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Scooped by Dr. Stefan Gruenwald!

Krubera, Earth's deepest cave mapped - it takes 1 month to decent to the bottom

Krubera, Earth's deepest cave mapped - it takes 1 month to decent to the bottom | Amazing Science |

The Krubera cave is located in the Arabika Massif mountain range on the edge of the Black Sea in Abkhazia, which some argue is part of Georgia.  It is said to be bottomless, but experts have managed to map Earth’s deepest cave. Intrepid explorers have charted every known twist and turn of the terrifying Krubera cave that measures 7,208ft (2,197meters) deep. And with every expedition the chasm seems to become deeper as divers plunge to new depths never visited by humans to extend the cave’s reach into the Earth.

The cave is called Voronya in Russia, which means crow's cave. The name was used as slang by Kiev cavers during the 1980s because of the number of crows nesting in the entrance pit. The Arabika Massif is one of the largest high-mountain limestone karst massifs (the main mass of an exposed structure) in the Western Caucasus, which is an area of southern Russia.  It is composed of Lower Cretaceous and Upper Jurassic limestones that dip continuously southwest to the Black Sea and plunge below the modern sea level. The cave, which is named after Russian geologist Alexander Krubera, is the only chasm on Earth that's known to be deeper than 6,561ft (2,000m).

In 2005 he organized a series of expeditions and his team of 56 carried some five tons of equipment into the chasm. Much like scaling a mountain, the team had to cover certain distances so they could set up camp at depth of 2,300, 3,986, 4,630, and 5,380ft (700, 1,215, 1,410, and 1,640metres). The explorers were able to cook meals, sleep in tents and huddle together for warmth before venturing down the limestone rock faces for up to 20 hours at a time, sometimes though extremely cold water. It takes about 1 month to climb down to the bottom.

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The search continues for dark photons, hypothetical messengers of an invisible universe hidden from us

The search continues for dark photons, hypothetical messengers of an invisible universe hidden from us | Amazing Science |

The matter we know accounts for less than 5 percent of the universe; the rest is filled with invisible dark matter and dark energy. Scientists working on a new experiment to be conducted at Thomas Jefferson National Accelerator Facility in Virginia hope to shed light on some of those cosmic unknowns. According to certain theories known as hidden-sector models, dark matter is thought to consist of particles that interact with regular matter through gravitation, which is why we know about it, but not through the electromagnetic, strong and weak fundamental forces (which is why it is hard to detect). Such dark matter would interact with regular matter and with itself through yet-to-be-discovered hidden-sector forces. Scientists believe that heavy photons—also called dark photons—might be mediators of such a dark force, just as regular photons are carriers of the electromagnetic force between normal charged particles.

The Heavy Photon Search at Jefferson Lab will hunt for these dark, more massive cousins of light.

“The heavy photon could be the key to a whole rich world with many new dark particles and forces,” says Rouven Essig, a Stony Brook University theoretical physicist who in recent years helped develop the theory for heavy-photon searches.  If heavy photons exist, researchers want to create them in the lab.

Theoretically, a heavy photon can transform into what is known as a virtual photon—a short-lived fluctuation of electromagnetic energy with mass—and vice versa. This should happen only very rarely and for a very short time, but it still means that experiments that produce virtual photons could in principle also generate heavy photons. Producing enormous numbers of virtual photons may create detectable amounts of heavy ones.

At Jefferson Lab’s Continuous Electron Beam Accelerator Facility, CEBAF, scientists will catapult electrons into a tungsten target, which will generate large numbers of virtual photons—and perhaps some heavy photons, too. The photon mass measured in the experiment matters because a heavy photon has a unique mass, whereas virtual photons appear with a broad range of masses. “The heavy photon would reveal itself as a sharp bump on top of a smooth background from the virtual photon decays,” says SLAC National Accelerator Laboratory’s John Jaros, another HPS spokesperson.

The location in which the electron-positron pair was produced also matters because virtual photons decay almost instantaneously within the target, says Timothy Nelson, project lead for the silicon detector, which is being built at SLAC. Heavy photons could decay more slowly, after traveling beyond the target. So photons that decay outside the target can only be heavy ones. The HPS silicon detector’s unique ability to identify outside-of-target decays sets it apart from other experiments currently participating in a worldwide hunt for heavy photons.

The HPS calorimeter, whose construction was led by researchers from the French Institut de Physique Nucléaire, the Italian Istituto Nazionale di Fisica Nucleare and Jefferson Lab, is currently being tested at Jefferson Lab, while scientists at SLAC plan to ship their detector early next year. The experiment is scheduled to begin in the spring of 2015.

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Tooth loss in birds occurred about 116 million years ago

Tooth loss in birds occurred about 116 million years ago | Amazing Science |

The absence of teeth or "edentulism" has evolved on multiple occasions within vertebrates including birds, turtles, and a few groups of mammals such as anteaters, baleen whales and pangolins. Where early birds are concerned, the fossil record is fragmentary. A question that has intrigued biologists is: Based on this fossil record, were teeth lost in the common ancestor of all living birds or convergently in two or more independent lineages of birds? A research team led by biologists at the University of California, Riverside and Montclair State University, NJ, has found an answer. Using the degraded remnants of tooth genes in birds to determine when birds lost their teeth, the team reports in the Dec. 12 issue ofScience that teeth were lost in the common ancestor of all living birds more than 100 million years ago.

"One of the larger lessons of our finding is that 'dead genes,' like the remnants of dead organisms that are preserved in the fossil record, have a story to tell," said Mark Springer, a professor of biology and one of the lead authors of the study along with Robert Meredith at Montclair State University who was previously a graduate student and postdoctoral researcher in Springer's laboratory. "DNA from the crypt is a powerful tool for unlocking secrets of evolutionary history."

Springer explained that edentulism and the presence of a horny beak are hallmark features of modern birds. "Ever since the discovery of the fossil bird Archaeopteryx in 1861, it has been clear that living birds are descended from toothed ancestors," he said. "However, the history of tooth loss in the ancestry of modern birds has remained elusive for more than 150 years."

All toothless/enamelless vertebrates are descended from an ancestor with enamel-capped teeth. In the case of birds, it is theropod dinosaurs. Modern birds use a horny beak instead of teeth, and part of their digestive tract to grind up and process food.

Tooth formation in vertebrates is a complicated process that involves many different genes. Of these genes, six are essential for the proper formation of dentin (DSPP) and enamel (AMTN, AMBN, ENAM, AMELX, MMP20).

The researchers examined these six genes in the genomes of 48 bird species, which represent nearly all living bird orders, for the presence of inactivating mutations that are shared by all 48 birds. The presence of such shared mutations in dentin and enamel-related genes would suggest a single loss of mineralized teeth in the common ancestor of all living birds.

Springer, Meredith, and other members of their team found that the 48 bird species share inactivating mutations in both dentin-related (DSPP) and enamel-related genes (ENAMAMELX, AMTNMMP20), indicating that the genetic machinery necessary for tooth formation was lost in the common ancestor of all modern birds.

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The fastest camera ever created records events at 100 billion frames per second

The fastest camera ever created records events at 100 billion frames per second | Amazing Science |
You can watch exactly how light interacts with objects using a camera that captures 100 billion frames per second.

The capture of transient scenes at high imaging speed has been long sought by photographers1-4, with early examples being the well known recording in 1878 of a horse in motion5 and the 1887 photograph of a supersonic bullet6. However, not until the late twentieth century were breakthroughs achieved in demonstrating ultrahigh-speed imaging (more than 105 frames per second)7. In particular, the introduction of electronic imaging sensors based on the charge-coupled device (CCD) or complementary metal–oxide–semiconductor (CMOS) technology revolutionized high-speed photography, enabling acquisition rates of up to 107 frames per second8. Despite these sensors’ widespread impact, further increasing frame rates using CCD or CMOS technology is fundamentally limited by their on-chip storage and electronic readout speed9. A team of scientists now demonstrate a two-dimensional dynamic imaging technique, compressed ultrafast photography (CUP), which can capture non-repetitive time-evolving events at up to 1011frames per second. Compared with existing ultrafast imaging techniques, CUP has the prominent advantage of measuring an xyt (xy, spatial coordinates; t, time) scene with a single camera snapshot, thereby allowing observation of transient events with temporal resolution as tens of picoseconds. Furthermore, akin to traditional photography, CUP is receive-only, and so does not need the specialized active illumination required by other single-shot ultrafast imagers23. As a result, CUP can image a variety of luminescent—such as fluorescent or bioluminescent—objects. Using CUP, we visualize four fundamental physical phenomena with single laser shots only: laser pulse reflection and refraction, photon racing in two media, and faster-than-light propagation of non-information (that is, motion that appears faster than the speed of light but cannot convey information). Given CUP’s capability, the researchers expect it to find widespread applications in both fundamental and applied sciences, including biomedical research.

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One dollar paper microscope from Stanford can detect parasites in contaminated water with 500x magnification

One dollar paper microscope from Stanford can detect parasites in contaminated water with 500x magnification | Amazing Science |

A team of engineers now describe an ultra-low-cost origami-based approach for large-scale manufacturing of microscopes, specifically demonstrating brightfield, darkfield, and fluorescence microscopes. Merging principles of optical design with origami enables high-volume fabrication of microscopes from 2D media. Flexure mechanisms created via folding enable a flat compact design. Structural loops in folded paper provide kinematic constraints as a means for passive self-alignment. This light, rugged instrument can survive harsh field conditions while providing a diversity of imaging capabilities, thus serving wide-ranging applications for cost-effective, portable microscopes in science and education.

Microscopes are ubiquitous tools in science, providing an essential, visual connection between the familiar macro-world and the remarkable underlying micro-world. Since the invention of the microscope, the field has evolved to provide numerous imaging modalities with resolution approaching 250 nm and smaller [1]. However, some applications demand non-conventional solutions due to contextual challenges and tradeoffs between cost and performance. For example, in situ examination of specimens in the field provides important opportunities for ecological studies, biological research, and medical screening. Further, ultra-low cost DIY microscopes provide means for hands-on science education in schools and universities. Finally, this platform could empower a worldwide community of amateur microscopists to capture and share images of a broad range of specimens.

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New 'high-entropy' alloy is as light as aluminum but as strong as titanium alloys

New 'high-entropy' alloy is as light as aluminum but as strong as titanium alloys | Amazing Science |

High-entropy alloys are materials that consist of five or more metals in approximately equal amounts. These alloys are currently the focus of significant attention in materials science and engineering because they can have desirable properties. The research team combined lithium, magnesium, titanium, aluminum and scandium to make a nanocrystalline high-entropy alloy that has low density, but very high strength.

"The density is comparable to aluminum, but it is stronger than titanium alloys," says Dr. Carl Koch, Kobe Steel Distinguished Professor of Materials Science and Engineering at NC State and senior author of a paper on the work. "It has a combination of high strength and low density that is, as far as we can tell, unmatched by any other metallic material. The strength-to-weight ratio is comparable to some ceramics, but we think it's tougher - less brittle - than ceramics."

There are a wide range of uses for strong, lightweight materials, such as in vehicles or prosthetic devices. "We still have a lot of research to do to fully characterize this material and explore the best processing methods for it," Koch says.

At this point, the primary problem with the alloy is that it is made of 20 percent scandium, which is extremely expensive.

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There's A Lab Where You Can Pay To Have Your Dog Cloned

There's A Lab Where You Can Pay To Have Your Dog Cloned | Amazing Science |

We’ve come a long way since scientists cloned the first adult mammal, a sheep named Dolly, in 1996. Now, you can pay to have your own dog duplicated using the same technique scientists used to make Dolly. But there’s a catch (aside, of course, from the whole ethical dilemma of incubating your recently deceased pet’s cells inside a random pup): It costs around $US100,000, and there’s only one lab in the world that does it. In South Korea.

To clone a dog, scientists at the Sooam Biotech Research Foundation laboratory do exactly what researchers did to make Dolly. First, they take a few cells from your pet and reprogram them to stop growing — effectively putting their DNA to sleep. Then, using a tiny straw-like device, they suck up the dormant cell and inject it inside another dog cell that’s been emptied of its nucleus, or command center. Then the scientists zap the new cell with electricity, coaxing the two parts to fuse into one cell. Once they make sure the new cell “works,” meaning it can divide and develop on its own, the scientists implant it inside a surrogate mama pup. In a few months, if all goes well, the surrogate dog will give birth to a puppy that looks just like yours.

The new animal won’t be absolutely identical, of course. Missing all the memories of the old animal, for starters. “When thinking of cloning, try to think of an identical twin,” Sooam biologist Insung Hwang explains. “The dog will not be 100% the same — the spots on a Dalmatian clone will be different, for example — but for breeds without such characteristics it will be very hard to tell them apart.”

The lab that oversees the procedure isn’t without controversy, however. Eight years after winning international acclaim for cloning the world’s first dog in 2005, Sooam founder and veterinarian by training Woo Suk Hwang was publically disgraced for falsifying research on human embryo cloning. Hwang (no relation to Insung Hwang) was expelled from Seoul National University, where he did the research, and is still facing criminal charges.

Despite the public outcry, Hwang’s supporters managed to gather more than $US3.5 million to help him start Sooam in 2006. Since then, the lab has cloned more than 400 dogs, mostly pets, reports Nature. In the past few years, Sooam researchers have picked up their pace, producing about 15 puppies a month.

Beyond Dog Cloning:

Some scientists want to use Sooam’s cloning technique to replicate far more than people’s deceased pups. Geneticist George Church and Sooam biologist Insung Hwang, for example, are exploring the possibility of bringing long-extinct animals back to life using samples of their DNA. Church and Hwang are part of a team of researchers who recently autopsied the body of a woolly mammoth who lived about 40,000 years ago and whose blood was surprisingly well preserved, along with her body, in Siberia. The autopsy is featured in detail in a recent Smithsonian documentary called “How To Clone A Woolly Mammoth.”

Andrea J Galan's curator insight, April 4, 2016 5:37 PM
So I clicked on this article because I have a debate on the topic of cloning humans and animals. I find it interesting how people wou.d actAlly spend so much money to create another look alike of their dead dog. Don't get me wrong I love my 13 year old Labrador but I don't think I could handle seeing another dog with her exact same features once she passed. I. Also curious about the welfare of the surrogate mothers. Are they constantly pregnant, do they get a break from being pregnant. I
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Time's Mysterious Past: New Theories Suggest Big Bang Was Not The Beginning

Time's Mysterious Past: New Theories Suggest Big Bang Was Not The Beginning | Amazing Science |

Tentative new work from Julian Barbour of the University of Oxford, Tim Koslowski of the University of New Brunswick and Flavio Mercati of the Perimeter Institute for Theoretical Physics suggests that perhaps the arrow of time doesn’t really require a fine-tuned, low-entropy initial state at all but is instead the inevitable product of the fundamental laws of physics. Barbour and his colleagues argue that it is gravity, rather than thermodynamics, that draws the bowstring to let time’s arrow fly. Their findings were published in October in Physical Review Letters.
The team’s conclusions come from studying an exceedingly simple proxy for our universe, a computer simulation of 1,000 pointlike particles interacting under the influence of Newtonian gravity. They investigated the dynamic behavior of the system using a measure of its "complexity," which corresponds to the ratio of the distance between the system’s closest pair of particles and the distance between the most widely separated particle pair. The system’s complexity is at its lowest when all the particles come together in a densely packed cloud, a state of minimum size and maximum uniformity roughly analogous to the big bang. The team’s analysis showed that essentially every configuration of particles, regardless of their number and scale, would evolve into this low-complexity state. Thus, the sheer force of gravity sets the stage for the system’s expansion and the origin of time’s arrow, all without any delicate fine-tuning to first establish a low-entropy initial condition.
From that low-complexity state, the system of particles then expands outward in both temporal directions, creating two distinct, symmetric and opposite arrows of time. Along each of the two temporal paths, gravity then pulls the particles into larger, more ordered and complex structures—the model’s equivalent of galaxy clusters, stars and planetary systems. From there, the standard thermodynamic passage of time can manifest and unfold on each of the two divergent paths. In other words, the model has one past but two futures. As hinted by the time-indifferent laws of physics, time’s arrow may in a sense move in two directions, although any observer can only see and experience one. “It is the nature of gravity to pull the universe out of its primordial chaos and create structure, order and complexity,” Mercati says. “All the solutions break into two epochs, which go on forever in the two time directions, divided by this central state which has very characteristic properties.”
Although the model is crude, and does not incorporate either quantum mechanics or general relativity, its potential implications are vast. If it holds true for our actual universe, then the big bang could no longer be considered a cosmic beginning but rather only a phase in an effectively timeless and eternal universe. More prosaically, a two-branched arrow of time would lead to curious incongruities for observers on opposite sides. “This two-futures situation would exhibit a single, chaotic past in both directions, meaning that there would be essentially two universes, one on either side of this central state,” Barbour says. “If they were complicated enough, both sides could sustain observers who would perceive time going in opposite directions. Any intelligent beings there would define their arrow of time as moving away from this central state. They would think we now live in their deepest past.”

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Germanium semiconductor milestone for creating ultrafast circuits

Germanium semiconductor milestone for creating ultrafast circuits | Amazing Science |

A laboratory at Purdue University provided a critical part of the world's first transistor in 1947 – the purified germanium semiconductor – and now researchers here are on the forefront of a new germanium milestone. The team has created the first modern germanium circuit – a complementary metal–oxide–semiconductor (CMOS) device – using germanium as the semiconductor instead of silicon.

"Bell Labs created the first transistor, but the semiconductor crystal made of purified germanium was provided by Purdue physicists," said Peide "Peter" Ye, a Purdue professor of electrical and computer engineering.

Germanium was superseded by silicon as the semiconductor of choice for commercial CMOS technology. However, the industry will soon reach the limit as to how small silicon transistors can be made, threatening future advances. Germanium is one material being considered to replace silicon because it could enable the industry to make smaller transistors and more compact integrated circuits, Ye said. Compared to silicon, germanium also is said to have a "higher mobility" for electrons and electron "holes," a trait that makes for ultra-fast circuits.

In new findings, Purdue researchers show how to use germanium to produce two types of transistors needed for CMOS electronic devices. The material had previously been limited to "P-type" transistors. The findings show how to use the material also to make "N-type" transistors. Because both types of transistors are needed for CMOS circuits, the findings point to possible applications for germanium in computers and electronics, he said.

Findings will be detailed in two papers being presented during the 2014 IEEE International Electron Devices Meeting on Dec. 15-17 in San Francisco. One paper was authored by Ye and graduate students Heng Wu, Nathan Conrad and Wei Luo, the same authors of the second paper together with graduate students Mengwei Si, Jingyun Zhang and Hong Zhou.

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WHO: Malaria deaths halved since 2000 in quest for total eradication

WHO: Malaria deaths halved since 2000 in quest for total eradication | Amazing Science |

The international health community is celebrating what may prove to be a turning point in the global fight against malaria. Deaths from the mosquito-borne disease have been almost halved since the turn of the millennium, according to a new report from the World Health Organization (WHO), with experts saying they’re confident the illness can one day be eradicated entirely.

However, although the malaria mortality rate fell by 47 percent globally and by 54 percent in Africa, the WHO warns that much more still needs to be done. Dozens of countries are reporting insecticide-resistance among their mosquito populations and in Africa — where 90 percent of malaria deaths occur — some 278 million people lack even the basic protection of an insecticide-treated mosquito net.

The disease also continues to disproportionately affect children in poor countries. Of the estimated global malaria death toll of 584,000 in 2013, some 437,000 of those cases were African children under the age of five. However, malaria infections in the African continent have decreased significantly since the year 2000, falling by 23 percent from 173 million to 128 million.

The WHO attributes these gains to the increased spread of established methods, including rapid diagnostic tests (which have risen globally from 46 million 319 million over the past five years); malarial treatment using artemisnin (392 million treatments were bought last year, up from 11 million in 2004); and access to insecticide-treated nets (427 million of which have been distributed in the last two years).

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Quantum Teleportation Reaches Farthest Distance Yet

Quantum Teleportation Reaches Farthest Distance Yet | Amazing Science |
Physicists have teleported a light particle 15 miles (25 kilometers), making it the farthest quantum teleportation yet.

Advances in quantum teleportation could lead to better Internet and communication security, and get scientists closer to developing quantum computers. About five years ago, researchers could only teleport quantum information, such as which direction a particle is spinning, across a few meters. Now, they can beam that information across several miles.

Physicists can't instantly transport matter, but they can instantly transport information through quantum teleportation. This works thanks to a bizarre quantum mechanics property called entanglement. Quantum entanglement happens when two subatomic particles stay connected no matter how far apart they are. When one particle is disturbed, it instantly affects the entangled partner. It's impossible to tell the state of either particle until one is directly measured, but measuring one particle instantly determines the state of its partner.

In the new, record-breaking experiment, researchers from the University of Geneva, NASA's Jet Propulsion Laboratory and the National Institute of Standards and Technology used a superfast laser to pump out photons. Every once in a while, two photons would become entangled. Once the researchers had an entangled pair, they sent one down the optical fiber and stored the other in a crystal at the end of the cable. Then, the researchers shot a third particle of light at the photon traveling down the cable. When the two collided, they obliterated each other.

Quantum information has already been transferred dozens of miles, but this is the farthest it's been transported using an optical fiber, and then recorded and stored at the other end. Other quantum teleportation experiments that beamed photons farther used lasers instead of optical fibers to send the information. But unlike the laser method, the optical-fiber method could eventually be used to develop technology like quantum computers that are capable of extremely fast computing, or quantum cryptography that could make secure communication possible.

Keith Wayne Brown's curator insight, December 10, 2014 1:48 PM

the future information

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Smoking Still Causes A Large Proportion of Cancer Deaths in the United States

Smoking Still Causes A Large Proportion of Cancer Deaths in the United States | Amazing Science |
More than 30 years ago, a groundbreaking analysis by famed British researchers, Richard Doll and Richard Peto, calculated that 30 percent of all cancer deaths in the United States were caused by smoking. Since that time, no new estimate of this percentage has been published in the scientific literature. During that same time, smoking rates have dropped, but new cancers have been added to the list of those established as caused by smoking and lung cancer death rates among female smokers have increased.

To provide a well-documented estimate for cigarette smoking and cancer mortality in the contemporary United States, researchers led by Eric J. Jacobs, PhD, looked at the most recent data on smoking rates from the National Health Interview Survey (NHIS) as well as data on the risks of smoking derived from epidemiologic studies, to estimate what is called the population attributable fraction (PAF), described as the proportion of cancer deaths in the population caused by smoking.

The authors found that the PAF for active cigarette smoking was 28.7% when estimated conservatively, including only deaths from the 12 cancers currently formally established as caused by smoking by the US Surgeon General. When estimated more comprehensively, including excess deaths from all cancers, the PAF was 31.7% percent. These estimates do not include additional potential cancer deaths from environmental tobacco smoke or other type of tobacco use such as cigars, pipes, or smokeless tobacco.

The authors say despite important declines in smoking prevalence, the PAF for smoking and cancer mortality estimated for 2010 is similar to the 30% estimated by Doll and Peto more than 30 years ago. But that does not indicate that declines in smoking rates have not made important contributions to reducing cancer mortality. Rather, other factors have contributed to increasing the PAF, including the addition of new cancers to the list of those counted as caused by smoking, increases over time in death rates from lung cancer among female smokers, and progress in reducing deaths from cancer caused by factors other than smoking.
Michael Mazo's curator insight, December 13, 2014 1:40 PM

Taking into consideration that most of the incredibly large and thriving tobacco companies are based in America its not surprise to see a large number of lung cancer related deaths to impact our nation. When these companies are reaping profits in any way possible, they will also do anything possible to continue this trend even if that means putting innocent people at risk. Although they pay a hefty tax on the cigarettes they sell, they still continue to large amounts of money and pay for advertising. If one were to stand the way of collecting their money, they would do anything in their power to remove you from the picture. In addition to being so rich, because of all their money it makes them very powerful. It doesn't take an individual to stop a company like this, it takes an entire nation.

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Small-Molecule Inhibition of BRDT for Male Contraception

Small-Molecule Inhibition of BRDT for Male Contraception | Amazing Science |

A pharmacologic approach to male contraception remains a longstanding challenge in medicine. Toward this objective, the spermatogenic effects of a selective small-molecule inhibitor (JQ1) of the bromodomain and extraterminal (BET) subfamily of epigenetic reader proteins are being explored. A team of scientists now reports potent inhibition of the testis-specific member BRDT, which is essential for chromatin remodeling during spermatogenesis. Biochemical and crystallographic studies confirm that occupancy of the BRDT acetyl-lysine binding pocket by JQ1 prevents recognition of acetylated histone H4. Treatment of mice with JQ1 reduced seminiferous tubule area, testis size, and spermatozoa number and motility without affecting hormone levels. Although JQ1-treated males mate normally, inhibitory effects of JQ1 evident at the spermatocyte and round spermatid stages cause a complete and reversible contraceptive effect. These data establish a new contraceptive that can cross the blood:testis boundary and inhibit bromodomain activity during spermatogenesis, providing a lead compound targeting the male germ cell for contraception.

National Microscope Exchange's comment, December 10, 2014 1:44 AM
Very Classic Defination
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Discovering the Undiscovered: The time is right to apply genomic technologies to discover new life on Earth

Discovering the Undiscovered: The time is right to apply genomic technologies to discover new life on Earth | Amazing Science |

In a perspective piece published November 6 in the journal Science,Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, along with Microbial Program Head Tanja Woyke, discusses why the time is right to apply genomic technologies to discover new life on Earth. In this perspective they propose the division of microbial life on Earth into three categories: explored, unexplored, and undiscovered. The first can be grown in the laboratory. The second encompasses the uncultivated organisms from environmental samples known only by their molecular signatures. The third, the focus of the perspective, is the yet-undiscovered life that up until now has eluded detection.

“We are poised, armed with a new toolkit of powerful genomic technologies to generate and mine the increasingly large datasets to discover new life that may be strikingly different from those that we catalogued thus far,” said Rubin. “Nature has been tinkering with life for at least three billion years and we now have a new set of ways to look for novel life that have so far eluded discovery.”

“Massive-scale metagenomic sequencing of environmental DNA and RNA samples should, in principle, generate sequence data from any entity for which nucleic acids can be extracted,” Rubin noted. “Analysis of these data to identify outliers to previously defined life represents a powerful means to explore the unknown.”

In addition, Rubin pointed to the advent of single-cell sequencing with microfluidic and cell sorting approaches, focused specifically on cells that lack genes that match previously identified ones, as another approach in the search for completely novel organisms.

“We also need to choose particularly suitable environmental niches so that we are not just looking, ‘under the street lamp’ — at environments that we have already previously studied.”

Rubin suggested targets for the discovery of novel life including extreme, inhospitable and isolated environments that are expected to be preferred niches for early life, potentially sheltered from more modern microbial competitors. This would include low oxygen subsurface sites with environmental conditions predating the Great Oxidation Event that occurred about 2.3 billion years ago when the atmosphere went from very low to high oxygen concentrations. Support for the idea that isolated low-oxygen environments may be preferred niches for early life comes from observations that anaerobic niches deep within Earth’s crust tend to harbor ancient branches within the domains of life.

Exploring the “undiscovered” classification is expected to be a boon for enriching the public data portals, Rubin said. He also noted that lurking among these difficult ones may well be the discovery of a “fourth domain” of life, to which a reasonable mariner, ancient or contemporary, may proclaim, “full speed ahead.”

Rubin presented recent work on “microbial dark matter” at the DOE Joint Genome Institute’s 2014 Genomics of Energy and Environment Meeting that can be viewed at The DOE JGI’s 10th Annual Meeting will be held March 24-26, 2015 and the list of preliminary speakers can be found here:

Dahl Winters's curator insight, December 18, 2014 8:00 AM

A big use of big data - exploring the genomes of life on Earth.  One of the biggest data sets in the world is the one we carry around with us and on us every day.

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Chemists Fabricate Novel Rewritable Paper Using Color Switching Redox Dyes

Chemists Fabricate Novel Rewritable Paper Using Color Switching Redox Dyes | Amazing Science |

First developed in China in about the year A.D. 150, paper has many uses, the most common being for writing and printing upon.  Indeed, the development and spread of civilization owes much to paper’s use as writing material. According to surveys, 90 percent of all information in businesses used today is retained on paper, even though the bulk of this printed paper is discarded after just one-time use. This is such a waste of paper and ink cartridges — not to mention the accompanying environmental problems such as deforestation and chemical pollution to air, water and land—could be curtailed if the paper were “rewritable,” that is, capable of being written on and erased multiple times.

Chemists at the University of California, Riverside have now fabricated in the lab just such novel rewritable paper, one that is based on the color switching property of commercial chemicals called redox dyes.  The dye forms the imaging layer of the paper.  Printing is achieved by using ultraviolet light to photobleach the dye, except the portions that constitute the text on the paper.  The new rewritable paper can be erased and written on more than 20 times with no significant loss in contrast or resolution.

“This rewritable paper does not require additional inks for printing, making it both economically and environmentally viable,” said Yadong Yin, a professor of chemistry, whose lab led the research. “It represents an attractive alternative to regular paper in meeting the increasing global needs for sustainability and environmental conservation.”

The rewritable paper is essentially rewritable media in the form of glass or plastic film to which letters and patterns can be repeatedly printed, retained for days, and then erased by simple heating.

The paper comes in three primary colors: blue, red and green, produced by using the commercial redox dyes methylene blue, neutral red and acid green, respectively.  Included in the dye are titania nanocrystals (these serve as catalysts) and the thickening agent hydroxyethyl cellulose (HEC).  The combination of the dye, catalysts and HEC lends high reversibility and repeatability to the film.

During the writing phase, ultraviolet light reduces the dye to its colorless state.  During the erasing phase, re-oxidation of the reduced dye recovers the original color; that is, the imaging material recovers its original color by reacting with ambient oxygen.  Heating at 115 C can speed up the reaction so that the erasing process is often completed in less than 10 minutes. “The printed letters remain legible with high resolution at ambient conditions for more than three days – long enough for practical applications such as reading newspapers,” Yin said. “Better still, our rewritable paper is simple to make, has low production cost, low toxicity and low energy consumption.”

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Strange Object in our Solar System: The Dwarf Planet Haumea

Strange Object in our Solar System: The Dwarf Planet Haumea | Amazing Science |

Haumea is the third closest dwarf planet to the Sun and is located beyond the orbit of Neptune. It has about 1/3 the mass of Pluto and was discovered in 2004 by a team of astronomers from Caltech at the Palomar Observatory in California working on a project headed by Mike Brown. However, Haumea was co-discovered in 2005 by a team headed by J. L. Ortiz at the Sierra Nevada Observatory in Spain.

Haumea claim to fame is because of its elongated shape making it the least spherical of all the dwarf planets. Haumea’s highly ellipsoid shape is believed to be the result of its rapid rotation. This rotational speed, along with its collisional origin make Haumea one of the densest dwarf planets discovered to date.

It was classified as dwarf planet by the International Astronomical Union (IAU) on September 17th, 2008 and was named after Haumea, the Hawaiian goddess of childbirth. Haumea has two small satellites by itself, called Hi’iaka & Namaka. These two little moons were discovered by Mike Brown’s team in 2005 through observations using the W.M. Keck Observatory.

Haumea’s moons are thought to be the result of a collision with a large object billions of years ago – causing pieces of Haumea to fragment and begin orbiting the planet. One day on Haumea lasts 3.9 Earth hours because it is one of the fastest rotating large objects in the solar system.

The dwarf planet is made from rock with a thick coating of ice. Haumea is the third brightest object in the Kuiper belt, after the dwarf planets Pluto and Makemake. On a clear night with a good quality telescope, it is possible to see Haumea in the night sky.

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Molecular Interferometry Makes a New Break

Molecular Interferometry Makes a New Break | Amazing Science |
A new technique in matter-wave interferometry using laser light to fragment molecules may open the door to interference demonstrations with large bio-molecules or nanoclusters.

Quantum mechanics has been spectacularly successful in explaining the microscopic realm, yet exactly how it interfaces to the everyday macroscopic world is still an open question. To this end, a long-standing goal in physics has been to realize a system like that envisaged by Erwin Schrödinger in the early days of quantum mechanics in which a large object like a cat simultaneously exists in two separate states (such as “dead” and “alive”) [1]. Schrödinger originally proposed his famous “gedanken experiment” to point out a problem with quantum theories that allow for the existence of cat states and other macroscopic superpositions, which in fact do not appear in everyday life. While progress has been made in exploring the quantum-classical boundary with nanomechanical systems [2], much still remains to be done. Now physicists at the University of Vienna, Austria, have developed a new technique for observing quantum effects in the external motion of large molecules. Nadine Dörre and co-workers used three standing waves of UV light as the optical elements in a matter-wave interferometer for molecules with masses as high as 2000 atomic mass units (amu) [3]. The method can potentially be extended to the interference of larger particles, such as complex organic molecules and even small “living” organisms like viruses.

In the current experiments, the researchers demonstrated interference with clusters of hexafluorobenzene or vanillin, both of which have single photon ionization energies significantly above 7.9eV. To observe interference of the molecular clusters, the authors used three loss gratings in an arrangement known as a time domain Talbot-Lau interferometer [7]. Here the gratings are pulsed standing waves of light separated by nearly equal time intervals. In a Talbot-Lau interferometer, the first grating produces an array of pointlike sources, which increases the spatial coherence of the initial, almost incoherent molecular beam. The matter waves are then diffracted by the second grating, which in the near field, produces the intricate “carpet” of interference shown in Fig. 2. At a certain time after the second grating pulse, the matter-wave field displays a pattern of dark and bright fringes that replicates the transmission profile of the second grating. This phenomenon, known as the Talbot effect [8], is the signature used to infer that interference is taking place. Unfortunately, directly observing the structure of the matter-wave intensity created by the Talbot effect is difficult because the scale of the patterns seen in the figure is on the order of 100nm. Instead, the third grating in a Talbot-Lau interferometer forms a transmission mask, which produces a signal at the detector that depends strongly on the timing between the second and third grating pulse. If this time is equal to the so-called Talbot time, then the detector signal will drop to a minimum. By combining the mass dependence of the Talbot time and the use of a mass spectrometer as part of their detector, Dörre et al. were able to select different cluster sizes for interference.

This research is published in Physical Review Letters.
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DNA-based memory can record multiple inputs from engineered gene circuits

DNA-based memory can record multiple inputs from engineered gene circuits | Amazing Science |

A new DNA-based recorder allows bioengineers to create cell cultures that detect information in their environment and store it for later use. Such 'designer' cells might in the future be used to monitor water quality in a village, or measure the amount of sugar a person eats. The technique is described this week in Science1.

In synthetic biology, genes are engineered to regulate each other's expression in such a way that they can perform logic operations similar to those in computer circuits. Memory storage has long been considered one of the key components needed to fulfil the promise of this technology.

“Building gene circuits requires not only computation and logic, but a way to store that information,” says bioengineer Timothy Lu of the Massachusetts Institute of Technology in Cambridge. “DNA provides a very stable form of memory and will allow us to do more complex computing tasks.”

In previous synthetic-biology attempts, data storage has been laborious to create. It also recorded only the presence or absence of one particular sensory input, and could be used only for limited applications. In the latest paper, Lu and his colleague Fahim Farzadfard describe how they can record many types of data simultaneously, and can register the accumulation of the input over time, like a car’s odometer counts kilometres. The stored information can then be read out by sequencing the DNA. They dub their method SCRIBE, for Synthetic Cellular Recorders Integrating Biological Events.

“It’s a nice addition to the toolbox”, which could complement other memory-storage techniques, says Jérôme Bonnet, a bioengineer at the Centre for Structural Biochemistry in Montpellier, France, who was not involved in the research. “There’s room for different types of memory in synthetic biology — as in computing you have the hard drive and the RAM.”

In a proof-of-concept experiment described in their latest paper, the team created a colony of Escherichia coli bacteria in which retrons responded to the presence of a chemical, flipping a switch in the E. coli genome that made it resistant to an antibiotic. This transformation did not happen to the same extent inside every E. coli cell in the colony, howeverThe higher the concentration of the triggering chemical, the greater was the proportion of cells that ended up antibiotic resistant.

Unlike previous methods that serve as a digital form of memory — turning on or off like a light switch — SCRIBE could work as an 'analog' form of memory that functions more like a dimmer switch. The memory is not contained in a single E. coli cell, but in the entire culture. “Distributing memory across this population becomes a powerful way of doing things.”

Mike Dele's curator insight, March 20, 2015 7:52 PM

i am thinking towards a situation where the human race will be able to use DNA recorders for combating crime. The idea seems to be an unrealistic one, but if it can be achieved the world might witness one of the  crime  free era of our history, because it will make a criminal investigation  a lot easier and it will also be able to record and give an accurate location of someone if been tracked. 

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NASA found ancient lake on Mars capable to support life for thousands of years

NASA found ancient lake on Mars capable to support life for thousands of years | Amazing Science |

An ancient lake on Mars was capable of supporting life for tens or hundreds of thousands of years, researchers reported today based on findings from NASA's Curiosity rover. In March, NASA announced that the lake was once capable of supporting microbial life, but little more was known. Now researchers have shown that the lake existed around 3.5-3.6 billion years ago and actually contained an "Earth-like" environment. "There would have been some snow, maybe ice up in the mountains around the crater rim," John Grotzinger, project scientist for Curiosity, said at a press conference this morning. "It's pretty darn similar to Earth.

Not long after touching down in the Gale Crater last August, NASA's Curiosity rover was driven over to Yellowknife Bay, a trough over 16 feet deep made up of basaltic sandstones. It's there, near the edges of the lake where lower levels of dirt are accessible, that researchers tested to see if microorganisms could have existed. In particular, they say that chemolithoautotrophs — a type of microorganism commonly found in caves on Earth — could have existed in the lake's environment, breaking down the area's rocks and minerals for energy as they do on Earth.

The Martian lake would have been around 30 miles long and 3 miles wide, or as Grotzinger puts it, "typical of a small Finger Lake of Upstate New York." The researchers say that liquid water once existed there, and they've previously speculated that it would actually have been drinkable because of its low salinity and neutral acidity level. Actual signs of microbial life haven't been detected yet, but researchers say that an elemental cocktail that would have supported them was certainly present.

The research was presented at the American Geophysical Union and is published in a series of papers in Science.

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New Explanation For Earth's Biggest Migration of Animals

New Explanation For Earth's Biggest Migration of Animals | Amazing Science |

Each day small sea creatures known as plankton rise from deep underwater to the ocean's surface during the night and then return to the depths in daytime. Zoologists describe this “diel” movement, named after the Latin word for day, as Earth’s biggest migration. The stimulus for this mass migration has long puzzled scientists. But a team from the European Molecular Biology Laboratory in Heidelberg, Germany has now discovered a likely answer: melatonin, the hormone that influences humans' sleep patterns so significantly that it's sometimes taken to relieve the effects of jet lag.

The team focused on larvae of the plankton species Platynereis dumerilii, a type of marine worm. “This is the only plankton model species amenable to molecular development, neurobiology, and behavioral studies,” said zoologist Detlev Arendt, who led the study. The team identified a group of brain cells in the larvae that respond to light, run an internal clock that differentiates day from night, and – most important – make melatonin during the night.

The melatonin, channeled through other types of neurons, apparently triggered the worms to begin dropping below the surface. During the day, however, the production of melatonin stops. That seemed to cause the plankton to move back up to the ocean surface.

To confirm melatonin’s role, the team influenced the behavior pattern artificially. “When we exposed the larvae to melatonin during the day, they switched towards night-time behavior,” team member Maria Antonietta Tosches said. “It’s as if they were jet-lagged.” The research, reported in the journal Cell, indicates that melatonin works by influencing the physical process responsible for the larvae’s up-and-down travels.

The process relies on a series of microscopic flippers, called cilia. Arranged in a belt around each larva’s middle, they drive the larvae upward by beating up and down at a rapid rate, rather like the flapping of birds’ wings. Once the larvae reach the surface at dusk, the beating slows down. As a result, the larvae start to sink. By morning, they have settled back down in the depths, which shelter them from the damaging ultraviolet rays that strike the water surface during daylight.

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The harlequin filefish uses 'smell camouflage' to hide from predators

The harlequin filefish uses 'smell camouflage' to hide from predators | Amazing Science |

The harlequin filefish is a master of disguise. The reef-dwelling fish (Oxymonacanthus longirostris) sports a brightly colored pattern that allows it to fade into the coral it calls home. Now, scientists have discovered that the filefish doesn’t just look like a branch of coral—it smells like one, too. The researchers report online today in the Proceedings of the Royal Society B that the animal picks up the smell of the corals it feeds on, which serves as a handy disguise from the cunning predators that use odor to hunt down their prey. To identify this chemical camouflage, the team placed cod—a common predator of reef fish—in tanks with filefish and a species of coral that either matched their diet or a coral species the fish hadn’t been feeding on. The filefish were hidden inside perforated containers within the aquarium so that the cod could only smell, and not see, their prey. The researchers found that cod were much less likely to hang out around the filefish container when the species of coral present matched the reef fish’s last meals. Exactly how the filefish retains the coral smell is still unknown, but the disguise even fooled coral-feeding crabs. When the researchers gave the crabs a choice between their favorite corals and a filefish that fed on their favorite corals, they often chose the filefish. Many invertebrate species, like caterpillars, are known to incorporate compounds from the plants they eat into the outer layer of their skin to hide from hungry predators. But the filefish is the first vertebrate species found to camouflage its smell, which means that the behavior could be even more widespread across the animal kingdom than previously thought.

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Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing

Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing | Amazing Science |

Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process.

A group of scientists now applied next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. The scientists conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

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Birds, bees, lizards, elephants, and chimpanzees all share a survival trait: They self-medicate

Birds, bees, lizards, elephants, and chimpanzees all share a survival trait: They self-medicate | Amazing Science |

Anyone who has seen a dog eat grass during a walk has witnessed self-medication. The dog probably has an upset stomach or a parasite. The grass helps them vomit up the problem or eliminate it with the feces.

The science of animal self-medication is called zoopharmacognosy, derived from the roots zoo (“animal”), pharma (“drug”), and gnosy (“knowing”). It’s not clear how much knowing or learning is involved, but many animals seem to have evolved an innate ability to detect the therapeutic constituents in plants. Although the evidence is entirely circumstantial, the examples are plentiful. The practice is spreading across the animal kingdom in sometimes surprising ways.

Most studies of animal self-medication, however, are in the great apes. In the 1960s, the Japanese anthropologist Toshisada Nishida observed chimpanzees in Tanzania eating aspella leaves, which had no nutritional value. Harvard primatologist Richard Wrangham saw the same behavior at Jane Goodall’s Gombe reserve, where chimps were swallowing leaves whole. Other scientists noted the same in other chimp colonies. Without chewing, the animals weren’t getting much nutritional benefit. So why do it?

In 1996, biologist Michael Huffman suggested the chimps were self-medicating. Huffman, an American who has worked for years in Japan at the Primate Research Institute at Kyoto University, first saw a parasite-ridden, constipated chimpanzee in Tanzania chew on the leaves of a noxious plant it would normally avoid. By the next day, the chimpanzee was completely recovered (1).

The plants had bristly leaves, rough to the touch. Huffman theorized the chimps were swallowing the plants to take advantage of that roughness, using the leaves and stems to scour their intestines and rid themselves of parasites. Other researchers observed the same practice among other apes across Africa.

Huffman established widely used criteria for judging when an animal is self-medicating. First, the plant eaten cannot be a regular part of the animal’s diet; it is used as medicine not food. Second, the plant must provide little or no nutritional value to the animal. Third, the plant must be consumed during those times of year—for example, the rainy season—when parasites are most likely to cause infections. Fourth, other animals in the group don’t participate (2, 3). If the activity meets these standards, it is safe to assume the animal is self-medicating, Huffman says. Researchers have observed the practice in 25 regions involving 40 different plants.

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Berkeley Lab Researchers Set World Record for Compact Particle Accelerator

Berkeley Lab Researchers Set World Record for Compact Particle Accelerator | Amazing Science |

Using one of the most powerful lasers in the world, researchers have accelerated subatomic particles to the highest energies ever recorded from a compact accelerator. The team, from the U.S. Department of Energy’s Lawrence Berkeley National Lab (Berkeley Lab), used a specialized petawatt laser and a charged-particle gas called plasma to get the particles up to speed. The setup is known as a laser-plasma accelerator, an emerging class of particle accelerators that physicists believe can shrink traditional, miles-long accelerators to machines that can fit on a table.

The researchers sped up the particles—electrons in this case—inside a nine-centimeter long tube of plasma. The speed corresponded to an energy of 4.25 giga-electron volts. The acceleration over such a short distance corresponds to an energy gradient 1000 times greater than traditional particle accelerators and marks a world record energy for laser-plasma accelerators.

“This result requires exquisite control over the laser and the plasma,” says Dr. Wim Leemans, director of the Accelerator Technology and Applied Physics Division at Berkeley Lab and lead author on the paper. The results appear in the most recent issue of Physical Review Letters.

Traditional particle accelerators, like the Large Hadron Collider at CERN, which is 17 miles in circumference, speed up particles by modulating electric fields inside a metal cavity. It’s a technique that has a limit of about 100 mega-electron volts per meter before the metal breaks down.

Laser-plasma accelerators take a completely different approach. In the case of this experiment, a pulse of laser light is injected into a short and thin straw-like tube that contains plasma. The laser creates a channel through the plasma as well as waves that trap free electrons and accelerate them to high energies. It’s similar to the way that a surfer gains speed when skimming down the face of a wave.

The record-breaking energies were achieved with the help of BELLA (Berkeley Lab Laser Accelerator), one of the most powerful lasers in the world. BELLA, which produces a quadrillion watts of power (a petawatt), began operation just last year.

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Where are my veins? World-first vein viewing technology

Where are my veins? World-first vein viewing technology | Amazing Science |

Do you have hard-to-find veins? Don’t let that stop you from donating blood.  In a world-first study, the Australian Red Cross Blood service is conducting research into the use of leading-edge technology to visualise blood donors’ veins during blood donation.

The vein visualization devices are portable, and project an image of the veins onto the skin’s surface using non-invasive near infra-red technology. The Blood Service is aiming to find out if this procedure reduces anxiety, improves donation comfort and makes donors more likely to donate again.

The study will assess the responses of 300 first-time and 600 return donors aged between 18 and 30 attending the Chatswood and Elizabeth Street Donor Centres in Sydney. "Donor Centre staff have found the technology particularly useful in cases where the vein is not visible to the naked eye” said Dr Dan Waller, one of the senior investigators on the trial.

“We are keen to retain our young donors, and it is important to test if this technology may help us do that.”

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