut off gene expression of its virulence toxins, so it’s another way that one could try to treat these infections,” says Benjamin Wang PhD ’21, one of the lead authors of the study.

Julie Takagi PhD ’22 is also a lead author of the paper. Katharina Ribbeck, the Andrew and Erna Viterbi Professor of Biological Engineering at MIT, is the senior author of the study, which appears today in the EMBO Journal.

Other key members of the research team are Rachel Hevey, a research associate at the University of Basel; Micheal Tiemeyer, a professor of biochemistry and molecular biology at the University of Georgia; and Fitnat Yildiz, a professor of microbiology and environmental toxicology at the University of California at Santa Cruz.

Taming microbes

In recent years, Ribbeck and others have discovered that mucus, which lines much of the body, plays a key role in controlling microbes. Ribbeck’s lab has showed that glycans — complex sugar molecules found in mucus — can disable bacteria such as Pseudomonas aeruginosa, and the yeast Candida albicans, preventing them from causing harmful infections.

Most of Ribbeck’s previous studies have focused on lung pathogens, but in the new study, the researchers turned their attention to a microbe that infects the gastrointestinal tract. Vibrio cholerae, which is often spread through contaminated drinking water, can cause severe diarrhea and dehydration. Vibrio cholerae comes in many strains, and previous research has shown that the microbe becomes pathogenic only when it is infected by a virus called CTX phage.

“That phage carries the genes that encode the cholera toxin, which is really what’s responsible for the symptoms of severe cholera infection,” Wang says.

In order for this “toxigenic conversion” to occur, the CTX phage must bind to a receptor on the surface of the bacteria known as the toxin co-regulated pilus (TCP). Working with mucin glycans purified from the pig gastrointestinal tract, the MIT team found that glycans suppress the bacteria’s ability to produce the TCP receptor, so the CTX phage can no longer infect it.

The researchers also showed that exposure to mucin glycans dramatically alters the expression of many other genes, including those required to produce the cholera toxin. When the bacteria were exposed to these glycans, they produced almost no cholera toxin.

When Vibrio cholerae infects the epithelial cells that line the gastrointestinal tract, the cells begin overproducing a molecule called cyclic AMP. This causes them to secrete massive amounts of water, leading to severe diarrhea. The researchers found that when they exposed human epithelial cells to Vibrio cholerae that had been disarmed by mucin glycans, the cells did not produce cyclic AMP or start leaking water.

Delivering glycans

The researchers then investigated which specific glycans might be acting on Vibrio cholerae. To do that, they worked with Hevey’s lab to create synthetic versions of the most abundant glycans found in the naturally occurring mucin samples they were studying. Most of the glycans they synthesized have structures known as core 1 or core 2, which differ slightly in the number and type of monosaccharides they contain.

The researchers found that core 2 glycans played the biggest role in taming cholera infection. It is estimated that 50 to 60 percent of people infected with Vibrio cholerae are asymptomatic, so the researchers hypothesize that the symptomatic cases may occur when these cholera-blocking mucins are missing.

“Our findings suggest that maybe infections occur when the mucus barrier is compromised and is lacking this particular glycan structure,” Ribbeck says.

She is now working on ways to deliver synthetic mucin glycans, possibly along with antibiotics, to infection sites. Glycans on their own cannot attach to the mucosal linings of the body, so Ribbeck’s lab is exploring the possibility of tethering the glycans to polymers or nanoparticles, to help them adhere to those linings. The researchers plan to begin with lung pathogens, but also hope to apply this approach to intestinal pathogens, including Vibrio cholerae.

“We want to learn how to deliver glycans by themselves, but also in conjunction with antibiotics, where you might need a two-pronged approach. That’s our main goal now because we see so many pathogens are affected by different glycan structures,” Ribbeck says.

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The research was funded by the National Institute of Biomedical Imaging and Bioengineering, the Materials Research Science and Engineering Centers Program of the U.S. National Science Foundation, the National Institute of Environmental Health Sciences, a Training Grant in Environmental Toxicology from the MIT Center for Environmental Health Sciences, the National Institutes of Health, and a Swiss National Science Foundation grant.

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JOURNAL

The EMBO Journal

ARTICLE TITLE

Host-derived O-glycans inhibit toxigenic conversion by a virulence-encoding phage in Vibrio cholerae

ARTICLE PUBLICATION DATE

12-Dec-2022

Uptick in prevalence of simultaneous cannabis and alcohol use in the US after states legalize recreational cannabis use

Peer-Reviewed Publication

COLUMBIA UNIVERSITY'S MAILMAN SCHOOL OF PUBLIC HEALTH

December 12, 2022-- Simultaneous cannabis and alcohol use, defined as using both substances at the same time so their effects overlap, increased in adults from 2008 to 2019, according to new research conducted at Columbia University Mailman School of Public Health. Shifts in cannabis legislation have raised questions about unintended effects on cannabis and alcohol use patterns, whereby policy changes might lead people to use both substances. Until now, the relationships between recreational cannabis laws (RCLs) and changes in simultaneous cannabis/alcohol use prevalence had remain untested.  The results are published online in the Journal of General Internal Medicine.

“Our findings are concerning considering that simultaneous cannabis and alcohol use is associated with more negative consequences (e.g., risk behaviors [driving under the influence], heavy patterns of substance use, increased risk for alcohol use disorders) to the individual and society,” said Priscilla Goncalves, PhD, a post-doctoral research fellow in Columbia Mailman School’s Department of Epidemiology, and first author. “Until this study, little had been known about the RCL and simultaneous use in adults in the U.S., where adult cannabis use and alcohol use are increasing in a changing cannabis policy environment.”

The researchers accessed restricted data from individuals aged 12+ from the 2008–2019 National Survey on Drug Use and Health (NSDUH) covering 817,359 participants. Data included respondents’ 2019 state of residence for state recreational cannabis law status. The final analysis included self-reporting of simultaneous cannabis and alcohol use.

From 2008 to 2019, the overall prevalence of simultaneous cannabis/alcohol use increased in adults. Comparing the period pre-RCL to post RCL, there were small but significant increases observed among those aged 21 and older. More specifically, the prevalence of simultaneous use among respondents aged 21-30 increased from 9.2 percent to 10.4 percent. Similarly, among participants aged 31-40 years and 41-50 years, prevalence increased from 5 percent to 6 percent and from 3 percent to 4.7 percent, respectively. However, for respondents aged 12–20 years old and 51 year-old and older, there were no significant associations between RCL and changes in the prevalence of simultaneous use.  

“The greater availability and opportunity to access cannabis through legal supply chains available for adults ages 21 and over such as dispensaries, present in most RCL states, may explain why we observed increases in simultaneous cannabis/alcohol use in those aged 21–50 but not 12–20 years after RCLs in this sample.,” noted Silvia Martins, MD, PhD, professor of epidemiology at Columbia Mailman School and senior author. “These findings build upon prior research showing that states allowing dispensaries had a greater likelihood of alcohol-related outcomes in adults aged 21+. Our work confirms these findings and extends them by reporting rising simultaneous use after RCL with cannabis supply implementation using a nationally representative sample across age groups over a long period (2008–2019).

“Finally, our study contributes to the understanding of age group changes in simultaneous cannabis/ alcohol use after the legalization of adult cannabis use in the U.S. beyond medical laws” says Gonçalves. “Therefore, there may be a need to develop strategies to reduce harms related to simultaneous cannabis/alcohol use in adults aged 21-50”.

Co-authors are Natalie Levy, Luis Segura, Emilie Bruzelius, and Pia Mauro, Columbia Mailman School; Anne Boustead, University of Arizona; and Deborah Hasin, Columbia Mailman School and Columbia University Irving Medical Center Department of Psychiatry.

The study was funded by the U.S. National Institutes of Health, National Institute on Drug Abuse (R01DA037866, T32DA031099, R01DA048860, and K01DA045224); and the National Center for Injury Prevention and Control, Centers for Disease Control and Prevention to the Center for Injury Epidemiology and Prevention at Columbia University (1 R49 CE002096-01).

Columbia University Mailman School of Public Health

Founded in 1922, the Columbia University Mailman School of Public Health pursues an agenda of research, education, and service to address the critical and complex public health issues affecting New Yorkers, the nation and the world. The Columbia Mailman School is the fourth largest recipient of NIH grants among schools of public health. Its nearly 300 multi-disciplinary faculty members work in more than 100 countries around the world, addressing such issues as preventing infectious and chronic diseases, environmental health, maternal and child health, health policy, climate change and health, and public health preparedness. It is a leader in public health education with more than 1,300 graduate students from 55 nations pursuing a variety of master’s and doctoral degree programs. The Columbia Mailman School is also home to numerous world-renowned research centers, including ICAP and the Center for Infection and Immunity. For more information, please visit www.mailman.columbia.edu.

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JOURNAL

Journal of General Internal Medicine

DOI

10.1007/s11606-022-07948-w 

ARTICLE TITLE

Cannabis Recreational Legalization and Prevalence of Simultaneous Cannabis and Alcohol Use in the United States