Dependable, detailed inundation estimates are vital for emergency managers to have enough situational awareness to quickly get the right resources and information to flood-impacted communities. In 2007, severe flooding in southeastern Kansas put a spotlight on the lack of timely, reliable projections for floodwater spread.

With heavy rains this spring (May 2019 was the wettest month ever recorded in Kansas), officials at the Kansas Water Office and Kansas Division of Emergency Management worked with Kastens, now a KU associate research professor with the Kansas Applied Remote Sensing Program at the Kansas Biological Survey, to get a more precise read on where floodwaters could rise to, based on his approach to integrating data from elevation maps, stream gauges and National Weather Service river stage forecasts.

“I worked with the Kansas Water Office in May,” Kastens said. “The ground was saturated, and the reservoirs were getting full, and with a lot more rain in the forecast, major flooding across central and eastern Kansas was looking imminent. Some years ago we’d developed this inundation library largely in collaboration with the Water Office and the Kansas GIS Policy Board but had never had the chance to put it through its paces in real time. It was based on the approach that I developed for my dissertation, and we had flood libraries for the greater eastern half of Kansas, based on the gauged stream network. For instance, if you drive south of Lawrence on Highway 59, you’ll see a USGS stream gauge box by the bridge over the Wakarusa River. There are about 200 gauges in Kansas that collect real-time stream stage information, and in times of flood, the National Weather Service provides stage forecasts several days out for a lot of these. We can take these data and map estimated current or future flooding, between gauges or around one.”

Kastens’ model (called FLDPLN, or “Floodplain”) maps potential inundation as a function of stage height using basic hydrologic principles and gridded elevation data. Because the approach requires so few inputs and little supervision, it has significant advantages for real-time mapping over existing methods such as the more precise but more complicated hydrodynamic models that FEMA uses to map 100-year floodplains.

Working with Kansas officials as historic rainfalls of 2019 threatened several areas of Kansas with flooding, mapping efforts were focused on three critical locations.

“We modeled the Neosho River south of John Redmond Reservoir in Coffey County down to Oklahoma, which is about a 100-mile stretch,” Kastens said. “We also modeled the Neosho and the Cottonwood rivers above John Redmond, centered around Emporia close to where those two rivers come together in Lyon County. The third area was around Salina, where flooding along the Saline River and Mulberry Creek was approaching historic levels.”

When John Redmond Reservoir just above Burlington on the Neosho River was nearly at capacity and the Army Corps of Engineers was planning the release of large volumes of water, Kastens’ efforts helped inform local leaders of the potential flooding extent — and they shared his flood maps with the public.

“Using projected discharge and stage information from the Corps, we modeled Neosho River flooding at Burlington and down through the rest of Coffey County,” Kastens said. “John Redmond was built by the Corps in the early 1960s to provide flood control along the Neosho, but the reservoir flood pool had reached capacity and needed to have some pressure released to avoid compromising the dam. With the Neosho already running high, city managers and commissioners had a lot of concern with how bad it was going to get because the Army Corps was going to have start releasing a very large quantity of water out of the reservoir. I made some maps using Corps projections supplied by the Kansas Water Office and also by the Coffey County GIS coordinator, Cara Mays. It helped greatly that Cara recently completed her master’s thesis at KU using the FLDPLN model to simulate the historic 1951 flood in Burlington, so she was well aware of its capabilities.”

Going forward, Kastens — who did a lot of this work during his free time in the evenings and weekends as a public service — hopes to automate the task of generating flood maps to lessen the workload when streams and rivers threaten to overspill their banks.

“With my other obligations at KBS, a lot of off-the-clock effort was needed to see this through,” he said. “Time is of the essence during major flood events. We need to develop software tools to help automate the mapping process and hand it off to these other agencies so they have the freedom to map whichever scenarios they want. I think our work in May demonstrated the value of our mapping approach, and hopefully we can pull together a project to help us move forward with the automation. So, when that next flood hits, emergency response personnel can just run the models as they see fit. That’s how we always envisioned this thing — we construct the inundation libraries for others to use during flood emergencies or simulations.”

Kastens’ novel approach to flood mapping has proven to be such an improvement, recently he’s worked with a private firm to commercialize the technology and provide services outside of Kansas to emergency management officials and entities with property in flood-prone areas.

“In 2015, we entered an agreement with Riverside Technology Inc. based in Fort Collins, Colorado, working through KU Center for Technology Commercialization to try to commercialize this stuff,” Kastens said. “They did their homework and market research and saw a real opportunity to develop inundation mapping solutions built around our flood libraries. Our contract with Riverside expires next year, so we will just have to see what happens after that. We made sure we carved out Kansas from the agreement, which allows us the freedom to provide direct assistance during flood events like we did in May.”

Kastens likens the projected inundation maps to predicted storm tracks or tornado watch or warning maps.

“They are never perfectly accurate, but then again neither are more sophisticated models. No two floods are the same, and a lot of resources are being expended in the public and private sectors to do what we are already capable of doing cheaply and efficiently right now here in Kansas.”

The Kansas Biological Survey, a KU Designated Research Center, was established at KU in 1911. It houses a diverse group of environmental research and remote sensing/GIS programs. The survey also manages the 3,700-acre KU Field Station, established in 1947; it offers sites for faculty and student study in the sciences, arts, humanities and professional schools.

In a new study published in the Journal of Burn Care & Research, a team of surgeons from the UNLV School of Medicine reviewed all pavement burn admissions into a Las Vegas area burn center over five years. The team compared the outdoor temperatures at the time of each patient admission to, in essence, determine how hot is too hot.

“Pavement burns account for a significant number of burn-related injuries, particularly in the Southwestern United States,” the study authors wrote. “The pavement can be significantly hotter than the ambient temperature in direct sunlight and can cause second-degree burns within two seconds.”

For the study, researchers identified 173 pavement-related burn cases between 2013 to 2017. Of those, 149 cases were isolated pavement burns and 24 involved other injuries, including those from motor vehicle accidents. More than 88 percent (153) of related incidents occurred when temps were 95 degrees or higher, with the risk increasing exponentially as temperatures exceeded 105 degrees.

That’s because pavement in direct sunlight absorbs radiant energy, making it significantly hotter and potentially dangerous. Study authors say that pavement on a 111-degree day, for example, can get as hot as 147 degrees in direct sunlight. For reference, a fried egg becomes firm at 158 degrees.

And while it seems like a no-brainer to stay off a hot sidewalk, for some it’s unavoidable — including victims of motor vehicle accidents, people with mobility issues or medical episodes who have fallen to the ground, or small children who may not know better.

The takeaway — summer in the desert is no joke, and more education is needed to warn people of the risks of hot pavement, particularly as temperatures creep above 100 degrees.

“This information is useful for burn centers in hotter climates, to plan and prepare for the coordination of care and treatment,” says study lead author Dr. Jorge Vega. “It can also be used for burn injury prevention and public health awareness, including increased awareness and additional training to emergency medical service and police personnel when attending to pavement burn victims in the field.”

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In their exploration of the evolutionary origins and history of RNA splicing and the human genome, UC San Diego biochemists Navtej Toor and Daniel Haack combined two-dimensional (2D) images of individual molecules to reconstruct a three-dimensional (3D) picture of a portion of RNA — what the scientists call group II introns. In so doing, they discovered a large-scale molecular movement associated with RNA catalysis that provides evidence for the origin of RNA splicing and its role in the diversity of life on Earth. Their breakthrough research is outlined in the current edition of Cell.

“We are trying to understand how the human genome has evolved starting from primitive ancestors. Every human gene has unwanted frames that are non-coding and must be removed before gene expression. This is the process of RNA splicing,” stated Toor, an associate professor in the Department of Chemistry and Biochemistry, adding that 15 percent of human diseases are the result of defects in this process.

Toor explained that his team works to understand the evolutionary origins of 70 percent of human DNA — a portion made up of two types of genetic elements, which are both thought to have evolved from group II introns. Specifically, spliceosomal introns, which make up about 25 percent of the human genome, are non-coding sequences that must be removed before gene expression. The other 45 percent is comprised of sequences derived from what are called retroelements. These are genetic elements that insert themselves into DNA and hop around the genome to replicate themselves via an RNA intermediate.

“Studying group II introns gives us insight into the evolution of a large portion of the human genome,” noted Toor.

Working with the group II intron RNA nanomachine, Toor and Haack, a postdoctoral scholar at UC San Diego and first author of the paper, were able to isolate the group II intron complexes from a species of blue-green algae that lives at high temperature.

“Using a group II intron from a high-temperature organism facilitated structure determination due to the innate stability of the complex from this species,” said Haack. “The evolution of this type of RNA splicing likely led to the diversification of life on Earth.”

Haack further explained that he and Toor discovered that the group II intron and the spliceosome share a common dynamic mechanism of moving their catalytic components during RNA splicing.

“This is the strongest evidence to date that the spliceosome evolved from a bacterial group II intron,” he said.

Additionally, the findings reveal how group II introns are able to insert themselves into DNA through a process called retrotransposition. This copy-and-paste process has resulted in selfish retroelements proliferating in human DNA to comprise a large portion of the genome.

“Replication of these retroelements has played a large role in shaping the architecture of the modern human genome and has even been implicated in the speciation of primates,” noted Toor.

The researchers used cryo-electron microscopy (cryo-EM) to extract a molecular structure of the group II intron. They froze the RNA in a layer of thin ice and then shot electrons through this sample. According to the scientists, the electron microscope can magnify the image 39,000 times. The resulting 2D images of individual molecules were then put together to come up with a 3D view of the group II intron.

“This is like molecular archaeology,” described Haack. “Group II introns are living fossils that give us a glimpse into how complex life first evolved on Earth.”

This research was supported by the National Institutes of Health (grants 1R01GM123275, 1R01GM033050, NIH DP5 OD021396 and U54GM103368).

The device, which is detailed July 24 in the journal Nature, could eventually lead to smaller, more efficient quantum computers that operate by manipulating sound rather than light.

“We expect this device to allow new types of quantum sensors, transducers and storage devices for future quantum machines,” said study leader Amir Safavi-Naeini, an assistant professor of applied physics at Stanford’s School of Humanities and Sciences.

Quantum of motion

First proposed by Albert Einstein in 1907, phonons are packets of vibrational energy emitted by jittery atoms. These indivisible packets, or quanta, of motion manifest as sound or heat, depending on their frequencies.

Like photons, which are the quantum carriers of light, phonons are quantized, meaning their vibrational energies are restricted to discrete values — similar to how a staircase is composed of distinct steps.

“Sound has this granularity that we don’t normally experience,” Safavi-Naeini said. “Sound, at the quantum level, crackles.”

The energy of a mechanical system can be represented as different “Fock” states — 0, 1, 2, and so on — based on the number of phonons it generates. For example, a “1 Fock state” consist of one phonon of a particular energy, a “2 Fock state” consists of two phonons with the same energy, and so on. Higher phonon states correspond to louder sounds.

Until now, scientists have been unable to measure phonon states in engineered structures directly because the energy differences between states — in the staircase analogy, the spacing between steps — is vanishingly small. “One phonon corresponds to an energy ten trillion trillion times smaller than the energy required to keep a lightbulb on for one second,” said graduate student Patricio Arrangoiz-Arriola, a co-first author of the study.

To address this issue, the Stanford team engineered the world’s most sensitive microphone — one that exploits quantum principles to eavesdrop on the whispers of atoms.

In an ordinary microphone, incoming sound waves jiggle an internal membrane, and this physical displacement is converted into a measurable voltage. This approach doesn’t work for detecting individual phonons because, according to the Heisenberg uncertainty principle, a quantum object’s position can’t be precisely known without changing it.

“If you tried to measure the number of phonons with a regular microphone, the act of measurement injects energy into the system that masks the very energy that you’re trying to measure,” Safavi-Naeini said.

Instead, the physicists devised a way to measure Fock states — and thus, the number of phonons — in sound waves directly. “Quantum mechanics tells us that position and momentum can’t be known precisely — but it says no such thing about energy,” Safavi-Naeini said. “Energy can be known with infinite precision.”

Singing qubits

The quantum microphone the group developed consists of a series of supercooled nanomechanical resonators, so small that they are visible only through an electron microscope. The resonators are coupled to a superconducting circuit that contains electron pairs that move around without resistance. The circuit forms a quantum bit, or qubit, that can exist in two states at once and has a natural frequency, which can be read electronically. When the mechanical resonators vibrate like a drumhead, they generate phonons in different states.

“The resonators are formed from periodic structures that act like mirrors for sound. By introducing a defect into these artificial lattices, we can trap the phonons in the middle of the structures,” Arrangoiz-Arriola said.

Like unruly inmates, the trapped phonons rattle the walls of their prisons, and these mechanical motions are conveyed to the qubit by ultra-thin wires. “The qubit’s sensitivity to displacement is especially strong when the frequencies of the qubit and the resonators are nearly the same,” said joint first-author Alex Wollack, also a graduate student at Stanford.

However, by detuning the system so that the qubit and the resonators vibrate at very different frequencies, the researchers weakened this mechanical connection and triggered a type of quantum interaction, known as a dispersive interaction, that directly links the qubit to the phonons.

This bond causes the frequency of the qubit to shift in proportion to the number of phonons in the resonators. By measuring the qubit’s changes in tune, the researchers could determine the quantized energy levels of the vibrating resonators — effectively resolving the phonons themselves.

“Different phonon energy levels appear as distinct peaks in the qubit spectrum,” Safavi-Naeini said. “These peaks correspond to Fock states of 0, 1, 2 and so on. These multiple peaks had never been seen before.”

Mechanical quantum mechanical

Mastering the ability to precisely generate and detect phonons could help pave the way for new kinds of quantum devices that are able to store and retrieve information encoded as particles of sound or that can convert seamlessly between optical and mechanical signals.

Such devices could conceivably be made more compact and efficient than quantum machines that use photons, since phonons are easier to manipulate and have wavelengths that are thousands of times smaller than light particles.

“Right now, people are using photons to encode these states. We want to use phonons, which brings with it a lot of advantages,” Safavi-Naeini said. “Our device is an important step toward making a ‘mechanical quantum mechanical’ computer.”

Other Stanford co-authors include graduate students Zhaoyou Wang, Wentao Jiang, Timothy McKenna and Jeremy Witmer, and postdoctoral researchers Marek Pechal and Raphël Van Laer.

The research was funded by the David and Lucile Packard Fellowship, the Stanford University Terman Fellowship and the U.S. Office of Naval Research.

A paper published in the journal Frontiers in Microbiology on — co-authored by researchers from Cornell University and the Mars Global Food Safety Center (GFSC), Beijing — illuminates breakthroughs.

“Salmonella is the foodborne pathogen with the biggest public health and economic impact globally. It’s one of the major causes of diarrhea all around the world,” said Martin Wiedmann, food safety professor and Cornell Institute for Food Systems faculty fellow. “Salmonella can be mild or it can cause death, as its severity depends on salmonella’s serotypes [distinct variations] — and that’s what we’re trying to find out.”

The paper describes how the food industry around the world should use molecular methods more often for subtyping and characterizing salmonella. The paper compared older subtyping practices — some practices going back to the 1930s — to the newer whole-genome sequencing, a method that can analyze a wider, more complete swath of the genome.

With this technique, scientists can more precisely identify a particular strain of salmonella and determine the origin and the path of the disease’s outbreak, Wiedmann said.

For example, in early July the U.S. Food and Drug Administration and the federal Centers for Disease Control and Prevention (CDC) used the technique, as they began investigating a suspected salmonella link between pig-ear dog treats and humans — due to people handling the treats. At the time, there were 45 cases of salmonella in 13 states, with 12 people hospitalized, according to the CDC.

“Whole-genome sequencing is rapidly becoming the method of choice for salmonella subtyping,” said microbiologist Silin Tang, the paper’s lead author and senior research scientist at the Mars Global Food Safety Center. “Foods often reach the consumer through increasingly complex supply chains, creating many opportunities where food safety could be compromised. Recent cases highlight the need to reinforce salmonella control measures in the food industry, including rapid and accurate tracking of contamination sources with appropriate subtyping tools.”

Tang said there is an opportunity for the food industry to create a talent pipeline of expertise in bioinformatics — the use of software tools to understand biological data — to harness the full potential of whole-genome sequencing technologies.

Further, Wiedmann said, this paper represents the translation of academic analysis into a useful industry application. “This will help industry implement better ways to proactively address the complications and complexity of salmonella,” he said.

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To meet the ever-increasing demands, low-cost and more efficient alternatives to silicon-based solar cells — currently the most widely used technology — are desirable. In the past decade, lead-halide perovskites have surged as the most promising class of alternative materials; however, they are unstable. They contain lead, which is toxic and poses potential health and environmental hazards such as groundwater contamination.

A team of engineers at Washington University in St. Louis has found what they believe is a more stable, less toxic semiconductor for solar applications using a novel double perovskite oxide discovered through data analytics and quantum-mechanical calculations.

Their work was published online June 11 in Chemistry of Materials.

Rohan Mishra, assistant professor of mechanical engineering & materials science in the McKelvey School of Engineering, led an interdisciplinary, international team that discovered the new semiconductor, made up of potassium, barium, tellurium, bismuth and oxygen (KBaTeBiO6). The lead-free double perovskite oxide was one of an initial 30,000 potential bismuth-based oxides. Of those 30,000, only about 25 were known compounds.

Using materials informatics and quantum mechanical calculations on one of the fastest supercomputers in the world, Arashdeep Singh Thind, a doctoral student in Mishra’s lab based at Oak Ridge National Laboratory, found KBaTeBiO6 to be the most promising out of the 30,000 potential oxides.

“We found that this looked to be the most stable compound and that it could be synthesized in the lab,” Mishra said. “More importantly, whereas most oxides tend to have a large band, we predicted the new compound to have a lower band gap, which is close to the halide perovskites, and to have reasonably good properties.”

The band gap is the energy barrier that electrons must overcome to form free carriers that, in the context of a solar cell, can be extracted to power an electrical device or stored in a battery for later use. The energy to overcome this barrier is provided by sunlight. The most promising compounds for solar cell applications have a band gap of about 1.5 eV, or electronvolt, Mishra said.

Mishra discussed the possibility of synthesizing KBaTeBiO6 with Pratim Biswas, assistant vice chancellor, the Lucy & Stanley Lopata Professor and chair of the Department of Energy, Environmental & Chemical Engineering. Shalinee Kavadiya, then a McKelvey Engineering doctoral student and now a postdoctoral research associate at Arizona State University, got to work on perfecting the recipe.

“Shalinee spent about six months synthesizing the material,” Mishra said. “Once she was able to synthesize it, as we had predicted, it was stable and had a band gap of 1.88 eV, which we also predicted.”

Mishra said these are first-generation solar cells that need more fine tuning of the band gap, but it is a good first step toward nontoxic solar cells.

“This shows that we can go away from these lead-halide perovskites,” Mishra said. “This opens up a really big space for designing semiconductors not just for solar cell applications but also for other semiconductor applications, such as LCD displays.”

Next, the team will study the role of any defects in this new semiconductor and look to more advanced synthesis techniques, including using aerosol techniques.

One condition that contributes to fainting and falls is atrial fibrillation. Atrial fibrillation occurs when the upper (atrial) part of your heart contracts rapidly and irregularly (fibrillates). Atrial fibrillation may be continuous or occasional and is the most common irregular heart rhythm in older adults. It occurs in three to five percent of people over age 65.

To prevent atrial fibrillation symptoms, health professionals may treat patients with medications to control their heart rate or rhythm. However, these medications can potentially raise the risk for falls and fainting, though the connection hasn’t studied significantly in the past.

To learn more, researchers in Denmark designed a study to learn more about the potential risk for falls and fainting among older adults taking medication for atrial fibrillation. Their study was published in the Journal of the American Geriatrics Society.

Using Danish health data, the researchers identified patients who were between the ages of 65 and 100 when they were first diagnosed with atrial fibrillation. The researchers examined the records of 100,935 atrial fibrillation patients 65 years or older who filled prescriptions for heart rhythm medications.

The researchers examined the medication the patients took to control their heart rhythms. Prescriptions were for beta-blockers, certain calcium channel blockers (diltiazem, verapamil), and digoxin. Other medications included amiodarone, flecainide, and propafenone.

Then the researchers looked for those patients who had emergency department visits or hospital admissions for fainting, fall-related injuries, or both. Fall-related injuries were defined as fractures of the thigh, elbow, forearm, wrist, shoulder or upper arm, pelvis, and skull, as well as major and minor head injuries.

The researchers followed the patients for about two and a half years. During the follow-up period:

• 17,132 (17 percent) had a fall-related injury
• 5,745 (5.7 percent) had a fainting episode
• 21,093 (20.9 percent) had either a fall-related or fainting-related injury

There were 40,447 deaths without a fall-related injury or fainting episode, which accounted for 40.1 percent of study participants.

The researchers reported that the medication amiodarone was significantly associated with increased risk, whether it was prescribed alone or with other heart rhythm drugs. The medication digoxin was slightly associated with fall-related injuries.

The researchers also learned that people were at higher risk for an injury within the first 90 days of treatment, and especially within the first 14 days of treatment.

“Our findings add evidence that, for older patients with atrial fibrillation, treatment with amiodarone is associated with a higher risk of fall-related injuries and fainting,” said the researchers. Additionally, the amiodarone connection was strongest within the first two weeks of the treatment but still present after long-term treatment.

The researchers concluded that being informed on the adverse risks of a given treatment is crucial to make shared decisions and provide quality patient care.

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“For the first time, we’ve found specific direct targets for LKB1 that prevent lung cancer and discovered — very unexpectedly — that inflammation plays a role in this tumor growth,” says Professor Reuben Shaw, director of the Salk Cancer Center and senior author of the paper. “With this knowledge we can hopefully develop new treatments for this large fraction of lung cancer patients.”

When functioning normally, LKB1 acts as a tumor suppressor, actively preventing cancer from forming in the first place. Scientists knew that the LKB1 gene worked like the captain of a relay team, passing cellular signals, like a baton, to enzymes called kinases, that then passed the signal to other enzymes in a chain reaction. LKB1 acts as the captain of a team consisting of 14 different kinase teammates. But which of these kinases is specifically responsible for carrying on LKB1’s tumor suppressive function has been unclear for the more than 15 years since LKB1 was first identified as a major gene disrupted in lung cancer. In 2018, the Shaw lab solved the first step of this molecular whodunnit by showing that 2 of the 14 teammates (the main enzymes known to control metabolism and growth) were surprisingly not as important to LKB1’s effects to block lung cancer as most scientists had assumed. That left 12 of their kinase teammates as potentially important, but almost nothing was known about them.

“This is was like a cancer detective case. We suspected that one of these 12 kinases was likely the key to the tumor suppressing effects of LKB1, but we were not sure which one,” says Pablo Hollstein, first author on the paper and a postdoctoral fellow at Salk.

To figure it out, the team used CRISPR technology combined with genetic analysis to inactivate each suspected kinase one at a time and then in combinations. They observed how the inactivations affected tumor growth and development in both cell cultures of NSCLC cells and in a genetic NSCLC mouse model. The experiments pointed the researchers to two kinases: one called SIK1 had the strongest effect in stopping tumors from forming. When SIK1 was inactivated, tumor growth increased; and when a related kinase, SIK3, was also inactivated, the tumor grew even more aggressively.

“Discovering that of the 14 kinases it was SIK1 and SIK3 that were the most critical players is like discovering that the relatively unknown backup quarterback who almost never plays is actually one of the most important quarterbacks in the history of the sport,” says Shaw.

LKB1 is also known to play a role in suppressing inflammation in cells generally, so the researchers were intrigued to discover that SIK1 and SIK3 were specifically inhibiting the cellular inflammation response in lung cancer cells. Thus, when LKB1 or SIK1 and SIK3 become mutated in tumors, inflammation is increased, driving tumor growth.

In a related vein, Salk Professor Marc Montminy recently published a paper along with Shaw, identifying metabolic switches to which SIK1 and SIK3 “pass the baton,” revealing three steps of the relay started by LKB1.

“By attacking the problem of lung cancer from different angles, we have now defined a single direct route that underpins how the disease develops in many patients,” says Shaw, who holds the William R. Brody Chair. “We have been working on this project since I started my lab in 2006, so it is incredibly rewarding and astonishing to find that inflammation is a driving force in tumor formation in this very clearly defined set of lung cancers. This discovery highlights the nature of scientific research and how important it is to commit to pursuing difficult, complicated problems, even if it takes over 10 years to get an answer.”

Next, the researchers plan to further investigate how these kinase-driven switches in inflammation trigger lung tumor growth in NSCLC.

The work was funded by the National Institutes of Health (R35CA220538 and P01CA120964), the Samuel Waxman Cancer Research Foundation, The Leona M. and Harry B. Helmsley Charitable Trust (grant #2012-PG-MED002) and the American Cancer Society (ACS#124183-PF-13-023-01-CSM and PF-15-037-01-DMC).

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