Tag Archives: University of Iowa

Chandra Sonifications (extraplanetary music and data sonification)

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I’m not sure why the astronomy community is so taken with creating music out of data but it seems to be the most active of the science communities in the field. This October 15. 2023 article by Elizabeth Hlavinka for Salon.com provides a little context before describing some of the latest work, Note: Links have been removed,

Christine Malec, who has been blind since birth, has always been a big astronomy buff, fascinated by major questions about the universe like what happens when a limit reaches infinity and whether things like space travel could one day become a reality. However, throughout her childhood, most astronomical information was only accessible to her via space documentaries or science fiction books.

Nearly a decade ago, Malec discovered a completely new way to experience astronomy when she saw astronomer and musician Matt Russo, Ph.D., give a presentation at a local planetarium in Toronto. Using a process called astronomical sonification, Russo had translated information collected from the TRAPPIST-1 solar system, which has seven planets locked in an orbital resonance, into something people who are blind or have low vision could experience: music. 

Russo’s song sent a wave of goosebumps through Malec’s body. Something she had previously understood intellectually but never had turned into a sensory experience was suddenly, profoundly felt.

“It was unforgettable,” Malec told Salon in a phone interview. “I compare it to what it might be like for a sighted person to look up at the night sky and get a sensory intuition of the size and nature of the cosmos. As a blind person, that’s an experience I hadn’t had.”

Through astronomical sonification, scientists map complex astronomical structures like black holes or exploded stars through the similarly expansive and multidimensional world of sound. Translating data from outer space into music not only expands access to astronomy for people who are blind or have low vision, but it also has the potential to help all scientists better understand the universe by leading to novel discoveries. Like images from the James Webb telescope that contextualize our tiny place in the universe, astronomical sonification similarly holds the power to connect listeners to the cosmos.

“It really does bring a connection that you don’t necessarily get when you’re just looking at a cluster of galaxies that’s billions of light years away from you that stretches across many hundreds of millions of light years,” said Kimberly Kowal Arcand, Ph.D., a data visualizer for NASA’s Chandra X-ray Observatory. “Having sound as a way of experiencing that type of phenomenon, that type of object, whatever it is, is a very valid way of experiencing the world around you and of making meaning.”

Malec serves as a consultant for Chandra Sonifications, which translates complex data from astronomical objects into sound. One of their most popular productions, which has been listened to millions of times, sonified a black hole in the Perseus cluster galaxy about 240 million light-years away. When presenting this sonification at this year’s [2023] SXSW festival in March, Russo, who works with Chandra through an organization he founded called SYSTEM Sounds, said this eerie sound used to depict the black hole had been likened to “millions of damned souls being sucked into the pits of hell.” 

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Here’s some of what the audience at the 2023 SXSW festival heard,

If you have the time , do read Hlavinka’s October 15. 2023 article as she tells a good story with many interesting tidbits such as this (Note: Links have been removed),

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William “Bill” Kurth, Ph.D., a space physicist at the University of Iowa, said the origins of astronomical sonification can be traced back to at least the 1970s when the Voyager-1 spacecraft recorded electromagnetic wave signals in space that were sent back down to his team on Earth, where they were processed as audio recordings.

Back in 1979, the team plotted the recordings on a frequency-time spectrogram similar to a voiceprint you see on apps that chart sounds like birds chirping, Kurth explained. The sounds emitted a “whistling” effect created by waves following the magnetic fields of the planet rather than going in straight lines. The data seemed to confirm what they had suspected: lightning was shocking through Jupiter’s atmosphere.

“At that time, the existence of lightning anywhere other than in Earth’s atmosphere was unknown,” Kurth told Salon in a phone interview. “This became the first time that we realized that lightning might exist on another planet.”

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And this (Note: Links have been removed),

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Beyond astronomy, sonification can be applied to any of the sciences, and health researchers are currently looking at tonifying DNA strands to better understand how proteins fold in multiple dimensions. Chandra is also working on constructing tactile 3-D models of astronomical phenomena, which also expands access for people who are blind or have low vision — those who have historically only been able to experience these sciences through words, Malec said.

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Chandra and other sonification projects

I found a brief and somewhat puzzling description of the Chandra sonification project on one of the of US National Aeronautics and Space Administration (NASA) websites. From a September 22, 2021 posting on the Marshall Science Research and Projects Division blog (Note: Links have been removed,)

On 9/16/21, a Chandra sonification image entitled “Jingle, Pluck, and Hum: Sounds from Space” was released to the public.  Since 2020, Chandra’s “sonification” project has transformed astronomical data from some of the world’s most powerful telescopes into sound.  Three new objects — a star-forming region, a supernova remnant, and a black hole at the center of a galaxy — are being released.  Each sonification has its own technique to translate the astronomical data into sound.

For more information visit: Data Sonifications: Westerlund 2 (Multiwavelength), Tycho’s Supernova Remnant, and M87. https://www.nasa.gov/missions_pages/chandra/main/index.html.

A Chandra article entitled “Data Sonification: Sounds from the Milky Way” was also released in the NASA STEM Newsletter.  This newsletter was sent to 54,951 subscribers and shared with the office of STEM engagements social media tools with approximately 1.7M followers. For more information visit: https://myemail.constantcontact.com/NASA-EXPRESS—-Your-STEM-Connection-for-Sept–9–2021.html?soid=1131598650811&aid=iXfzAJk6x_s

I’m a little puzzled by the reference to a Chandra sonification image but I’m assuming that they also produce data visualizations. Anyway, as Hlavinka notes Chandra is a NASA X-ray Observatory and they have a number of different projects/initiatives.

Getting back to data sonification, Chandra offers various audio files on its A Universe of Sound webpage,

Here’s a sampling of three data sonification posts (there are more) here,

Enjoy!

XSEDE: the most advanced, powerful integrated digital resources in the world and nanomaterials

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The University of Iowa does not jump to mind when considering powerhouse nanomaterial research; it seems that’s a mistake. An Oct. 19, 2016 news item on Nanowerk sets the record straight,

Chemists at the University of Iowa will research the effects of nanomaterials on the environment and human health using a network of supercomputers funded by the U.S. National Science Foundation.

Sara E. Mason, assistant professor in the Department of Chemistry, won an NSF award that grants her team access to the Extreme Science and Engineering Discovery Environment (XSEDE). The XSEDE project links computers, data, and people from around the world to establish a single, virtual system that scientists can interactively use to conduct research. It was started in 2011 and was renewed by the NSF last August.

The NSF says it “will be the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world.”

An Oct. 12, 2016 University of Iowa (UI) news release by Richard C. Lewis, which originated the news item, provides a little more detail,

The UI grant, valued at $72,503, essentially gives Mason’s team time on the supercomputer network, which they can access from their desktops. The researchers will use that time to study nanoparticles—matter far too small to be seen by the naked eye and present in a range of products, from sunscreen to advanced batteries for hybrid and electric vehicles.

The team hopes to better define the atom-to-atom interactions of various nanoparticles. Mason says the grant will “super charge” her computational research.

“To me, having four concurrent NSF research grants is a big deal, and now, having the boost of the computer time allows us to do even more,” Mason says. “XSEDE allows us to run simulations using quantum mechanics and highly parallelized computers. The outcome is new chemical insight into natural or widely used nanoparticles. We can then connect the chemistry to broader issues, such as human health and the behavior of nanomaterials in the environment.”

Mason’s group aims to find and design nanomaterials that are more benign to the environment and human health. Part of the search means trying out new elements in computational designs to find out how they interact, as well as their side effects, good or bad.

The XSEDE computers will give them far more computing horsepower to carry out those computational experiments.

“We can collectively get a lot more done in a shorter period of time,” says Joseph Bennett, co-principal investigator on the grant and a post-doctoral researcher in Mason’s group.

The UI is one of 15 institutions affiliated with the NSF-funded Center for Sustainable Nanotechnology, devoted to investigating the fundamental molecular mechanisms by which nanoparticles interact with biological systems.

I wish them good luck.

Center for Sustainable Nanotechnology or how not to poison and make the planet uninhabitable

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I received notice of the Center for Sustainable Nanotechnology’s newest deal with the US National Science Foundation in an August 31, 2015 email University of Wisconsin-Madison (UWM) news release,

The Center for Sustainable Nanotechnology, a multi-institutional research center based at the University of Wisconsin-Madison, has inked a new contract with the National Science Foundation (NSF) that will provide nearly $20 million in support over the next five years.

Directed by UW-Madison chemistry Professor Robert Hamers, the center focuses on the molecular mechanisms by which nanoparticles interact with biological systems.

Nanotechnology involves the use of materials at the smallest scale, including the manipulation of individual atoms and molecules. Products that use nanoscale materials range from beer bottles and car wax to solar cells and electric and hybrid car batteries. If you read your books on a Kindle, a semiconducting material manufactured at the nanoscale underpins the high-resolution screen.

While there are already hundreds of products that use nanomaterials in various ways, much remains unknown about how these modern materials and the tiny particles they are composed of interact with the environment and living things.

“The purpose of the center is to explore how we can make sure these nanotechnologies come to fruition with little or no environmental impact,” explains Hamers. “We’re looking at nanoparticles in emerging technologies.”

In addition to UW-Madison, scientists from UW-Milwaukee, the University of Minnesota, the University of Illinois, Northwestern University and the Pacific Northwest National Laboratory have been involved in the center’s first phase of research. Joining the center for the next five-year phase are Tuskegee University, Johns Hopkins University, the University of Iowa, Augsburg College, Georgia Tech and the University of Maryland, Baltimore County.

At UW-Madison, Hamers leads efforts in synthesis and molecular characterization of nanomaterials. soil science Professor Joel Pedersen and chemistry Professor Qiang Cui lead groups exploring the biological and computational aspects of how nanomaterials affect life.

Much remains to be learned about how nanoparticles affect the environment and the multitude of organisms – from bacteria to plants, animals and people – that may be exposed to them.

“Some of the big questions we’re asking are: How is this going to impact bacteria and other organisms in the environment? What do these particles do? How do they interact with organisms?” says Hamers.

For instance, bacteria, the vast majority of which are beneficial or benign organisms, tend to be “sticky” and nanoparticles might cling to the microorganisms and have unintended biological effects.

“There are many different mechanisms by which these particles can do things,” Hamers adds. “The challenge is we don’t know what these nanoparticles do if they’re released into the environment.”

To get at the challenge, Hamers and his UW-Madison colleagues are drilling down to investigate the molecular-level chemical and physical principles that dictate how nanoparticles interact with living things.
Pedersen’s group, for example, is studying the complexities of how nanoparticles interact with cells and, in particular, their surface membranes.

“To enter a cell, a nanoparticle has to interact with a membrane,” notes Pedersen. “The simplest thing that can happen is the particle sticks to the cell. But it might cause toxicity or make a hole in the membrane.”

Pedersen’s group can make model cell membranes in the lab using the same lipids and proteins that are the building blocks of nature’s cells. By exposing the lab-made membranes to nanomaterials now used commercially, Pedersen and his colleagues can see how the membrane-particle interaction unfolds at the molecular level – the scale necessary to begin to understand the biological effects of the particles.

Such studies, Hamers argues, promise a science-based understanding that can help ensure the technology leaves a minimal environmental footprint by identifying issues before they manifest themselves in the manufacturing, use or recycling of products that contain nanotechnology-inspired materials.

To help fulfill that part of the mission, the center has established working relationships with several companies to conduct research on materials in the very early stages of development.

“We’re taking a look-ahead view. We’re trying to get into the technological design cycle,” Hamers says. “The idea is to use scientific understanding to develop a predictive ability to guide technology and guide people who are designing and using these materials.”

What with this initiative and the LCnano Network at Arizona State University (my April 8, 2014 posting; scroll down about 50% of the way), it seems that environmental and health and safety studies of nanomaterials are kicking into a higher gear as commercialization efforts intensify.

US Dept. of Agriculture awards $3.8M for nanotechnology research grants

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I wonder just how much funding the US Dept. of Agriculture (USDA) is devoting to nanotechnology this year (2015). I first came across an announcement of $23M in the body of a news item about Zinkicide (my April 7, 2015 posting),

Found in Florida orchards in 2005, a citrus canker, citrus greening, poses a serious threat to the US state’s fruit industry. An April 2, 2105 news item on phys.org describes a possible solution to the problem,

Since it was discovered in South Florida in 2005, the plague of citrus greening has spread to nearly every grove in the state, stoking fears among growers that the $10.7 billion-a-year industry may someday disappear.

Now the U.S. Department of Agriculture has awarded the University of Florida a $4.6 million grant aimed at testing a potential new weapon in the fight against citrus greening: Zinkicide, a bactericide invented by a nanoparticle researcher at the University of Central Florida.

An April 29, 2015 article by Diego Flammini for Farm.com describes the latest USDA nanotechnology funding announcement,

In an effort to increase America’s food security, nutrition, food safety and environmental protection, the United States Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA) announced $3.8 million in nanotechnology research grants.

Flammini lists three of the eight recipients,

University of Georgia
With $496,192, the research team will develop different sensors that are able to detect fungal pathogens in crops. The project will also develop a smartphone app for farmers to have so they can access their information whenever necessary.

Rutgers University
The school will use its $450,000 to conduct a nationwide survey about nanotechnology and gauge consumer beliefs about it and its relationship to health. Among the specifics it will touch on is the use of visuals to communicate nanotechnology.

University of Massachusetts
The researchers will concentrate their $444,200 on developing a platform to detect pathogens in food that is better than the current methods.

A full list of the recipients can be found in the April 27, 2015 USDA news release featuring the $3.8M in awards,

  • The University of Georgia, Athens, Ga., $496,192
  • University of Iowa, Iowa City, Iowa., $496,180
  • University of Kentucky Research Foundation, Lexington, Ky., $450,000
  • University of Massachusetts, Amherst, Mass., $444,200
  • North Dakota State University, Fargo, N.D., $149,714
  • Rutgers University, New Brunswick. N.J., $450,000
  • Pennsylvania State University, University Park, University Park, Pa., $447,788
  • West Virginia University, Morgantown, W. Va., $496,168
  • University of Wisconsin-Madison, Madison, Wis., $450,100

You can find more details about the awards in this leaflet featuring the USDA project descriptions for the eight recipients.

A vaccine for dust-mite allergies

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I like the illustration which the University of Iowa has used to illustrate work on a nanscale vaccine for dust-mite allergies,

Dust mites are tiny and ubiquitous, but they cause big allergic reactions for many people. University of Iowa researchers have created a vaccine that may provide relief to dust-mite allergies. Illustration by Austin Smoldt-Sáenz. [downloaded from http://now.uiowa.edu/2014/06/researchers-create-vaccine-dust-mite-allergies?utm_source=News&utm_medium=dustmiteallergiesvacine&utm_campaign=UI%20Home%20Page]

Dust mites are tiny and ubiquitous, but they cause big allergic reactions for many people. University of Iowa researchers have created a vaccine that may provide relief to dust-mite allergies. Illustration by Austin Smoldt-Sáenz. [downloaded from http://now.uiowa.edu/2014/06/researchers-create-vaccine-dust-mite-allergies?utm_source=News&utm_medium=dustmiteallergiesvacine&utm_campaign=UI%20Home%20Page]

A July 23, 2014 news item on Azonano tells more about the vaccine,

If you’re allergic to dust mites (and chances are you are), help may be on the way.

Researchers at the University of Iowa have developed a vaccine that can combat dust-mite allergies by naturally switching the body’s immune response. In animal tests, the nano-sized vaccine package lowered lung inflammation by 83 percent despite repeated exposure to the allergens, according to the paper, published in the AAPS (American Association of Pharmaceutical Scientists) Journal. One big reason why it works, the researchers contend, is because the vaccine package contains a booster that alters the body’s inflammatory response to dust-mite allergens.

“What is new about this is we have developed a vaccine against dust-mite allergens that hasn’t been used before,” says Aliasger Salem, professor in pharmaceutical sciences at the UI and a corresponding author on the paper.

A July 22, 2014 University of Iowa news release by Richard C. Lewis provides information on dust mites and gives insight into the body’s immune responses and the proposed vaccine’s circumvention of those responses,

Dust mites are ubiquitous, microscopic buggers who burrow in mattresses, sofas, and other homey spots. They are found in 84 percent of households in the United States, according to a published, national survey. Preying on skin cells on the body, the mites trigger allergies and breathing difficulties among 45 percent of those who suffer from asthma, according to some studies. Prolonged exposure can cause lung damage.

Treatment is limited to getting temporary relief from inhalers or undergoing regular exposure to build up tolerance, which is long term and holds no guarantee of success.

“Our research explores a novel approach to treating mite allergy in which specially-encapsulated miniscule particles are administered with sequences of bacterial DNA that direct the immune system to suppress allergic immune responses,” says Peter Thorne, public health professor at the UI and a contributing author on the paper. “This work suggests a way forward to alleviate mite-induced asthma in allergy sufferers.”

The UI-developed vaccine takes advantage of the body’s natural inclination to defend itself against foreign bodies. A key to the formula lies in the use of an adjuvant—which boosts the potency of the vaccine—called CpG. The booster has been used successfully in cancer vaccines but never had been tested as a vaccine for dust-mite allergies. Put broadly, CpG sets off a fire alarm within the body, springing immune cells into action. Those immune cells absorb the CpG and dispose of it.

This is important, because as the immune cells absorb CpG, they’re also taking in the vaccine, which has been added to the package, much like your mother may have wrapped a bitter pill around something tasty to get you to swallow it. In another twist, combining the antigen (the vaccine) and CpG causes the body to change its immune response, producing antibodies that dampen the damaging health effects dust-mite allergens generally cause.

In lab tests, the CpG-antigen package, at 300 nanometers in size, was absorbed 90 percent of the time by immune cells, the UI-led team reports. The researchers followed up those experiments by giving the package to mice and exposing the animals to dust-mite allergens every other day for nine days total. In analyses conducted at the UI College of Public Health, packages with CpG yielded greater production of the desirable antibodies, while lung inflammation was lower than particles that did not contain CpG, the researchers report.

“This is exactly what we were hoping for,” says Salem, whose primary appointment is in the College of Pharmacy.

The researchers will continue to test the vaccine in the hope that it can eventually be used to treat patients.

I wonder what “eventually” means. Three to five years? Five to 10? In any event, here’s a link to and a citation for the paper,

Development of a Poly (lactic-co-glycolic acid) Particle Vaccine to Protect Against House Dust Mite Induced Allergy by Vijaya B. Joshi, Andrea Adamcakova-Dodd, Xuefang Jing, Amaraporn Wongrakpanich, Katherine N. Gibson-Corley, Peter S. Thorne, and Aliasger K. Salem. The AAPS Journal (Themed Issue: Nanoparticles in Vaccine Delivery) Pages: 1-11 DOI: 10.1208/s12248-014-9624-5 Published online July 1, 2014

This paper is behind a paywall.

I last mentioned Aliasger K. Salem in a Nov. 8, 2013 posting about bone bio-patches.

Bone bio-patches from the University of Iowa

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Let’s take a look at the bone patch developed at the University Iowa,

Researchers at the University of Iowa have created a bio patch to regenerate missing or damaged bone. The patch has been shown to nearly fully regrow missing skull, seen in the image above. Image courtesy of Satheesh Elangovan. & University of Iowa

Researchers at the University of Iowa have created a bio patch to regenerate missing or damaged bone. The patch has been shown to nearly fully regrow missing skull, seen in the image above. Image courtesy of Satheesh Elangovan. & University of Iowa

A Nov. 7, 2013 news item on Nanowerk provides information explaining the bone bio-patch,

Researchers at the University of Iowa have created a bio patch to regenerate missing or damaged bone by putting DNA into a nano-sized particle that delivers bone-producing instructions directly into cells.

The bone-regeneration kit relies on a collagen platform seeded with particles containing the genes needed for producing bone. In experiments, the gene-encoding bio patch successfully regrew bone fully enough to cover skull wounds in test animals. It also stimulated new growth in human bone marrow stromal cells in lab experiments.

The study is novel in that the researchers directly delivered bone-producing instructions (using piece of DNA that encodes for a platelet-derived growth factor called PDGF-B) to existing bone cells in vivo, allowing those cells to produce the proteins that led to more bone production. Previous attempts had relied on repeated applications from the outside, which is costly, intensive, and harder to replicate consistently.

The Nov. 6, 2013 University of Iowa news piece, which originated the news item and was written by Richard C. Lewis, provides some insight from the researchers (Note: Links have been removed),

“We delivered the DNA to the cells, so that the cells produce the protein and that’s how the protein is generated to enhance bone regeneration,” explains Aliasger Salem, professor in the College of Pharmacy and a co-corresponding author on the paper, published in the journal Biomaterials. ”If you deliver just the protein, you have keep delivering it with continuous injections to maintain the dose. With our method, you get local, sustained expression over a prolonged period of time without having to give continued doses of protein.”

The researchers believe the patch has several potential uses in dentistry. For instance, it could be used to rebuild bone in the gum area that serves as the concrete-like foundation for dental implants. That prospect would be a “life-changing experience” for patients who need implants and don’t have enough bone in the surrounding area, says Satheesh Elangovan, assistant professor in the UI’s College of Dentistry and a joint first author, as well as co-corresponding author, on the paper. It also can be used to repair birth defects where there’s missing bone around the head or face.

“We can make a scaffold in the actual shape and size of the defect site, and you’d get complete regeneration to match the shape of what should have been there,” Elangovan says.

The news article goes on to provide details about how the bio-patch was created,

The team started with a collagen scaffold. The researchers then loaded the bio patch with synthetically created plasmids, each of which is outfitted with the genetic instructions for producing bone. They then inserted the scaffold on to a 5-millimeter by 2-millimeter missing area of skull in test animals. Four weeks later, the team compared the bio patch’s effectiveness to inserting a scaffold with no plasmids or taking no action at all.

The plasmid-seeded bio patch grew 44-times more bone and soft tissue in the affected area than with the scaffold alone, and was 14-fold higher than the affected area with no manipulation. Aerial and cross-sectional scans showed the plasmid-encoded scaffolds had spurred enough new bone growth to nearly close the wound area, the researchers report.

The plasmid does its work by entering bone cells already in the body – usually those located right around the damaged area that wander over to the scaffold. The team used a polymer to shrink the particle’s size (like creating a zip file, for example) and to give the plasmid the positive electrical charge that would make it easier for the resident bone cells to take them in.

“The delivery mechanism is the scaffold loaded with the plasmid,” Salem says. “When cells migrate into the scaffold, they meet with the plasmid, they take up the plasmid, and they get the encoding to start producing PDGF-B, which enhances bone regeneration.”

The researchers also point out that their delivery system is nonviral. That means the plasmid is less likely to cause an undesired immune response and is easier to produce in mass quantities, which lowers the cost.

“The most exciting part to me is that we were able to develop an efficacious, nonviral-based gene-delivery system for treating bone loss,” says Sheetal D’mello, a graduate student in pharmacy and a joint first author on the paper.

Elangovan and Salem next hope to create a bio platform that promotes new blood vessel growth– needed for extended and sustained bone growth.

Here’s a link to and a citation for the published paper,

The enhancement of bone regeneration by gene activated matrix encoding for platelet derived growth factor by Satheesh Elangovan, Sheetal R. D’Mello, Liu Hong, Ryan D. Ross, Chantal Allamargot, Deborah V. Dawson, Clark M. Stanford, Georgia K. Johnson, D. Rick Sumnerd,& Aliasger K. Salem. Biomaterials Volume 35, Issue 2, January 2014, Pages 737–747 DOI: 10.1016/j.biomaterials.2013.10.021

This paper is behind a paywall.