Amazing Science

Famous landmarks like the Arc Du Triumph, the Pyramids of Giza, and the Sagrada Familia have been photographed countless times by photographers from around the world.

First, according to Rice University engineers, get a nanotube hole. Then insert water. If the nanotube is just the right width, the water molecules will align into a square rod.

Molecular models of nanotube ice produced by engineers at Rice University show how forces inside a carbon nanotube at left and a boron nitride nanotube at right pressure water molecules into taking on the shape of a square tube. The phenomenon is dependent upon the diameter of the nanotube. Courtesy of the Multiscale Materials Laboratory

Rice materials scientist Rouzbeh Shahsavari and his team used molecular models to demonstrate their theory that weak van der Waals forces between the inner surface of the nanotube and the water molecules are strong enough to snap the oxygen and hydrogen atoms into place.

Shahsavari referred to the contents as two-dimensional “ice,” because the molecules freeze regardless of the temperature. He said the research provides valuable insight on ways to leverage atomic interactions between nanotubes and water molecules to fabricate nanochannels and energy-storing nanocapacitors.

A paper on the research appears in the American Chemical Society journal Langmuir.

Shahsavari and his colleagues built molecular models of carbon and boron nitride nanotubes with adjustable widths. They discovered boron nitride is best at constraining the shape of water when the nanotubes are 10.5 angstroms wide. The researchers already knew that hydrogen atoms in tightly confined water take on interesting structural properties. Recent experiments by other labs showed strong evidence for the formation of  nanotube ice and prompted the researchers to build density functional theory models to analyze the forces responsible.

Shahsavari’s team modeled water molecules, which are about 3 angstroms wide, inside carbon and boron nitride nanotubes of various chiralities (the angles of their atomic lattices) and between 8 and 12 angstroms in diameter. They discovered that nanotubes in the middle diameters had the most impact on the balance between molecular interactions and van der Waals pressure that prompted the transition from a square water tube to ice.

“If the nanotube is too small and you can only fit one water molecule, you can’t judge much,” Shahsavari said. “If it’s too large, the water keeps its amorphous shape. But at about 8 angstroms, the nanotubes’ van der Waals force starts to push water molecules into organized square shapes.” He said the strongest interactions were found in boron nitride nanotubes due to the particular polarization of their atoms.

Shahsavari said nanotube ice could find use in molecular machines or as nanoscale capillaries, or foster ways to deliver a few molecules of water or sequestered drugs to targeted cells, like a nanoscale syringe.

Previous research in animal shelters has determined the breeds of dogs living in shelters by their visual appearance. However the genetic breed testing of such dogs is seldom conducted, and few studies have compared the breed labels assigned by shelter staff to the results of this testing.

In the largest sampling of shelter dogs’ breed identities to-date, 459 dogs at Arizona Animal Welfare League & SPCA (AAWL) in Phoenix, Arizona, and 460 dogs at San Diego Humane Society & SPCA (SDHS) in San Diego, California, were genetically tested using a commercially available product to determine their breed heritage. In a recent sample, genetic analyses identified 125 distinct breeds with 91 breeds present at both shelters, and 4.9% of the dogs identified as purebreds. The three most common breed signatures, in order of prevalence, American Staffordshire Terrier, Chihuahua, and Poodle, accounted for 42.5% or all breed identifications at the great grandparent level.

During their stay at the shelter, dogs with pit bull-type ancestries waited longer to be adopted than other dogs. When researchers compared shelter breed assignment as determined by visual appearance to that of genetic testing, staff at SDHS was able to successfully match at least one breed in the genetic heritage of 67.7% of dogs tested; however their agreement fell to 10.4% when asked to identify more than one breed. Lastly, the scientists found that as the number of pit bull-type relatives in a dog’s heritage increased, so did the shelter’s ability to match the results of DNA analysis.

Studies by researchers at Uppsala University indicate that just one night of sleep loss can trigger tissue-specific epigenetic, gene expression, and metabolic changes that are associated with the loss of lean muscle mass and an increase in fat. The research, involving human volunteers who were allowed either a good night sleep or who were kept awake all night, hints at molecular mechanisms and disruption to the circadian clock that may underpin the previously identified link between chronic sleep loss, weight gain, metabolic syndrome, and type 2 diabetes.

"Our research group was the first to demonstrate that acute sleep loss in and of itself results in epigenetic changes in the so-called clock genes that within each tissue regulate its circadian rhythm,” comments Jonathan Cedernaes, Ph.D., a researcher at Uppsala University, department of neuroscience, who led the new study. “Our new findings indicate that sleep loss causes tissue-specific changes to the degree of DNA methylation in genes spread throughout the human genome. Our parallel analysis of both muscle and adipose tissue further enabled us to reveal that DNA methylation is not regulated similarly in these tissues in response to acute sleep loss.”

Dr. Cedernaes and colleagues at Uppsala University, Karolinska University, together with collaborators in Sweden. China, Germany, and the U.S., describe their work in Science Advances, in a paper titled, “Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans.”

Loss of sleep in humans has previously been linked with weight gain and loss of lean muscle mass (catabolism), and with an increased risk for diabetes and metabolic syndrome, the authors note. “Even minor weekly shifts in sleep timing, or as few as five consecutive nights of short sleep, have been associated with an increased risk of weight gain in healthy humans.” However, the underlying mechanisms aren’t well understood.

To try and identify the genetic and molecular basis of these observations, the Uppsala University-led team investigated epigenetic, gene expression, and metabolic changes in subcutaneous adipose tissue and skeletal muscle taken from healthy volunteers either after a good night’s sleep, or after a night of being kept awake. “… as a model of shift work that often entails overnight wakefulness, we hypothesized that acute sleep loss (that is, overnight wakefulness) would induce tissue-specific alterations at the genomic and physiological levels in pathways regulating metabolic substrate utilization and anabolic versus catabolic state,” they write.

Their analyses of adipose tissue in sleep-deprived individuals identified a number of differentially methylated regions (DMR)—either increased or decreased DNA methylation—in stretches of the genome that have been linked with altered lipid metabolism and DNA damage response pathways. Interestingly, one of the most hypermethylated DNA regions in adipose tissue of sleep-deprived participants was located near to the transcription start site (TSS) of a gene known as CD36, the expression of which is dysregulated in obese and type 2 diabetic patients.

In contrast, there were no specific DMRs in skeletal muscle following sleep loss, when compared with the sleep-allowed participants. “This finding could indicate that other epigenetic modifications—that may also respond to environmental changes (for example, at the chromatin level) regulate the transcriptional response to sleep loss in skeletal muscle or, alternatively, that DNA methylation changes occur at, for example, earlier or later time points in our intervention,” the authors write.

"It is interesting that we saw changes in DNA methylation only in adipose tissue, and specifically for genes that have also been shown to be altered at the DNA methylation level in metabolic conditions such as obesity and type 2 diabetes,” Dr. Cedernaes points out. “Epigenetic modifications are thought to be able to confer a sort of metabolic "memory" that can regulate how metabolic programs operate over longer time periods. We, therefore, think that the changes we have observed in our new study can constitute another piece of the puzzle of how chronic disruption of sleep and circadian rhythms may impact the risk of developing, for example, obesity.”

Further data from transcriptomic RNA sequencing of both adipose and skeletal muscle tissue showed that acute sleep loss changed the expression of 117 mRNA transcripts in skeletal muscle and 96 in subcutaneous adipose tissue. A comparison of the two tissue types indicated that many of the transcripts exhibited tissue-specific directionalities in response to sleep or no sleep. “In addition, almost no overlap was found between the two tissues for mRNA transcripts that were differentially expressed, further highlighting the tissue specificity of the response to acute sleep loss in human metabolic tissue,” the researchers note.

Further gene set enrichment analysis (GSEA) of skeletal muscle and adipose tissue samples from the sleep-allowed and sleep-deprived participants highlighted tissue-specific changes in metabolic genes that are also altered in prediabetic and diabetic patients, and changes to the transcription of inflammatory genes and genes that impact on insulin signaling.

Subsequent analysis of skeletal tissue samples using mass spectrometry indicated that acute sleep loss causes tissue-specific changes in cell respiration and anabolic/catabolic pathways, and there was a shift in glycolytic protein levels that correlated with altered systemic insulin sensitivity. The results from oral glucose tolerance tests (OGTT) showed that sleep-deprivation was associated with higher postprandial levels of glucose, but not insulin, and with 15% reduced insulin sensitivity.

An international team of researchers discovered a new species of dinosaur, Xiyunykus pengi, during an expedition to Xinjiang, China. The discovery is the latest stemming from a partnership between the George Washington University and the Chinese Academy of Sciences.

An international team of researchers discovered a new species of dinosaur, Xiyunykus pengi, during an expedition to Xinjiang, China. The discovery is the latest stemming from a partnership between the George Washington University and the Chinese Academy of Sciences. The findings were published today in Current Biology along with the description of a second new intermediate species, Bannykus wulatensis.

Xiyunykus and Bannykus are both alvarezsaurs, an enigmatic group of dinosaurs that share many characteristics with birds. Their bodies are slender, with a bird-like skull and many small teeth instead of the usual large, sharp cutting teeth of their meat-eating relatives.

“When we described the first well-known alvarezsaur, Mononykus, in 1993, we were amazed at the contrast between its mole-like arms and its roadrunner-like body, but there were few fossils connecting it back to other theropod groups,” James Clark, the Ronald Weintraub Professor of Biology at the GW Columbian College of Arts and Sciences, said.

However, alvarezsaurs did not always look this way. Early members of the group had relatively long arms with strong-clawed hands and typical meat-eating teeth. Over time, the alvarezsaurs evolved into dinosaurs with mole-like arms and a single claw. The discovery of the new specimens allowed the researchers to uncover an important shift in how the specialized features of the alvarezsaurs evolved.

"It can be hard to pin down the relationships of highly specialized animals. But fossil species with transitional features, like Xiyunykus and Bannykus, are tremendously helpful because they link bizarre anatomical features to more typical ones," Jonah Choiniere, an associate professor at Wits University and member of the research team, said.

New research boosts the case for quantum entanglement. Scientists have used distant quasars, one of which emitted its light 7.8 billion years ago and the other 12.2 billion years ago, to determine the measurements to be made on pairs of entangled photons. They found correlations among more than 30,000 pairs of photons -- far exceeding the limit for a classically based mechanism.

Last year, physicists at MIT, the University of Vienna, and elsewhere provided strong support for quantum entanglement, the seemingly far-out idea that two particles, no matter how distant from each other in space and time, can be inextricably linked, in a way that defies the rules of classical physics.

Take, for instance, two particles sitting on opposite edges of the universe. If they are truly entangled, then according to the theory of quantum mechanics their physical properties should be related in such a way that any measurement made on one particle should instantly convey information about any future measurement outcome of the other particle — correlations that Einstein skeptically saw as “spooky action at a distance.”

In the 1960s, the physicist John Bell calculated a theoretical limit beyond which such correlations must have a quantum, rather than a classical, explanation. But what if such correlations were the result not of quantum entanglement, but of some other hidden, classical explanation? Such “what-ifs” are known to physicists as loopholes to tests of Bell’s inequality, the most stubborn of which is the “freedom-of-choice” loophole: the possibility that some hidden, classical variable may influence the measurement that an experimenter chooses to perform on an entangled particle, making the outcome look quantumly correlated when in fact it isn’t.

Last February, the MIT team and their colleagues significantly constrained the freedom-of-choice loophole, by using 600-year-old starlight to decide what properties of two entangled photons to measure. Their experiment proved that, if a classical mechanism caused the correlations they observed, it would have to have been set in motion more than 600 years ago, before the stars’ light was first emitted and long before the actual experiment was even conceived.  

Now, in a paper published today in Physical Review Letters, the same team has vastly extended the case for quantum entanglement and further restricted the options for the freedom-of-choice loophole. The researchers used distant quasars, one of which emitted its light 7.8 billion years ago and the other 12.2 billion years ago, to determine the measurements to be made on pairs of entangled photons. They found correlations among more than 30,000 pairs of photons, to a degree that far exceeded the limit that Bell originally calculated for a classically based mechanism.

For the first time in decades, researchers have identified a new anatomical structure within the immune system – and they say it’s an important step towards understanding how to make better vaccines.

Chris Doe’s UO lab has mapped the neurons responsible for the insects' rapid direction changes. In the fruit fly, a single pair of brain neurons command backward locomotion in both larvae and adults, researchers report.

The mapping of descending circuitry that can smoothly and rapidly switch movement from forward to backward is unprecedented, said Chris Doe, a biology professor and co-director of the University of Oregon's Institute of Neuroscience. He was principal investigator on the project, detailed in a paper published Aug. 2, 2018 in the journal eLife.

Australia has seen an unprecedented number of widespread, catastrophic transformations in response to extreme weather events.

To the chagrin of the tourist industry, the Great Barrier Reef has become a notorious victim of climate change. But it is not the only Australian ecosystem on the brink of collapse. Research, recently published in Nature Climate Change, describes a series of sudden and catastrophic ecosystem shifts that have occurred recently across Australia. These changes, caused by the combined stress of gradual climate change and extreme weather events, are overwhelming ecosystems’ natural resilience.

Variable climate

Australia is one of the most climatically variable places in the world. It is filled with ecosystems adapted to this variability, whether that means living in scorching heat, bitter cold or a climate that cycles between the two. Despite land clearing, mining and other activities that transform the natural landscape, Australia retains large tracts of near-pristine natural systems.

Many of these regions are iconic, sustaining tourism and outdoor activities and providing valuable ecological services – particularly fisheries and water resources. Yet even here, the combined stress of gradual climate change and extreme weather events is causing environmental changes. These changes are often abrupt and potentially irreversible.

They include wildlife and plant population collapses, the local extinction of native species, the loss of ancient, highly diverse ecosystems and the creation of previously unseen ecological communities invaded by new plants and animals.

Australia’s average temperature (both air and sea) has increased by about 1°C since the start of the 19th century. We are now experiencing longer, more frequent and more intense heatwaves, more extreme fire weather and longer fire seasons, changes to rainfall seasonality, and droughts that may be historically unusual.

Crumble is a newly published NGS compression method by James Bonfield, Shane McCarthy, Richard Durbin of the Sanger Institute. Crumble provides size savings of 20-70% for BAM and CRAM files from HiSeq2500, HiSeqX, and NovaSeq Whole Genome Sequencing (WGS) and exomes. The resulting variant calls, showing generally similar results when using Crumble, even slightly improving variant-calling accuracy on the same sequencing data.

Among computational fields, genomics is especially data-heavy. For a 30x WGS sample, the size of the BAM file can easily exceed 100 GB. The collective size of genomics projects is growing at a tremendous rate. One highly cited work by Stephens et al. projects that, with current trends, the volume of NGS data in 2025 will exceed the data footprint of YouTube, Twitter, and astronomy. Most of the data footprint is in BAM files. In this format, the data footprint is divided between Read Names, the Sequence itself, Quality Values (QV) and Tags. The CRAM format uses lossless reference compression for the sequence, pushing the relative data footprint toward storing the quality values (see our Readshift blog for background on QV).

In an uncompressed (SAM) file, each quality value occupies a bin with a fixed amount of space. The BAM format compresses this data with a standard method similar to gzip. To simplify compression methods greatly, they identify recurring patterns within the data that can be used to pack elements together. More irregular data (data with higher entropy) is harder to compress.

This blog from Dropbox contains interesting examples on how compression methods can work. As Illumina has progressively increased instrument throughput, it has fought the growing friction in managing data footprint by decreasing the range of possible QV (HiSeq2500 – 40, HiSeqX – 8, NovaSeq – 4). The figure illustrate how packing a stream of QV pieces together is easier when there are fewer types of QVs and these types are more similar. These changes are generally synergistic with other advanced compression technologies such as Petagene.

Humans are clever, but without intending to, we have created massive sustainability problems for future generations. Fortunately, solutions to these global challenges are all around us.

Biomimicry is an approach to innovation that seeks sustainable solutions to human challenges by emulating nature’s time-tested patterns and strategies. The goal is to create products, processes, and policies—new ways of living—that are well-adapted to life on earth over the long haul.

The core idea is that nature has already solved many of the problems we are grappling with. Animals, plants, and microbes are the consummate engineers. After billions of years of research and development, failures are fossils, and what surrounds us is the secret to survival.

EMBL researchers visualize the proteins needed to capture molecules and bring them into a cell, during the process of endocytosis.

EMBL scientists have used super-resolution microscopy to see the protein machinery used by cells to ‘eat’ nutrients and other molecules. The research, published in Cell, clarifies how 23 of the most important proteins involved in this task organize and assemble themselves. EMBL group leader Jonas Ries led the research alongside collaborators Marko Kaksonen and François Nédélec.

Researchers imaged more than 100,000 sites on yeast cell membranes, where molecules are taken into the cell in a process known as endocytosis. They discovered that different proteins gather at the membrane in a precise set of ring shapes. These act as a template to recruit proteins known as actin to pull the membrane inwards and surround external molecules, ready to bring them inside the cell. Computer simulations allowed them to get a glimpse of how actin makes endocytosis so efficient. This information could also help researchers understand what happens on the cell surface when cells move or divide, both in yeast and human cells at the nanoscale level.

Anyone who still thinks blockchain’s encrypted ledger technology is just an account book for cryptocurrencies is in for a squirt of high-octane disruptive diesel in the eye. Its potential to decentralize businesses and organizations could be the biggest technology wave to crash since cloud computing infrastructure.

Erasing the middleman from all kinds of transactions could create a whole new peer-to-peer economy. There are beginning signs of it disrupting and decentralizing cloud and even making regular folks’ laptops and smartphones the world’s new compute providers.

Blockchain’s momentum is building palpably in Silicon Valley and beyond, and it won’t be long before it changes the game in many domains, according to Al Burgio (pictured, left), founder of the DigitalBits Project, Fusechain Inc. and Console Connect Inc. “It’s a matter of moments, not years,” he said. “If you’re not paying attention, you need to be paying attention, including if you’re in the cloud industry.”

Burgio and Matthew Roszak, co-founder of Bloq Inc., spoke with John Furrier, host of theCUBE, SiliconANGLE Media’s mobile livestreaming studio, during the Global Cloud and Blockchain Summit in Toronto last week. They discussed blockchain’s prime position to disrupt industries around the globe, regulatory speed bumps and the decentralization of cloud.  Enterprise customers of all sorts will soon be exploring what blockchain can do for their businesses and applications, Burgio pointed out. Along with consumers, they make up a rich vein of people who will be using blockchain technology. The question is: To whom will they turn?

Major cloud providers such as Amazon Web Services Inc. have partnerships with blockchain companies. And Microsoft Corp. just announced a simplified blockchain-as-a-service offering. But some might argue that these moves are too shallow and cursory to compete with blockchain startups obsessing day in and day out over the technology’s innards. 

“Today, the lightweight version is to say, ‘Yeah. I have a blockchain as a service strategy,’ and that’s like, ‘Well done’ and check the box,” Burgio said. “Now, the question is: How far in this new world will they go down?”

Blockchain startups decentralizing storage and compute resources are posing big, potentially threatening questions about the future of cloud computing. Will megarich, megapowerful cloud providers meet the challenge and swing the pendulum in their favor? Or will the decentralized, peer-to-peer revolution steamroll them into history? 

Currently, blockchain is not exactly the bread and butter of most companies. Just 1 percent of surveyed chief executive officers have adopted any blockchain technology in their organizations, and only 8 percent are entertaining short-term plans to do so, according to Gartner’s 2018 CIO Agenda Survey. “This year’s Gartner CIO Survey provides factual evidence about the massively hyped state of blockchain adoption and deployment,” said David Furlonger, vice president and Gartner fellow. “It is critical to understand what blockchain is and what it is capable of today compared to how it will transform companies, industries and society tomorrow.”

This may be because the technology is complicated, and the pool of people who get it is still somewhat limited. This does not mean that there aren’t people getting ridiculously rich from it and from the cryptocurrency market already. Bitmain Technologies Ltd. is the world’s biggest supplier of the virtual pickaxes workers use to mine bitcoin. This month, it nailed a $1 billion pre-IPO round of funding that valued the company at $14 billion. “And the amount of money they’ll raise will eclipse what Facebook raised,” Burgio said. 

The global blockchain technology market will reach $7.6 billion by 2024, according to a report from Grand View Research Inc. What must take place in the interim for blockchain to hit that number The ecosystem around blockchain will likely pour more efforts into simplifying and democratizing the technology, according to Burgio. Microsoft’s announcement is an important milestone that suggests blockchain is on the cusp of going mainstream.

Air pollution shortens human lives by more than a year, according to a new study led by engineers at UT Austin.

Air pollution shortens human lives by more than a year, according to a new study from a team of leading environmental engineers and public health researchers. Better air quality could lead to a significant extension of lifespans around the world. This is the first time that data on air pollution and lifespan has been studied together in order to examine the global variations in how they affect overall life expectancy.

The researchers looked at outdoor air pollution from particulate matter (PM) smaller than 2.5 microns. These fine particles can enter deep into the lungs, and breathing PM2.5 is associated with increased risk of heart attacks, strokes, respiratory diseases and cancer. PM2.5 pollution comes from power plants, cars and trucks, fires, agriculture and industrial emissions.

Led by Joshua Apte in the Cockrell School of Engineering at The University of Texas at Austin, the team used data from the Global Burden of Disease Study to measure PM2.5 air pollution exposure and its consequences in 185 countries. They then quantified the national impact on life expectancy for each individual country as well as on a global scale.

The findings were published Aug. 22, 2018 in Environmental Science & Technology Letters.

Scientists have shown that water is likely to be a major component of those exoplanets (planets orbiting other stars) which are between two to four times the size of Earth. It will have implications for the search of life in our Galaxy.

Scientists have shown that water is likely to be a major component of those exoplanets (planets orbiting other stars) which are between two to four times the size of Earth. It will have implications for the search of life in our Galaxy. The work is presented at the Goldschmidt conference in Boston.

The 1992 discovery of exoplanets orbiting other stars has sparked interest in understanding the composition of these planets to determine, among other goals, whether they are suitable for the development of life. Now a new evaluation of data from the exoplanet-hunting Kepler Space Telescope and the Gaia mission indicates that many of the known planets may contain as much as 50% water. This is much more than the Earth's 0.02% (by weight) water content.

"It was a huge surprise to realize that there must be so many water-worlds," said lead researcher Dr Li Zeng (Harvard University),

Physicists show first proof of Dicke cooperativity in a matter-matter system.

After their recent pioneering experiments to couple light and matter to an extreme degree, Rice University scientists decided to look for a similar effect in matter alone. They didn't expect to find it so soon.

Rice physicist Junichiro Kono, graduate student Xinwei Li and their international colleagues have discovered the first example of Dicke cooperativity in a matter-matter system, a result reported in Science just recently. The discovery could help advance the understanding of spintronics and quantum magnetism, Kono said. On the spintronics side, he said the work will lead to faster information processing with lower power consumption and will contribute to the development of spin-based quantum computing.

The team's findings on quantum magnetism will lead to a deeper understanding of the phases of matter induced by many-body interactions at the atomic scale. Instead of using light to trigger interactions in a quantum well, a system that produced new evidence of ultrastrong light-matter coupling earlier this year, the Kono lab at Rice used a magnetic field to prompt cooperativity among the spins within a crystalline compound made primarily of iron and erbium.

"This is an emerging subject in condensed matter physics," Kono said. "There's a long history in atomic and molecular physics of looking for the phenomenon of ultrastrong cooperative coupling. In our case, we'd already found a way to make light and condensed matter interact and hybridize, but what we're reporting here is more exotic."

Dicke cooperativity, named for physicist Robert Dicke, happens when incoming radiation causes a collection of atomic dipoles to couple, like gears in a motor that don't actually touch. Dicke's early work set the stage for the invention of lasers, the discovery of cosmic background radiation in the universe and the development of lock-in amplifiers used by scientists and engineers.

"Dicke was an unusually productive physicist," Kono said. "He had many high-impact papers and accomplishments in almost all areas of physics. The particular Dicke phenomenon that's relevant to our work is related to superradiance, which he introduced in 1954. The idea is that if you have a collection of atoms, or spins, they can work together in light-matter interaction to make spontaneous emission coherent. This was a very strange idea.

"When you stimulate many atoms within a small volume, one atom produces a photon that immediately interacts with another atom in the excited state," Kono said. "That atom produces another photon. Now you have coherent superposition of two photons. "This happens between every pair of atoms within the volume and produces macroscopic polarization that eventually leads to a burst of coherent light called superradiance," he said. Taking light out of the equation meant the Kono lab had to find another way to excite the material's dipoles, the compass-like magnetic force inherent in every atom, and prompt them to align. Because the lab is uniquely equipped for such experiments, when the test material showed up, Kono and Li were ready.

"The sample was provided by my colleague (and co-author) Shixun Cao at Shanghai University," Kono said. Characterization tests with a small or no magnetic field performed by another co-author, Dmitry Turchinovich of the University of Duisburg-Essen, drew little response. "But Dmitry is a good friend, and he knows we have a special experimental setup that combines terahertz spectroscopy, low temperatures and high magnetic field," Kono said. "He was curious to know what would happen if we did the measurements."

"Because we have some experience in this field, we got our initial data, identified some interesting details in it and thought there was something more we could explore in depth," Li added. "But we certainly didn't predict this," Kono said.

In the largest known brain imaging study, scientists from Amen Clinics (Costa Mesa, CA), Google, John's Hopkins University, University of California, Los Angeles and the University of California, San Francisco evaluated 62,454 brain SPECT (single photon emission computed tomography) scans of more than 30,000 individuals from 9 months old to 105 years of age to investigate factors that accelerate brain aging. SPECT tomography) evaluates regional cerebral blood flow in the brain that is reduced in various disorders.

Lead author, psychiatrist Daniel G. Amen, MD, founder of Amen Clinics, commented, "Based on one of the largest brain imaging studies ever done, we can now track common disorders and behaviors that prematurely age the brain. Better treatment of these disorders can slow or even halt the process of brain aging. The cannabis abuse finding was especially important, as our culture is starting to see marijuana as an innocuous substance. This study should give us pause about it."

The current study used brain SPECT imaging to determine aging trajectories in the brain and which common brain disorders predict abnormally accelerated aging. It examined these functional neuroimaging scans from a large multi-site psychiatric clinic from patients who had many different psychiatric disorders, including bipolar disorder, schizophrenia and attention deficit hyperactivity disorder (ADHD).

Researchers studied 128 brain regions to predict the chronological age of the patient. Older age predicted from the scan compared to the actual chronological age was interpreted as accelerated aging. The study found that a number of brain disorders and behaviors predicted accelerated aging, especially schizophrenia, which showed an average of 4 years of premature aging, cannabis abuse (2.8 years of accelerated aging), bipolar disorder (1.6 years accelerated aging), ADHD (1.4 years accelerated aging) and alcohol abuse (0.6 years accelerated aging). Interestingly, the researchers did not observe accelerated aging in depression and aging, which they hypothesize may be due to different types of brain patterns for these disorders.

Commenting on the study, George Perry, PhD, Chief Scientist at the Brain Health Consortium from the University of Texas at San Antonio, said, "This is one of the first population-based imaging studies, and these large studies are essential to answer how to maintain brain structure and function during aging. The effect of modifiable and non-modifiable factors of brain aging will further guide advice to maintain cognitive function."

Co-investigator Sachit Egan, Google Inc. (Mountain View, CA), said, "This paper represents an important step forward in our understanding of how the brain operates throughout the lifespan. The results indicate that we can predict an individual's age based on patterns of cerebral blood flow. Additionally, groundwork has been laid to further explore how common psychiatric disorders can influence healthy patterns of cerebral blood flow."

MIT researchers are employing novel machine-learning techniques to improve the quality of life for patients by reducing toxic chemotherapy and radiotherapy dosing for glioblastoma, the most aggressive form of brain cancer.

Glioblastoma is a malignant tumor that appears in the brain or spinal cord, and prognosis for adults is no more than five years. Patients must endure a combination of radiation therapy and multiple drugs taken every month. Medical professionals generally administer maximum safe drug doses to shrink the tumor as much as possible. But these strong pharmaceuticals still cause debilitating side effects in patients.

In a paper being presented next week at the 2018 Machine Learning for Healthcare conference at Stanford University, MIT Media Lab researchers detail a model that could make dosing regimens less toxic but still effective. Powered by a “self-learning” machine-learning technique, the model looks at treatment regimens currently in use, and iteratively adjusts the doses. Eventually, it finds an optimal treatment plan, with the lowest possible potency and frequency of doses that should still reduce tumor sizes to a degree comparable to that of traditional regimens.

In simulated trials of 50 patients, the machine-learning model designed treatment cycles that reduced the potency to a quarter or half of nearly all the doses while maintaining the same tumor-shrinking potential. Many times, it skipped doses altogether, scheduling administrations only twice a year instead of monthly.

“We kept the goal, where we have to help patients by reducing tumor sizes but, at the same time, we want to make sure the quality of life — the dosing toxicity — doesn’t lead to overwhelming sickness and harmful side effects,” says Pratik Shah, a principal investigator at the Media Lab who supervised this research.

The paper’s first author is Media Lab researcher Gregory Yauney.

Rewarding good choices

The researchers’ model uses a technique called reinforced learning (RL), a method inspired by behavioral psychology, in which a model learns to favor certain behavior that leads to a desired outcome. The technique comprises artificially intelligent “agents” that complete “actions” in an unpredictable, complex environment to reach a desired “outcome.” Whenever it completes an action, the agent receives a “reward” or “penalty,” depending on whether the action works toward the outcome. Then, the agent adjusts its actions accordingly to achieve that outcome.

Rewards and penalties are basically positive and negative numbers, say +1 or -1. Their values vary by the action taken, calculated by probability of succeeding or failing at the outcome, among other factors. The agent is essentially trying to numerically optimize all actions, based on reward and penalty values, to get to a maximum outcome score for a given task.

The approach was used to train the computer program DeepMind that in 2016 made headlines for beating one of the world’s best human players in the game “Go.” It’s also used to train driverless cars in maneuvers, such as merging into traffic or parking, where the vehicle will practice over and over, adjusting its course, until it gets it right.

The researchers adapted an RL model for glioblastoma treatments that use a combination of the drugs temozolomide (TMZ) and procarbazine, lomustine, and vincristine (PVC), administered over weeks or months.

Russian bots and trolls took to Twitter and other social media platforms to try to turn Americans against vaccines. But in addition to spreading false information and interfering in the election, a new study reports, a significant number of these malevolent actors tried to sow discord over vaccines.

An analysis of Twitter accounts previously identified as having been operated by Russian bots and trolls found they dove into the vaccine debate as early as January 2015, the researchers reported. They did not take one side or the other, but seemed to tweet pro-vaccine and anti-vaccine messages in roughly equal measure.

On a variety of issues, the overall aim of the Russian campaign appeared to be to erode social cohesion and generate confusion by amplifying the number of voices taking part in these debates on social media. But in the case of vaccines, that could have increased the misperception that the science on their safety and effectiveness isn’t settled — as is the case — but rather that it is still subject to debate.

“We do have a very strong suspicion that these accounts were attempting to generate discord,” said David Broniatowski, assistant professor in George Washington University’s department of engineering management and systems engineering and lead author of the study.

In the study, published Thursday in the American Journal of Public Health, Broniatowski and his co-authors focused on Twitter, analyzing tweets from accounts that had been identified as having been operated by Russian trolls, bots, and so-called content polluters whose aim is to disseminate spam and malware. The article is titled “Weaponized Health Communications: Twitter Bots and Russian Trolls Amplify the Vaccine Debate.”

The researchers compared tweets from the accounts to a selection of tweets from other users to see if the trolls and bots commented on vaccines more frequently than average Twitter accounts. They did.We found that, yeah, indeed, this was something that does seem to be part of the lexicon of what some of these bots and trolls use,” Broniatowski told STAT.

Even though the division of pro- and anti-vacccine tweets was roughly equal, that still skewed the picture of views on vaccines on Twitter, he noted, pointing to data from the Pew Trust that shows the vast majority of Americans support vaccination. “We’ve always been a little puzzled why social media looks like there are so many anti-vaxxers,” said Broniatowski. “So even if somebody’s posting 50-50, compared to the Pew data, there are going to be more anti-vaxxers.”

Dr. Amesh Adalja, an infectious diseases physician and senior scholar at the Center for Health Security at Johns Hopkins Bloomberg School of Public Health, said any skepticism about the safety of vaccines risks feeding the concerns of parents who are worried about having their children vaccinated. “The more the vaccine ‘debate’… is amplified it gains an undeserved sense of legitimacy and gives vaccine-hesitant individuals a pretense to forgo vaccination for themselves and their children,” said Adalja, who was harshly critical of the use of vaccinations in efforts to turn people against each other, calling it “overtly nihilistic.”

Other experts were unsurprised that Russian trolls and bots would delve into vaccines discussions, given the heat the topic can generate. “Vaccination links to deep values around protection, health, harm, and the social contract,” said Julie Leask, an associate professor at the University of Sydney’s Susan Wakil School of Nursing and Midwifery who researches vaccine refusal. “People become highly invested in the discussion, and highly reactive to the notion that people refuse vaccines. The expression of sentiment at the margins — very pro- and very anti-vaccine — generates emotional energy and clicks.”

Adam Dunn, an associate professor in the Center for Health Informatics at Australia’s Macquarie University, said responding to this type of activity by internet bots and trolls would be challenging for public health authorities and may rely on the rooting out of the malicious accounts.

A team led by researchers at St. Jude Children's Research Hospital has conducted an multi-faceted integrated analysis of rhabdomyosarcoma (RMS) samples, a relatively rare but deadly childhood cancer.  The strategy involved transcriptomic, epigenomic, proteomic, and phospho-proteomic data analysis, leading the authors of the study to conclude that a number of deregulated pathways could be addressed therapeutically. Based on further preclinical testing, the researchers also found the WEE1 kinase to be a promising target for treating high-risk RMS.

The study, which is part of the St. Jude-Washington University Pediatric Cancer Genomic Project and was led by senior author Michael Dyer, chair of the Department of Developmental Neurobiology at St. Jude's, was recently published in Cancer Cell.

"This research offers a template for exploring the origins and vulnerabilities of solid tumors by looking not only at somatic mutations, but also at epigenetic changes and ultimately differences in how those changes are manifest in protein expression and activity," Dyer said in a statement, adding that it "also highlights how preclinical models and extensive preclinical testing can help prioritize and streamline drug development."

Rhabdomyosarcoma is a relatively rare childhood solid tumor that involves muscle and soft tissue and affects about 350 patients in the US each year. While the cure rate is 75 percent for patients with localized tumors, survival is only 30 percent for patient with metastatic disease and just 17 percent for those with recurring disease. Survival numbers have not improved much in the last 15 years. The majority of RMS cases are embryonal (ERMS), while most others are of the alveolar (ARMS) type.

For their study, the researchers focused on 17 so-called orthotopic patient-derived xenografts (O-PDX) of pediatric solid tumors that had previously been studied at the genomic level, as well as on primary human myoblasts, myotubes, and fetal skeletal muscle samples. Specifically, they performed whole-genome bisulfite sequencing, RNA sequencing, and chromatin immunoprecipitation and sequencing (ChIP-seq).

In addition, they used 10-plex isobaric labeling mass spectrometry to quantify the proteome and phospho-proteome of 12 O-PDXs and several human myoblasts and myotubes in replicated experiments. In total, they analyzed more than 16,500 human proteins and almost 63,000 phosphorylation events on about 7,200 proteins.

They then analyzed the data across multiple platforms, using two approaches. In one, they looked at differentially expressed proteins and mRNAs in tumors and myoblasts and performed co-expression clustering of those genes and proteins that were conserved across the two platforms. For the other, they integrated transcriptomic, epigenomic, proteomic, and phospho-proteomic data with order statistics. Their analyses showed that the RAS pathway, the unfolded protein response pathway, and the G2/M-mitotic spindle checkpoint pathway were the most affected pathways in the RMS samples.

Through extensive preclinical testing, which involved screening more than 1,700 drug-tumor combinations, they found that AZD1775, which inhibits the WEE1 enzyme in the G2/M pathway, shows promise as a treatment for high-risk RMS. As a result, the Children's Oncology Group has expanded a multicenter phase I/II clinical trial of AZD1775 and the drug irinotecan to include high-risk rhabdomyosarcoma patients, according to St. Jude.