How to train a robot (using AI and supercomputers)

UT Arlington computer scientists use TACC systems to generate synthetic objects for robot training

UNIVERSITY OF TEXAS AT AUSTIN, TEXAS ADVANCED COMPUTING CENTER

Research News

IMAGE: EXAMPLES OF 3D POINT CLOUDS SYNTHESIZED BY THE PROGRESSIVE CONDITIONAL GENERATIVE ADVERSARIAL NETWORK (PCGAN) FOR AN ASSORTMENT OF OBJECT CLASSES. PCGAN GENERATES BOTH GEOMETRY AND COLOR FOR POINT CLOUDS, WITHOUT... view more 

CREDIT: [WILLIAM BEKSI, UT ARLINGTON]

Before he joined the University of Texas at Arlington as an Assistant Professor in the Department of Computer Science and Engineering and founded the Robotic Vision Laboratory there, William Beksi interned at iRobot, the world's largest producer of consumer robots (mainly through its Roomba robotic vacuum).

To navigate built environments, robots must be able to sense and make decisions about how to interact with their locale. Researchers at the company were interested in using machine and deep learning to train their robots to learn about objects, but doing so requires a large dataset of images. While there are millions of photos and videos of rooms, none were shot from the vantage point of a robotic vacuum. Efforts to train using images with human-centric perspectives failed.

Beksi's research focuses on robotics, computer vision, and cyber-physical systems. "In particular, I'm interested in developing algorithms that enable machines to learn from their interactions with the physical world and autonomously acquire skills necessary to execute high-level tasks," he said.

Years later, now with a research group including six PhD computer science students, Beksi recalled the Roomba training problem and begin exploring solutions. A manual approach, used by some, involves using an expensive 360 degree camera to capture environments (including rented Airbnb houses) and custom software to stitch the images back into a whole. But Beksi believed the manual capture method would be too slow to succeed.

Instead, he looked to a form of deep learning known as generative adversarial networks, or GANs, where two neural networks contest with each other in a game until the 'generator' of new data can fool a 'discriminator.' Once trained, such a network would enable the creation of an infinite number of possible rooms or outdoor environments, with different kinds of chairs or tables or vehicles with slightly different forms, but still -- to a person and a robot -- identifiable objects with recognizable dimensions and characteristics.

"You can perturb these objects, move them into new positions, use different lights, color and texture, and then render them into a training image that could be used in dataset," he explained. "This approach would potentially provide limitless data to train a robot on."

"Manually designing these objects would take a huge amount of resources and hours of human labor while, if trained properly, the generative networks can make them in seconds," said Mohammad Samiul Arshad, a graduate student in Beksi's group involved in the research.

CAPTION

Examples of 3D point clouds synthesized by a progressive conditional generative adversarial network (PCGAN).

CREDIT

William Beksi, Mohammad Samiul Arshad, UT Arlington

GENERATING OBJECTS FOR SYNTHETIC SCENES

After some initial attempts, Beksi realized his dream of creating photorealistic full scenes was presently out of reach. "We took a step back and looked at current research to determine how to start at a smaller scale - generating simple objects in environments."

Beksi and Arshad presented PCGAN, the first conditional generative adversarial network to generate dense colored point clouds in an unsupervised mode, at the International Conference on 3D Vision (3DV) in Nov. 2020. Their paper, "A Progressive Conditional Generative Adversarial Network for Generating Dense and Colored 3D Point Clouds," shows their network is capable of learning from a training set (derived from ShapeNetCore, a CAD model database) and mimicking a 3D data distribution to produce colored point clouds with fine details at multiple resolutions.

"There was some work that could generate synthetic objects from these CAD model datasets," he said. "But no one could yet handle color."

In order to test their method on a diversity of shapes, Beksi's team chose chairs, tables, sofas, airplanes, and motorcycles for their experiment. The tool allows the researchers to access the near-infinite number of possible versions of the set of objects the deep learning system generates.

"Our model first learns the basic structure of an object at low resolutions and gradually builds up towards high-level details," he explained. "The relationship between the object parts and their colors -- for examples, the legs of the chair/table are the same color while seat/top are contrasting -- is also learned by the network. We're starting small, working with objects, and building to a hierarchy to do full synthetic scene generation that would be extremely useful for robotics."

They generated 5,000 random samples for each class and performed an evaluation using a number of different methods. They evaluated both point cloud geometry and color using a variety of common metrics in the field. Their results showed that PCGAN is capable of synthesizing high-quality point clouds for a disparate array of object classes.

SIM2REAL

Another issue that Beksi is working on is known colloquially as 'sim2real.' "You have real training data, and synthetic training data, and there can be subtle differences in how an AI system or robot learns from them," he said. "'Sim2real' looks at how to quantify those differences and make simulations more realistic by capturing the physics of that scene - friction, collisions, gravity -- and by using ray or photon tracing."

The next step for Beksi's team is to deploy the software on a robot, and see how it works in relationship to the sim-to-real domain gap.

The training of the PCGAN model was made possible by TACC's Maverick 2 deep learning resource, which Beksi and his students were able to access through the University of Texas Cyberinfrastructure Research (UTRC) program, which provides computing resources to researchers at any of the UT System's 14 institutions.

"If you want to increase resolution to include more points and more detail, that increase comes with an increase in computational cost," he noted. "We don't have those hardware resources in my lab, so it was essential to make use of TACC to do that."

In addition to computation needs, Beksi required extensive storage for the research. "These datasets are huge, especially the 3D point clouds," he said. "We generate hundreds of megabytes of data per second; each point cloud is around 1 million points. You need an enormous amount of storage for that."

While Beksi says the field is still a long way from having really good robust robots that can be autonomous for long periods of time, doing so would benefit multiple domains, including health care, manufacturing, and agriculture.

"The publication is just one small step toward the ultimate goal of generating synthetic scenes of indoor environments for advancing robotic perception capabilities," he said

Appearance, social norms keep students off Zoom cameras

CORNELL UNIVERSITY

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ITHACA, N.Y. - When the semester shifted online amid the COVID-19 pandemic last spring, Cornell University instructor Mark Sarvary, and his teaching staff decided to encourage - but not require - students to switch on their cameras.

It didn't turn out as they'd hoped.

"Most of our students had their cameras off," said Sarvary, director of the Investigative Biology Teaching Laboratories in the College of Agriculture and Life Sciences (CALS).

"Students enjoy seeing each other when they work in groups. And instructors like seeing students, because it's a way to assess whether or not they understand the material," Sarvary said. "When we switched to online learning, that component got lost. We wanted to investigate the reasons for that."

Sarvary and co-instructor Frank Castelli, a CALS Active Learning Initiative education postdoctoral researcher, surveyed the 312 students in the class at the end of the semester to figure out why they weren't using their cameras - and to try to come up with ways to turn that trend around.

They found that while some students had concerns about the lack of privacy or their home environment, 41% of the 276 respondents cited their appearance, and more than half of those who selected "other" as their reason for keeping their camera off explained that it was the norm. This suggested that explicitly encouraging camera use could boost participation without adverse effects, the researchers said.

"We felt it would create an undue burden and add stress in an already stressful time to require the cameras to be on, and we found this could disproportionately affect certain groups of students, such as underrepresented minorities," said Castelli, first author of "Why Students Do Not Turn on Their Video Cameras During Online Classes and an Equitable and Inclusive Plan to Encourage Them to Do So," which published Jan. 10 in Ecology and Evolution.

In the survey, Castelli and Sarvary found that among underrepresented minorities, 38% said they were concerned about other people being seen behind them, and 26% were concerned about their physical location being visible; while among non-underrepresented minorities, 24% were worried about people behind them and 13% about their physical locations.

"It's a more inclusive and equitable strategy to not require the cameras but to instead encourage them, such as through active learning exercises," Castelli said. "This has to be done carefully so it doesn't create an environment where you're making those without cameras on feel excluded. But at the same time, if you don't explicitly ask for the cameras and explain why, that can lead to a social norm where the camera is always off. And it becomes a spiral of everyone keeping it off, even though many students want it on."

Establishing camera use as the norm, explaining the reasons that cameras improve the class and employing active learning techniques and icebreakers, such as beginning each class with a show-and-tell, are techniques that could boost participation, the authors suggested in the study.

"Active learning plays an important role in online learning environments," Sarvary said. "Students may feel more comfortable turning on their cameras in breakout rooms. Polling software or Zoom chats are alternatives that can help the instructor assess student learning, even without seeing nodding or smiling or confused expressions."

The authors also suggested instructors address potential distractions, give breaks to help maintain attention, and poll their students to learn about other potential barriers to camera use or participation.

Though they have not yet formally studied the effect, the instructors in the 24 sections of the laboratory class all observed improved camera participation when they used some of these strategies last fall.

"We wanted to develop an engaging and inclusive virtual learning environment, using the best pedagogical methods," Sarvary said. "That's why we wanted to know why the students are not turning their cameras on, rather than just assuming or, as some instructors do, requiring them to turn their cameras on. We wanted to take an education research approach and figure out the best practices."

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The research was supported by the CALS Active Learning Initiative Grants Program.

Making microwaves safer for children

New journal article recounts Rush pediatricians' campaign to protect children from severe burns

RUSH UNIVERSITY MEDICAL CENTER

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A 15-year research and advocacy effort to make microwave ovens safer has led to a change in national manufacturing standards that will make microwaves more difficult for young children to open, protecting them from the severe microwave-related burns that scar hundreds of kids under 5 years old in the United States each year. Researchers at Rush University Medical Center and other leaders of the campaign, who worked diligently to document the frequency and severity of these injuries and young children's vulnerability to them, published the results of their efforts in The Journal of Pediatrics on Jan. 20.

"The efforts we have made over the last 15 years have recently led to a change in how microwaves are made. In 2023, manufacturers will be required to incorporate two distinct actions into opening the door of a microwave oven," said Kyran Quinlan MD, MPH, a professor of pediatrics and the director of the Division of General Pediatrics at Rush University Medical Center. Quinlan and fellow Rush pediatrician Gina Lowell, MD, worked closely with colleagues from the University of Chicago Medical Center Burn Unit to achieve the goal of child resistant microwave doors.

"We believed that if young children were less able to open microwave oven doors, they would be less likely to be able to remove the heated items, such as liquids and noodle soups, and they would therefore be less at risk for severe burns," Quinlan added. 'These burns are terribly painful, require burn unit care, and can be life-changing because of the permanent scarring that often results."

An abstract presenting the results from the advocacy effort was chosen as the Program Description Abstract of the Year during the annual conference of the Injury Free Coalition for Kids in December 2019.

According to the American Burn Association, 22.5% of the patients in burn units across the United States are children, and most of the children are admitted for scalds rather than burns suffered in fires.

The researchers' 15-year journey began with documenting the issue, and learning how microwave ovens are regulated and how to effectively advocate for child-resistant microwave oven doors. In 2008, the researchers published an analysis of three years of burn unit data that found that a significant percentage of burns involved young children opening a microwave themselves and removing and spilling the oven's heated contents.

In that report, the youngest child burned was 18 months old, and nearly half of the cases required skin grafts -- a process of removing skin from one part of the body to cover the section of skin that was burned.

The researchers then evaluated and documented the abilities of healthy young children ages 15 months to 4 years to use microwave ovens. They recorded whether the children could open the microwave oven door with either a push mechanism or a pull mechanism, turn on the microwave and remove its contents.

The study revealed that children as young as 17 months could open both a push- and a pull-open microwave oven door, remove what was in the microwave, and even turn it on. Nearly all children were able to perform each of these tasks by the age of 2.

The researchers then worked to submit a proposed change in the design requirements of microwave oven doors to make them more difficult for young children to open. Quinlan and Lowell worked with the child product safety advocacy group Kids in Danger to enlist college engineering students to design child-resistant microwave doors to demonstrate their feasibility. The team also presented their research at national meetings and created a short video to put a face with the statistics about microwave-related childhood burns.

Eventually, Quinlan and Marla Robinson MSc, OTR/L, assistant director of therapy services at University of Chicago Medical Center and a partner in the advocacy campaign, became voting members of the Underwriters Laboratories Standards Technical Panel for microwave ovens, which sets the standards required for any microwave sold in the United States.

After previous failed attempts to change the standard for microwave oven doors, the panel passed the change by a single vote in September 2018. The new microwave ovens also will be required to include labels warning families of the risk of severe scalds to young children.

"Early on, we felt that making microwave oven doors harder to open would truly protect young children from these burns, which were frequently severe," Quinlan said. "This took longer than we expected, but it was so worth it.

"We knew we had work to do to share this idea and to provide enough information to convince others who could be a part of the change we sought, but ultimately, our idea was a good one, and with persistence we realized our goal."

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Breakthrough in understanding 'tummy bug' bacteria

UNIVERSITY OF EXETER

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IMAGE: SCANNING ELECTRON MICROSCOPE (SEM) IMAGE OF HEALTHY, GROWING VIBRIO PARAHAEMOLYTICUS. view more 

CREDIT: UNIVERSITY OF EXETER BIOIMAGING UNIT

Scientists have discovered how bacteria commonly responsible for seafood-related stomach upsets can go dormant and then "wake up".

Vibrio parahaemolyticus is a marine bacterium that can cause gastroenteritis in humans when eaten in raw or undercooked shellfish such as oysters and mussels.

Some of these bacteria are able to turn dormant in poor growth conditions such as cold temperatures - and can remain in that state of hibernation for long periods before resuscitating.

University of Exeter scientists have identified a population of these dormant cells that are better at waking up, and have discovered an enzyme involved in that waking up process.

"Most of these bacteria die when they encounter poor growth conditions, but we identified sub-populations of bacteria that are able to stay dormant for long periods of time," said lead author Dr Sariqa Wagley, of the University of Exeter.

"We found that this population has a better ability to revive when conditions improve.

"Our tests show that when these dormant bacteria are revived they are just as virulent and able to cause disease."

The findings could have implications for seafood safety, as dormant cells are not detectable using routine microbiological screening tests and the true bacterial load (amount of bacteria) could be underestimated.

"When they go dormant, these bacteria change shape, reduce respiration activities and they don't grow like healthy bacteria on agar plates used in standard laboratory tests, so they are much harder to detect," Dr Wagley explained.

"Using a range of tools, we were able to find dormant bacteria in seafood samples and laboratory cultures and look at their genetic content to look for clues in how they might survive for long periods.

"It is important to note that thorough cooking kills bacteria in seafood.

"Our results may also help us predict the conditions that dormant bacteria need in order to revive."

Working with the seafood industry, the Exeter team identified a lactate dehydrogenase enzyme that breaks down lactic acid into pyruvate, a key component of several metabolic pathways (chemical reactions in a cell).

CAPTION

Scanning Electron Microscope (SEM) image of dormant Vibrio parahaemolyticus.

CREDIT

University of Exeter Bioimaging Unit

The findings suggest that lactate dehydrogenase is essential both for maintaining bacterial dormancy and resuscitation back to an active form.

Vibrio parahaemolyticus usually grows in warm and tropical marine environments, although Dr Wagley said that due to rising sea temperatures in recent years it is now prevalent in UK waters during the summer months.

During the winter, it is not detected in the marine environment around the UK and it is thought to die due to the cold winter temperatures.

This study could explain how Vibrio parahaemolyticus is able remerge in the environment during the summer.

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The study was partly funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional funding and support from Lyons Seafoods.

The paper, published in the journal PLOS Pathogens, is entitled: "Bacterial dormancy: a subpopulation of viable but non-culturable cells demonstrates better fitness for revival."

CAPTION

Scanning Electron Microscope (SEM) image of dormant Vibrio parahaemolyticus

Exploration of toxic Tiger Rattlesnake venom advances use of genetic science techniques

In deciphering a simple, but particularly deadly venom, the research opens avenues for exploration of how genes produce traits

UNIVERSITY OF SOUTH FLORIDA (USF INNOVATION)

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VIDEO: A RESEARCH TEAM LED BY THE UNIVERSITY OF SOUTH FLORIDA STUDIED THE GENOME OF THE TIGER RATTLESNAKE. view more 

CREDIT: MICHAEL P. HOGAN, FLORIDA STATE UNIVERSITY

The Tiger Rattlesnake possesses the simplest, yet most toxic venom of any rattlesnake species, and now new research from a team lead by a University of South Florida biologist can explain the genetics behind the predator's fearsome bite.

Published in the new edition of "Proceedings of the National Academy of Sciences," USF Department of Integrative Biology Assistant Professor Mark Margres and colleagues across the southeastern United States have sequenced the genome of the Tiger Rattlesnake to understand the genotype of the venom trait. Despite the simplicity of the Tiger Rattlesnake's venom, Margres says it is roughly 40 times more toxic than the venom of the Eastern Diamondback Rattlesnakes here in Florida.

Their work is the most complete characterization of the venom gene-regulatory network to date and its identification of key mechanisms in producing the particularly toxic venom will help scientists explain a wide array of genetic questions.

"Simple genotypes can produce complex traits," Margres said. "Here, we have shown the opposite is also true - a complex genotype can produce simple traits."

CAPTION

Mark Margres photographs an Eastern Diamondback Rattlesnake at Caladesi Island, Florida.

CREDIT

University of South Florida

Margres collaborated with colleagues at Clemson University, Florida State University and the University of South Alabama, in the project, which sought to explain whether trait differences are derived from differences in the number of genes, their sequence or how they are regulated. Their work is only the second time a rattlesnake genome has been decoded.

An organism's genotype is the set of genes it carries, and its phenotype is all of its observable characteristics, which can be influenced by its genes, the environment in which it lives, and other factors. Evolutionary biologists work to understand how genes influence the variation in phenotype among otherwise similar organisms. In this case, they looked at why different species of rattlesnakes differ in venom composition and toxicity.

Tiger Rattlesnakes are native to the Sonoran Desert of southern Arizona and northern Mexico where the relatively small pit viper preys on lizards and rodents. While some species of rattlesnakes have complex venoms that are the result of scores of genes, Margres said the Tiger Rattlesnake's venom is quite simple - as few as 15 of its 51 toxic-producing genes actively drive the production of proteins and peptides that attacks its prey's nervous system, forces blood pressure to drop and causes blood clotting to cease.

The team found that the number of venom genes greatly exceeds the number of proteins produced in the simple phenotype, indicating a complex process was at the heart of the toxic venom and the Tiger Rattlesnakes even has toxic genes to spare.

CAPTION

Tiger Rattlesnake used in the study was found in the Santa Rita Mountains in Arizona.

"Only about half of the venom genes in the genotype were expressed," Margres said. "To me, the interesting part is why are the non-expressed genes still present? These genes can make functional toxins, they just don't. That needs to be explored further."

Beyond understanding this one species of venomous snake, Margres said the research will help advance genetic science by showing the techniques more commonly used on genetic research on mice and fruit flies, organisms that are often used in genetic studies, can also work when applied to less-studied organisms like snakes. The team used genetic sequencing techniques that are common in human genetics research and in doing so, opened the door for scientists to understand the genotype-phenotype relationship in many other organisms.

Another potential side benefit of the research, Margres said, is that snake venom is used in medicine for humans to combat stroke and high blood pressure. The more scientists understand about venom, the better medical engineering can apply that knowledge in drug discovery and development.

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The research was funded by the National Science Foundation and Clemson University.

Disease threatens to decimate western bats

White-nose syndrome predicted to drastically impact hibernating bat species in the West

WILDLIFE CONSERVATION SOCIETY

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IMAGE: A RESEARCHER ABOUT TO HANDLE A HIBERNATING TOWNSEND'S BIG-EARED BAT IN AN ABANDONED MINE IN NEVADA. view more 

CREDIT: KIM RAFF

BOZEMAN, Montana (January 19, 2021) - A four-year study recently published in Ecology and Evolution concludes that the fungal disease, white-nose syndrome, poses a severe threat to many western North American bats.

Since it was first detected in 2006, white-nose syndrome has killed millions of bats in eastern and central North America. The spread of the fungal pathogen that causes white-nose syndrome in hibernating bats has reached several western U.S. states, mostly likely through bat-to-bat spread, and is presently threatening western species.

Bats with white-nose syndrome have fungus growing on their nose and wings, as the name implies, but the fungal infection also triggers a higher frequency of arousals from hibernation. Each arousal involves an increase in body temperature from as low as near freezing (when bats use torpor) to an active mammalian body temperature (~98?F or 38?C), which uses a significant amount of energy. Bats have limited fat stored for the winter, and if this is used up before the end of winter, death by starvation occurs.

The researchers' aim was to provide managers with information on which western bat species may suffer high mortality and extinction risk if infected with the disease. To do so they combined an unprecedented field data collection effort with a mechanistic model that explains how energy is consumed during hibernation and how the causal fungus impacts this energy consumption. By comparing their new knowledge of how long bats infected with white-nose syndrome could hibernate against the duration of winter that they would need to hibernate with the disease, the authors predicted survival outcomes for each species. If a bat did not have sufficient energy to live beyond the duration of winter the simulation recorded a mortality.

Three years of intensive fieldwork resulted in 946 bat captures (all released after measuring). Bat energetic measurements paired with hibernaculum environmental data were gathered for nine species that were sampled at eight sites scattered throughout the West (see Figure A). The researchers then assessed how the arrival of white-nose syndrome might affect hibernation energy use, and subsequently each species' ability to survive hibernation with the disease. Combining data on the host, the environment they select for hibernation, and how the pathogen grows at different temperature and humidity conditions the authors simulated how many days infected populations could hibernate under field conditions.

The study revealed there are white-nose syndrome threats to all the small Myotis species examined, including M. ciliolabrum (western small-footed bat), M. evotis (long-eared bat), M. lucifugus (little brown bat), M. thysanodes (fringed myotis), and M. volans (long-legged bat), as well as Perimyotis subflavus (tricolored bat). In comparison, larger species like M. velifer (cave bat), Corynorhinus townsendii (Townsend's big-eared bat) and Eptesicus fuscus (big brown bat) are predicted to be less impacted. Further analysis showed body mass (and relatedly body-fat as these attributes are correlated) as well as hibernaculum water vapor deficit (i.e. relative humidity) explained over half the variation observed in bat survival.

Dr. Catherine Haase, now Assistant Professor of Biology at Austin Peay State University and the study's lead author said: "Our results indicate the need to take a holistic view on conservation, as it is not just one thing that determines survival from white-nose syndrome, but rather the combination of bat, environment, and disease variables."

All of the western bat species studied were insectivores, meaning they prey on insects, including those that are pests to agricultural crops. In addition to providing valuable ecosystem services, they are incredibly fascinating species, from their ability to echolocate to their unique immune system.

Dr. Sarah Olson, Wildlife Conservation Society Health Program co-author and project Principle Investigator said: "This study demonstrates the value of collecting baseline data to pre-emptively understand a threat posed by a wildlife disease, like white-nose syndrome, to western bats, so that more proactive conservation measures can be taken to protect these species. Here, an all hands on deck approach is needed. Western states can take steps now to put protections in place before anticipated severe declines are observed, like reducing habitat loss and restricting access to hibernacula, as well as investing in research and surveillance."

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The study was funded by an award from the Strategic Environmental Research and Development Program(SERDP;) - the Department of Defense's environmental science and technology program that is executed in partnership with the Department of Energy and the Environmental Protection Agency. The research involved a consortium of partners including Texas Tech University, Montana State University, Massey University in New Zealand, Wildlife Conservation Society Canada, Conservation Science Partners and the Wildlife Conservation Society.

About the WCS (Wildlife Conservation Society)

The Wildlife Conservation Society (WCS) is a US non-profit, tax-exempt, private organization established in 1895 that saves wildlife and wild places by understanding critical issues, crafting science-based solutions, and taking conservation actions that benefit nature and humanity. With more than a century of experience, long-term commitments in dozens of landscapes, presence in more than 60 nations, and experience helping to establish over 150 protected areas across the globe, WCS has amassed the biological knowledge, cultural understanding and partnerships to ensure that vibrant, wild places and wildlife thrive alongside local communities. Working with local communities and organizations, that knowledge is applied to address species, habitat and ecosystem management issues critical to improving the quality of life of poor rural people whose livelihoods depend on the direct utilization of natural resources. WCS was the first conservation organization with a dedicated team of wildlife veterinarians and other health professionals deployed around the world. The WCS Health Program is central to delivering on our mission to save wildlife and wild places around the globe. Wildlife, livestock, and human diseases will likely have a significant impact on the future development of sustainable land uses, protected areas, transboundary natural resource management, other biodiversity conservation approaches, and livelihood opportunities in many of the landscapes and seascapes where we work. Our work at the interface of wildlife, domestic animal, and human health has demonstrated that a One Health approach can build new constituencies for conservation and strengthen existing ones, while mitigating a key threat to conservation. Today, WCS Health Programs are globally recognized for excellence in zoological and wildlife medicine, pathology, and global health conservation initiatives. Visit: newsroom.wcs.org Follow: @WCSNewsroom. For more information: 347-840-1242.

About Austin Peay State University

Austin Peay State University (APSU; apsu.edu) is a moderately-sized state university located in middle Tennessee. APSU serves a large population of diverse students with several degree options at the associates, bachelor's, master's and doctoral levels. Many of these degrees can be pursued on campus and online. APSU is home to the state's only Center of Excellence for Field Biology, which enables students to work with professional field biologists in the study of mammals, insects, fish, plants and more.

About WCS Canada Wildlife Conservation Society (WCS) Canada was incorporated as a conservation organization in Canada in 2004. The mission of WCS Canada is to conserve wildlife and wild places by understanding the issues, developing science-based solutions, and working with others to carry out conservation actions across Canada. WCS Canada is distinguished from other environmental organizations through their role in generating science through field and applied research, and by using results to encourage collaboration among scientific communities, organizations and policy makers to achieve conservation results.

About TTU

A new era of excellence is dawning at Texas Tech University as it stands on the cusp of being one of the nation's premier research institutions. Research and enrollment numbers are at record levels, which cement Texas Tech's commitment to attracting and retaining quality students. In fall 2020, the university achieved a goal more than a decade in the making, reaching a total student population of more than 40,000. In 2018, the Carnegie Classification of Institutions of Higher Education again placed Texas Tech among its top doctoral universities in the nation in the "Very High Research Activity" category. Texas Tech is one of 94 public institutions nationally and 131 overall to achieve this prestigious recognition. Quality students need top-notch faculty. Texas Tech is home to a diverse, highly revered pool of educators who excel in teaching, research and service. The university strives to foster an environment that celebrates student accomplishment above all else. Texas Tech is large enough to provide the best in facilities and academics but prides itself on being able to focus on each student individually.

The momentum for excellence at Texas Tech has never been greater.

About MSU

Montana State University is a public university located in Bozeman, Montana. It was founded in 1893 as the state's land-grant institution and prides itself on its tripartite mission of excellence in teaching and learning, research and creative projects and outreach and service. With an enrollment of more than 15,600 students, MSU is the largest university in the state. It is also the largest research university in Montana and the largest research and development entity of any kind in Montana, with annual research expenditures typically exceeding $100 million annually. Through its colleges, MSU offers baccalaureate degrees in more than 50 fields, master's degrees in more than 40 fields, and doctoral degrees in approximately 20 fields. To learn more, visit http://www.montana.edu/.

About Massey U

Massey University is New Zealand's largest and most influential educational institution with around 32,500 students. It calls itself New Zealand's defining university because its areas of specialized teaching and world-class research reflect what New Zealand and New Zealanders are best known for - agrifood innovation and the associated disciplines such as public health, animal welfare, farming and food technology, design, creative arts, social sciences, and business. It has five colleges (faculties), around 3000 full-time equivalent staff and the nation's largest university-based distance education program, allowing students to study from anywhere in the world.

About CSP

Conservation Science Partners (CSP; csp-inc.org) is a nonprofit scientific collective established to meet the analytical and research needs of diverse stakeholders in conservation outcomes on public and private lands. The mission of CSP is to apply human ingenuity to the preservation of species, populations, and ecosystems using scientific principles, innovative approaches, and lasting partnerships with conservation practitioners. CSP connects the best minds in conservation science to solve environmental problems in a comprehensive, flexible, and service-oriented manner. The core capabilities of CSP span a wide spectrum of geospatial and statistical techniques, from custom ecological and environmental data development (GIS and remote sensing based) to advanced analyses of landscape patterns and changes at multiple spatial and temporal scales.

Study identifies a nonhuman primate model that mimics severe COVID-19 similar to humans

New research published in The American Journal of Pathology suggests that aged African green monkeys may be suitable models for the study of severe forms of COVID-19

ELSEVIER

Research News

 

IMAGE: ACUTE RESPIRATORY DISTRESS SYNDROME (ARDS) IN SARS-COV-2 INFECTED AGED, AFRICAN GREEN MONKEY. A. RADIOGRAPHIC CHANGES NOTED FOLLOWING A RAPID CLINICAL DECLINE WITHIN A 24-HOUR PERIOD. B. MICROSCOPIC FINDINGS SHOWING DIFFUSE... view more 

CREDIT: THE AMERICAN JOURNAL OF PATHOLOGY

Philadelphia, January 19, 2021 - Aged, wild-caught African green monkeys exposed to the SARS-CoV-2 virus developed acute respiratory distress syndrome (ARDS) with clinical symptoms similar to those observed in the most serious human cases of COVID-19, report researchers in The American Journal of Pathology, published by Elsevier. This is the first study to show that African green monkeys can develop severe clinical disease after SARS-CoV-2 infection, suggesting that they may be useful models for the study of COVID-19 in humans.

"Animal models greatly enhance our understanding of diseases. The lack of an animal model for severe manifestations of COVID-19 has hampered our understanding of this form of the disease," explained lead investigator Robert V. Blair, DVM, PhD, Dip ACVP, Tulane National Primate Research Center, Covington, LA, USA. "If aged green monkeys prove to be a consistent model of severe COVID-19, studying the disease pathobiology in them would improve our understanding of the disease and allow testing treatment options."

The researchers exposed four aged rhesus macaques and four aged African green monkeys to SARS-CoV-2. Older animals (13-16 years of age) were specifically chosen to see if they would develop the severe form of the disease that is observed more frequently in elderly individuals. All of the monkeys developed a spectrum of disease from mild to severe COVID-19. A day after routine screening found no remarkable symptoms, two of the African green monkeys developed rapid breathing that quickly progressed to severe respiratory distress. Radiographic studies found the two African green monkeys had widespread opacities in the lungs, in stark contrast to images taken the day before, highlighting the rapid development of the disease. Such opacities are a hallmark of ARDS in humans.

The African green monkeys that progressed to severe disease had notable increases in plasma cytokines that are compatible with cytokine storm, which is thought to underlie the development of ARDS in some patients. All four African green monkeys had elevated levels of interferon gamma; the two that had progressed to ARDS had the highest plasma concentration. Plasma cytokines were not increased in the rhesus macaques. Dr. Blair suggested that elevated interferon gamma could be explored as a potential predictive biomarker for advanced disease in patients and a possible therapeutic target.

Dr. Blair said, "Our data suggest that both rhesus monkeys and African green monkeys are capable of modeling mild manifestations of SARS-CoV-2 infection, and aged African green monkeys may additionally be capable of modeling severe disease manifestations, including ARDS."

HIV/AIDS WAS FIRST DISCOVERED IN GREEN MONKEYS IN AFRICA

Stealing the spotlight in the field and kitchen

AMERICAN SOCIETY OF AGRONOMY

Research News

 

IMAGE: BEANS IN THE UC DAVIS BREEDING PROGRAM, WHOSE VARIETIES HAVE BEEN SELECTED TO COMBINE EXCELLENT CULINARY WITH IMPROVED YIELDS AND RESISTANCE TO BEAN COMMON MOSAIC VIRUS. view more 

CREDIT: TRAVIS PARKER

January 20, 2021 - Plant breeders are constantly working to develop new bean varieties to meet the needs and desires of the food industry. But not everyone wants the same thing.

Many consumers desire heirloom-type beans, which have great culinary quality and are visually appealing. On the other hand, farmers desire beans with better disease resistance and higher yield potential.

The bean varieties that farmers want to grow are usually different than the varieties consumers want to purchase. Until now.

Travis Parker, a plant scientist at University of California, Davis, has worked with a team of researchers to release five new varieties of dry beans that combine the most desirable traits.

The new varieties, UC Sunrise, UC Southwest Red, UC Tiger's Eye, UC Rio Zape, and UC Southwest Gold, were recently highlighted in the Journal of Plant Registrations, a publication of the Crop Science Society of America.

"Our new beans combine the best of both worlds for farmers and consumers," says Parker. "They combine the better qualities of heirloom-type beans with the better qualities of commercial types."

Heirloom-type beans often represent older bean types that are known for culinary qualities and seed patterns. These are highly desired by consumers. Heirloom types often fetch a higher market value than other beans.

Commercial dry beans often have higher yields, shorter maturity times, and improved disease resistance. While they possess qualities desirable to producers, they don't fetch as high of a market price compared to their heirloom counterparts.

"Our goal was to improve field characteristics of the heirloom beans without losing culinary characteristics," said Parker. "We have an interest in higher-value varieties and want them to grow well."

Farmers growing the heirloom dry beans often sell the beans to health-conscious consumers or high-end restaurants. This sale often leads to a higher price point. However, these beans are prone to disease and don't perform well in the field.

"We know that existing heirloom beans don't usually do well in terms of yield," said Parker. "Breeding beans for high yields is a major improvement for farmers. The new varieties are high-yielding, heat-tolerant, and are also resistant to bean common mosaic virus."

CAPTION

A comparison of the heirloom variety "Tiger's Eye" (left, with virus symptoms) and the newly released "UC Tiger's Eye" (right, healthy leaves). These varieties have similar culinary qualities, but UC Tiger's Eye is resistant to the common mosaic virus and has higher yields.

Incorporating disease resistance was essential when developing the new bean varieties. Bean common mosaic virus is a well-known problem that is hard to control in the field.

"The only real effective means to handle the virus is through genetic resistance," explains Parker.

The new varieties, such as UC Sunrise, satisfy the need for farmers to have a bean that is disease resistant while also yielding 50% more than heirloom types. In addition, the beans do not take as long to grow between planting and harvest.

Commercial and heirloom beans come from the same species, but they are in different market classes. The heirloom varieties are bred with intimate knowledge of what tastes good and what works well in the kitchen.

"In recent decades, there has been less attention paid to consumer desires during the bean breeding process," says Parker. "There are more layers between the breeder and the consumer. We are trying to make sure to keep consumers in mind while incorporating qualities that are beneficial to the farmer."

With consumer desires in mind, the research team used cross-pollination to breed plants with key characteristics they selected. As Parker and the team continued the breeding process, they performed taste tests to ensure the beans met the level of culinary quality expected of an heirloom-type bean, in terms of flavor and visual appeal.

CAPTION

A detailed view of UC Sunrise, one of the new varieties the heirloom-like dry bean. The colorful pattern is desirable to consumers. 

This research was supported by the Clif Bar Family Foundation, Lundberg Family Farms, the United States Department of Agriculture Organic Agriculture Research & Extension Initiative, and the United States Department of Agriculture Western Sustainable Agriculture Research and Education program.

American Society of Agronomy, Soil Science Society of America, Crop Science Society of America: Collectively, these Societies represent more than 12,000 individual members around the world. Members are researchers and professionals in the areas of growing our world's food supply while protecting our environment. Together we work toward solutions to advance scientific knowledge in the areas of agronomy, crop science, and soil science.

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