Saturday, May 18, 2024

NCSA upgrades granite to expand availability to access, Illinois researchers

Granite’s capacity will increase 4.5 times and nearly double its performance thanks to a $500,000 NSF grant

NATIONAL CENTER FOR SUPERCOMPUTING APPLICATIONS

As the capabilities of technology continue to expand and grow, so does the need for data storage. Researchers across the country and on the University of Illinois Urbana-Champaign campus continue to generate large datasets that need to be stored and shared long-term. New innovations in artificial intelligence and processing algorithms also mean that training and reprocessing of previously collected datasets is becoming more and more common.

The National Center for Supercomputing Applications understands these critical needs for researchers and, with a $500,000 grant from the U.S. National Science Foundation, will upgrade its primary active archive system, Granite.

Granite is a cutting-edge tape-based data subsystem that allows researchers to store and retrieve data in both traditional and newer, more flexible methods. It’s closely integrated with Taiga – NCSA’s global file system – to provide users with a place to store longer-term archive datasets.

The funding allows NCSA to upgrade Granite’s tape drives and media from the TS1140 tape drive to the latest-available LTO-9. The new hardware will provide 4.5 times greater density of the library and almost double the system’s performance.

Researchers continue to generate large volumes of data that need to be stored and shared for long periods of time. These upgrades allow researchers to store data for future reprocessing using new algorithms and allow data to be made available to other researchers for reproducibility purposes and to gain further insight.
J.D. Maloney, Senior Research Storage Engineer at NCSA and principal investigator of the award

“There is an urgent need to explore pragmatic data archiving strategies,” said University of Illinois Urbana-Champaign’s Research Data Service Director Heidi Imker. “In a world of infinite resources, all data would be just one click away. But that’s not feasible – or even necessary – for many datasets, especially large ones. This grant will allow us to explore alternative strategies and pilot what implementation would look like in practice.”

Imker and NCSA’s Associate Director of Integrated Cyberinfrastructure Tim Boerner are both co-principal investigators on the NSF funding for Granite, which will strengthen the ability for Illinois researchers and the national research community – through the NSF cyberinfrastructure program ACCESS – to store, share and utilize their data in the ways they need. Eighty percent of allocations on Granite will go to Illinois researchers and the remaining 20 percent will be allocated through ACCESS. Granite’s upgrades are expected to be completed by mid-summer 2024.

ABOUT NCSA

The National Center for Supercomputing Applications at the University of Illinois Urbana-Champaign provides supercomputing, expertise and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students and collaborators from around the globe use innovative resources to address research challenges for the benefit of science and society. NCSA has been assisting many of the world’s industry giants for over 35 years by bringing industry, researchers and students together to solve grand challenges at rapid speed and scale.

ABOUT ACCESS

The Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) program is a U.S. National Science Foundation-funded virtual organization that facilitates cyberinfrastructure (CI) support for research. Through ACCESS, researchers can request time allocated from an extensive network of CI resources such as advanced computing, data resources and analysis, visualization, and storage. The ACCESS CI ecosystem is essential to computational and data-intensive research with a goal of providing seamless collaboration between resources and researchers.

STAR sees a magnetic imprint on deconfined nuclear matter

Data from heavy ion collisions give new insight into the electromagnetic properties of quark-gluon plasma “deconfined” from protons and neutrons

DOE/US DEPARTMENT OF ENERGY

STAR Sees a Magnetic Imprint on Deconfined Nuclear Matter — IMAGE:
COLLISIONS OF HEAVY IONS GENERATE AN IMMENSELY STRONG MAGNETIC FIELD THAT IN TURN INDUCES ELECTROMAGNETIC EFFECTS IN THE QUARK-GLUON PLASMA, A “SOUP” OF QUARKS AND GLUONS LIBERATED FROM THE COLLIDING PROTONS AND NEUTRONS.
view more
CREDIT: IMAGE COURTESY OF TIFFANY BOWMAN AND JEN ABRAMOWITZ/BROOKHAVEN NATIONAL LABORATORY

The Science

Scientists have the first direct evidence that the powerful magnetic fields created in off-center collisions of atomic nuclei induce an electric current in “deconfined” nuclear matter. This is a plasma “soup” of quarks and gluons that have been set free, or “deconfined,” from nuclear matter—protons and neutrons—in the particle collisions. The magnetic fields in deconfined nuclear matter are a billion times stronger than a typical refrigerator magnet, but their effects can be hard to detect. This new study’s evidence is from measuring the way particles with an electric charge are deflected when they emerge from the collisions. The study provides proof that the powerful magnetic fields exist. It also offers a new way to measure the electrical conductivity in the quark-gluon plasma (QGP).

The Impact

Scientists can infer the value of the QGP’s electrical conductivity from how much the electromagnetic field deflects charged particles such as electrons, quarks, and protons. The stronger a particular type of deflection is, the stronger the conductivity. Conductivity is an important property of matter, but scientists have not been able to measure it in QGP before. Understanding the electromagnetic properties of the QGP may help physicists unravel the mysteries of the phase transition between QGP and ordinary nuclear matter made of protons and neutrons. The work will also aid in explorations of other magnetic effects in the QGP.

Summary

Off-center collisions of atomic nuclei at the Relativistic Heavy Ion Collider (RHIC), a Department of Energy particle accelerator user facility at Brookhaven National Laboratory, should generate powerful magnetic fields. That’s because some of the non-colliding positively charged protons are set swirling as the nuclei sideswipe one another at close to the speed of light. The fields are expected to be stronger than those of neutrons stars and much more powerful than Earth’s. But measuring magnetic fields in the QGP is challenging because this deconfined nuclear matter doesn’t last very long. So, instead, scientists measure the QGP’s properties indirectly, for example by using RHIC’s STAR detector to track the impact of the magnetic field on charged particles streaming from the collisions.

The STAR physicists saw a pattern of charged-particle deflection that could only be caused by an electromagnetic field and current induced in the QGP. This was clear evidence that the magnetic fields exist. The degree of deflection is directly related to the strength of the induced current. Scientists will now use this method to measure the conductivity of the QGP. That, in turn, may help them unravel mysteries of the phase transition between deconfined quarks and gluons and composite particles such as protons and neutrons.

Funding

This research was funded by the Department of Energy Office of Science, the National Science Foundation, and a range of international organizations and agencies listed in the scientific paper. The STAR team used computing resources at the Scientific Data and Computing Center at Brookhaven National Laboratory, the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, and the Open Science Grid consortium.

JOURNAL

Physical Review X

DOI

10.1103/PhysRevX.14.011028

METHOD OF RESEARCH

Experimental study

ARTICLE TITLE

Leading the way for Southeastern dairies

UTIA’s Center for Dairy Advancement and Sustainability to be hub for information

UNIVERSITY OF TENNESSEE INSTITUTE OF AGRICULTURE

Liz Eckelkamp, associate professor in the University of Tennessee Department of Animal Science — IMAGE:
UTIA'S NEW CENTER FOR DAIRY ADVANCEMENT AND SUSTAINABILITY (CDAS) IS LED BY LIZ ECKELKAMP, ASSOCIATE PROFESSOR OF ANIMAL SCIENCE AND EXTENSION DAIRY SPECIALIST.
view more
CREDIT: PHOTO BY H. HARBIN, COURTESY UTIA.

The Southeast’s dairy industry has faced many challenges over the past several decades, and the number of dairy farm numbers across the region has fallen to historic lows. Fewer than 2,000 are operating, with many teetering on the edge of profitability. In an effort to help local producers survive economically, as well as to keep their beloved dairy products available to consumers, the University of Tennessee Institute of Agriculture has formed the Center for Dairy Advancement and Sustainability (CDAS).

While the CDAS has been “open” for several months, now is the perfect time to highlight the center’s operations and goals as the nation begins celebrations for June Dairy Month.

The new center is led by Liz Eckelkamp, associate professor of animal science and Extension Dairy specialist. Eckelkamp has been the successful director of the Southest Dairy Business Innovation Initiative since 2020, which is a USDA-funded effort to revitalize the regional dairy industry through value-added products. The new CDAS will help with that and more. It is expected to be a hub of research, extension, and teaching with the goal of providing Real. Life. Solutions.™ to the Southeast dairy industry. Building on SDBII as well as additional funding, the CDAS is set to position UTIA as leader in innovative dairy solutions for both large and small ruminants, for example dairy cows and goats.

Eckelkamp, who also coordinates and provides curricula for the Tennessee Master Dairy Program (utdairy.tennessee.edu/master-dairy), says dairy farmers in the Southeast are faced with high costs of production. “On average they lose $6 for every hundred pounds of milk they sell commercially. In the face of these elevated costs and to thin negative profit margins, producers and processors must find alternative ways to remain in business and support their families, employees and communities,” she stresses. “The CDAS will focus on facing these challenges head on through alternatives revenue sources such as farmstead creameries, alternative inputs such as non-traditional forages, technologies to reduce labor costs and access issues, marketing and outreach tools and leadership training for existing dairy businesses.”

Center members consist of UTIA and other UT Knoxville faculty with the expertise to support the advancement and sustainability of the dairy industry through a dairy systems approach that includes topics under the areas of animal husbandry, precision dairy technologies, dairy foods, labor management, leadership, marketing, branding, and small business economics. Eckelkamp says, “We envision establishing UTIA as a leader in dairy precision technology and alternative income strategies addressing the needs of farmers, processors and producer/processors through Extension, research and teaching with University and industry synergistic partnerships.”

To raise awareness and grow the industry, CDAS will also provide opportunities to students through internships, conference travel, and research experiences. Center members will also have the opportunity to apply for seed grant funding through CDAS to answer pressing questions for the dairy industry.

Neal Schrick, professor and head of the UT Department Head of Animal Science, remarks, “Dr. Eckelkamp and her team have developed the Center for Dairy Advancement and Sustainability to provide focus and additional resources toward providing solutions for southeast dairy producers to help them overcome the many obstacles in their path toward sustainability of the industry. With Dr. Eckelkamp at the helm of the center and with the team she has organized across the Southeast, I see great opportunities across many difference facets of the dairy industry in the knowledge and initiatives that CDAS will provide.”

For more information, contact Eckelkamp at eeckelka@tennessee.edu or visit the UT Dairy website (utdairy.tennessee.edu) or the SBDII website (sdbii.tennessee.edu).

The University of Tennessee Institute of Agriculture is comprised of the Herbert College of Agriculture, UT College of Veterinary Medicine, UT AgResearch and UT Extension. Through its land-grant mission of teaching, research and outreach, the Institute touches lives and provides Real. Life. Solutions. to Tennesseans and beyond. utia.tennessee.edu.

NIH study shows chronic wasting disease unlikely to move from animals to people

Study of cerebral organoids reinforces evidence for substantial species barrier

NIH/NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES

Human Cerebral Organoids — IMAGE:
A RESEARCHER HOLDS A FLASK CONTAINING HUMAN CEREBRAL ORGANOIDS SIMILAR TO THOSE USED IN THE CWD STUDY
view more
CREDIT: NIAID

WHAT:
A new study of prion diseases, using a human cerebral organoid model, suggests there is a substantial species barrier preventing transmission of chronic wasting disease (CWD) from cervids—deer, elk and moose—to people. The findings, from National Institutes of Health scientists and published in Emerging Infectious Diseases, are consistent with decades of similar research in animal models at the NIH’s National Institute of Allergy and Infectious Diseases (NIAID).

Prion diseases are degenerative diseases found in some mammals. These diseases primarily involve deterioration of the brain but also can affect the eyes and other organs. Disease and death occur when abnormal proteins fold, clump together, recruit other prion proteins to do the same, and eventually destroy the central nervous system. Currently, there are no preventive or therapeutic treatments for prion diseases.

CWD is a type of prion disease found in cervids, which are popular game animals. While CWD has never been found in people, a question about its transmission potential has lingered for decades: Can people who eat meat from CWD-infected cervids develop prion disease? The question is important because during the mid-1980s and mid-1990s a different prion disease – bovine spongiform encephalopathy (BSE), or mad cow disease – emerged in cattle in the United Kingdom (U.K.) and cases also were detected in cattle in other countries, including the United States. Over the next decade, 178 people in the U.K. who were thought to have eaten BSE-infected beef developed a new form of a human prion disease, variant Creutzfeldt-Jakob Disease, and died. Researchers later determined that the disease had spread among cattle through feed tainted with infectious prion protein. The disease transmission path from feed to cattle to people terrified U.K. residents and put the world on alert for other prion diseases transmitted from animals to people, including CWD. CWD is the most transmissible of the prion disease family, showing highly efficient transmission between cervids.

Historically, scientists have used mice, hamsters, squirrel monkeys and cynomolgus macaques to mimic prion diseases in people, sometimes monitoring animals for signs of CWD for more than a decade. In 2019, NIAID scientists at Rocky Mountain Laboratories in Hamilton, Montana, developed a human cerebral organoid model of Creutzfeldt-Jakob Disease to evaluate potential treatments and to study specific human prion diseases.

Human cerebral organoids are small spheres of human brain cells ranging in size from a poppy seed to a pea. Scientists grow organoids in dishes from human skin cells. The organization, structure, and electrical signaling of cerebral organoids are similar to brain tissue. They are currently the closest available laboratory model to the human brain. Because organoids can survive in a controlled environment for months, scientists use them to study nervous system diseases over time. Cerebral organoids have been used as models to study other diseases, such as Zika virus infection, Alzheimer’s disease, and Down syndrome.

In the new CWD study, the bulk of which was done in 2022 and 2023, the research team validated the study model by successfully infecting human cerebral organoids with human CJD prions (positive control). Then, using the same laboratory conditions, they directly exposed healthy human cerebral organoids for seven days with high concentrations of CWD prions from white-tailed deer, mule deer, elk, and normal brain matter (negative control). The researchers then observed the organoids for up to six months, and none became infected with CWD.

This indicates that even following direct exposure of human central nervous system tissues to CWD prions there is a substantial resistance or barrier to the propagation of infection, according to researchers. The authors acknowledge the limitations of their research, including the possibility that a small number of people may have genetic susceptibility that was not accounted for, and that emergence of new strains with a lesser barrier to infection remains possible. They are optimistic that the inference of these current data is that humans are extremely unlikely to contract a prion disease because of inadvertently eating CWD-infected cervid meat.

ARTICLES:
B Groveman and K Williams et al. Lack of Transmission of Chronic Wasting Disease Prions to Human Cerebral Organoids. Emerging Infectious Diseases DOI: 10.3201/eid3006.231568 (2024).

B Groveman and NC Ferreira et al. Human Cerebral Organoids as a Therapeutic Drug Screening Model for Creutzfeldt-Jakob Disease. Scientific Reports DOI: 10.1038/s41598-021-84689-6 (2021).

B Race et al. Lack of Transmission of Chronic Wasting Disease to Cynomolgus Macaques. Journal of Virology DOI: 10.1128/JVI.00550-18 (2018).

B Race et al. Susceptibilities of Nonhuman Primates to Chronic Wasting Disease. Emerging Infectious Diseases DOI: 10.3201/eid1509.090253 (2009).

NIAID conducts and supports research—at NIH, throughout the United States, and worldwide—to study the causes of infectious and immune-mediated diseases, and to develop better means of preventing, diagnosing and treating these illnesses. News releases, fact sheets and other NIAID-related materials are available on the NIAID website.

About the National Institutes of Health (NIH): NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit http://www.nih.gov/.

NIH...Turning Discovery Into Health®

The top frames show the validated study model, where CJD brain matter (in red) infected the organoid. The bottom frames show the uninfected organoid after exposure to infectious CWD matter.

CREDIT

NIAID