The Earth is the moon's single mother, according to a new "paternity test" done on Apollo lunar rock samples.
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Scientists believe they are close to a blood test for pancreatic cancer - one of the hardest tumours to detect and treat. The test, which they describe as "a major advance", hunts for tiny spheres of fat that are shed by the cancers. Early results published in the journal Nature showed the test was 100% accurate.
Experts said the findings were striking and ingenious, but required refinement before they could become a cancer test. The number of people who survive 10 years after being diagnosed with pancreatic cancer is less than 1% in England and Wales compared with 78% for breast cancer. The tumor results in very few symptoms in its early stages and by the time people become unwell, the cancer has often spread around the body and become virtually untreatable.
A cell surface proteoglycan, glypican-1 (GPC1), on circulating exosomes may serve as a potential noninvasive diagnostic and screening tool to detect early stages of pancreatic cancer, according to research published online June 24 in Nature.
Raghu Kalluri, M.D., Ph.D., chair of cancer biology at the MD Anderson Cancer Center in Houston, and colleagues analyzed blood samples from about 250 pancreatic cancer patients and 32 breast cancer patients. For comparison, they used blood samples from healthy donors and small groups of people with other conditions, such as pancreatitis.
The researchers found that exosomes from cancer cells, but not other cell types, harbored high levels of the GPC1 protein. "Any time we identified GPC1-enriched exosomes, we could tell it was a cancer cell," Kalluri told HealthDay. And while many breast tumors released high amounts of GPC1, all pancreatic tumors did -- including early-stage cancers.
"GPC1+ circulating exosomes may serve as a potential noninvasive diagnostic and screening tool to detect early stages of pancreatic cancer to facilitate possible curative surgical therapy," the authors write. "These results encouraged us to perform further analyses to potentially inform on the utility of GPC1+ circulating exosomes as a detection and monitoring tool for pancreatic ductal adenocarcinoma."
Extraordinary advances have turned cancer from an apparent death sentence into a manageable chronic illness for many. But what does it mean to live with a terminal disease...interminably?
Several broad forces have contributed to the transformation of cancer over the past two decades. The first is early detection. The preponderance of screening tests along with new, more refined imaging technologies have led to the discovery of tumors earlier than ever, often before they’ve spread beyond the original site. And even in the case of metastasized tumors, catching them early can improve a person’s ability to weather treatment and fight the disease.
There have also been remarkable medical advances, including targeted therapies, which are drugs designed to act against particular molecules involved in cancer-cell growth in specific types of cancer; personalized medicine, which allows doctors to identify and respond to genetic and biological abnormalities in an individual patient’s cancer; and targeted immunotherapy, a new type of treatment that harnesses the body’s own immune system to destroy cancer cells.
Last is the growing field of psycho-oncology, which has led to an expanded understandingof cancer patients’ emotional and social needs and has been shown to add not just to the quality of their years but to the quantity as well. Being better informed and supported can motivate people to work on their overall physical wellness and opt to participate in experimental treatments and clinical trials, which can be life-extending.
All these developments are factors in the increasing number of people whose cancer can be considered cured, a nebulous term that generally describes those who are cancer-free five years after their diagnosis. But at the same time, they’re enabling more and more people like Brad Slocum to live longer with active or persistent cancer, including tumors that are controlled without being eliminated or tumors that go through continuous cycles of remission and recurrence.
“It’s very different from being cured,” says Michael Fisch, chair of general oncology at the MD Anderson Cancer Center in Houston. “Being cured becomes a story like, ‘Back in 2002, I had a small breast tumor, and they took care of it,’ or ‘I had a small melanoma removed five years ago, and I live a normal life now.’ It’s a line item on a medical history that maybe isn’t too important. But taking Sutent, or periodically having surgeries, or having a lot of CT scans, or having a fear of recurrence or progression, or being on maintenance chemotherapy—that’s a different experience.”
Via Susan Zager
An MIT physicist has proposed the provocative idea that life exists because the law of increasing entropy drives matter to acquire lifelike physical properties.
Why does life exist? Popular hypotheses credit a primordial soup, a bolt of lightning and a colossal stroke of luck. But if a provocative new theory is correct, luck may have little to do with it. Instead, according to the physicist proposing the idea, the origin and subsequent evolution of life follow from the fundamental laws of nature and “should be as unsurprising as rocks rolling downhill.”
From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.
“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant,” England said. England’s theory is meant to underlie, rather than replace, Darwin’s theory of evolution by natural selection, which provides a powerful description of life at the level of genes and populations. “I am certainly not saying that Darwinian ideas are wrong,” he explained. “On the contrary, I am just saying that from the perspective of the physics, you might call Darwinian evolution a special case of a more general phenomenon.”
His idea, detailed in a recent paper and further elaborated in a talk he is delivering at universities around the world, has sparked controversy among his colleagues, who see it as either tenuous or a potential breakthrough, or both.
England has taken “a very brave and very important step,” said Alexander Grosberg, a professor of physics at New York University who has followed England’s work since its early stages. The “big hope” is that he has identified the underlying physical principle driving the origin and evolution of life, Grosberg said.
England’s theoretical results are generally considered valid. It is his interpretation — that his formula represents the driving force behind a class of phenomena in nature that includes life — that remains unproven. But already, there are ideas about how to test that interpretation in the lab. “He’s trying something radically different,” said Mara Prentiss, a professor of physics at Harvard who is contemplating such an experiment after learning about England’s work. “As an organizing lens, I think he has a fabulous idea. Right or wrong, it’s going to be very much worth the investigation.”
At the heart of England’s idea is the second law of thermodynamics, also known as the law of increasing entropy or the “arrow of time.” Hot things cool down, gas diffuses through air, eggs scramble but never spontaneously unscramble; in short, energy tends to disperse or spread out as time progresses. Entropy is a measure of this tendency, quantifying how dispersed the energy is among the particles in a system, and how diffuse those particles are throughout space. It increases as a simple matter of probability: There are more ways for energy to be spread out than for it to be concentrated. Thus, as particles in a system move around and interact, they will, through sheer chance, tend to adopt configurations in which the energy is spread out. Eventually, the system arrives at a state of maximum entropy called “thermodynamic equilibrium,” in which energy is uniformly distributed. A cup of coffee and the room it sits in become the same temperature, for example. As long as the cup and the room are left alone, this process is irreversible. The coffee never spontaneously heats up again because the odds are overwhelmingly stacked against so much of the room’s energy randomly concentrating in its atoms.
Although entropy must increase over time in an isolated or “closed” system, an “open” system can keep its entropy low — that is, divide energy unevenly among its atoms — by greatly increasing the entropy of its surroundings. In his influential 1944 monograph “What Is Life?” the eminent quantum physicist Erwin Schrödinger argued that this is what living things must do. A plant, for example, absorbs extremely energetic sunlight, uses it to build sugars, and ejects infrared light, a much less concentrated form of energy. The overall entropy of the universe increases during photosynthesis as the sunlight dissipates, even as the plant prevents itself from decaying by maintaining an orderly internal structure.
Via SIN JONES
A team of researchers led by UCLA electrical engineers has demonstrated a new way to harness light particles, or photons, that are connected to each other and act in unison no matter how far apart they are —a phenomenon known as quantum entanglement.
In the new study, researchers demonstrated that they could slice up and entangle each photon pair into multiple dimensions using quantum properties such as the photons' energy and spin. This method, called hyperentanglement, allows each photon pair to carry much more data than was possible with previous methods.
Quantum entanglement could allow users to send data through a network and know immediately whether that data had made it to its destination without being intercepted or altered. With hyperentanglement, users could send much denser packets of information using the same networks.
The research, published today in Nature Photonics, was led by Zhenda Xie, a research scientist in the lab of Chee Wei Wong, a UCLA associate professor of electrical engineering who was the research project's principal investigator. Researchers from MIT, Columbia University, the University of Maryland and the National Institute of Standards and Technology were also part of the team.
Albert Einstein famously described quantum entanglement as "spooky action at a distance" because it seems so improbable that what happens to one particle in an entangled pair also happens instantly to the other particle, even over great distances. The phenomenon exceeds the speed of light.
In the new study, researchers sent hyperentangled photons in a shape known as a biphoton frequency comb, essentially breaking up entangled photons into smaller parts. In secure data transfer, photons sent over fiber optic networks can be encrypted through entanglement. With each dimension of entanglement, the amount of information carried on a photon pair is doubled, so a photon pair entangled by five dimensions can carry 32 times as much data as a pair entangled by only one. The result greatly extends from wavelength multiplexing, the method for carrying many videos over a single optical fiber.
"We show that an optical frequency comb can be generated at single photon level," Xie said. "Essentially, we're leveraging wavelength division multiplexing concepts at the quantum level."
Scientists at the University of Exeter say they've developed a way to make graphene better, cheaper, faster -- and at mass scale. Lead researcher Monica Craciun says the technology, known as the nanoCVD system, promises to usher in "a graphene-driven industrial revolution."
Graphene is a single layer of carbon atoms, organized a honeycomb like structure. The material is super strong, flexible and conductive.
"The vision for a 'graphene-driven industrial revolution' is motivating intensive research on the synthesis of high quality and low cost graphene," Craciun said in a press release. "Currently, industrial graphene is produced using a technique called chemical vapor deposition (CVD). Although there have been significant advances in recent years in this technique, it is still an expensive and time consuming process."
Craciun and her colleagues, in cooperation with U.K.-based graphene company Moorfield, have tweaked CVD technology to develop a "cold wall" device. CVD technology mixes volatile vapors to create a desired deposited material (like a film of graphene) on a substrate.
The research team's new nanoCVD system reportedly grows graphene at a rate 100 times faster than traditional methods, and at one percent of the cost.
"We are very excited about the potential of this breakthrough using Moorfield's technology and look forward to seeing where it can take the graphene industry in the future," said Jon Edgeworth, the company's technical director.
Results shore up the importance of cancer-associated Ras proteins in aging.
A cancer drug that boosts the lifespan of fruit flies is the latest addition to a small roster of compounds shown to lengthen life — although none has yet been proven in humans. Trametinib (Mekinist), which was developed by the London-based pharmaceutical firm GlaxoSmithKline, is already used to treat advanced melanoma. It extends the lifespan of adult fruit flies by about 12%, although the later in life the drug is started, the less effect it has, says Linda Partridge, a geneticist at University College London and the Max Planck Institute for Biology of Ageing in Cologne, Germany, who led the work. Her team’s research is reported on 25 June inCell1. But Partridge cautions against rushing to take trametinib in search of a longer life. “That would be mad,” she says. “We just don’t know enough about the long-term consequences.”
Trametinib’s effects are connected to a biochemical pathway controlled by a family of proteins collectively called Ras which seem to be important to both cancer and aging. They are activated when cells need to grow and proliferate, for example to replace damaged tissue. Mutations in the proteins are associated with cancer — which has led to a decades-long pursuit of drugs that target Ras.
At the same time, Ras proteins are involved in other pathways that have been firmly linked to ageing. In yeast, deleting a gene for Ras extends lifespan2, notes Valter Longo, director of the University of Southern California’s Longevity Institute in Los Angeles.
And Partridge’s team showed that trametinib’s benefits in fruit flies depended on suppressing a pathway regulated by Ras. Flies genetically modified to have this pathway permanently switched on did not live longer on trametinib.
Partridge hopes to extend her Ras studies to mammalian cells grown in culture and to mice. “We don’t know in mammals at the moment what the situation is,” she says. Although many of Ras’s functions are similar in flies and mammals, Partridge notes that cellular pathways in mammals are often more complex than the analogous pathways in flies, with multiple alternative routes available to compensate if one branch of the pathway is shut down.
Stringing together meaningless sounds to create meaningful signals was previously thought to be the preserve of humans alone, but a new study has revealed that babbler birds are also able to communicate in this way.
Researchers at the Universities of Exeter and Zurich discovered that the chestnut-crowned babbler -- a highly social bird found in the Australian Outback -- has the ability to convey new meaning by rearranging the meaningless sounds in its calls. This babbler bird communication is reminiscent of the way humans form meaningful words. The research findings, which are published in the journal PLOS Biology, reveal a potential early step in the emergence of the elaborate language systems we use today.
"In contrast to most songbirds, chestnut-crowned babblers do not sing. Instead its extensive vocal repertoire is characterised by discrete calls made up of smaller acoustically distinct individual sounds." she added.
"We think that babbler birds may choose to rearrange sounds to code new meaning because doing so through combining two existing sounds is quicker than evolving a new sound altogether." said co-author Professor Andy Russell from the University of Exeter who has been studying the babblers since 2004.
The researchers noticed that chestnut-crowned babblers reused two sounds "A" and "B" in different arrangements when performing specific behaviors. When flying, the birds produced a flight call "AB," but when feeding chicks in the nest they emitted "BAB" prompt calls.
When the researchers played the sounds back, the listening birds showed they were capable of discriminating between the different call types by looking at the nests when they heard a feeding prompt call and by looking out for incoming birds when they heard a flight call. This was also the case when the researchers switched elements between the two calls: making flight calls from prompt elements and prompt calls from flight elements, indicating that the two calls were indeed generated from rearrangements of the same sounds.
Making new materials with micro-explosions
Scientists have made exotic new materials by creating laser-induced micro-explosions in silicon, the common computer chip material (Nature Communications, "Experimental evidence of new tetragonal polymorphs of silicon formed through ultrafast laser-induced confined microexplosion").
The new technique could lead to the simple creation and manufacture of superconductors or high-efficiency solar cells and light sensors, said leader of the research, Professor Andrei Rode, from The Australian National University (ANU)."We've created two entirely new crystal arrangements, or phases, in silicon and seen indications of potentially four more," said Professor Rode, a laser physicist at the ANU Research School of Physics and Engineering (RSPE). "Theory predicts these materials could have very interesting electronic properties, such as an altered band gap, and possibly superconductivity if properly doped."
By focusing lasers onto silicon buried under a clear layer of silicon dioxide, the group have perfected a way to reliably blast tiny cavities in the solid silicon. This creates extremely high pressure around the explosion site and forms the new phases.The phases have complex structures, which took the team of physicists from ANU and University College London a year to understand.Using a combination of electron diffraction patterns and structure predictions, the team discovered the new materials have crystal structures that repeat every 12, 16 or 32 atoms respectively, said Professor Jim Williams, from the Electronic Material Engineering group at RSPE."The micro-explosions change silicon's simplicity to much more complex structures, which opens up possibility for unusual and unexpected properties," he said.These complex phases are often unstable, but the small size of the structures means the materials cool very quickly and solidify before they can decay, said Professor Eugene Gamaly, also from the ANU Research School of Physics and Engineering. The new crystal structures have survived for more than a year now."These new discoveries are not an accident, they are guided by a deep understanding of how lasers interact with matter," he said.
Measles kills about 140,000 people worldwide every year, but the millions of kids who have survived the disease aren’t in the clear. A new epidemiological study suggests that they remain susceptible to other infections for more than 2 years, much longer than researchers anticipated. The results bolster a hypothesis that the measles virus undermines the immune system’s memory—and indicate that the measles vaccine protects against other deadly diseases as well.
Researchers have long known that measles inhibits the immune system, but they generally thought this effect wore off after a few months at the most. However, studies of children in developing countries, where most cases occur, found that measles vaccination reduces the overall death rate from infections for up to 5 years, suggesting that preventing the disease somehow provides protection against other illnesses.
One possible explanation for this benefit is that the measles vaccine somehow spurs the immune system to produce defenses against these other diseases. But work on monkeys recovering from measles spawned an alternative hypothesis. In 2012, Rik de Swart of Erasmus MC in Rotterdam, Netherlands, and colleagues revealed that the measles virus kills large numbers of memory cells, white blood cells that prevent subsequent infections by the same pathogen. Thus, the measles virus might cause what the scientists termed immunological amnesia, impairing the immune system’s ability to remember and quickly eliminate other microbes it has already beaten. As a result, “you are vulnerable to diseases you shouldn’t be vulnerable to,” says Michael Mina, lead author of the new paper and a medical student at Emory University School of Medicine in Atlanta.
To test this explanation, a team that included De Swart and Mina, then a postdoc at Princeton University, obtained data on the numbers of measles cases and deaths from other infectious diseases in the United States, Denmark, and part of the United Kingdom. Measles vaccination started in the 1960s in the United Kingdom and United States and in the 1980s in Denmark, and the researchers had statistics from before and after its introduction.
The team’s mathematical analysis tried to determine whether there was a relationship between the number of measles cases and the number of kids who died from other diseases. If the virus inhibits immunity for only a short time, for example, the number of deaths from other infections in a specific year might correlate to the number of measles cases in that year. But if the virus triggers a prolonged immune amnesia, the number of deaths in a particular year might correlate to the total number of cases in that year and the previous year or two.
Using this approach, the researchers calculated that children who survive measles remain vulnerable to other diseases for an average of 2.5 years. The value was almost the same for all three countries, the team reports online today in Science. “Our results suggest that the adverse effects of measles are much more lasting,” Mina says.
Watch out, Google. Facebook is gunning for the title of World’s Coolest Place to Work. And its arsenal includes unmanned drones, lasers, satellites and virtual reality headsets. Mark Zuckerberg, co-founder and chief executive of Facebook, announced on Thursday that the company was creating a new lab of up to 50 aeronautics experts and space scientists to figure out how to beam Internet access down from solar-powered drones and other “connectivity aircraft.”
To start the effort, Facebook is buying Ascenta, a small British company whose founders helped to create early versions of an unmanned solar-powered drone, the Zephyr, which flew for two weeks in July 2010 and broke a world record for time aloft.
“We want to think about new ways of connectivity that dramatically reduce the cost,” said Yael Maguire, engineering director for the new Facebook Connectivity Lab. “We want to explore whether there are ways from the sky to deliver the Internet access.”
It’s the second head-spinning announcement from Facebook this week and the third this year. On Tuesday, the company said it would spend at least $2 billion to buy Oculus VR, a Southern California start-up that is developing virtual reality headsets for playing games and other uses. Last month, it said it would buy WhatsApp, a messaging app that offers free texting around the world, for as much as $19 billion.
The lab is part of Mr. Zuckerberg’s ambitious Internet.org project to bring the Internet to the two-thirds of the world’s population without Internet access. With partners like Qualcomm and Nokia, Facebook is working on technology to compress Internet data, cut the cost of mobile phones and extend connections to people who can’t afford them or live in places that are too difficult to reach.
That last part of the problem — reaching the 10 percent of the world’s population that are in areas difficult to reach via traditional Internet solutions — is the initial focus of the connectivity lab, said Mr. Maguire.
Currently, satellites can deliver Internet to sparsely populated areas with spotty Internet connections, but the cost is very high, said Mr. Maguire.
Facebook wants to explore whether access could be delivered more cheaply through both new types of satellites and unmanned aircraft.
The company envisions drones that could stay aloft for months, even years, at a time at an altitude of more than 12 miles from the surface of the earth — far above other planes and the ever-changing weather.
New Milestone Will Enable System to Address Larger and More Complex Problems
D-Wave Systems Inc., the world's first quantum computing company, today announced that it has broken the 1000 qubit barrier, developing a processor about double the size of D-Wave’s previous generation and far exceeding the number of qubits ever developed by D-Wave or any other quantum effort.
This is a major technological and scientific achievement that will allow significantly more complex computational problems to be solved than was possible on any previous quantum computer.
D-Wave’s quantum computer runs a quantum annealing algorithm to find the lowest points, corresponding to optimal or near optimal solutions, in a virtual “energy landscape.” Every additional qubit doubles the search space of the processor. At 1000 qubits, the new processor considers 21000possibilities simultaneously, a search space which dwarfs the 2512 possibilities available to the 512-qubit D-Wave Two. In fact, the new search space contains far more possibilities than there are particles in the observable universe.
“For the high-performance computing industry, the promise of quantum computing is very exciting. It offers the potential to solve important problems that either can’t be solved today or would take an unreasonable amount of time to solve,” said Earl Joseph, IDC program vice president for HPC. “D-Wave is at the forefront of this space today with customers like NASA and Google, and this latest advancement will contribute significantly to the evolution of the Quantum Computing industry.”
As the only manufacturer of scalable quantum processors, D-Wave breaks new ground with every succeeding generation it develops. The new processors, comprising over 128,000 Josephson tunnel junctions, are believed to be the most complex superconductor integrated circuits ever successfully yielded. They are fabricated in part at D-Wave’s facilities in Palo Alto, CA and at Cypress Semiconductor’s wafer foundry located in Bloomington, Minnesota.
“Temperature, noise, and precision all play a profound role in how well quantum processors solve problems. Beyond scaling up the technology by doubling the number of qubits, we also achieved key technology advances prioritized around their impact on performance,” said Jeremy Hilton, D-Wave vice president, processor development. “We expect to release benchmarking data that demonstrate new levels of performance later this year.”
The 1000-qubit milestone is the result of intensive research and development by D-Wave and reflects a triumph over a variety of design challenges aimed at enhancing performance and boosting solution quality. Beyond the much larger number of qubits, other significant innovations include:
Die-offs in such creatures could have ramifications up the food chain in some of the most productive fisheries in the world and provide a preview of what is in store for the rest of the world’s oceans down the road.
“The Arctic can be a great indicator” of future issues, oceanographer Jeremy Mathis, of the Pacific Marine Environmental Laboratory, said.
Ocean acidification is a process happening in tandem with the warming of the planet and is driven by the same human-caused increase of carbon dioxide in the atmosphere that is trapping excess heat. The oceans absorb much of that excess CO2, where it dissolves and reacts with water to form carbonic acid.
As CO2 emissions have continued to grow, so has the amount of carbonic acid in the oceans, decreasing their pH. The ocean generally has a pH of 8.2, making it slightly basic (a neutral pH is 7, while anything above is basic and anything below is acidic). An ocean that is becoming less basic is a problem for the creatures like shellfish and coral that depend on specific ocean chemistry to have enough of the mineral calcium carbonate to make their hard shells and skeletons.
Small snails the size of a human fingernail in polar coastal waters can react very quickly to increased acidity, with their shells dissolving. Such tiny creatures are often the linchpins of marine ecosystems, causing a domino effect up the food chain when they collapse. That’s a major concern in an area that has some of the globe’s most productive fisheries, especially the Bering Sea.
The polar oceans are particularly threatened by ocean acidification, as cold water is better at absorbing CO2 than warm water is. And in regions near the coast, this process is helped along by glacier melt and river runoff that also shift the water’s chemistry toward increased CO2 absorption.
Methyltransferases are enzymes that facilitate the transfer of a methyl (-CH3) group to specific nucleophilic sites on proteins, nucleic acids or other biomolecules. They share a reaction mechanism in which the nucleophilic acceptor site attacks the electrophilic carbon of S-adenosyl-L-methionine (SAM) in an SN2 displacement reaction that produces a methylated biomolecule and S-adenosyl-L-homocysteine (SAH) as a byproduct. Methylation reactions are essential transformations in small-molecule metabolism, and methylation is a common modification of DNA and RNA. The recent discovery of dynamic and reversible methylation of amino acid side chains of chromatin proteins, particularly within the N-terminal tail of histone proteins, has revealed the importance of methyl 'marks' as regulators of gene expression. Human protein methyltransferases (PMTs) fall into two major families - protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) - that are distinguishable by the amino acid that accepts the methyl group and by the conserved sequences of their respective catalytic domains. Given their involvement in many cellular processes, PMTs have attracted attention as potential drug targets, spurring the search for small-molecule PMT inhibitors. Several classes of inhibitors have been identified, but new specific chemical probes that are active in cells will be required to elucidate the biological roles of PMTs and serve as potent leads for PMT-focused drug development.
Protein lysine methyltransferases (PKMTs)
The phylogenetic tree shows 51 genes predicted to encode PKMTs, which are positioned in the tree on the basis of the similarities of their amino acid sequences. This tree excludes one validated PKMT, DOT1L, which lacks a SET domain - the catalytic domain conserved in this family - and clusters more closely with the PRMTs. The tree has four major branches, and each branch contains enzymes with validated methyltransferase activity (highlighted in red). Some PKMTs add a single methyl group, resulting in a mono-methylated product (Kme), whereas others produce di-(Kme2) or tri-methylated (Kme3) lysine modifications. Many of the validated PKMTs methylate lysines on histones, though nonhistone substrates have also been identified.
Protein arginine methyltransferases (PRMTs)
The human PRMT phylogenetic tree comprises 45 predicted enzymes including the PKMT DOT1L. There are two major types of PRMTs; both catalyze the formation of mono-methylarginine (Rme1) but distinct reaction mechanisms yield symmetric (Rme2s) or asymmetric (Rme2a) dimethylarginine. A small number of predicted PRMTs have validated activity (highlighted in blue). In addition to PRMTs, this tree includes validated RNA methyltransferases (highlighted in green) and biosynthetic enzymes (highlighted in violet). It remains uncertain whether these latter enzymes have PRMT activity, despite their shared structural features. Substrates for the enzymes shown include RNA, metabolites, histones and RNA-binding and spiceosomal proteins.
The day will officially be a bit longer than usual on Tuesday, 30 June 2015, because an extra second, or “leap” second, will be added.
Typically, a leap second is inserted either on 30 June or 31 December. Normally, the clock would move from 23:59:59 to 00:00:00 the next day. But with the leap second on 30 June, UTC will move from 23:59:59 to 23:59:60, and then to 00:00:00 on 1 July. In practice, many systems are instead turned off for one second. Previous leap seconds have created challenges for some computer systems and generated some calls to abandon them altogether. One reason is that the need to add a leap second cannot be anticipated far in advance.
“In the short term, leap seconds are not as predictable as everyone would like,” said Chopo Ma, a geophysicist at Goddard and a member of the directing board of the International Earth Rotation and Reference Systems Service. “The modelling of the Earth predicts that more and more leap seconds will be called for in the long-term, but we can’t say that one will be needed every year.”
From 1972, when leap seconds were first implemented, through 1999, leap seconds were added at a rate averaging close to one per year. Since then, leap seconds have become less frequent. This June’s leap second will be only the fourth to be added since 2000. Before 1972, adjustments were made in a different way.
Scientists don’t know exactly why fewer leap seconds have been needed lately. Sometimes, sudden geological events, such as earthquakes and volcanic eruptions, can affect Earth’s rotation in the short-term, but the big picture is more complex.
A team from the UK, the Netherlands, and Ireland has identified a form of inherited obesity and type 2 diabetes that appears to stem from a mutation in a single enzyme-coding gene. As they reported online in PLOS One, the researchers did exome sequencing on members of a consanguineous family affected by a condition characterized by extreme obesity, type 2 diabetes, intellectual disability, and other features. Their search led to truncating mutations affecting both copies of a gene that codes for a peptide-processing enzyme called carboxypeptidase E.
That enzyme normally plays a role in regulating hormone and neuropeptide peptides, the team explained. And past mouse studies suggest that mutations that alter the enzyme's ability to regulate such peptides can throw off appetite control, normal glucose metabolism, and other physiological processes.
"There are now an increasing number of single-gene causes of obesity and diabetes known," corresponding author Alexandra Blakemore, a diabetes, endocrinology, and metabolism researcher at the Imperial College of Medicine, said in a statement.
"We don't know how many more have yet to be discovered, or what proportion of the severely obese people in our population have these diseases — it is not possible to tell just by looking," Blakemore added, explaining that such inherited conditions can affect individuals' bodies and their ability to appropriately respond to hunger and fullness signals.
In an effort to track down new genes that contribute to inherited, single-gene forms of obesity, the researchers performed exome sequencing on members of a Sudanese family found through a genetic obesity clinic at a UK hospital.
Using the Agilent SureSelectXT Human All Exon V4+UTR kit, the team isolated protein-coding DNA from an affected family member — a morbidly obese 21-year-old woman with childhood-onset obesity, type 2 diabetes, intellectual disability, and reproductive problems — along with her mother and sister. After sequencing these exomes with the Illumina HiSeq 2500, the researchers scrutinized the sequences for single nucleotide changes, small insertions and deletions, and copy number variants.
The search ultimately led to a truncating frameshift mutation in the first exon of the CPE gene. With the help of Sanger sequencing, the team determined that the affected woman carried two copies of this mutation, while her mother, sister, and two brothers had one copy of the altered CPE gene. Similarly, when researchers used real-time PCR to track expression of the gene in blood samples from family members and female controls, they did not detect CPE transcripts in blood samples from the affected women. A sister with one copy of the mutation had lower-than-usual CPE expression compared to six control individuals.
The study's authors argued that the newly detected mutation, together with those in other genes involved in monogenic forms of obesity, should provide opportunities to find the basis of disease in ever more individuals with inherited obesity.
"Diagnosis is very valuable to the patient. It helps to set realistic expectations, and can help them get the best possible treatment," Blakemore noted, explaining that such diagnoses also make it possible to provide genetic counseling and advice to other members of affected families.
As inquisitive beings, we are constantly questioning and quantifying the speed of various things. With a fair degree of accuracy, scientists have quantified the speed of light, the speed of sound, the speed at which the earth revolves around the sun, the speed at which hummingbirds beat their wings, the average speed of continental drift….
These values are all well-characterized. But what about the speed of thought? It’s a challenging question that’s not easily answerable – but we can give it a shot. To quantify the speed of anything, one needs to identify its beginning and end. For our purposes, a “thought” will be defined as the mental activities engaged from the moment sensory information is received to the moment an action is initiated. This definition necessarily excludes many experiences and processes one might consider to be “thoughts.”
Here, a “thought” includes processes related to perception (determining what is in the environment and where), decision-making (determining what to do) and action-planning (determining how to do it). The distinction between, and independence of, each of these processes is blurry. Further, each of these processes, and perhaps even their sub-components, could be considered “thoughts” on their own. But we have to set our start- and endpoints somewhere to have any hope of tackling the question.
Finally, trying to identify one value for the “speed of thought” is a little like trying to identify one maximum speed for all forms of transportation, from bicycles to rockets. There are many different kinds of thoughts that can vary greatly in timescale. Consider the differences between simple, speedy reactions like the sprinter deciding to run after the crack of the starting pistol (on the order of 150 milliseconds [ms]), and more complex decisions like deciding when to change lanes while driving on a highway or figuring out the appropriate strategy to solve a math problem (on the order of seconds to minutes).
Via Steven Krohn
Less than three minutes into its flight, SpaceX's Falcon 9 rocket disintegrated along with the cargo it was carrying to the ISS.
In the eternal war between SpaceX’s reusable rockets and SpaceX’s robot boat, the rockets lost again. Elon Musk’s company loaded up a Dragon capsule full of supplies this morning in what would have been its seventh mission to the International Space Station—and its third attempt to salvage the capsule’s rocket, Falcon 9, by landing on an autonomous barge. But the poor thing didn’t even get the chance to try. Less than three minutes into flight, the rocket and its cargo exploded, their disintegrating parts cloaked by a huge cloud of smoke. Astronaut Scott Kelly, watching the catastrophic failure from his perch in the ISS above, said it right: “Space is hard.”
It’s not clear yet what caused the rocket to break up. At the time of “launch vehicle failure,” in NASA-speak, Falcon was still firing all of its nine first-stage engines, with the Dragon capsule and second stage Merlin vacuum engine attached. Right now, the NASA mishap and anomaly teams are trying to piece together video analysis of the flight path with the two minutes or so of data sent from the craft before it exploded. Canadian astronaut Chris Hadfield speculated that the failure might have started at the front of the craft—near the second stage engine and the Dragon capsule.
In a NASA press conference today, SpaceX president and COO Gwynne Shotwell confirmed that a problem occurred in that general location, noting an overpressurization event in the liquid oxygen tank in the second stage of the rocket. But SpaceX doesn’t know yet what caused it. Even the typically speculation-happy Musk can’t say more yet, tweeting only that their “data suggests [a] counterintuitive cause.”
The Dragon capsule was carrying more than 4,000 pounds of supplies for the ISS. This is the third resupply mission to fail in the last eight months; at the end of April, a Russian Progress spacecraft and its Soyuz rocket similarly failed early in their launch, and last October, an Antares rocket from Orbital Sciences blew up right on the launch pad.
While that might seem to indicate a troubling trend, “there’s no commonality across these three events other than that it’s space and it’s difficult to fly,” says NASA’s associate administrator for Human Exploration and Operations William Gerstenmaier.
An international team of scientists has discovered the deepest underground dwelling centipede. The animal was found by members of the Croatian Biospeleological Society in three caves in Velebit Mts, Croatia. Recorded as deep as -1100 m the new species was namedGeophilus hadesi, after Hades, the God of the Underworld in the Greek Mythology. The research was published in the open access journal ZooKeys.
Lurking in the dark vaults of some of the world's deepest caves, the Hades centipede has also had its name picked to pair another underground-dwelling relative named after Persephone, the queen of the underworld. Centipedes are carnivores that feed on other invertebrate animals. They are common cave inhabitants but members of this particular order, called geophilomorphs, usually find shelter there only occasionally. Species with an entire life cycle confined to cave environments are exceptionally rare in the group.
In fact, so far the Hades and Persephone centipedes are the only two geophilomorphs that have adapted to live exclusively in caves, thus rightfully bearing the titles of a queen and king of the underworld.
Like most cave-dwellers, the newly discovered centipede shows unusual traits, some of which commonly found in cave-dwelling arthropods, including much elongated antennae, trunk segments and leg claws. Equipped with powerful jaws bearing poison glands and long curved claws allowing to grasp and tightly hold its prey, the Hades centipede is among the top predators crawling in the darkness of the cave.
The new species is yet another addition to the astonishing cave critters that live in the Velebit, a mountain that stretches over 145 km in the Croatian Dinaric Karst, which is as a whole considered a hot spot of subterranean diversity. The deepest record comes from the Lukina jama - Trojama cave system, which is 1431 meters deep and is currently ranked the 15th deepest cave in the world.
Virtual Private Networks (VPNs) are legal and increasingly popular for individuals wanting to circumvent censorship, avoid mass surveillance or access geographically limited services like Netflix and BBC iPlayer. Used by around 20 per cent of European internet users they encrypt users’ internet communications, making it more difficult for people to monitor their activities.
Few physical systems are better understood than the interference of two planar waves—like ripples on a pond. Proving that there are still secrets to be discovered even in such fundamentally well-known systems, RIKEN researchers Konstantin Bliokh, Aleksandr Bekshaev and Franco Nori have used theory to reveal a new, hidden force in this system that acts on particles in an unexpected way ("Transverse Spin and Momentum in Two-Wave Interference").
Two-dimensional waves have been studied for centuries: initially to understand the intrinsic behavior of waves and more recently to understand the fundamental mechanics of quantum physics. “The interference between two plane waves has always provided an important model for understanding the basic features of waves,” notes Bliokh. “It is difficult to find a simpler and more thoroughly studied system in physics. We show that such a basic system still exhibits unexpected and unusual features.”
Recent research has showed that interfering planar waves can have unusual properties on a small scale. For over a century, waves such as light beams have been known to carry both momentum and angular momentum in the direction of the propagating wave and this momentum can be used to move and rotate small particles. This is consistent with the common understanding of photons as particles carrying momentum and spin. On the local scale in non-plane-wave optical fields, however, light can also impart forces and torques perpendicular to the light beam, counterintuitive to our everyday experience. These unusual effects have been noticed in highly confined near-field radiation known as evanescent waves, but so far they have not turned up in freely propagating light waves.
In a comprehensive theoretical study, the scientists, from the RIKEN Center for Emergent Matter Science and Interdisciplinary Theoretical Science Research Group (iTHES), revisited the concept of two propagating waves interfering in the same plane. Their mathematical analysis of this system revealed that even this well-studied example of interfering waves can exert a force and torque on a small particle perpendicular to both waves (see figure). Both the force and torque are strongly dependent on the polarization of the two interfering waves, which differs to the conventional experience of waves carrying the same momentum irrespective of their polarizations.
The possibility of realizing such an effect in an actual experimental system and to potentially control it through parameters such as polarization is attractive and, Nori predicts, practically feasible. “Our findings offer a new vision for the fundamental properties of propagating optical fields and pave the way for novel optical manipulations of small particles.”
A group of University of Wisconsin-Madison engineers and a collaborator from China have developed a nanogenerator that harvests energy from a car's rolling tire friction.
An innovative method of reusing energy, the nanogenerator ultimately could provide automobile manufacturers a new way to squeeze greater efficiency out of their vehicles.
The researchers reported their development, which is the first of its kind, in a paper published May 6, 2015, in the journal Nano Energy.
Xudong Wang, the Harvey D. Spangler fellow and an associate professor of materials science and engineering at UW-Madison, and his PhD student Yanchao Mao have been working on this device for about a year.
The nanogenerator relies on the triboelectric effect to harness energy from the changing electric potential between the pavement and a vehicle's wheels. The triboelectric effect is the electric charge that results from the contact or rubbing together of two dissimilar objects. Wang says the nanogenerator provides an excellent way to take advantage of energy that is usually lost due to friction.
"The friction between the tire and the ground consumes about 10 percent of a vehicle's fuel," he says. "That energy is wasted. So if we can convert that energy, it could give us very good improvement in fuel efficiency." The nanogenerator relies on an electrode integrated into a segment of the tire. When this part of the tire surface comes into contact with the ground, the friction between those two surfaces ultimately produces an electrical charge-a type of contact electrification known as the triboelectric effect.
The ray-finned fishes, so called because their fins are supported by bony spines or rays, make up more than 95% of all fish species. They come in all shapes and sizes, from the showy lionfish (pictured above) to the delicious Atlantic salmon. Yet paleontologists have been unsure when and why ray-finned fishes exploded into such prominence, in large part because the preservation of fish fossils is a very hit-or-miss affair. Now, researchers have taken a new approach to the problem: They looked at marine sediments taken from deep-sea cores at six sites around the world, including the Atlantic and Pacific oceans. To figure out when ray-finned fish numbers took off, they calculated the ratio of fossilized teeth from ray-finned fishes to the fossilized scales from another major group of fish: sharks.
As they report online this week in the Proceedings of the National Academy of Sciences (PNAS), this ratio shows that sharks well outnumbered the ray-finned fish at the end of the Cretaceous, about 66 million years ago. That was when dinosaurs, ammonites, and most marine reptiles went extinct, probably because of a large asteroid hitting Earth. After the extinction event, the ratio of these ray-finned fish remains shot up dramatically, quickly outnumbering those of sharks. Although the sharks also survived the end of the Cretaceous, their numbers appear to have remained flat, whereas the size and diversity of ray-finned fish populations took off. The researchers suggest that the mass extinction, especially of ammonites (which probably competed with fish for food), allowed the ray-fins to exploit new ecological niches and launched what the authors call a “new age of fish.”
Deep neural networks are an approach to machine learning that has revolutionized computer vision and speech recognition in the last few years, blowing the previous state of the art results out of the water. They’ve also brought promising results to many other areas, including language understanding and machine translation. Despite this, it remains challenging to understand what, exactly, these networks are doing.
Understanding neural networks is just scratching the surface, however, because understanding the network is fundamentally tied to understanding the data it operates on. The combination of neural networks and dimensionality reduction turns out to be a very interesting tool for visualizing high-dimensional data – a much more powerful tool than dimensionality reduction on its own.
Paragraph vectors, introduced by Le & Mikolov (2014), are vectors that represent chunks of text. Paragraph vectors come in a few variations but the simplest one, which we are using here, is basically some really nice features on top of a bag of words representation.
With word embeddings, we learn vectors in order to solve a language task involving the word. With paragraph vectors, we learn vectors in order to predict which words are in a paragraph.
Concretely, the neural network learns a low-dimensional approximation of word statistics for different paragraphs. In the hidden representation of this neural network, we get vectors representing each paragraph. These vectors have nice properties, in particular that similar paragraphs are close together.
Now, Google has some pretty awesome people. Andrew Dai, Quoc Le, and Greg Corrado decided to create paragraph vectors for some very interesting data sets. One of those was Wikipedia, creating a vector for every English Wikipedia article. The result is that we get a visualization of the entirety of Wikipedia. A map of Wikipedia. A large fraction of Wikipedia’s articles fall into a few broad topics: sports, music (songs and albums), films, species, and science.
The Advanced Camera for Surveys, one of the Hubble’s advanced instruments, has taken a spectacularly detailed image of a galaxy called SBS 1415+437.
Discovered in 1995 by a team of astronomers from the United States and Ukraine, SBS 1415+437 lies in the constellation Boötes at a distance of about 45.3 million light-years. It is a galaxy type known as a cometary blue compact dwarf galaxy. Astronomers initially thought that SBS 1415+437 was a truly young galaxy that did not start to form stars until 100 million years ago, but a recent study has suggested that the galaxy is in fact older, containing stars 1.3 billion years old.
SBS 1415+437, otherwise known as PGC 51017, SBSG 1415+437 or SDSS CGB 12067.1, also belongs to a rare group of starburst galaxies called Wolf–Rayet galaxies. The galaxy has an unusually high number of extremely hot and massive Wolf–Rayet stars. These stars are among the largest and shortest lived stars known, typically over 20 solar masses with surface temperatures well over 25,000 K. Many of the brightest and most massive stars in the Milky Way are Wolf–Rayet stars.
These massive stars are in the stage of their stellar evolution where they undergo heavy mass loss. A typical Wolf–Rayet star can lose a mass equal to that of our Sun in just 100,000 years. Because of this it is unusual to find more than a few of these stars per galaxy – except in Wolf–Rayet galaxies, like the one in this image.
From fun-house mirrors to holograms, we have all experienced incredible optical illusions. Right now, scientists are fascinated by the prospect of finding a way to perform an even more challenging trick: hiding things in plain sight. We've made some metamaterials that have refractive indices that can redirect particular wavelengths of light. But one issue scientists have found particularly difficult to address is how to mask corners. Sharp corners are pretty common, and it's difficult to figure out ways to guide the surface waves of light around corners, as the light experiences scattering loss when encountering sharp corners.
That's because there is a large mismatch in momentum of the light waves at the surface of an object before and after passing around the corner of an extremely compact shape. Though scientists have successfully developed a few materials that can perform scattering-free guidance of surface waves around corners, these methods are limited. They rely on photonic crystals with a large magnetic response, which limits the types of waves it can influence.
When waves encounter a sharp corner, they pass through compact space, which causes the change in momentum (yes, photons have momentum). More advanced cloaking methods have focused on compensating for this change in momentum by curving the electromagnetic space in a way that tricks light waves into behaving as if they're moving in a straight line. Through this method, transformative optics has made strides towards developing a real invisibility cloak.
In the new work, scientists have demonstrated a way of bending surface light waves around sharp corners, one that works across a broad range of wavelengths, exhibiting almost ideal transmission. This method is able to bend the waves in a way that does not disturb other wave properties, such as the amplitude and phase. This could actually allow for the development of an invisibility cloak.
The scientists created bending adaptors that were essentially “corner cloaks”—able to hide corners as the waves traveled around them. Physically, the corner cloaks are triangular pieces that can be placed over a sharp corner. The cloaks are made of layered structures of subwavelength foam and ceramic materials that had a refractive index that's able to redirect light. Experimental results show that the cloaks almost completely conceal their presence from anyone looking at the light that passed through them. It appears that the ultimate Harry Potter fantasy might be right around the corner for some of us.