Forget Fracking, Let’s Blow Shit Up

still-gaslandThe Environmental Protection Agency and President Obama are making headlines today with the announcement of an initiative to slash coal pollution. The aim is to get each state to individually cut its current carbon dioxide emissions by 30 percent, with each state choosing how best to go about its business. You can be sure, though, that at least part of the cut would have to come from the coal-fired electrical plants that dot the black eyes of the American landscape.

You can also be sure that the whole thing will end up in court for several years and that the next President and congress could very likely repeal it before it sees the light of day. After all, no news is American news. But that’s neither here nor there.

With the coal industry once again in the news—as well as Canadian oil’s route through Nebraska in hot debate—it seems that hydraulic fracking isn’t getting nearly the amount of time on the 24-hour “news” channels that it should. I mean, I’ve almost gone consecutive bowel movements without hearing the term fracking, and America just can’t stand for that.

So I’m here to balance the equation and point out a recent study from Northwestern University that suggests we’re going about fracturing shale all wrong. We shouldn’t be using pressurized water. Oh no. Instead we should be blowing it up with an electric pulse arc.

An arc is basically what happens when a shit-ton of electricity jumps out of one wire and enters its nearby neighbor. The heat and electricity ionizes the gas between, creating a small space of plasma. Electric arcs get used in welding a lot, but on a much smaller scale than what would be needed to blow apart solid shale.

The ability of an electric pulse arc to blow apart shale sounds shaky to me, but I’m no expert. Zdenek P. Bazant sure sounds like a name that knows what its talking about when it comes to science, though, so I will defer to the physics outlined in the paper he wrote.

The idea is to use the kinetic energy of high-rate shearing generated by an underground explosion caused by an electric pulse arc to reduce the rock to small fragments. Since there’s no water being pumped underground, there’s little risk of contamination issues. But would it work?

Bazant has already shown that the basic idea works well in the laboratory with exploding concrete instead of shale. And he claims that the mathematics between the concrete and shale is similar, indicating that it’s at least a viable thought. But would it really work?

“This theory is not proven for fracturing shale—we don’t know whether it would work—but it is an idea that is worth investigating,” Bažant said. “An oil company or a national laboratory would need to conduct experiments and learn how to handle the practical issues.”

My money would be on a national laboratory. I’m pretty sure oil companies are far too busy spending their billions of dollars on lobbyists to keep the status quo and their money flowing in rather than looking for ways to fundamentally change everything they do in the name of the environment.

But I for one sure would like to see somebody do some follow up studies.

The paper published in the Proceedings of the National Academy of Sciences is titled “Comminution of solids caused by kinetic energy of high shear strain rate, with implications for impact, shock, and shale fracturing.” Bažant and Ferhun C. Caner are co-authors of the paper. -

Posted in Northwestern | Leave a comment

Screening for Autism: There’s an App for That

autismscreeningMost schools across the United States provide simple vision tests to their students–not to prescribe glasses, but to identify potential problems and recommend a trip to the optometrist. Researchers are now on the cusp of providing the same kind of service for autism.

Researchers at Duke University have developed software that tracks and records infants’ activity during videotaped autism screening tests. Their results show that the program is as good at spotting behavioral markers of autism as experts giving the test themselves, and better than non-expert medical clinicians and students in training.

The results appear online in the journal Autism Research and Treatment.

“We’re not trying to replace the experts,” said Jordan Hashemi, a graduate student in computer and electrical engineering at Duke. “We’re trying to transfer the knowledge of the relatively few autism experts available into classrooms and homes across the country. We want to give people tools they don’t currently have, because research has shown that early intervention can greatly impact the severity of the symptoms common in autism spectrum disorders.”

The study focused on three behavioral tests that can help identify autism in very young children.

In one test, an infant’s attention is drawn to a toy being shaken on the left side and then redirected to a toy being shaken on the right side. Clinicians count how long it takes for the child’s attention to shift in response to the changing stimulus. The second test passes a toy across the infant’s field of view and looks for any delay in the child tracking its motion. In the last test, a clinician rolls a ball to a child and looks for eye contact afterward — a sign of the child’s engagement with their play partner.

In all of the tests, the person administering them isn’t just controlling the stimulus, he or she is also counting how long it takes for the child to react — an imprecise science at best. The new program allows testers to forget about taking measurements while also providing more accuracy, recording reaction times down to tenths of a second.

“The great benefit of the video and software is for general practitioners who do not have the trained eye to look for subtle early warning signs of autism,” said Amy Esler, an assistant professor of pediatrics and autism researcher at the University of Minnesota, who participated in some of the trials highlighted in the paper.

Guillermo Sapiro

Guillermo Sapiro

“The software has the potential to automatically analyze a child’s eye gaze, walking patterns or motor behaviors for signs that are distinct from typical development,” Esler said. “These signs would signal to doctors that they need to refer a family to a specialist for a more detailed evaluation.”

According to Hashemi and his adviser, Guillermo Sapiro, professor of electrical and computer engineering at Duke, because the program is non-invasive, it could be useful immediately in homes and clinics. Neither, however, expects it to become widely used — not because clinicians, teachers and parents aren’t willing, but because the researchers are working on an even more practical solution.

Later this year, the Duke team (which includes students and faculty from engineering and psychiatry) plans to test a new tablet application that could do away with the need for a person to administer any tests at all. The program would watch for physical and facial responses to visual cues played on the screen, analyze the data and automatically report any potential red flags. Any parent, teacher or clinician would simply need to download the app and sit their child down in front of it for a few minutes.

The efforts are part of the Information Initiative at Duke, which connects researchers from disparate fields to experts in computer programming to help analyze large data sets.

“We’re currently working with autism experts at Duke Medicine to determine what sorts of easy tests could be used on just a computer or tablet screen to spot any potential concerns,” said Sapiro. “The goal is to mimic the same sorts of social interactions that the tests with the toys and balls measure, but without the toys and balls. The research has shown that the earlier autism can be spotted, the more beneficial intervention can be. And we want to provide everyone in the world with the ability to spot those signs as early as possible.”

This research was supported by the National Science Foundation (1039741, 1028076), CAPES (BEX 1018/11-6), and FAPESP (2011/01434-9) Ph.D. scholarships from Brazil and the U.S. Department of Defense.

###

“Computer vision tools for low-cost and non-invasive measurement of autism-related behaviors in infants,” Hashemi, J.; Tepper, M.; Spina, T.V.; Esler, A.; Morellas, V.; Papanikolopoulos, N.; Egger, H.; Dawson, G.; Sapiro, G. Autism Research and Treatment, 2014.

Posted in Duke | 1 Comment

Microchip-Like Technology Allows Single-Cell Analysis

lgthumb_singlecellassayA U.S. and Korean research team has developed a chip-like device that could be scaled up to sort and store hundreds of thousands of individual living cells in a matter of minutes. The system is similar to a random access memory chip, but it moves cells, rather than electrons.

Researchers at Duke University and Daegu Gyeongbuk Institute of Science and Technology (DGIST) in the Republic of Korea hope the cell-sorting system will revolutionize research by allowing the fast, efficient control and separation of individual cells that could then be studied in vast numbers.

“Most experiments grind up a bunch of cells and analyze genetic activity by averaging the population of an entire tissue rather than looking at the differences between single cells within that population,” said Benjamin Yellen, an associate professor of mechanical engineering and materials science at Duke’s Pratt School of Engineering. “That’s like taking the eye color of everyone in a room and finding that the average color is grey, when not a single person in the room has grey eyes. You need to be able to study individual cells to understand and appreciate small but significant differences in a similar population.”

The study appears May 14 online in Nature Communications.

Yellen and his collaborator, Cheol Gi Kim of DGIST, printed thin electromagnetic components onto a slide akin to those found on microchips. These patterns create magnetic tracks and elements like switches, transistors and diodes that guide magnetic beads and single cells tagged with magnetic nanoparticles through a thin liquid film.

Like a series of small conveyer belts, localized rotating magnetic fields move the beads and cells along specific directions etched into a track, while built-in switches direct traffic to storage sites on the chip. The result is an integrated circuit that controls small magnetic objects much like the way electrons are controlled on computer chips.

In the study, the engineers demonstrate a three-by-three grid of compartments that allow magnetic beads to enter but not leave. By tagging cells with magnetic particles and directing them to different compartments, the cells can be separated, sorted, stored, studied and retrieved.

Benjamin Yellen

Benjamin Yellen

In a random access memory chip, similar logic circuits manipulate electrons on a nanometer scale, controlling billions of compartments in a square inch. But cells are much larger than electrons, which would limit the new devices to hundreds of thousands of storage spaces per square inch.

But Yellen and Kim say that’s still plenty small for their purposes.

“You need to analyze thousands of cells to get the statistics necessary to understand which genes are being turned on and off in response to pharmaceuticals or other stimuli,” said Yellen. “And if you’re looking for cells exhibiting rare behavior, which might be one cell out of a thousand, then you need arrays that can control hundreds of thousands of cells.”

As an example, Yellen points to cells afflicted by HIV or cancer. In both diseases, most afflicted cells are active and can be targeted by therapeutics. A few rare cells, however, remain dormant, biding their time and avoiding destruction before activating and bringing the disease out of remission. With the new technology, the researchers hope to watch millions of individual cells, pick out the few that become dormant, quickly retrieve them and analyze their genetic activity.

“Maybe then we could find a way to target the dormant cells,” said Yellen.

Kim added, “Our technology can offer new tools to improve our basic understanding of cancer metastasis at the single cell level, how cancer cells respond to chemical and physical stimuli, and to test new concepts for gene delivery and metabolite transfer during cell division and growth.”

The researchers now plan to demonstrate a larger grid of 8×8 or 16×16 compartments with cells, and then to scale it up to hundreds of thousands of compartments. If successful, their technology would lend itself well to manufacturing, giving scientists around the world access to single-cell experimentation.

“Our idea is a simple one,” said Kim. “Because it is a system similar to electronics and is based on the same technology, it would be easy to fabricate. That makes the system relevant to commercialization.”

“There’s another technique paper we need to do as a follow-up before we get to actual biological applications,” added Yellen. “But they’re on their way.”

“Magnetophoretic circuits for digital control of single particles and cells,” Byeonghwa Lim, Venu Reddy, XingHao Hu, KunWoo Kim, Mital Jadhav, Roozbeh Abedini-Nassab, Young-Woock Noh, Yong Taik Lim, Benjamin B. Yellen, CheolGi Kim. Nature Communications, 2014. DOI: 10.1038/ncomms4846

Posted in Duke | Leave a comment

First Ever Analysis of Super-Earth Exoplanet Atmosphere Reveals… Clouds

An artist's rendering of GJ 1214b. Image courtesy NASA.

An artist’s rendering of GJ 1214b. Image courtesy NASA.

Back in 2009, astronomers discovered an exoplanet by the name of GJ 1214b orbiting a star some 40 light-years away, practically making it our neighbor in galactic terms. The planet orbits its star every 38 hours, which is part of the reason it was able to be discovered in the first place.

Planets orbiting other stars are spotted by carefully watching the amount of light reaching our telescopes. When a planet passes between us and the parent star, it blocks a little bit of the light, dimming the star’s appearance from our perspective. The faster the planet orbits, the more times it passes between us and its star, and the easier it is to detect its presence.

According to measurements, GJ 1214b was a super-Earth, meaning its size lies somewhere between that of Earth’s and Neptune’s, our solar systems next biggest planet after ours. That description is quite broad, however, seeing as how Neptune is 3.9 times bigger than Earth. And seeing as how no planets in our own solar system lie in that size range, scientists can only speculate what a super-Earth-sized planet is likely to look like.

Since the planet is in of an interesting size, not that far away and orbits its star so quickly, it was an excellent choice for further studies. Scientists took an even closer look at the planet by carefully analyzing the light reaching us after having passed through its atmosphere. Based on what bands of light make it through the atmosphere, researchers could guess what the atmosphere is made out of.

A size comparison of Earth, Neptune and GJ1214b.

A size comparison of Earth, Neptune and GJ1214b.

The preliminary results were inconclusive, most likely because there’s a crap-ton of clouds blocking our view. Naturally, this answer wasn’t precise enough, so we pointed Hubble at it.

The Hubble observations used 96 hours of telescope time spread over 11 months. This was the largest Hubble program ever devoted to studying a single exoplanet. And now the results are in.

The Hubble spectra revealed no chemical fingerprints whatsoever in the planet’s atmosphere. This allowed the astronomers to rule out cloud-free atmospheres made of water vapor, methane, nitrogen, carbon monoxide, or carbon dioxide. The best explanation for the new data is that there are high-altitude clouds in the atmosphere of the planet, though their composition is unknown. Models of super-Earth atmospheres predict clouds could be made out of potassium chloride or zinc sulfide at the scorching temperatures of 450 degrees Fahrenheit found on GJ 1214b.

“You would expect very different kinds of clouds to form than you would expect, say, on Earth,” said Laura Kriedberg, a graduate student at the University of Chicago and first author on the paper.

The launch of NASA’s next major space telescope, the 6.5 meter James Webb Space Telescope, later this decade should reveal more about such worlds, Kreidberg said. “Looking forward, JWST will be transformative,” she said. “The new capabilities of this telescope will allow us to peer through the clouds on planets like GJ 1214b. But more than that, it may open the door to studies of Earth-like planets around nearby stars.”

The study, “Clouds in the atmosphere of the super-Earth exoplanet GJ 1214b,” was published in Nature by Laura Kreidberg, Jacob L. Bean, Jean-Michel Désert, Björn Benneke, Drake Deming, Kevin B. Stevenson, Sara Seager, Zachory Berta-Thompson, Andreas Seifahrt, and Derek Homeier.

Posted in Chicago | Leave a comment

Transforming Ambulances to Trains to Repair the Brain

Imagine your brain as a giant system of metro rail lines with trains constantly zipping through. Now imagine an earthquake crumbles many of the lines; obviously we’re talking about some sort of brain damage here such as trauma or Alzheimer’s disease. In the real world, ambulances, fire trucks and eventually construction vehicles appear on the scene to clean up the mess and get the whole system back on track.

Your brain has analogous cells as well called glial cells that appear on the scene to repair damaged neurons. But now imagine that the entire emergency response system of New York shows up for damaged lines in Queens and then refuse to get out of the way once the job is done. Sure, the damage may be somewhat repaired, but the vehicles are blocking the paths.

This is sort of what happens with glial scarring. The glial cells that support healthy neurons build up on a damaged site and don’t let any more trains pass. But researchers at Penn State hope they have found a solution. They have demonstrated the ability to convert ambulances and police cars to rail trains, freeing up the transportation system once more.

The researchers accomplished this feat using genetic engineering techniques, introducing a retrovirus to glial cells to deliver a protein called NeuroD1, which is known to be important in the formation of nerve cells in the hippocampus area of adult brains. They hypothesized that expressing NeuroD1 protein into the reactive glial cells at the injury site might help to generate new neurons — just as it does in the hippocampus.

In one test, the team showed that the retrovirus could coax glial cells into becoming functional neural cells in adult mice. What’s more, they found that two types of glial cells can be converted into both excitatory and inhibitory neurons, which is important for proper brain function. While some neurons in your brain are excitatory, passing signals on to their neighbors, others are inhibitory, telling them to calm the hell down.

In a second test, the team showed that the same could be done in adult mouse models of Alzheimer’s disease, even when the mice were 14 months old, which is 60 in human years. “Therefore, the conversion technology that we have demonstrated in the brains of mice potentially may be used to regenerate functional neurons in people with Alzheimer’s disease,” said Gong Chen, a professor of biology, the Verne M. Willaman Chair in Life Sciences at Penn State, and the leader of the research team.

Finally, Chen and his colleagues showed that the same technique could work for human glial cells in a laboratory experiment. “Within 3 weeks after expression of the NeuroD1 protein, we saw in the microscope that human glial cells were reinventing themselves: they changed their shape from flat sheet-like glial cells into normal-looking neurons with axon and dendritic branches,” Chen said. The scientists further tested the function of these newly converted human neurons and found that, indeed, they were capable of both releasing and responding to neurotransmitters.

 

“Our dream is to develop this in vivo conversion method into a useful therapy to treat people suffering from neural injury or neurological disorders,” Chen said. “Our passionate motivation for this research is the idea that an Alzheimer’s patient, who for a long time was not able to remember things, could start to have new memories after regenerating new neurons as a result of our in vivo conversion method, and that a stroke victim who could not even move his legs might start to walk again.”

Of course, caveats abound for projects like this. Just because something works in a mouse model does not mean it will work in an actual human brain. And even if it does, the potential side effects are numerous. And even converting excess glial cells into active neural cells likely can’t repair all of the damage done by debilitating diseases.

Can transformed glial cells actually integrate into the existing neural network harmoniously? Can they even be transformed at all? This is just a first step, and most first steps lead to nowhere. But still, it’s a cool and exciting first step nonetheless.

The paper, “In Vivo Direct Reprogramming of Reactive Glial Cells into Functional Neurons after Brain Injury and in an Alzheimer’s Disease Model,” was published in the journal Cell by Chen and his colleagues Ziyuan Guo, Lei Zhang, Zheng Wu, Yuchen Chen, and Fan Wang, all from Penn State.

Posted in Penn State | Leave a comment

The Duck-Billed Platypus of the Plant World

Amborella

Amborella

Flowering plants are pretty important. Besides giving us a way to try to make amends for acting like less civilized versions of ourselves while in a state of extreme inebriation, they also provide the plants responsible for creating the opportunity to get to that inebriated state to begin with. That, and they pretty much provide all of the fruits and vegetables we consume on a daily basis. So yeah, you might say they’re pretty important.

Interestingly enough, the fossil record shows that flowering plants didn’t make an appearance on this planet until about 200 million years ago. But once they did, the proliferated extremely quickly, covering the globe and diversifying into the more than 300,000 species prospering today. That’s roses, corn, cherries, apples, dandelions – you name it.

new_caledoniaIn a recent issue of Science, researchers report on the genome sequencing of one of the more interesting lineages still alive and kicking. Amborella trichopoda is a shrub that grows in one place and one place only – the bustling metropolis that is New Caledonia. What makes Amborella interesting is that it split from the evolutionary tree of flowering plants not long after they appeared at all.

It’s sort of like the duck-billed platypus of the flowering kingdom. It’s still technically a flower, but it’s quite different from many of its distant cousins because of how long ago it branched away into a new evolutionary direction.

Reading the shrub’s DNA has given researchers a possible insight into how flowering plants evolved in the first place. They believe now that it all started with a gene-doubling event. In other words, a few of our flowers’ ancient ancestors accidentally and suddenly created cells with a whole lot of extra copies of genes. And that situation is exactly what you need for an explosion in evolution.

If you have a gene that codes for the chloroplasts that convert sunlight into energy and it gets horribly mutated, what happens? It breaks down and the plant dies. But what happens if there are two of those genes? Even if one is broken, the other can pick up the slack and keep the organism alive. That gives the genetic duplicates the freedom to mutate and change into weird and exciting new forms without putting the plant at risk. And eventually at least a few of those mutating genes will become something new and useful, like, for example, the pistols and pollen of a flowering plant.

Genome doubling may offer an explanation for the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period,” said Claude dePamphilis, professor of biology at Penn State, the overall principal investigator for the project, and the corresponding author for the paper. “Generations of scientists have worked to solve this puzzle, known as Darwin’s “abominable mystery.”

The paper, “The Amborella Genome and the Evolution of Flowering Plants,” was published in Science by dePamphilis and a whole host of other researchers from many other institutions, including Penn State University, the University at Buffalo, the University of Florida, the University of Georgia, and the University of California-Riverside.

Posted in Penn State | Leave a comment

Powering a Pacemaker with the Heart it Keeps in Rhythm

The implant contains a flexible piezoelectric film and a tiny rechargeable battery. (Credit: John Rogers, University of Illinois)

The implant contains a flexible piezoelectric film and a tiny rechargeable battery. (Credit: John Rogers, University of Illinois)

It’s beginning to become pretty apparent to me that Yonggang Huang of Northwestern University and John Rogers of the University of Illinois are two of the biggest science rock stars in the Big Ten. And when you put the two of them together in collaboration, amazing things will soon follow. The duo have a longstanding collaboration that researchers flexible electronics.

Take, for example, my post from 2011 about stick-on “tattoos” that are basically fully functioning, wireless computer chips just 40 micrometers thick that stick to human skin without any sort of adhesive. These could act as an EEG or EMG sensor to monitor nerve and muscle activity, or a sensor to monitor brain waves, sleeping patterns and other brain functions. Current methods require sticky gel pads to be placed all over the body with long, clunky wires attached to computers and power sources. But the new electronic tattoos have all of that built in. You could walk around all day, sleep on your sofa and go for a run without even noticing that you’re wearing medical devices.

Or there’s my post from 2012 on similarly thin electronic strips with all the wiring embedded that dissolve away completely in the presence of water. The possibilities are endless. Medical implants – sensors or thermal therapeutic devices, for example – could simply vanish once they are no longer needed. Environmental sensors could be deployed without the need to retrieve them ever. Hell, cell phones could disintegrate away into thin air once the next model gets released.

Or the post from 2013 on radically new camera lenses that integrate many cameras on a spherical surface much like a bug’s eye to create a wide field of vision. Again, flexible electronics that can conform to the shape of a sphere were integral to the project.

Well, they’re at it again, folks, this time with some piezoelectric magic.

Piezo comes from the Greek word for pressure, while electric means exactly what you think it is. So these materials are able to generate electricity through the pressures exerted on them and the deformations those pressures cause. There are a lot of projects out there trying to harness energy from wearable electronics embedded in your shoes or clothing, so that natural everyday movements could charge electronic devices.

But for their new project, Huang and Rogers went for something even more intrinsic to your everyday life – the beating of a human heart.

The duo have now demonstrated a thin-film, all-in-one electronic device that can adhere to the surface of a heart and generate electricity from its constant beating. Such a device could power pacemakers, defibrillators and heart-rate monitors naturally and reliably and reduce or eliminate the need for batteries.

You could see this sort of advance coming by looking at their previous work. Thin film electronics, biocompatible materials, adhesive films—it all adds up to implantable microdevices. In their study, the team attached their prototype to the hearts, lungs, and diaphragms of living animals and produced enough electricity to charge a 3.8-volt battery.

“This work is a great demonstration of engineers working with doctors and taking advantage of the natural properties of a beating heart,” Huang said. “We envision this device being used to power a pacemaker with the energy coming right from the heart.”

With a proof-of-concept in the bag, the pair are now working to optimize different design layouts of the stretchable mechanical energy harvester to facilitate its easy use. This is step one toward having everything mentioned above actually available in humans.

So stay tuned.

The paper, “Conformal piezoelectric energy harvesting and storage from motions of the heart, lung, and diaphragm,” was published in the Proceedings of the National Academy of Sciences by Huang and Rogers, and, of course, an entire slew of brilliant team members.

Posted in Illinois, Northwestern | Leave a comment