Hollow bones that let dinosaurs become giants evolved at least three times independently

The study analyzed fossilized bones from three Brazilian species of the Late Triassic (about 233 million years ago), the period in which the dinosaurs emerged. All the bones were found in recent decades in Rio Grande do Sul, Brazil’s southernmost state

Peer-Reviewed Publication

FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO

 

IMAGE: GNATHOVORAX CABREIRAI WAS A HERRERASAURID, A LINEAGE THAT BECAME EXTINCT NOT LONG AFTER THE PERIOD IN WHICH IT LIVED view more 

CREDIT: ILLUSTRATION: MÁRCIO CASTRO

Dinosaurs as big as buses or five-story buildings would not be possible if their bones were dense and heavy like ours. Like present-day birds, dinosaurs had hollow bones with inner structures known as air sacs, which made their skeletons lighter and less dense. These structures were apparently so advantageous that they emerged at least three times during the evolution of dinosaurs and pterosaurs (flying reptiles), according to a study supported by FAPESP and described in an article in Scientific Reports.

“Less dense bones containing more air gave the dinosaurs and pterosaurs [and still give birds] more oxygen circulating in their blood, as well as more agility to hunt, flee and fight, or even to fly. They not only used less energy but also kept their bodies cool more efficiently,” said Tito Aureliano, first author of the article. The study was part of his PhD research at the State University of Campinas’s Institute of Geosciences (IG-UNICAMP).

Aureliano analyzed fossilized bones from three Brazilian species of the Late Triassic (about 233 million years ago), the period in which the dinosaurs emerged. All the bones were found in recent decades in Rio Grande do Sul, Brazil’s southernmost state.

Detailed knowledge of specimens belonging to different groups and dating from an early stage in their evolution provides a basis for understanding when certain traits were developed. In this case, the researchers were looking for signs of the presence of air sacs, which were commonplace in geologically more recent (and more studied) species, such as tyrannosauruses or velociraptors, and are found in present-day birds, as noted earlier. Air sacs are found in bones throughout the body next to the spinal column.

Computerized tomography was used to visualize the fossils’ internal structures. Small spaces in the vertebrae were identified as foramina for veins, arteries and marrow, and attachment points for muscles and tendons could be seen, but none appeared capable of serving as pneumatic chambers through which air might have flowed continuously. 

“The Triassic was very warm and dry. What’s now Rio Grande do Sul was far from the sea in the heart of the supercontinent Pangea. In that context, more oxygen circulating in the blood would cool the body more efficiently and certainly afford a welcome advantage, so much so that it evolved at least three times independently,” said Fresia Ricardi-Branco, penultimate author of the article, a professor at IG-UNICAMP, and principal investigator for the FAPESP-funded project of which the study was part.

Pneumaticity

The fossils analyzed were found between 2011 and 2019 by researchers at the Federal University of Santa Maria (UFSM) in an area known as Quarta Colônia near Santa Maria in Rio Grande do Sul. Some of those researchers are co-authors of the article. 

The fossils belonged to three species: Buriolestes schultzi, Pampadromaeus barberenai and Gnathovorax cabreirai. The first two were sauropodomorphs, the group of long-necked dinosaurs that became the largest animals to walk the planet. The third was a herrerasaurid, one of the earliest carnivorous dinosaurs. The lineage became extinct shortly after the period in which this specimen lived.

A study published in 2021 by researchers from South Africa, the United Kingdom, the United States and Canada had already shown that another dinosaur lineage, the ornithischians, also lacked structures that could have housed air sacs. This order of dinosaurs probably emerged later, in the Jurassic (between 201 million and 145 million years ago), and included the popular Triceratops. 

The data collected on ornithischians, herrerasaurids and sauropods showed that air sacs evolved independently in each group. “We discovered that no common ancestor had this trait. All three groups must have developed air sacs independently,” Aureliano said.

The other groups that had air sacs were the pterosaurs (including pterodactyls) and the theropods (including tyrannosaurs and velociraptors, as well as extant birds). Although they descended from B. schultzi and P. barberenai, in the long-necked lineage, hollow bones only evolved later. Exactly when is not yet known.

“The oldest dinosaurs in the world are in South America and have been discovered only in the past two decades,” Ricardi-Branco said. “More of this kind of research needs to be done to show how the dominant organisms of the period coped with a much warmer climate than ours.”

About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.

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JOURNAL

Scientific Reports

DOI

10.1038/s41598-022-25067-8 

ARTICLE TITLE

The absence of an invasive air sac system in the earliest dinosaurs suggests multiple origins of vertebral pneumaticity

Rensselaer researcher breaks through the clouds to advance satellite communication

New method enables effective free-space optical communication regardless of weather

Peer-Reviewed Publication

RENSSELAER POLYTECHNIC INSTITUTE

 

IMAGE: MOUSSA N'GOM view more 

CREDIT: RENSSELAER POLYTECHNIC INSTITUTE

Rensselaer Polytechnic Institute’s Moussa N’Gom, assistant professor of physics, applied physics, and astronomy, has devised a method to make communications between satellites and the ground more effective no matter the weather. In research recently published, N’Gom and his team used ultrafast, femtosecond lasers to cut through the clouds and rain that commonly cause losses in free-space optical communication (FSO).

“The lasers we use are so energetic that they change the environment in which they propagate,” N’Gom said. “The environment starts to change the laser that is changing it, and they have a light-matter interaction. It becomes a cascading effect that creates a long filament of light.”

The filament of light is accompanied by a shockwave, along the lines of a sonic boom. The laser filament propagates through clouds and the accompanying shockwave clears the space around the filament, providing an open pathway for visible light. N’Gom uses structured light, in the form of a spiral with a hole at its center, to propagate through the pathway.

“The Laguerre–Gauss beam travels through this empty space without interacting with the filament and is unobstructed by the clouds,” N’Gom said. “Normally, light travels in one, flat wave, but the light we create travels in a spiral. Imagine it like curling a flat piece of paper with scissors.”

On top of facilitating transmission through clouds, the spiral shape of the light also allows for more information to be transmitted.

The method presents a significant advance for FSO, which already has substantially higher capacity than radio frequency communication. Previous attempts to overcome the persistent obstacle of rain and clouds required substantial energy, large investments, or were less effective.

“Dr. N’Gom’s innovative research shows how to overcome a fundamental barrier in free-space optical communication,” said Curt Breneman, dean of the Rensselaer School of Science. “I expect free-space optical communication technology of this type to enable hyper-speed secure worldwide quantum communications.”

N’Gom was joined in research by doctoral students Tianhong Wang, Saad Bin Ali Reza, Finn Buldt, and postdoctoral associate Pascal Bassène. The work was funded by the National Geospatial Agency.

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About Rensselaer Polytechnic Institute:

Founded in 1824, Rensselaer Polytechnic Institute is America’s first technological research university. Rensselaer encompasses five schools, over 30 research centers, more than 140 academic programs including 25 new programs, and a dynamic community made up of over 6,800 students and 104,000 living alumni. Rensselaer faculty and alumni include upwards of 155 National Academy members, six members of the National Inventors Hall of Fame, six National Medal of Technology winners, five National Medal of Science winners, and a Nobel Prize winner in Physics. With nearly 200 years of experience advancing scientific and technological knowledge, Rensselaer remains focused on addressing global challenges with a spirit of ingenuity and collaboration. To learn more, please visit www.rpi.edu.

Contact: 
Katie Malatino
Sr. Communications Specialist
malatk@rpi.edu
838-240-5691

For general inquiries: newsmedia@rpi.edu

Visit the Rensselaer research and discovery blog: https://everydaymatters.rpi.edu/

Follow us on Twitter: @RPINews

 

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JOURNAL

Journal of Applied Physics

DOI

10.1063/5.0129902 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Structured light signal transmission through clouds

Elegantly modeling earth’s abrupt glacial transitions

Simple and intuitive model illustrates how climate cycles are influenced by our planet’s orbit.

Peer-Reviewed Publication

AMERICAN INSTITUTE OF PHYSICS

WASHINGTON, March 7, 2023 – Proxy data – indirect records of the Earth’s climate found in unlikely places like coral, pollen, trees, and sediments – show interesting oscillations approximately every 100,000 years starting about 1 million years ago. Strong changes in global ice volume, sea level, carbon dioxide concentration, and surface temperature indicate cycles of a long, slow transition to a glacial period and an abrupt switch to a warm and short interglacial period.

Milutin Milankovitch hypothesized that the timing of these cycles was controlled by the orbital parameters of the Earth, including the shape of its path around the sun and the tilt of the planet. A slightly closer orbit or more tilted planet could create a small increase in solar radiation and a feedback loop that leads to massive changes in climate. This idea suggests that there may be some predictability in the climate, a notoriously complex system.

In Chaos, by AIP Publishing, Stefano Pierini of Parthenope University of Naples proposed a new paradigm to simplify the verification of the Milankovitch hypothesis.

“The main motivation behind this study was the wish to characterize and illustrate the Milankovitch hypothesis in a simple, elegant, and intuitive way,” Pierini said.

Many models suggest that Milankovitch is correct; however, such methods are often detailed and study specific. They incorporate climate feedback loops – for example, increased ice cover reflects more radiation back into space, leading to further cooling and more ice cover – as threshold crossing rules. This means that an abrupt jump in climate only occurs once a parameter reaches a given tipping point.  

Pierini’s “deterministic excitation paradigm” combines the physics concepts of relaxation oscillation and excitability to link Earth’s orbital parameters and the glacial cycles in a more generic way. The relaxation oscillation component describes how the climate slowly returns to its original glacier state after it is disturbed. At that point, the excitability piece of the model captures the external orbital changes and triggers the next glacial cycle.

By using his own threshold crossing rules and adopting a classical energy-balance model, Pierini obtained correct and robust timing of the most recent glacial cycles.

“The application of the deterministic excitation paradigm in the present basic formulation can explain the timing of the last four glacial terminations,” he said. “Extending the same analysis to the whole Pleistocene will be the subject of a future investigation.”

Pierini believes similar methods could be used in other fields of nonlinear science and in connection with other climate phenomena.

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The article “The deterministic excitation paradigm and the late Pleistocene glacial terminations” is authored by Stefano Pierini. It will appear in Chaos on March 7, 2023 (DOI: 10.1063/5.0127715). After that date, it can be accessed at https://doi.org/10.1063/5.0127715.

ABOUT THE JOURNAL

Chaos is devoted to increasing the understanding of nonlinear phenomena in all areas of science and engineering and describing their manifestations in a manner comprehensible to researchers from a broad spectrum of disciplines. See https://aip.scitation.org/journal/cha.

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JOURNAL

Chaos An Interdisciplinary Journal of Nonlinear Science

DOI

10.1063/5.0127715 

ARTICLE TITLE

The deterministic excitation paradigm and the late Pleistocene glacial terminations

ARTICLE PUBLICATION DATE

7-Mar-2023

Drunk mice sober up after a hormone shot

Peer-Reviewed Publication

CELL PRESS

 

IMAGE: FGF21 COUNTERACTS ALCOHOL INTOXICATION BY ACTIVATING THE NORADRENERGIC NERVOUS SYSTEM view more 

CREDIT: CELL METABOLISM/CHOI ET AL.

A hormone called fibroblast growth factor 21 (FGF21) protects mice against ethanol-induced loss of balance and righting reflex, according to a study publishing on March 7 in the journal Cell Metabolism.

“We’ve discovered that the liver is not only involved in metabolizing alcohol but that it also sends a hormonal signal to the brain to protect against the harmful effects of intoxication, including both loss of consciousness and coordination,” says co-senior study author Steven Kliewer of the University of Texas Southwestern Medical Center.

“We’ve further shown that by increasing FGF21 concentrations even higher by injection, we can dramatically accelerate recovery from intoxication. FGF21 does this by activating a very specific part of the brain that controls alertness,” says Kliewer.

The consumption of ethanol produced by the natural fermentation of simple sugars in ripening fruits and nectars can cause intoxication, impairing mobility and judgement. Animals that consume fructose and other simple sugars have evolved liver enzymes to break down ethanol.

FGF21 is a hormone that is induced in the liver by a variety of metabolic stresses, including starvation, protein deficiency, simple sugars, and ethanol. In humans, ethanol is by far the most potent inducer of FGF21 described to date. Previous studies showed that FGF21 suppresses ethanol preference, induces water drinking to prevent dehydration, and protects against alcohol-induced liver injury.

In the new study, Kliewer and co-senior study author David Mangelsdorf of the University of Texas Southwestern Medical Center show that FGF21 plays a broader role in defending against the harmful consequences of ethanol exposure than previously thought. In mice, FGF21 stimulated arousal from intoxication without changing the breakdown of ethanol. Mice lacking FGF21 took longer than their littermates to recover their righting reflex and balance following ethanol exposure. Conversely, pharmacologic FGF21 administration reduced the time needed for mice to recover from ethanol-induced unconsciousness and lack of muscle coordination.

Surprisingly, FGF21 did not counteract sedation caused by ketamine, diazepam, or pentobarbital, indicating specificity for ethanol. FGF21 mediated its anti-intoxicant effects by directly activating noradrenergic neurons in the locus coeruleus region in the brain, which regulates arousal and alertness. Taken together, the results suggest that the FGF21 liver-brain pathway evolved to protect against ethanol-induced intoxication. According to the authors, this pathway may modulate a variety of cognitive and emotional functions to enhance survival under stressful conditions.

Yet it remains to be determined whether activation of the noradrenergic system contributes to FGF21’s other effects, including those on metabolism and ethanol and sweet preference. Although both FGF21 and noradrenergic nervous system activity are induced by ethanol in humans, additional studies will also be required to determine whether FGF21’s anti-intoxicant activity translates to humans.

“Our studies reveal that the brain is the major site of action for FGF21’s effects,” Mangelsdorf says. “We are now exploring in greater depth the neuronal pathways by which FGF21 exerts its sobering effect.”

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This work was supported by the National Institutes of Health, the Robert A. Welch Foundation, and the Howard Hughes Medical Institute. Information about potential conflicts of interest can be found in the paper text.

Cell Metabolism, Choi et al. “FGF21 counteracts alcohol intoxication by activating the noradrenergic nervous system” https://www.cell.com/cell-metabolism/fulltext/S1550-4131(23)00041-4

Cell Metabolism (@Cell_Metabolism), published by Cell Press, is a monthly journal that publishes reports of novel results in metabolic biology, from molecular and cellular biology to translational studies. The journal aims to highlight work addressing the molecular mechanisms underlying physiology and homeostasis in health and disease. Visit http://www.cell.com/cell-metabolism. To receive Cell Press media alerts, contact press@cell.com.

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JOURNAL

Cell Metabolism

DOI

10.1016/j.cmet.2023.02.005 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

FGF21 Counteracts Alcohol Intoxication by Activating the Noradrenergic Nervous System

ARTICLE PUBLICATION DATE

7-Mar-2023

The case for female mice in neuroscience research

Findings reveal that female mice have more stable exploratory behavior than male mice

Peer-Reviewed Publication

HARVARD MEDICAL SCHOOL

At a glance:

• New research suggests female mice show more stable exploratory behavior than male mice, despite hormone cycles
• The results challenge a long-held assumption that hormones have a broad effect on behavior in female mice, making them less suitable for research
• The findings make a strong scientific case for increasing the inclusion of female mice in neuroscience and other experiments

Mice have long been a central part of neuroscience research, providing a flexible model that scientists can control and study to learn more about the intricate inner workings of the brain. Historically, researchers have favored male mice over female mice in experiments, in part due to concern that the hormone cycle in females causes behavioral variation that could throw off results.

But new research from Harvard Medical School challenges this notion and suggests that for many experiments, the concern may not be justified.

The study results, published March 7 in Current Biology, reveal that female mice, despite ongoing hormonal fluctuations, exhibit exploratory behavior that is more stable than that of their male peers.

Using a strain of mice commonly studied in lab settings, the researchers analyzed how the animals behaved as they freely explored an open space. They found that the hormone cycle had a negligible effect on behavior and that differences in behavior between individual female mice were much greater. Moreover, differences in behavior were even greater for males than for females, both within and between mice. 

The results underscore the importance of incorporating both sexes into mouse studies, the research team said.

“I think this is really powerful evidence that if you’re studying naturalistic, spontaneous exploratory behavior, you should include both sexes in your experiments — and it leads to the argument that in this setting,  if you can only pick one sex to work on, you should actually be working on females,” said Sandeep Robert Datta, professor of neurobiology in the Blavatnik Institute at HMS, who co-led the study with Rebecca Shansky of Northeastern University.

From rodents to humans: A history of bias

As neuroscientists strive to better understand the human brain, they routinely turn to the mouse, which Datta considers “the flagship vertebrate model for understanding how the brain works.”

This is because mouse and human brains share a considerable amount of structural organization and genetic information, so scientists can easily manipulate the mouse genome to address specific experimental questions and to build models of human diseases.

“Much of what we understand about the relationship between genes and neural circuits, and between neural activity and behavior, comes from basic research in the mouse, and mouse models are likely going to be really central tools in our fight against a broad array of neurological and psychological diseases,” Datta said.

For more than 50 years, researchers have preferentially used male mice in experiments, and nowhere has this practice been more prominent than in neuroscience. In fact, a 2011 analysis found that there were over five times as many single-sex neuroscience studies of male mice than of female mice. Over time, this practice has resulted in a poorer understanding of the female brain, likely contributing to the misdiagnosis of mental and neurological conditions in women, as well as the development of drugs that have more side effects for women — issues outlined by Shansky in a 2021 perspective in Nature Neuroscience.

The disparity in sex representation common in animal research has also been historically mirrored in research involving human subjects.

“This bias starts in basic science, but the repercussions are rolled into drug development, and lead to bias in drugs being produced, and how drugs are suited for the different sexes,” said lead author Dana Levy, a research fellow in neurobiology at HMS. For example, Levy noted that conditions such as anxiety, depression, and pain are known to manifest differently in female mice and women than in the male mice that are more often used in early-stage drug testing.

To address the problem of sex bias in scientific research, the National Institutes of Health published a policy in 2016 requiring researchers to include male and female subjects and samples in experiments. However, follow-up studies that look across scientific disciplines and examine neuroscience specifically indicate that progress has been slow.

The reasons for such a long-standing bias in neuroscience are complicated, Datta said: “Part of it is just plain old sexism, and part of it is conservatism in the sense that people have studied male mice for so long that they don’t want to make a change.”

Yet perhaps the biggest reason for excluding female mice, Datta said, stems from a widespread assumption that their behavior is broadly affected by cyclic variations in hormones such as estrogen and progesterone — the rodent version of a menstrual cycle, known as the estrous cycle. According to Datta and Levy, estrous status is known to have a strong effect on certain social and sexual behaviors in mice. However, data on the influence of estrous status in other behavioral contexts have been mixed, resulting in what Datta calls “a genuine disagreement in the literature.”

“We wanted to measure how much the estrous cycle seemed to influence basic patterns of exploration,” Datta said. “Our question was whether these ongoing changes in the hormonal state of the mouse affect other neural circuits in a way that’s confusing for researchers.”

“We assumed, like everybody else, that adding females was just going to complicate our experiments,” Levy added, “And so we said, ‘why not test this.’”

Testing assumptions

The researchers studied genetically identical males and females from a common strain of lab mouse in a circular open field — a standard lab setup for behavioral neuroscience experiments. In practice, the test involved placing a mouse in a 5-gallon Home Depot bucket for 20 minutes and using a camera to record the mouse’s movements and behaviors in 3D as it freely explored the space. The researchers swabbed each female mouse to determine its estrous status and repeated the bucket test with the same individual multiple times.

The team analyzed the videos with MoSeq, an artificial intelligence technology previously developed by the lab. The technology uses machine learning algorithms to break down a mouse’s movements into around 50 different “syllables,” or components of body language: short, single motions such as rearing up, pausing, stepping, or turning. With MoSeq, the researchers gathered in-depth, high-resolution data about the structure and pattern of mouse behavior during each session.

The researchers found that estrous status had very little effect on exploratory behavior in female mice. Instead, patterns of behavior tended to vary much more across female mice than they did throughout the estrous cycle.

“If you give me any random video from our pile, I can tell you which mouse it is. That’s how individualized the pattern of behavior is,” Datta said, which suggests that in behavioral studies, “a dominant aspect of variation in the data is the fact that individuals have subtly different life histories.”

When the researchers compared female and male mice, they found something that surprised them: Males also exhibited individuality of behavior, but they had more behavioral variation within a single mouse and between mice than females.

“People have been making this assumption that we can use male mice to reliably make comparisons within and across experiments, but our data suggest that female mice are more stable in terms of behavior despite the fact that they have the estrous cycle,” Datta said.

A case for change

Scientists generally agree that including female mice is important from a fairness perspective, Datta noted, yet some have remained concerned that it could complicate their research. For him, the new findings make a strong scientific case for using female mice in experiments.

“The fact that female behavior is more reliable suggests that including females might actually decrease the overall variability in your data under many circumstances,” Datta said.

Based on their findings, researchers in the Datta lab have already switched from male mice to mixed groups or female mice in their other experiments that involve circular, open-field testing.

Datta cautioned that the study looks at only one mouse strain in one lab setup, and so the results cannot be generalized to other strains and setups without further testing. However, he noted that the strain and setup are commonly used in neuroscience research, including in early-stage drug development to test how a potential drug affects mouse locomotion.

Datta said that the findings “should encourage folks who are interested in drug development in this context to include both sexes in their analysis.”

Now, Datta and Levy are interested in exploring how internal states beyond hormonal status, such as hunger, thirst, pain, and illness, affect exploratory behavior in mice.

“The question is, who wins in this tug-of-war between your current internal state and your individual identity,” Levy explained.

They also want to delve deeper into the neural basis of the individuality of mouse behavior that they saw in the study.

“I was shocked by how much stable variation between individuals we were observing — it’s like these mice really are individuals,” Datta said. “We’re used to thinking of lab mice as interchangeable widgets, but they’re not at all. So, what is controlling these individualized patterns of behavior?”

“We want to understand the mechanisms of individuality: how variability between individuals comes about, how it affects behavior, what can alter it, and what brain regions support it,” Levy added.

To this end, the Datta lab is examining mouse behavior from birth until death to understand how individualized patterns of behavior emerge and crystallize during development, and how they change throughout life.

The researchers also hope that their work will open the door for more rigorous, quantitative research on whether and how the estrous cycle affects mouse behavior in other contexts, such as completing complex tasks.

“This is a very interesting example of how assumptions that affect the way that we conduct and design our science are sometimes just assumptions — and it is important to directly test them, because sometimes they’re not true,” Levy said.

Authorship, funding, disclosures

Additional authors include Nigel Hunter, Sherry Lin, Emma Robinson, Winthrop Gillis, Eli Conlin, and Rockwell Anyoha of HMS.

The research was supported by the NIH (U19NS113201; RF1AG073625; R01NS114020), the Brain Research Foundation, the Simons Collaboration on the Global Brain, the Simons Collaboration for Plasticity in the Aging Brain, the Human Frontier Science Program, and the Zuckerman STEM Leadership Program.

Datta is on the scientific advisory boards of Neumora, Inc., and Gilgamesh Pharmaceuticals, which have licensed the MoSeq technology.

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JOURNAL

Current Biology

DOI

10.1016/j.cub.2023.02.035 

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Mouse spontaneous behavior reflects individual variation rather than estrous state

ARTICLE PUBLICATION DATE

7-Mar-2023

Telemedicine use by rural vs urban VA beneficiaries before, after onset COVID-19

JAMA Network Open

Peer-Reviewed Publication

JAMA NETWORK

About The Study: The findings of this study suggest that despite initial telemedicine gains at rural Veterans Affairs (VA) health care sites, the pandemic was associated with an increase in the rural-urban telemedicine divide across the VA health care system. To ensure equitable access to care, the VA health care system’s coordinated telemedicine response may benefit from addressing rural disparities in structural capacity (e.g., internet bandwidth) and from tailoring technology to encourage adoption among rural users. 

Authors: Lucinda B. Leung, M.D., Ph.D., M.P.H., of the Veterans Affairs Greater Los Angeles Healthcare System in Los Angeles, is the corresponding author. 

http://jamanetwork.com/journals/jamanetworkopen/fullarticle/10.1001/jamanetworkopen.2023.1864?utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_term=030723

About JAMA Network Open: JAMA Network Open is an online-only open access general medical journal from the JAMA Network. On weekdays, the journal publishes peer-reviewed clinical research and commentary in more than 40 medical and health subject areas. Every article is free online from the day of publication.

 

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JOURNAL

JAMA Network Open

Counting heads: how deep learning can simplify tedious agricultural tasks

Scientists show how machine learning models can be used to automatically detect the heads of sorghum plants in drone images to derive agricultural metrics

Peer-Reviewed Publication

NANJING AGRICULTURAL UNIVERSITY THE ACADEMY OF SCIENCE

The selective breeding of grain crops is one of the main reasons why domesticated plants produce such excellent yields. Selecting the best candidates for breeding is, however, a remarkably complex task. On one hand, it requires a skilled breeder with trained eyes to assess plant resistance to disease and pests, crop growth, and other factors. On the other hand, it also requires precise tool-assisted measurements such as grain size, mass, and quality.

Although all these standard measures are useful, none of them takes into account the number of panicles or ‘heads’ per plant. Head density is closely related to crop yield in most cases, and it could easily be a staple characteristic to measure in breeding programs. However, estimating the number of heads per plant and per unit area is very time consuming and requires tedious manual work.

To address this issue, many researchers have developed machine learning models that can automatically detect individual heads on grain crops in images taken either at ground level or by drones. While these models are aimed at simplifying the otherwise manual counting process in the field, the reality is that they are usually trained in limited testing conditions and focus exclusively on head detection without providing more metrics. In other words, using these models outside of the context in which they were developed and trained can be difficult, tedious, and even yield poor results.

Against this backdrop, a research team including Professor Scott Chapman from The University of Queensland, Australia, sought to promote deep-learning models for head counting by providing a detailed pipeline outlining their use. As explained in their paper, which was recently published in Plant Phenomics, this pipeline covers most of the quirks and challenges that one could find when using these models. “We took various real-world variables into consideration, including data preparation, model validation, inference, and how to derive yield-specific metrics,” explains Prof. Chapman, “We aimed to outline a practical and end-to-end pipeline for head detection in sorghum.”

There are two variants to the proposed pipeline, which are demonstrated by way of two independent illustrative experiments. In the first one, the researchers show how one should proceed if one needed to prepare training, testing, and validation datasets for a given machine learning model from scratch. This is usually the case when publicly available datasets are not suitable for the target field, which can happen, for example, when one is dealing with a different stage in plant development than the available datasets.

In the second experiment, the team showcases the steps required to use various pre-trained deep-learning models for sorghum head detection and/or counting. They demonstrate how the detection results (that is, the output of models that only outline sorghum heads on a set of given images) can be ‘stitched together’ into larger mosaic images. This enables one to observe and analyze large areas more easily and calculate important metrics, such as head density per tilling row or per square meter. “Our pipeline produces a high-resolution head density map that can be used for the diagnosis of agronomic variability within a field without relying on commercial software,” highlights Prof. Chapman.

Overall, this study will be useful to researchers and people involved in the agricultural industry alike. Not only it explains how deep learning models can be leveraged to assess grain crops more efficiently, but it also helps unlock new functionalities for camera-equipped drones in agriculture. Worth noting, the proposed pipeline could be adapted to other plants besides sorghum, as Prof. Chapman remarks: “Although we demonstrated our pipeline in a sorghum field, it can be generalized to other grain species. In future works, we intend to test our pipeline on tasks involving other grain types, such as wheat and maize yield estimation.”

Let us hope this work help us bridge the field of agriculture with machine learning to improve crop breeding and, thus, secure better food supplies.

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Reference

Authors

Chrisbin James1, Yanyang Gu2, Andries Potgieter3, Etienne David4, Simon Madec4, Wei Guo5, Frédéric Baret6, Anders Eriksson2, and Scott Chapman1

Affiliations

1School of Agriculture and Food Sciences, The University of Queensland

2School of Information Technology and Electrical Engineering, The University of Queensland

3Queensland Alliance for Agriculture and Food Innovation, The University of Queensland

4Arvalis, Institut du Végétal

5Graduate School of Agricultural and Life Sciences, The University of Tokyo

6Institut National de la Recherche Agronomique

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JOURNAL

Plant Phenomics

DOI

10.34133/plantphenomics.0017 

ARTICLE TITLE

From Prototype to Inference: A Pipeline to Apply Deep Learning in Sorghum Panicle Detection

MMMMM MICROBES

Evidence for the health benefits of consuming more live microbes

New study shows lower weight and better overall health in those who consume more live microorganisms daily

Peer-Reviewed Publication

INTERNATIONAL SCIENTIFIC ASSOCIATION FOR PROBIOTICS AND PREBIOTICS

Safe live microorganisms are found in a variety of foods we eat every day, from yogurt and other fermented foods, to raw fruits and vegetables. Despite the widespread idea that these mixtures of live microbes contribute to health, convincing evidence linking live dietary microbes to health benefits has been lacking.

A new study provides some of the first real-world evidence that higher consumption of live microbes may promote health. A group of scientists led by the International Scientific Association for Probiotics and Prebiotics (ISAPP) classified over 9,000 individual foods listed in the US National Health and Nutrition Examination Survey (NHANES) into three categories based on their abundance of live microbes, and then used NHANES participants’ reported food intake to quantify the food they ate that contained medium or high levels of microbes. Then they determined how these intakes correlated with various markers of health such as blood pressure and weight.

The scientists found that increased consumption of live microbes in the diet was linked with multiple measurements of better health: more favorable blood pressure, better blood glucose and insulin, lower inflammation, as well as lower waist circumference and body mass index. This established that those who consumed higher quantities of live dietary microbes showed tangible, if modest, health benefits.

While the scientific approach did not allow researchers to conclude that the live dietary microorganisms directly caused the health benefits, the results are consistent with plausible arguments that dietary exposure to live microorganisms in general could benefit health by increasing the diversity of microbes in the gut or by supporting immune function. In the past century, a reduction in the amount of fermented foods in the diet and increased consumption of processed foods has led to a dramatic reduction in the number of microbes most people consume on a daily basis. This trend may be reversing, however, since the dietary data used in the study showed that US adults have gradually increased their live microbe consumption over the 18-year study period. This may bode well for the health of the population.

This study built on two previous published papers, here and here, which conducted the preliminary work necessary to make this assessment of live dietary microbes and health.

”Although the dose-response associations we found were relatively modest, it was notable that these estimated benefits applied to several plausible and important health outcomes and were robust to adjustment for available confounders, including body mass index,” says co-lead author Prof. Dan Tancredi, PhD, of University of California - Davis. “More research that extends these findings to other populations and research that uses study designs that permit stronger causal claims is needed, especially given the potential benefits that might be available by simply substituting into the diet more foods that have safe live microbes.”

ISAPP Executive Science Officer Mary Ellen Sanders, PhD, points out the research focused not just on probiotics, but on all microbes in foods, including environmental microbes associated with raw fruits and vegetables as well as lactic acid bacteria associated with fermented foods. Thus, the study differs from probiotic research, which focuses on microbes defined to the strain level, specific dose and proven health benefits.

Co-first author Prof. Colin Hill, PhD, of University College Cork, Ireland, says it's possible that dietary advice of the future could include a recommendation for the daily consumption of high levels of live dietary microbes. “Those foods with high levels of microbes (fermented foods, raw vegetables and fruits) are all nutritionally valuable parts of a healthy and diverse diet,” he says. “Secondly, these same foods could be providing an additional, hitherto unrecognised, health benefit due to live microbes themselves that enter the gut and interact with the host microbiome, immune system and even the enteric nervous system”.

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JOURNAL

Journal of Nutrition

DOI

10.1016/j.tjnut.2023.02.019 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Positive health outcomes associated with live microbe intake from foods, including fermented foods, assessed using NHANES databas

COI STATEMENT

This research was funded by the International Scientific Association for Probiotics and Prebiotics.