The "Star-Spangled Banner" stirs pride. Ed Sheeran's "The Shape of You" sparks joy. And "ooh là là!" best sums up the seductive power of George Michael's "Careless Whispers."
Scientists at the University of California, Berkeley, have surveyed more than 2,500 people in the United States and China about their emotional responses to these and thousands of other songs from genres including rock, folk, jazz, classical, marching band, experimental and heavy metal.
The upshot? The subjective experience of music across cultures can be mapped within at least 13 overarching feelings: Amusement, joy, eroticism, beauty, relaxation, sadness, dreaminess, triumph, anxiety, scariness, annoyance, defiance, and feeling pumped up.
"Imagine organizing a massively eclectic music library by emotion and capturing the combination of feelings associated with each track. That's essentially what our study has done," said study lead author Alan Cowen, a UC Berkeley doctoral student in neuroscience.
The findings are set to appear this week in the journal Proceedings of the National Academy of Sciences.
"We have rigorously documented the largest array of emotions that are universally felt through the language of music," said study senior author Dacher Keltner, a UC Berkeley professor of psychology.
Cowen translated the data into an interactive audio map, where visitors can move their cursors to listen to any of thousands of music snippets to find out, among other things, if their emotional reactions match how people from different cultures respond to the music.
Potential applications for these research findings range from informing psychological and psychiatric therapies designed to evoke certain feelings to helping music streaming services like Spotify adjust their algorithms to satisfy their customers' audio cravings or set the mood.
While both U.S. and Chinese study participants identified similar emotions -- such as feeling fear hearing the "Jaws" movie score -- they differed on whether those emotions made them feel good or bad.
"People from different cultures can agree that a song is angry, but can differ on whether that feeling is positive or negative," said Cowen, noting that positive and negative values, known in psychology parlance as "valence," are more culture-specific.
Furthermore, across cultures, study participants mostly agreed on general emotional characterizations of musical sounds, such as angry, joyful and annoying. But their opinions varied on the level of "arousal," which refers in the study to the degree of calmness or stimulation evoked by a piece of music.
For the study, more than 2,500 people in the United States and China were recruited via Amazon Mechanical Turk's crowdsourcing platform.
First, volunteers scanned thousands of videos on YouTube for music evoking a variety of emotions. From those, the researchers built a collection of audio clips to use in their experiments.
Next, nearly 2,000 study participants in the United States and China each rated some 40 music samples based on 28 different categories of emotion, as well as on a scale of positivity and negativity, and for levels of arousal.
Using statistical analyses, the researchers arrived at 13 overall categories of experience that were preserved across cultures and found to correspond to specific feelings, such as being "depressing" or "dreamy."
To ensure the accuracy of these findings in a second experiment, nearly 1,000 people from the United States and China rated over 300 additional Western and traditional Chinese music samples that were specifically intended to evoke variations in valence and arousal. Their responses validated the 13 categories.
Vivaldi's "Four Seasons" made people feel energized. The Clash's "Rock the Casbah" pumped them up. Al Green's "Let's Stay Together" evoked sensuality and Israel Kamakawiwo?ole's "Somewhere over the Rainbow" elicited joy.
Meanwhile, heavy metal was widely viewed as defiant and, just as its composer intended, the shower scene score from the movie "Psycho" triggered fear.
Researchers acknowledge that some of these associations may be based on the context in which the study participants had previously heard a certain piece of music, such as in a movie or YouTube video. But this is less likely the case with traditional Chinese music, with which the findings were validated.
Cowen and Keltner previously conducted a study in which they identified 27 emotions in response to evocative YouTube video clips. For Cowen, who comes from a family of musicians, studying the emotional effects of music seemed like the next logical step.
"Music is a universal language, but we don't always pay enough attention to what it's saying and how it's being understood," Cowen said. "We wanted to take an important first step toward solving the mystery of how music can evoke so many nuanced emotions."
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Jan 7, 2020
Need to control blood sugar? There's a drink for that
With more people with diabetes and pre-diabetes looking for strategies to help control blood sugar, new research from UBC's Okanagan campus suggests that ketone monoester drinks -- a popular new food supplement -- may help do exactly that.
"There has been a lot of excitement and interest in ketone drinks and supplements, which have really only been on the market and available to consumers for the last couple of years," says Jonathan Little, associate professor at UBC Okanagan's School of Health and Exercise Sciences and study lead author. "Because they're so new, there's very little research on how they can influence metabolism and we're among the first to look at their use in non-athletes."
Little says that Type 2 diabetes is a disease whereby the body is unable to control the level of sugar in the blood because defects in the functioning of a hormone called insulin.
"It's a disease that's becoming alarmingly common in Canada and approaching what many would consider epidemic levels," he says. "While Type 2 diabetes can be controlled with medications or injectable insulin, many people are looking to options that don't require taking pills every day or that are less invasive."
Ketone supplements are proving fertile ground for research into Type 2 diabetes because, according to Little, ketones are the natural fuel source of the body when it's in ketosis -- the metabolic byproduct of consuming a low carbohydrate, ketogenic diet.
"There is mounting evidence that a low carbohydrate ketogenic diet is very effective in controlling blood sugar and even reversing Type 2 diabetes," says Little. "We wanted to know what would happen if artificial ketones were given to those with obesity and at risk for Type 2 diabetes but who haven't been dieting."
To test the idea, Little and his team asked 15 people to consume a ketone drink after fasting overnight. After 30 minutes, they were then asked to drink a fluid containing 75 grams of sugar while blood samples were taken.
"It turns out that the ketone drink seemed to launch participants into a sort of pseudo-ketogenic state where they were better able to control their blood sugar levels with no changes to their insulin," explains Little. "It demonstrates that these supplements may have real potential as a valuable tool for those with Type 2 diabetes."
Little is quick to point out that ketone supplements are not a magic bullet in managing the disease.
"There are a number of problems that we still have to work out, including the fact that we still don't know what the long-term effects of consuming ketones are," he says. "And not to mention that the drink itself tastes absolutely terrible."
Read more at Science Daily
"There has been a lot of excitement and interest in ketone drinks and supplements, which have really only been on the market and available to consumers for the last couple of years," says Jonathan Little, associate professor at UBC Okanagan's School of Health and Exercise Sciences and study lead author. "Because they're so new, there's very little research on how they can influence metabolism and we're among the first to look at their use in non-athletes."
Little says that Type 2 diabetes is a disease whereby the body is unable to control the level of sugar in the blood because defects in the functioning of a hormone called insulin.
"It's a disease that's becoming alarmingly common in Canada and approaching what many would consider epidemic levels," he says. "While Type 2 diabetes can be controlled with medications or injectable insulin, many people are looking to options that don't require taking pills every day or that are less invasive."
Ketone supplements are proving fertile ground for research into Type 2 diabetes because, according to Little, ketones are the natural fuel source of the body when it's in ketosis -- the metabolic byproduct of consuming a low carbohydrate, ketogenic diet.
"There is mounting evidence that a low carbohydrate ketogenic diet is very effective in controlling blood sugar and even reversing Type 2 diabetes," says Little. "We wanted to know what would happen if artificial ketones were given to those with obesity and at risk for Type 2 diabetes but who haven't been dieting."
To test the idea, Little and his team asked 15 people to consume a ketone drink after fasting overnight. After 30 minutes, they were then asked to drink a fluid containing 75 grams of sugar while blood samples were taken.
"It turns out that the ketone drink seemed to launch participants into a sort of pseudo-ketogenic state where they were better able to control their blood sugar levels with no changes to their insulin," explains Little. "It demonstrates that these supplements may have real potential as a valuable tool for those with Type 2 diabetes."
Little is quick to point out that ketone supplements are not a magic bullet in managing the disease.
"There are a number of problems that we still have to work out, including the fact that we still don't know what the long-term effects of consuming ketones are," he says. "And not to mention that the drink itself tastes absolutely terrible."
Read more at Science Daily
A fast radio burst tracked down to a nearby galaxy
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| Gemini telescopes, Mauna Kea, Hawaii. |
In results published in the January 9 edition of Nature, the European VLBI Network (EVN) used eight telescopes spanning locations from the United Kingdom to China to simultaneously observe the repeating radio source known as FRB 180916.J0158+65. Using a technique known as Very Long Baseline Interferometry (VLBI), the researchers achieved a level of resolution high enough to localize the FRB to a region approximately seven light years across -- a feat comparable to an individual on Earth being able to distinguish a person on the Moon.
A 'very different' location for an FRB
With that level of precision, the research team was able to train an optical telescope onto the location to learn more about the environment from which the burst emanated. What they found has added a new chapter to the mystery surrounding the origins of FRBs.
"We used the eight-metre Gemini North telescope in Hawaii to take sensitive images that showed the faint spiral arms of a Milky-Way-like galaxy and showed that the FRB source was in a star-forming region in one of those arms," said co-author Shriharsh Tendulkar, a former McGill University postdoctoral researcher who co-led the optical imaging and spectroscopic analyses of the FRB's location.
"This is a very different environment for a repeating FRB, compared to the dwarf galaxy in which the first repeating FRB 121102 was discovered to reside."
CHIME team's hypotheses in line with observed data
The discovery lined up with a number of ideas CHIME/FRB researchers had put forward following their initial detection of the burst in 2018.
"The FRB is among the closest yet seen and we even speculated that it could be a more conventional object in the outskirts of our own galaxy," said co-author Mohit Bhardwaj, a McGill University doctoral student and CHIME team member.
"However the EVN observation proved that it's in a relatively nearby galaxy, making it still a puzzling FRB, but close enough to now study using many other telescopes."
Zooming in on the radio sky
Since it began operation in the summer of 2018, CHIME has detected dozens of fast radio bursts, greatly accelerating the rate of discovery of these transient astrophysical phenomena. With over 1,000 antennas, CHIME's large field of view gives it a much greater chance of picking up fleeting bursts than conventional radio telescopes that are able to observe only a small area of the sky at a time.
When it came to pinpointing FRB 180916, the CHIME/FRB team worked closely with their EVN colleagues to determine exactly where to point the VLBI telescopes.
"By recording and processing the raw signal from each of the antenna elements that make up CHIME, we were able to refine the source position to a level close enough for EVN to successfully observe and localize multiple bursts from this FRB source," said co-author Daniele Michilli, a McGill University postdoctoral researcher and CHIME/FRB team member.
FRB's proximity opens the way for further study
At half-a-billion light years from Earth, the source of FRB 180916 is around seven times closer than the only other repeating burst to have been localized, and more than 10 times closer than any of the few non-repeating FRBs scientists have managed to pinpoint. That's exciting for astronomers because it will enable more detailed study that may help narrow down the possible explanations for FRBs.
"We have a new chance to perhaps detect emissions at other wavelengths -- x-ray or visible light, for instance," said McGill University astrophysicist Victoria Kaspi, a leading member of the CHIME/FRB collaboration. "And if we did, that would be hugely constraining of the models."
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NASA planet hunter finds Earth-size habitable-zone world
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| This illustration of TOI 700 d is based on several simulated environments for an ocean-covered version of the planet. |
TOI 700 d is one of only a few Earth-size planets discovered in a star's habitable zone so far. Others include several planets in the TRAPPIST-1 system and other worlds discovered by NASA's Kepler Space Telescope.
"TESS was designed and launched specifically to find Earth-sized planets orbiting nearby stars," said Paul Hertz, astrophysics division director at NASA Headquarters in Washington. "Planets around nearby stars are easiest to follow-up with larger telescopes in space and on Earth. Discovering TOI 700 d is a key science finding for TESS. Confirming the planet's size and habitable zone status with Spitzer is another win for Spitzer as it approaches the end of science operations this January."
TESS monitors large swaths of the sky, called sectors, for 27 days at a time. This long stare allows the satellite to track changes in stellar brightness caused by an orbiting planet crossing in front of its star from our perspective, an event called a transit.
TOI 700 is a small, cool M dwarf star located just over 100 light-years away in the southern constellation Dorado. It's roughly 40% of the Sun's mass and size and about half its surface temperature. The star appears in 11 of the 13 sectors TESS observed during the mission's first year, and scientists caught multiple transits by its three planets.
The star was originally misclassified in the TESS database as being more similar to our Sun, which meant the planets appeared larger and hotter than they really are. Several researchers, including Alton Spencer, a high school student working with members of the TESS team, identified the error.
"When we corrected the star's parameters, the sizes of its planets dropped, and we realized the outermost one was about the size of Earth and in the habitable zone," said Emily Gilbert, a graduate student at the University of Chicago. "Additionally, in 11 months of data we saw no flares from the star, which improves the chances TOI 700 d is habitable and makes it easier to model its atmospheric and surface conditions."
Gilbert and other researchers presented the findings at the 235th meeting of the American Astronomical Societyin Honolulu, and three papers -- one of which Gilbert led -- have been submitted to scientific journals.
The innermost planet, called TOI 700 b, is almost exactly Earth-size, is probably rocky and completes an orbit every 10 days. The middle planet, TOI 700 c, is 2.6 times larger than Earth -- between the sizes of Earth and Neptune -- orbits every 16 days and is likely a gas-dominated world. TOI 700 d, the outermost known planet in the system and the only one in the habitable zone, measures 20% larger than Earth, orbits every 37 days and receives from its star 86% of the energy that the Sun provides to Earth. All of the planets are thought to be tidally locked to their star, which means they rotate once per orbit so that one side is constantly bathed in daylight.
A team of scientists led by Joseph Rodriguez, an astronomer at the Center for Astrophysics | Harvard & Smithsonian in Cambridge, Massachusetts, requested follow-up observations with Spitzer to confirm TOI 700 d.
"Given the impact of this discovery -- that it is TESS's first habitable-zone Earth-size planet -- we really wanted our understanding of this system to be as concrete as possible," Rodriguez said. "Spitzer saw TOI 700 d transit exactly when we expected it to. It's a great addition to the legacy of a mission that helped confirm two of the TRAPPIST-1 planets and identify five more."
The Spitzer data increased scientists' confidence that TOI 700 d is a real planet and sharpened their measurements of its orbital period by 56% and its size by 38%. It also ruled out other possible astrophysical causes of the transit signal, such as the presence of a smaller, dimmer companion star in the system.
Rodriguez and his colleagues also used follow-up observations from a 1-meter ground-based telescope in the global Las Cumbres Observatory network to improve scientists' confidence in the orbital period and size of TOI 700 c by 30% and 36%, respectively.
Because TOI 700 is bright, nearby, and shows no sign of stellar flares, the system is a prime candidate for precise mass measurements by current ground-based observatories. These measurements could confirm scientists' estimates that the inner and outer planets are rocky and the middle planet is made of gas.
Future missions may be able to identify whether the planets have atmospheres and, if so, even determine their compositions.
While the exact conditions on TOI 700 d are unknown, scientists can use current information, like the planet's size and the type of star it orbits, to generate computer models and make predictions. Researchers at NASA's Goddard Space Flight Center in Greenbelt, Maryland, modeled 20 potential environments of TOI 700 d to gauge if any version would result in surface temperatures and pressures suitable for habitability.
Their 3D climate models examined a variety of surface types and atmospheric compositions typically associated with what scientists regard to be potentially habitable worlds. Because TOI 700 d is tidally locked to its star, the planet's cloud formations and wind patterns may be strikingly different from Earth's.
One simulation included an ocean-covered TOI 700 d with a dense, carbon-dioxide-dominated atmosphere similar to what scientists suspect surrounded Mars when it was young. The model atmosphere contains a deep layer of clouds on the star-facing side. Another model depicts TOI 700 d as a cloudless, all-land version of modern Earth, where winds flow away from the night side of the planet and converge on the point directly facing the star.
When starlight passes through a planet's atmosphere, it interacts with molecules like carbon dioxide and nitrogen to produce distinct signals, called spectral lines. The modeling team, led by Gabrielle Englemann-Suissa, a Universities Space Research Association visiting research assistant at Goddard, produced simulated spectra for the 20 modeled versions of TOI 700 d.
"Someday, when we have real spectra from TOI 700 d, we can backtrack, match them to the closest simulated spectrum, and then match that to a model," Englemann-Suissa said. "It's exciting because no matter what we find out about the planet, it's going to look completely different from what we have here on Earth."
TESS is a NASA Astrophysics Explorer mission led and operated by MIT in Cambridge, Massachusetts, and managed by NASA's Goddard Space Flight Center. Additional partners include Northrop Grumman, based in Falls Church, Virginia; NASA's Ames Research Center in California's Silicon Valley; the Harvard-Smithsonian Center for Astrophysics in Cambridge, Massachusetts; MIT's Lincoln Laboratory; and the Space Telescope Science Institute in Baltimore. More than a dozen universities, research institutes and observatories worldwide are participants in the mission.
The Jet Propulsion Laboratory in Pasadena, California, manages the Spitzer Space Telescope mission for NASA's Science Mission Directorate in Washington. Science operations are conducted at the Spitzer Science Center at Caltech in Pasadena. Space operations are based at Lockheed Martin Space in Littleton, Colorado. Data are archived at the Infrared Science Archive housed at IPAC at Caltech. Caltech manages JPL for NASA.
Read more at Science Daily
Jan 6, 2020
Astronomers find wandering massive black holes in dwarf galaxies
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| Artist's conception of a dwarf galaxy, its shape distorted, most likely by a past interaction with another galaxy, and a massive black hole in its outskirts (pullout). The black hole is drawing in material that forms a rotating disk and generates jets of material propelled outward. |
These dwarf galaxies, more than 100 times less massive than our own Milky Way, are among the smallest galaxies known to host massive black holes. The scientists expect that the black holes in these smaller galaxies average about 400,000 times the mass of our Sun.
"We hope that studying them and their galaxies will give us insights into how similar black holes in the early Universe formed and then grew, through galactic mergers over billions of years, producing the supermassive black holes we see in larger galaxies today, with masses of many millions or billions of times that of the Sun," said Amy Reines of Montana State University.
Reines and her colleagues used the National Science Foundation's Karl G. Jansky Very Large Array (VLA) to make the discovery, which they are reporting at the American Astronomical Society's meeting in Honolulu, Hawaii.
Reines and her collaborators used the VLA to discover the first massive black hole in a dwarf starburst galaxy in 2011. That discovery was a surprise to astronomers and spurred a radio search for more.
The scientists started by selecting a sample of galaxies from the NASA-Sloan Atlas, a catalog of galaxies made with visible-light telescopes. They chose galaxies with stars totalling less than 3 billion times the mass of the Sun, about equal to the Large Magellanic Cloud, a small companion of the Milky Way. From this sample, they picked candidates that also appeared in the National Radio Astronomy Observatory's Faint Images of the Radio Sky at Twenty centimeters (FIRST) survey, made between 1993 and 2011.
They then used the VLA to make new and more sensitive, high-resolution images of 111 of the selected galaxies.
"The new VLA observations revealed that 13 of these galaxies have strong evidence for a massive black hole that is actively consuming surrounding material. We were very surprised to find that, in roughly half of those 13 galaxies, the black hole is not at the center of the galaxy, unlike the case in larger galaxies," Reines said
The scientists said this indicates that the galaxies likely have merged with others earlier in their history. This is consistent with computer simulations predicting that roughly half of the massive black holes in dwarf galaxies will be found wandering in the outskirts of their galaxies.
"This work has taught us that we must broaden our searches for massive black holes in dwarf galaxies beyond their centers to get a more complete understanding of the population and learn what mechanisms helped form the first massive black holes in the early Universe," Reines said.
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Study finds dopamine, biological clock link to snacking, overeating and obesity
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| Clock and eating concept. |
Coinciding with this increase in weight are ever-rising rates of heart disease, diabetes, cancer and health complications caused by obesity, such as hypertension. Even Alzheimer's disease may be partly attributable to obesity and physical inactivity.
"The diet in the U.S. and other nations has changed dramatically in the last 50 years or so, with highly processed foods readily and cheaply available at any time of the day or night," Ali Güler, a professor of biology at the University of Virginia, said. "Many of these foods are high in sugars, carbohydrates and calories, which makes for an unhealthy diet when consumed regularly over many years."
In a study published Thursday in the journal Current Biology, Güler and his colleagues demonstrate that the pleasure center of the brain that produces the chemical dopamine, and the brain's separate biological clock that regulates daily physiological rhythms, are linked, and that high-calorie foods -- which bring pleasure -- disrupt normal feeding schedules, resulting in overconsumption. Using mice as study models, the researchers mimicked the 24/7 availability of a high-fat diet, and showed that anytime snacking eventually results in obesity and related health problems.
Güler's team found that mice fed a diet comparable to a wild diet in calories and fats maintained normal eating and exercise schedules and proper weight. But mice fed high-calorie diets laden with fats and sugars began "snacking" at all hours and became obese.
Additionally, so-called "knockout" mice that had their dopamine signaling disrupted -- meaning they didn't seek the rewarding pleasure of the high-fat diet -- maintained a normal eating schedule and did not become obese, even when presented with the 24/7 availability of high-calorie feeds.
"We've shown that dopamine signaling in the brain governs circadian biology and leads to consumption of energy-dense foods between meals and during odd hours," Güler said.
Other studies have shown, Güler said, that when mice feed on high-fat foods between meals or during what should be normal resting hours, the excess calories are stored as fat much more readily than the same number of calories consumed only during normal feeding periods. This eventually results in obesity and obesity-related diseases, such as diabetes.
Speaking of the modern human diet, Güler said, "The calories of a full meal may now be packed into a small volume, such as a brownie or a super-size soda. It is very easy for people to over-consume calories and gain excessive weight, often resulting in obesity and a lifetime of related health problems.
"Half of the diseases that affect humans are worsened by obesity. And this results in the need for more medical care and higher health care costs for individuals, and society."
Güler said the human body, through thousands of years of evolution, is hard-wired to consume as much food as possible as long as it's available. He said this comes from a long earlier history when people hunted or gathered food and had brief periods of plenty, such as after a kill, and then potentially lengthy periods of famine. Humans also were potential prey to large animals and so actively sought food during the day, and sheltered and rested at night.
"We evolved under pressures we no longer have," Güler said. "It is natural for our bodies as organisms to want to consume as much as possible, to store fat, because the body doesn't know when the next meal is coming.
"But, of course, food is now abundant, and our next meal is as close as the kitchen, or the nearest fast-food drive-through, or right here on our desk. Often, these foods are high in fats, sugars, and therefore calories, and that's why they taste good. It's easy to overconsume, and, over time, this takes a toll on our health."
Additionally, Güler said, prior to the advent of our electricity-powered society, people started the day at dawn, worked all day, often doing manual labor, and then went to sleep with the setting of the sun. Human activity, therefore, was synchronized to day and night. Today, we are working, playing, staying connected -- and eating -- day and night. This, Guler said, affects our body clocks, which were evolved to operate on a sleep-wake cycle timed to daytime activity, moderate eating and nighttime rest.
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Animal life thriving around Fukushima
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| Fukushima, Japan map. |
The camera study, published in the Journal of Frontiers in Ecology and the Environment, reports that over 267,000 wildlife photos recorded more than 20 species, including wild boar, Japanese hare, macaques, pheasant, fox and the raccoon dog -- a relative of the fox -- in various areas of the landscape.
UGA wildlife biologist James Beasley said speculation and questions have come from both the scientific community and the general public about the status of wildlife years after a nuclear accident like those in Chernobyl and Fukushima.
This recent study, in addition to the team's research in Chernobyl, provides answers to the questions.
"Our results represent the first evidence that numerous species of wildlife are now abundant throughout the Fukushima Evacuation Zone, despite the presence of radiological contamination," said Beasley, associate professor at the Savannah River Ecology Laboratory and the Warnell School of Forestry and Natural Resources.
Species that are often in conflict with humans, particularly wild boar, were predominantly captured on camera in human-evacuated areas or zones, according to Beasley.
"This suggests these species have increased in abundance following the evacuation of people."
The team, which included Thomas Hinton, professor at the Institute of Environmental Radioactivity at Fukushima University, identified three zones for the research.
Photographic data was gathered from 106 camera sites from three zones: humans excluded due to the highest level of contamination; humans restricted due to an intermediate level of contamination; and humans inhabited, an area where people have been allowed to remain due to "background" or very low levels of radiation found in the environment.
The researchers based their designations on zones previously established by the Japanese government after the 2011 Fukushima Daiichi accident.
For 120 days, cameras captured over 46,000 images of wild boar. Over 26,000 of those images were taken in the uninhabited area, compared to approximately 13,000 in the restricted and 7,000 in the inhabited zones.
Other species seen in higher numbers in the uninhabited or restricted zones included raccoons, Japanese marten and Japanese macaque or monkeys.
Anticipating questions about physiological condition of the wildlife, Hinton said their results are not an assessment of an animal's health.
"This research makes an important contribution because it examines radiological impacts to populations of wildlife, whereas most previous studies have looked for effects to individual animals," said Hinton.
The uninhabited zone served as the control zone for the research.
The scientists said although there is no previous data on wildlife populations in the evacuated areas, the close proximity and similar landscape of the human-inhabited zone made the area the ideal control for the study.
The team evaluated the impact of other variables: distance to road, time of activity as captured by the cameras' date-time stamps, vegetation type and elevation.
"The terrain varies from mountainous to coastal habitats, and we know these habitats support different types of species. To account for these factors, we incorporated habitat and landscape attributes such as elevation into our analysis," Beasley said.
"Based on these analyses, our results show that level of human activity, elevation and habitat type were the primary factors influencing the abundance of the species evaluated, rather than radiation levels."
The study's results indicate the activity pattern of most species aligned with their well-known history or behavior patterns. Raccoons, who are nocturnal, were more active during the night, while pheasants, which are diurnal animals, were more active during the day. However, wild boar inside the uninhabited area were more active during the day than boar in human-inhabited areas, suggesting they may be modifying their behavior in the absence of humans.
One exception to these patterns was the Japanese serow, a goat-like mammal. Normally far-removed from humans, they were most frequently seen on the camera footage in rural human-inhabited upland areas. The researchers suggest this might be a behavioral adjustment to avoid the rapidly growing boar population in the evacuated zone.
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Some genetic sequencing fail to analyze large segments of DNA
Children who undergo expansive genetic sequencing may not be getting the thorough DNA analysis their parents were expecting, say experts at UT Southwestern Medical Center.
A review of clinical tests from three major U.S. laboratories shows whole exome sequencing routinely fails to adequately analyze large segments of DNA, a potentially critical deficiency that can prevent doctors from accurately diagnosing potential genetic disorders, from epilepsy to cancer.
The reanalysis by UT Southwestern shows each lab on average adequately examined less than three-quarters of the genes -- 34, 66, and 69 percent coverage -- and had startlingly wide gaps in their ability to detect specific disorders.
Researchers say they conducted the study because they believe vast differences in testing quality are endemic in clinical genetic sequencing but have not been well documented or shared with clinicians.
"Many of the physicians who order these tests don't know this is happening," says Jason Park, M.D., Ph.D., associate professor of pathology at UT Southwestern. "Many of their patients are young kids with neurological disorders, and they want to get the most complete diagnostic test. But they don't realize whole exome sequencing may miss something that a more targeted genetic test would find."
Whole exome sequencing, a technique for analyzing protein-producing genes, is increasingly used in health care to identify genetic mutations that cause disease -- mostly in children but also in adults with rare or undiagnosed diseases. However, Park says the process of fully analyzing the approximately 18,000 genes in an exome is inherently difficult and prone to oversights. About half the tests do not pinpoint a mutation.
The new study published in Clinical Chemistry gives insight into why some analyses may be coming back negative.
Researchers re-analyzed 36 patients' exome tests conducted between 2012 and 2016 -- 12 from each of the three national clinical laboratories -- and found starkly contrasting results and inconsistency with which genes were completely analyzed. A gene was not considered completely analyzed unless the lab met an industry-accepted threshold for adequate analysis of all DNA that encodes protein, which is defined as sequencing that segment at least 20 times per test.
Notably, less than 1.5 percent of the genes were completely analyzed in all 36 samples. A review of one lab's tests showed 28 percent of the genes were never adequately examined and only 5 percent were always covered. Another lab consistently covered 27 percent of the genes.
"And things really start to fall apart when you start thinking about using these tests to rule out a disease," Park says. "A negative exome result is meaningless when so many of the genes are not thoroughly analyzed."
For example, the chances of detecting an epileptic disorder from any of the 36 tests varied widely depending on which genes were analyzed. One lab conducted several patient tests that fully examined more than three quarters of the genes associated with epilepsy, but the same lab had three other patient samples in which less than 40 percent were completely analyzed.
Three tests from another lab came in at under 20 percent.
"When we saw this data we made it a regular practice to ask the labs about coverage of specific genes," says Garrett Gotway, M.D., Ph.D., a clinical geneticist at UT Southwestern who is the corresponding author of the study. "I don't think you can expect complete coverage of 18,000 genes every time, but it's fair to expect 90 percent or more."
The findings build upon previous research that showed similar gaps and disparities in whole genome sequencing, a technique that examines all types of genes, regardless of whether they produce proteins.
Gotway says he hopes the findings will prompt more physicians to ask labs about which genes were covered and push for improved consistency in testing quality. He also encourages physicians -- even before ordering the test -- to consider whether whole exome sequencing is the best approach for the patient.
"Clinical exomes can be helpful in complex cases, but you probably don't need one if a kid has epilepsy and doesn't have other complicating clinical problems," Gotway says. "There's a decent chance the exome test will come back negative and the parents are still left wondering about the genetic basis for their child's disease."
Read more at Science Daily
A review of clinical tests from three major U.S. laboratories shows whole exome sequencing routinely fails to adequately analyze large segments of DNA, a potentially critical deficiency that can prevent doctors from accurately diagnosing potential genetic disorders, from epilepsy to cancer.
The reanalysis by UT Southwestern shows each lab on average adequately examined less than three-quarters of the genes -- 34, 66, and 69 percent coverage -- and had startlingly wide gaps in their ability to detect specific disorders.
Researchers say they conducted the study because they believe vast differences in testing quality are endemic in clinical genetic sequencing but have not been well documented or shared with clinicians.
"Many of the physicians who order these tests don't know this is happening," says Jason Park, M.D., Ph.D., associate professor of pathology at UT Southwestern. "Many of their patients are young kids with neurological disorders, and they want to get the most complete diagnostic test. But they don't realize whole exome sequencing may miss something that a more targeted genetic test would find."
Whole exome sequencing, a technique for analyzing protein-producing genes, is increasingly used in health care to identify genetic mutations that cause disease -- mostly in children but also in adults with rare or undiagnosed diseases. However, Park says the process of fully analyzing the approximately 18,000 genes in an exome is inherently difficult and prone to oversights. About half the tests do not pinpoint a mutation.
The new study published in Clinical Chemistry gives insight into why some analyses may be coming back negative.
Researchers re-analyzed 36 patients' exome tests conducted between 2012 and 2016 -- 12 from each of the three national clinical laboratories -- and found starkly contrasting results and inconsistency with which genes were completely analyzed. A gene was not considered completely analyzed unless the lab met an industry-accepted threshold for adequate analysis of all DNA that encodes protein, which is defined as sequencing that segment at least 20 times per test.
Notably, less than 1.5 percent of the genes were completely analyzed in all 36 samples. A review of one lab's tests showed 28 percent of the genes were never adequately examined and only 5 percent were always covered. Another lab consistently covered 27 percent of the genes.
"And things really start to fall apart when you start thinking about using these tests to rule out a disease," Park says. "A negative exome result is meaningless when so many of the genes are not thoroughly analyzed."
For example, the chances of detecting an epileptic disorder from any of the 36 tests varied widely depending on which genes were analyzed. One lab conducted several patient tests that fully examined more than three quarters of the genes associated with epilepsy, but the same lab had three other patient samples in which less than 40 percent were completely analyzed.
Three tests from another lab came in at under 20 percent.
"When we saw this data we made it a regular practice to ask the labs about coverage of specific genes," says Garrett Gotway, M.D., Ph.D., a clinical geneticist at UT Southwestern who is the corresponding author of the study. "I don't think you can expect complete coverage of 18,000 genes every time, but it's fair to expect 90 percent or more."
The findings build upon previous research that showed similar gaps and disparities in whole genome sequencing, a technique that examines all types of genes, regardless of whether they produce proteins.
Gotway says he hopes the findings will prompt more physicians to ask labs about which genes were covered and push for improved consistency in testing quality. He also encourages physicians -- even before ordering the test -- to consider whether whole exome sequencing is the best approach for the patient.
"Clinical exomes can be helpful in complex cases, but you probably don't need one if a kid has epilepsy and doesn't have other complicating clinical problems," Gotway says. "There's a decent chance the exome test will come back negative and the parents are still left wondering about the genetic basis for their child's disease."
Read more at Science Daily
Jan 5, 2020
Researchers learn more about teen-age T.Rex
Without a doubt, Tyrannosaurus rex is the most famous dinosaur in the world. The 40-foot-long predator with bone crushing teeth inside a five-foot long head are the stuff of legend. Now, a look within the bones of two mid-sized, immature T. rex allow scientists to learn about the tyrant king's terrible teens as well.
In the early 2000s, the fossil skeletons of two comparatively small T. rex were collected from Carter County, Montana, by Burpee Museum of Natural History in Rockford, Illinois. Nicknamed "Jane" and "Petey," the tyrannosaurs would have been slightly taller than a draft horse and twice as long.
The team led by Holly Woodward, Ph.D., from Oklahoma State University Center for Health Sciences studied Jane and Petey to better understand T. rex life history.
The study "Growing up Tyrannosaurus rex: histology refutes pygmy 'Nanotyrannus' and supports ontogenetic niche partitioning in juvenile Tyrannosaurus" appears in the peer-reviewed journal Science Advances.
Co-authors include Jack Horner, presidential fellow at Chapman University; Nathan Myhrvold, founder and CEO of Intellectual Ventures; Katie Tremaine, graduate student at Montana State University; Scott Williams, paleontology lab and field specialist at Museum of the Rockies; and Lindsay Zanno, division head of paleontology at the North Carolina Museum of Natural Sciences. Supplemental histological work was conducted at the Diane Gabriel Histology Labs at Museum of the Rockies/Montana State University.
"Historically, many museums would collect the biggest, most impressive fossils of a dinosaur species for display and ignore the others," said Woodward. "The problem is that those smaller fossils may be from younger animals. So, for a long while we've had large gaps in our understanding of how dinosaurs grew up, and T. rex is no exception."
The smaller size of Jane and Petey is what make them so incredibly important. Not only can scientists now study how the bones and proportions changed as T. rex matured, but they can also utilize paleohistology -- the study of fossil bone microstructure -- to learn about juvenile growth rates and ages. Woodward and her team removed thin slices from the leg bones of Jane and Petey and examined them at high magnification.
"To me, it's always amazing to find that if you have something like a huge fossilized dinosaur bone, it's fossilized on the microscopic level as well," Woodward said. "And by comparing these fossilized microstructures to similar features found in modern bone, we know they provide clues to metabolism, growth rate, and age."
The team determined that the small T. rex were growing as fast as modern-day warm-blooded animals such as mammals and birds. Woodward and her colleagues also found that by counting the annual rings within the bone, much like counting tree rings, Jane and Petey were teenaged T.rex when they died; 13 and 15 years old, respectively.
There had been speculation that the two small skeletons weren't T. rex at all, but a smaller pygmy relative Nanotyrannus. Study of the bones using histology led the researchers to the conclusion that the skeletons were juvenile T. rex and not a new pygmy species.
Instead, Woodward points out, because it took T. rex up to twenty years to reach adult size, the tyrant king probably underwent drastic changes as it matured. Juveniles such as Jane and Petey were fast, fleet footed, and had knife-like teeth for cutting, whereas adults were lumbering bone crushers. Not only that, but Woodward's team discovered that growing T. rex could do a neat trick: if its food source was scarce during a particular year, it just didn't grow as much. And if food was plentiful, it grew a lot.
"The spacing between annual growth rings record how much an individual grows from one year to the next. The spacing between the rings within Jane, Petey, and even older individuals is inconsistent -- some years the spacing is close together, and other years it's spread apart," said Woodward.
Read more at Science Daily
In the early 2000s, the fossil skeletons of two comparatively small T. rex were collected from Carter County, Montana, by Burpee Museum of Natural History in Rockford, Illinois. Nicknamed "Jane" and "Petey," the tyrannosaurs would have been slightly taller than a draft horse and twice as long.
The team led by Holly Woodward, Ph.D., from Oklahoma State University Center for Health Sciences studied Jane and Petey to better understand T. rex life history.
The study "Growing up Tyrannosaurus rex: histology refutes pygmy 'Nanotyrannus' and supports ontogenetic niche partitioning in juvenile Tyrannosaurus" appears in the peer-reviewed journal Science Advances.
Co-authors include Jack Horner, presidential fellow at Chapman University; Nathan Myhrvold, founder and CEO of Intellectual Ventures; Katie Tremaine, graduate student at Montana State University; Scott Williams, paleontology lab and field specialist at Museum of the Rockies; and Lindsay Zanno, division head of paleontology at the North Carolina Museum of Natural Sciences. Supplemental histological work was conducted at the Diane Gabriel Histology Labs at Museum of the Rockies/Montana State University.
"Historically, many museums would collect the biggest, most impressive fossils of a dinosaur species for display and ignore the others," said Woodward. "The problem is that those smaller fossils may be from younger animals. So, for a long while we've had large gaps in our understanding of how dinosaurs grew up, and T. rex is no exception."
The smaller size of Jane and Petey is what make them so incredibly important. Not only can scientists now study how the bones and proportions changed as T. rex matured, but they can also utilize paleohistology -- the study of fossil bone microstructure -- to learn about juvenile growth rates and ages. Woodward and her team removed thin slices from the leg bones of Jane and Petey and examined them at high magnification.
"To me, it's always amazing to find that if you have something like a huge fossilized dinosaur bone, it's fossilized on the microscopic level as well," Woodward said. "And by comparing these fossilized microstructures to similar features found in modern bone, we know they provide clues to metabolism, growth rate, and age."
The team determined that the small T. rex were growing as fast as modern-day warm-blooded animals such as mammals and birds. Woodward and her colleagues also found that by counting the annual rings within the bone, much like counting tree rings, Jane and Petey were teenaged T.rex when they died; 13 and 15 years old, respectively.
There had been speculation that the two small skeletons weren't T. rex at all, but a smaller pygmy relative Nanotyrannus. Study of the bones using histology led the researchers to the conclusion that the skeletons were juvenile T. rex and not a new pygmy species.
Instead, Woodward points out, because it took T. rex up to twenty years to reach adult size, the tyrant king probably underwent drastic changes as it matured. Juveniles such as Jane and Petey were fast, fleet footed, and had knife-like teeth for cutting, whereas adults were lumbering bone crushers. Not only that, but Woodward's team discovered that growing T. rex could do a neat trick: if its food source was scarce during a particular year, it just didn't grow as much. And if food was plentiful, it grew a lot.
"The spacing between annual growth rings record how much an individual grows from one year to the next. The spacing between the rings within Jane, Petey, and even older individuals is inconsistent -- some years the spacing is close together, and other years it's spread apart," said Woodward.
Read more at Science Daily
Researchers build a particle accelerator that fits on a chip
On a hillside above Stanford University, the SLAC National Accelerator Laboratory operates a scientific instrument nearly 2 miles long. In this giant accelerator, a stream of electrons flows through a vacuum pipe, as bursts of microwave radiation nudge the particles ever-faster forward until their velocity approaches the speed of light, creating a powerful beam that scientists from around the world use to probe the atomic and molecular structures of inorganic and biological materials.
Now, for the first time, scientists at Stanford and SLAC have created a silicon chip that can accelerate electrons -- albeit at a fraction of the velocity of that massive instrument -- using an infrared laser to deliver, in less than a hair's width, the sort of energy boost that takes microwaves many feet.
Writing in the Jan. 3 issue of Science, a team led by electrical engineer Jelena Vuckovic explained how they carved a nanoscale channel out of silicon, sealed it in a vacuum and sent electrons through this cavity while pulses of infrared light -- to which silicon is as transparent as glass is to visible light -- were transmitted by the channel walls to speed the electrons along.
The accelerator-on-a-chip demonstrated in Science is just a prototype, but Vuckovic said its design and fabrication techniques can be scaled up to deliver particle beams accelerated enough to perform cutting-edge experiments in chemistry, materials science and biological discovery that don't require the power of a massive accelerator.
"The largest accelerators are like powerful telescopes. There are only a few in the world and scientists must come to places like SLAC to use them," Vuckovic said. "We want to miniaturize accelerator technology in a way that makes it a more accessible research tool."
Team members liken their approach to the way that computing evolved from the mainframe to the smaller but still useful PC. Accelerator-on-a-chip technology could also lead to new cancer radiation therapies, said physicist Robert Byer, a co-author of the Science paper. Again, it's a matter of size. Today, medical X-ray machines fill a room and deliver a beam of radiation that's tough to focus on tumors, requiring patients to wear lead shields to minimize collateral damage.
"In this paper we begin to show how it might be possible to deliver electron beam radiation directly to a tumor, leaving healthy tissue unaffected," said Byer, who leads the Accelerator on a Chip International Program, or ACHIP, a broader effort of which this current research is a part.
Inverse design
In their paper, Vuckovic and graduate student Neil Sapra, the first author, explain how the team built a chip that fires pulses of infrared light through silicon to hit electrons at just the right moment, and just the right angle, to move them forward just a bit faster than before.
To accomplish this, they turned the design process upside down. In a traditional accelerator, like the one at SLAC, engineers generally draft a basic design, then run simulations to physically arrange the microwave bursts to deliver the greatest possible acceleration. But microwaves measure 4 inches from peak to trough, while infrared light has a wavelength one-tenth the width of a human hair. That difference explains why infrared light can accelerate electrons in such short distances compared to microwaves. But this also means that the chip's physical features must be 100,000 times smaller than the copper structures in a traditional accelerator. This demands a new approach to engineering based on silicon integrated photonics and lithography.
Vuckovic's team solved the problem using inverse design algorithms that her lab has developed. These algorithms allowed the researchers to work backward, by specifying how much light energy they wanted the chip to deliver, and tasking the software with suggesting how to build the right nanoscale structures required to bring the photons into proper contact with the flow of electrons.
"Sometimes, inverse designs can produce solutions that a human engineer might not have thought of," said R. Joel England, a SLAC staff scientist and co-author on the Science paper.
The design algorithm came up with a chip layout that seems almost otherworldly. Imagine nanoscale mesas, separated by a channel, etched out of silicon. Electrons flowing through the channel run a gantlet of silicon wires, poking through the canyon wall at strategic locations. Each time the laser pulses -- which it does 100,000 times a second -- a burst of photons hits a bunch of electrons, accelerating them forward. All of this occurs in less than a hair's width, on the surface of a vacuum-sealed silicon chip, made by team members at Stanford.
The researchers want to accelerate electrons to 94 percent of the speed of light, or 1 million electron volts (1MeV), to create a particle flow powerful enough for research or medical purposes. This prototype chip provides only a single stage of acceleration, and the electron flow would have to pass through around 1,000 of these stages to achieve 1MeV. But that's not as daunting at it may seem, said Vuckovic, because this prototype accelerator-on-a-chip is a fully integrated circuit. That means all of the critical functions needed to create acceleration are built right into the chip, and increasing its capabilities should be reasonably straightforward.
The researchers plan to pack a thousand stages of acceleration into roughly an inch of chip space by the end of 2020 to reach their 1MeV target. Although that would be an important milestone, such a device would still pale in power alongside the capabilities of the SLAC research accelerator, which can generate energy levels 30,000 times greater than 1MeV. But Byer believes that, just as transistors eventually replaced vacuum tubes in electronics, light-based devices will one day challenge the capabilities of microwave-driven accelerators.
Read more at Science Daily
Now, for the first time, scientists at Stanford and SLAC have created a silicon chip that can accelerate electrons -- albeit at a fraction of the velocity of that massive instrument -- using an infrared laser to deliver, in less than a hair's width, the sort of energy boost that takes microwaves many feet.
Writing in the Jan. 3 issue of Science, a team led by electrical engineer Jelena Vuckovic explained how they carved a nanoscale channel out of silicon, sealed it in a vacuum and sent electrons through this cavity while pulses of infrared light -- to which silicon is as transparent as glass is to visible light -- were transmitted by the channel walls to speed the electrons along.
The accelerator-on-a-chip demonstrated in Science is just a prototype, but Vuckovic said its design and fabrication techniques can be scaled up to deliver particle beams accelerated enough to perform cutting-edge experiments in chemistry, materials science and biological discovery that don't require the power of a massive accelerator.
"The largest accelerators are like powerful telescopes. There are only a few in the world and scientists must come to places like SLAC to use them," Vuckovic said. "We want to miniaturize accelerator technology in a way that makes it a more accessible research tool."
Team members liken their approach to the way that computing evolved from the mainframe to the smaller but still useful PC. Accelerator-on-a-chip technology could also lead to new cancer radiation therapies, said physicist Robert Byer, a co-author of the Science paper. Again, it's a matter of size. Today, medical X-ray machines fill a room and deliver a beam of radiation that's tough to focus on tumors, requiring patients to wear lead shields to minimize collateral damage.
"In this paper we begin to show how it might be possible to deliver electron beam radiation directly to a tumor, leaving healthy tissue unaffected," said Byer, who leads the Accelerator on a Chip International Program, or ACHIP, a broader effort of which this current research is a part.
Inverse design
In their paper, Vuckovic and graduate student Neil Sapra, the first author, explain how the team built a chip that fires pulses of infrared light through silicon to hit electrons at just the right moment, and just the right angle, to move them forward just a bit faster than before.
To accomplish this, they turned the design process upside down. In a traditional accelerator, like the one at SLAC, engineers generally draft a basic design, then run simulations to physically arrange the microwave bursts to deliver the greatest possible acceleration. But microwaves measure 4 inches from peak to trough, while infrared light has a wavelength one-tenth the width of a human hair. That difference explains why infrared light can accelerate electrons in such short distances compared to microwaves. But this also means that the chip's physical features must be 100,000 times smaller than the copper structures in a traditional accelerator. This demands a new approach to engineering based on silicon integrated photonics and lithography.
Vuckovic's team solved the problem using inverse design algorithms that her lab has developed. These algorithms allowed the researchers to work backward, by specifying how much light energy they wanted the chip to deliver, and tasking the software with suggesting how to build the right nanoscale structures required to bring the photons into proper contact with the flow of electrons.
"Sometimes, inverse designs can produce solutions that a human engineer might not have thought of," said R. Joel England, a SLAC staff scientist and co-author on the Science paper.
The design algorithm came up with a chip layout that seems almost otherworldly. Imagine nanoscale mesas, separated by a channel, etched out of silicon. Electrons flowing through the channel run a gantlet of silicon wires, poking through the canyon wall at strategic locations. Each time the laser pulses -- which it does 100,000 times a second -- a burst of photons hits a bunch of electrons, accelerating them forward. All of this occurs in less than a hair's width, on the surface of a vacuum-sealed silicon chip, made by team members at Stanford.
The researchers want to accelerate electrons to 94 percent of the speed of light, or 1 million electron volts (1MeV), to create a particle flow powerful enough for research or medical purposes. This prototype chip provides only a single stage of acceleration, and the electron flow would have to pass through around 1,000 of these stages to achieve 1MeV. But that's not as daunting at it may seem, said Vuckovic, because this prototype accelerator-on-a-chip is a fully integrated circuit. That means all of the critical functions needed to create acceleration are built right into the chip, and increasing its capabilities should be reasonably straightforward.
The researchers plan to pack a thousand stages of acceleration into roughly an inch of chip space by the end of 2020 to reach their 1MeV target. Although that would be an important milestone, such a device would still pale in power alongside the capabilities of the SLAC research accelerator, which can generate energy levels 30,000 times greater than 1MeV. But Byer believes that, just as transistors eventually replaced vacuum tubes in electronics, light-based devices will one day challenge the capabilities of microwave-driven accelerators.
Read more at Science Daily
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