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Peta, Exa, Yotta And Beyond: Big Data Reaches Cosmic Proportions

Peta, Exa, Yotta And Beyond: Big Data Reaches Cosmic Proportions | Amazing Science | Scoop.it
Since the advent of big data, it's been a struggle for some to get a real sense of just how big big data really is. You hear strange terms like "peta," exa" and "yotta"… but what does all that really mean? When managing massive amounts of data, the scales were talking about can quickly reach astronomical proportions.

 

Coming from Indiana, where the value of Pi might have once legally been 3, it would be easy to just slap the label "gi-fracking-normous" on the scales we're talking about, but I'm going to push past my native upbringing and focus on recent efforts to quantify big data. A recent infographic from clearCi is one such effort, outlining the scale of data produced on the Internet each day: 2.5 quintillion bytes of data. Storage vendor Seagate figures that a total of 450 exabytes of storage shipped in 2011.

 

How Big Can Data Get? It will get bigger, of course. The next level of data will be the brontobyte, which is 10E27 bytes. The human body contains 7 octillion atoms. If each atom were a byte of information, that's 7 brontobytes of data.

 

No one company, not even Google, will every get to the upper ends of these scales. But with terabyte amounts of data an everyday occurrence and petabytes not so rare anymore, a lot of companies will need to wrap their heads around the notion of what the big in big data really means and bring it down to Earth.

 

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Scientists identify single-gene mutations (CARD11) that lead to atopic dermatitis

Scientists identify single-gene mutations (CARD11) that lead to atopic dermatitis | Amazing Science | Scoop.it

Researchers have identified mutations in a gene called CARD11 that lead toatopic dermatitis, or eczema, an allergic skin disease. Scientists from the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, and other institutions discovered the mutations in four unrelated families with severe atopic dermatitis and studied the resulting cell-signaling defects that contribute to allergic disease. Their findings, reported in Nature Genetics, also suggest that some of these defects potentially could be corrected by supplementation with the amino acid glutamine.

 

The scientists analyzed the genetic sequences of patients with severe atopic dermatitis and identified eight individuals from four families with mutations in the CARD11 gene, which provides instructions for production of a cell-signaling protein of the same name. While some people with these mutations had other health issues, such as infections, others did not, implying that mutations in CARD11 could cause atopic dermatitis without leading to other medical issues often found in severe immune system syndromes.

The scientists next set out to understand how the newly discovered CARD11 mutations contribute to atopic dermatitis.

 

Each of the four families had a distinct mutation that affected a different region of the CARD11 protein, but all the mutations had similar effects on T-cell signaling. With cell culture and other laboratory experiments, the researchers determined that the mutations led to defective activation of two cell-signaling pathways, one of which typically is activated in part by glutamine.  

 

Growing cultured T cells from patients with CARD11 mutations with excess glutamine boosted mTORC1 activation, a key part of one of the affected pathways, suggesting the potential to partially correct the cell-signaling defects that may contribute to atopic dermatitis. The scientists now are planning a study to assess the effect of supplemental glutamine and leucine, another amino acid that activates mTORC1, in people with atopic dermatitis with and without CARD11 mutations.

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Crystal ‘domain walls’ may lead to tinier electronic devices

Crystal ‘domain walls’ may lead to tinier electronic devices | Amazing Science | Scoop.it

Queen’s University Belfast physicists have discovered a radical new way to modify the conductivity (ease of electron flow) of electronic circuits — reducing the size of future devices. This new research takes another approach: Altering the properties of a crystal to eliminate the need for multiple circuits in devices.

 

To do that, the scientists used “ferroelectric copper-chlorine boracite” crystal sheets, which are almost as thin as graphene. The researchers discovered that squeezing the crystal sheets with a sharp needle at a precise location causes a jigsaw-puzzle-like pattern of “domains walls” to develop around the contact point.

Then, using external applied electric fields, these writable, erasable domain walls can be repeatedly moved around in the crystal to create a variety of new electronic properties. They can appear, disappear, or move around within the crystal, all without permanently altering the crystal itself.

 

Eliminating the need for multiple circuits may reduce the size of future computers and other devices, according to the researchers. The team’s findings have been published in an open-access paper in Nature Communications.

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A molecular plaster to repair DNA

A molecular plaster to repair DNA | Amazing Science | Scoop.it

All cells are confronted with DNA damage, for example by exposure of the skin to UV rays, chemical byproducts of nerve cells consuming sugar, or immune cells destroying bacteria. If these DNA lesions are not - or badly - repaired, they may initiate tumor formation. Thankfully, cells have evolved an elaborate control system to correct these DNA anomalies. Uli Rass and Nico Thomä at the FMI, together with colleagues at the University of Geneva (UNIGE), have now discovered the key role of a protein called Rif1 in the protection, stabilization and repair of damaged DNA. This study, published in the journal Nature Structural & Molecular Biology, uncovers a DNA maintenance function likely to be present in all eukaryotes because the region of Rif1 that enables the formation of a protective sheath around DNA lesions is similar in humans and yeast.


Via Integrated DNA Technologies
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Close-up View of DNA Replication Yields Surprises

Close-up View of DNA Replication Yields Surprises | Amazing Science | Scoop.it

Almost all life on earth is based on DNA being copied, or replicated, and understanding how this process works could lead to a wide range of discoveries in biology and medicine. Now for the first time scientists have been able to watch individual steps in the replication of a single DNA molecule, with some surprising findings. For one thing, there’s a lot more randomness at work than has been thought.

 

“It’s a different way of thinking about replication that raises new questions,” said Stephen Kowalczykowski, distinguished professor in microbiology and molecular genetics at the University of California, Davis, and at the UC Davis Comprehensive Cancer Center. The work is published June 15 in the journal Cell with co-authors James Graham, postdoctoral researcher at UC Davis, and Kenneth Marians, Sloan Kettering Cancer Center.

 

Using sophisticated imaging technology and a great deal of patience, the researchers were able to watch DNA from E. coli bacteria as it replicated and measure how fast enzyme machinery worked on the different strands.


Via Integrated DNA Technologies
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China's quantum satellite clears a major hurdle on the way to ultrasecure communications

China's quantum satellite clears a major hurdle on the way to ultrasecure communications | Amazing Science | Scoop.it

The Chinese satellite is one giant step for the quantum internet. Just months into its mission, the world’s first quantum-communications satellite has achieved one of its most ambitious goals.

Researchers report in Science1 that, by beaming photons between the satellite and two distant ground stations, they have shown that particles can remain in a linked quantum state at a record-breaking distance of more than 1,200 kilometers. That phenomenon, known as quantum entanglement, could be used as the basis of a future secure quantum-communications network.

 

The feat is the first result reported from China’s Quantum Experiments at Space Scale (QUESS) mission, also known as Micius after an ancient Chinese philosopher. Launched last August, the craft is designed to demonstrate principles underlying quantum communication. The team is likely to launch more quantum-enabled satellites to start building a network.


Quantum communication is secure because any interference is detectable. Two parties can exchange secret messages by sharing an encryption key encoded in the properties of entangled particles; any eavesdropper would affect the entanglement and so be detected.

 

The Micius team has already done experiments exploring whether it is possible to create such encryption keys using entangled photons, and even 'teleport' information securely between Earth and space, says Pan Jian-Wei, a physicist at the University of Science and Technology of China in Hefei and the main architect of the probe. But he says that his team is not yet ready to announce the results.

 

In theory, entangled particles should remain linked at any separation. That can be checked using a classic experiment called a Bell test. Central to QUESS's experiments is a laser beam mounted on the satellite. For the Bell test, the beam was split to generate pairs of photons that share a common quantum state, in this case related to polarization. The entangled photons were funneled into two onboard telescopes that fired them at separate stations on the ground: one in Delingha, on the northern Tibetan Plateau, and the other 1,203 kilometers south, at Gaomeigu Observatory in Lijiang. Once the particles arrived, the team used the Bell test to confirm that they were still entangled.

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Zika virus evolution and spread in the Americas

Zika virus evolution and spread in the Americas | Amazing Science | Scoop.it

One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.

 

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention1, 2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. A group of researchers now addresses this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. They analyzed the timing and patterns of introductions into distinct geographic regions. Their documented phylogenetic evidence suggests a rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. Furthermore, they find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. The group succeeded to identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.


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The world’s fastest supercomputer signals new dominance for Chinese hardware

The world’s fastest supercomputer signals new dominance for Chinese hardware | Amazing Science | Scoop.it
China now has more supercomputers among the world’s top 500 fastest machines than any other nation.

 

Housed in the National Supercomputing Center in Wuxi, China, TaihuLight is capable of performing 93 quadrillion calculations per second. That makes it three times faster than the previous number one, Tianhe-2—also from China—which achieves speeds of 33 quadrillion calculations per second.

 

TaihuLight uses 41,000 chips, each with 260 processor cores, to give it a grand total of 10.65 million cores. There’s also 1.3 petabytes of RAM—slightly less than Tianhe-2. The new computing champ is more efficient than its predecessor, too, drawing 15.3 megawatts of power, compared to 17.8 megawatts.

 

Today’s news also delivers two blows to American supercomputer dominance. Notably, it's the first time that more of the world’s top 500 supercomputers are Chinese than American. China now boasts 167 systems in the rankings, while the U.S. has 165. No other country rivals either nation: third on the list is Japan, with 29 systems.

 

Even more striking is the fact that TaihuLight doesn’t rely on Western hardware. In the past, the world’s fastest supercomputers have been built using U.S.-designed chips, with hardware from Intel or International Business Machines, or else silicon manufactured under license from Sun Microsystems. TaihuLight, however, uses Chinese-made processors.

 

In fact, the supercomputer was funded by China’s 863 program, sometimes known as the State High-Tech Development Plan. The program was set up in 1986 by the government of the People's Republic of China, with the aim of growing the nation’s domestic technology sectors and making China independent of other countries for its hardware.

 

To date, China’s wider chip business has lagged behind that of the U.S. and far, far behind those of Japan and South Korea. But in March the country announced it was investing $24 billion into its home-grown semiconductor industry. The state-owned chip maker XMC is already building facilities that will manufacture NAND flash-memory and DRAM chips, the first of which is expected to be operational in 2017.


Via Ben van Lier
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How DNA-encoded libraries are revolutionizing drug discovery

How DNA-encoded libraries are revolutionizing drug discovery | Amazing Science | Scoop.it

With the bar-coding technology, drugmakers leverage the chemistry of large numbers.  Forty trillion is the kind of number that gives one pause. Consider it written out with its 13 zeros: 40,000,000,000,000. Assembling and maintaining a collection of 40 trillion of anything seems like a mind-bogglingly massive task. But in February the Danish biopharmaceutical company Nuevolution announced that it had created a library of 40 trillion unique molecules—quite possibly the largest collection of synthetic compounds in the world.

 

You might think it would require every building in Copenhagen to store batches of 40 trillion different compounds. Not so, says Alex Haahr Gouliaev, Nuevolution’s chief executive officer. “All of that fits into an Eppendorf tube and is handled by one person for screening,” he says.

 

The substance that makes it possible to maintain this multitudinous mixture of molecules is the same substance that contains the code of life—DNA.

 

Nuevolution covalently attaches a short, unique strand of DNA to each of its 40 trillion compounds. Instead of holding the directions for life, though, these DNA strands encode the recipe used to synthesize each linked molecule. This trick enables the firm to store all the compounds as a mixture in a small volume and later sequence, or read, them out. As the cost for DNA sequencing plummets and the repertoire of DNA-compatible chemical reactions grows, these so-called DNA-encoded libraries are becoming a go-to resource for finding new drug candidates and research tools for large pharmaceutical companies, small biotech companies, and academics alike.


Via Integrated DNA Technologies
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New open-source website provides microfluidics for the masses

New open-source website provides microfluidics for the masses | Amazing Science | Scoop.it

A new MIT-designed open-source website might well be the Pinterest of microfluidics. The site, Metafluidics.org, is a free repository of designs for lab-on-a-chip devices, submitted by all sorts of inventors, including trained scientists and engineers, hobbyists, students, and amateur makers. Users can browse the site for devices ranging from simple cell sorters and fluid mixers, to more complex chips that analyze ocular fluid and synthesize gene sequences.

 

The site also serves as a social platform for the microfluidics community: Any user can log in to submit a design; they can also like, comment on, and download design files to reproduce a featured device or improve on it.

 

David S. Kong, director of the MIT Media Lab’s new Community Biotechnology Initiative, says the new site is designed to accelerate innovation in microfluidic design, which until now has followed a conventional, academically peer-reviewed route.

 

“There’s a familiar experience for people in microfluidics: You see a really amazing paper that shows you a design, but if you want to try to copy the design, the actual design files that are a critical part of reproducing or remixing a device are not shared in any systematic way,” Kong says. “As a result, researchers around the world are in parallel reinventing the wheel. It’s one of the reasons why open-source in general is a very powerful set of principles. It can really accelerate the diffusion of technology.”

 

Kong and his colleagues outlined the open-source platform in a paper published last week in the journal Nature Biotechnology. His co-authors are Todd Thorsen, Peter Carr, and Scott Wick of MIT’s Lincoln Laboratory; Jonathan Babb and Jeremy Gam in the Department of Biological Engineering; and Ron Weiss, professor of biological engineering and of electrical engineering and computer science.

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Apple Is Focusing on an Autonomous Car System to Revolutionize Industry

Apple Is Focusing on an Autonomous Car System to Revolutionize Industry | Amazing Science | Scoop.it
After years toiling away in secret on its car project, Apple Inc. Chief Executive Officer Tim Cook has for the first time laid out exactly what the company is up to in the automotive market: It’s concentrating on self-driving technology.

“We’re focusing on autonomous systems,” Cook said in a June 5 interview on Bloomberg Television that amounted to his most detailed comments yet on Apple’s automotive plans. “It’s a core technology that we view as very important.” He likened the effort to “the mother of all AI projects,” saying it’s “probably one of the most difficult AI projects to work on.”

The prospect of self-driving cars has seen a slew of technology companies push into the auto industry, according to McKinsey & Co. Alphabet Inc.’s Waymo unit has signed partnerships with Fiat Chrysler Automobiles NV and Lyft Inc. to develop the technology. And carmakers from BMW AG to General Motors Co. have opened sizable Silicon Valley offices and dedicated hundreds of millions of dollars to acquire autonomous vehicle startups.

Apple had initially been seeking to build its own car, before recalibrating those ambitions last year to prioritize the underlying technology for autonomous driving, Bloomberg News reported. The iPhone maker had hired more than 1,000 engineers to work on Project Titan, as the car team is known internally, after it started in 2014.

Ballooning costs and headcount led to Apple veteran Bob Mansfield being given the reins of the team in 2016. Cook has never before openly outlined Apple’s plans, though public filings have surfaced in recent months that provided snapshots of Apple’s efforts.

The iPhone maker secured a permit from the California Department of Motor Vehicles in April to test three self-driving sports-utility vehicles, photos of which emerged several weeks later. A half-dozen vehicles had been surreptitiously testing the autonomous technology on public roads in and around the San Francisco Bay area for at least a year, according to someone familiar with Project Titan. Apple spokesman Tom Neumayr declined to comment on how long the company has been conducting road tests.

In December, Steve Kenner, Apple’s director of product integrity, penned a letter to the National Highway Traffic Safety Administration revealing the company’s interest in automotive technology. It became public when it was published on a federal website. In the letter, Kenner wrote about the company’s excitement surrounding the potential for automated systems in fields like transportation.

“There is a major disruption looming there,” Cook said on Bloomberg Television, citing self-driving technology, electric vehicles and ride-hailing. “You’ve got kind of three vectors of change happening generally in the same time frame.”
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Scientists discover a 2-D magnet

Scientists discover a 2-D magnet | Amazing Science | Scoop.it

Magnetic materials form the basis of technologies that play increasingly pivotal roles in our lives today, including sensing and hard-disk data storage. But as our innovative dreams conjure wishes for ever-smaller and faster devices, researchers are seeking new magnetic materials that are more compact, more efficient and can be controlled using precise, reliable methods.

 

A team led by the University of Washington and the Massachusetts Institute of Technology has for the first time discovered magnetism in the 2-D world of monolayers, or materials that are formed by a single atomic layer. The findings, published June 8 in the journal Nature, demonstrate that magnetic properties can exist even in the 2-D realm -- opening a world of potential applications.

 

"What we have discovered here is an isolated 2-D material with intrinsic magnetism, and the magnetism in the system is highly robust," said Xiaodong Xu, a UW professor of physics and of materials science and engineering, and member of the UW's Clean Energy Institute. "We envision that new information technologies may emerge based on these new 2-D magnets."

 

Xu and MIT physics professor Pablo Jarillo-Herrero led the international team of scientists who proved that the material -- chromium triiodide, or CrI3 -- has magnetic properties in its monolayer form. Other groups, including co-author Michael McGuire at the Oak Ridge National Laboratory, had previously shown that CrI3 -- in its multilayered, 3-D, bulk crystal form -- is ferromagnetic. In ferromagnetic materials, the "spins" of constituent electrons, analogous to tiny, subatomic magnets, align in the same direction even without an external magnetic field.

 

But no 3-D magnetic substance had previously retained its magnetic properties when thinned down to a single atomic sheet. In fact, monolayer materials can demonstrate unique properties not seen in their multilayered, 3-D forms. "You simply cannot accurately predict what the electric, magnetic, physical or chemical properties of a 2-D monolayer crystal will be based on the behavior of its 3-D bulk counterpart," said co-lead author and UW doctoral student Bevin Huang.

 

Atoms within monolayer materials are considered "functionally" two-dimensional because the electrons can only travel within the atomic sheet, like pieces on a chessboard. To discover the properties of CrI3 in its 2-D form, the team used Scotch tape to shave a monolayer of CrI3 off the larger, 3-D crystal form. "Using Scotch tape to exfoliate a monolayer from its 3-D bulk crystal is surprisingly effective," said co-lead author and UW doctoral student Genevieve Clark. "This simple, low-cost technique was first used to obtain graphene, the 2-D form of graphite, and has been used successfully since then with other materials."

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Miracle material could end cracked phone screen era

Miracle material could end cracked phone screen era | Amazing Science | Scoop.it

Currently, most parts of a smart phone are made of silicon and other compounds, which are expensive and break easily, but with almost 1.5 billion smart phones purchased worldwide last year, manufacturers are on the lookout for something more durable and less costly.

 

Dr Elton Santos from Queen's University's School of Mathematics and Physics, has been working with a team of top-notch scientists from Stanford University, University of California, California State University and the National Institute for Materials Science in Japan, to create new dynamic hybrid devices that are able to conduct electricity at unprecedented speeds and are light, durable and easy to manufacture in large scale semiconductor plants.

 

The team found that by combining semiconducting molecules C60 with layered materials, such as graphene and hBN, they could produce a unique material technology, which could revolutionise the concept of smart devices. The winning combination works because hBN provides stability, electronic compatibility and isolation charge to graphene while C60 can transform sunlight into electricity. Any smart device made from this combination would benefit from the mix of unique features, which do not exist in materials naturally. This process, which is called van der Waals solids, allows compounds to be brought together and assembled in a pre-defined way.

 

Dr Elton Santos explains: "Our findings show that this new 'miracle material' has similar physical properties to Silicon but it has improved chemical stability, lightness and flexibility, which could potentially be used in smart devices and would be much less likely to break.

 

"The material also could mean that devices use less energy than before because of the device architecture so could have improved battery life and less electric shocks." He added: "By bringing together scientists from across the globe with expertise in chemistry, physics and materials science we were able to work together and use simulations to predict how all of the materials could function when combined -- and ultimately how these could work to help solve every day problems.

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Icelandic family of 10 suffering from psychosis helps to identify RBM12 as lead causative candidate

Icelandic family of 10 suffering from psychosis helps to identify RBM12 as lead causative candidate | Amazing Science | Scoop.it

A team from Iceland, Finland, and Germany have found evidence that links some forms of psychosis to mutations that lop off the end of the RNA-binding motif protein 12-coding gene RBM12.

 

As they reported in Nature Genetics, the researchers used genotyping and imputation-based long-range phasing to search for risky variants in a family from Iceland that included six individuals with of schizophrenia and two family members apiece with schizoaffective disorder or psychotic bipolar disorder. They also profiled seven psychosis-affected family members by whole-genome sequencing.

 

With genetic data from that family — and from a psychosis-affected family from Finland — the team narrowed in on a rare, psychosis-related truncation mutation in RBM12. Although that mutation did segregate with psychosis, it did not appear to be fully penetrant. Instead, the group reported that some individuals carrying the mutation did share non-psychosis-related psychiatric and neuropsychological features with their affected relatives.

 

"In addition to identifying RBM12 … the work reported here provides a template for future familial studies of psychosis, suggesting that the mutations involved are likely to be recent, may be incompletely penetrant for psychosis, but lead to related phenotypes in carriers unaffected by psychosis, and are likely to act in concert with other sequence variants," corresponding author Kari Stefansson, with Decode/Amgen and the University of Iceland, and his colleagues wrote.

 

Based on array-based genotypes, long-range phasing, and/or genome sequence data for the 10 individuals with psychosis from the first family, the researchers narrowed in on a shared nonsense mutation in the last coding exon of RBM12 that was verified with Sanger sequencing. The alteration did not turn up in the Genome Aggregation Database (gnomAD), they reported, and was identified in fewer than two dozen other Icelanders, all descended from the family in question.

 

Along with experiments done to gauge expression of the RBM12 in lymphoblast cell lines from several individuals who did or did not carry mutated versions of the gene, the team scoured sequence databases for other suspicious looking changes in RBM12, narrowing in on another mutation in the gene in an individual from Finland who had been diagnosed with schizophrenia.

 

That individual also carried a chromosome 22 deletion already associated with psychosis, the authors noted. But the same deletion was not present in four siblings with psychosis who shared RBM12 with the first Finnish family member. Conversely, unaffected siblings did carry the chromosome 22 deletion. The RBM12 mutation did not turn up in the unaffected Finnish family members, though findings from the Icelandic family indicated that mutations in that gene are not fully penetrant. 

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Graphene-based computer would be 1,000 times faster than silicon-based, use 100th the power

Graphene-based computer would be 1,000 times faster than silicon-based, use 100th the power | Amazing Science | Scoop.it

A future graphene-based transistor using spintronics could lead to tinier computers that are a thousand times faster and use a hundredth of the power of silicon-based computers. The radical transistor concept, created by a team of researchers at Northwestern University, The University of Texas at Dallas, University of Illinois at Urbana-Champaign, and University of Central Florida, is explained this month in an open-access paper in the journal Nature Communications.

 

Transistors act as on and off switches. A series of transistors in different arrangements act as logic gates, allowing microprocessors to solve complex arithmetic and logic problems. But the speed of computer microprocessors that rely on silicon transistors has been relatively stagnant since around 2005, with clock speeds mostly in the 3 to 4 gigahertz range.

 

The researchers discovered that by applying a magnetic field to a graphene ribbon (created by unzipping a carbon nanotube), they could change the resistance of current flowing through the ribbon. The magnetic field — controlled by increasing or decreasing the current through adjacent carbon nanotubes — increased or decreased the flow of current.

 

A cascading series of graphene transistor-based logic circuits could produce a massive jump, with clock speeds approaching the terahertz range — a thousand times faster.* They would also be smaller and substantially more efficient, allowing device-makers to shrink technology and squeeze in more functionality, according to Ryan M. Gelfand, an assistant professor in The College of Optics & Photonics at the University of Central Florida.

 

The researchers hope to inspire the fabrication of these cascaded logic circuits to stimulate a future transformative generation of energy-efficient computing.

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Mapping gene expression, one cell at a time

Mapping gene expression, one cell at a time | Amazing Science | Scoop.it

EMBL researchers have succeeded in creating a molecular atlas of a whole organism, studying the expression patterns of more than 100 important genes in each cell of the marine worm Platynereis dumerilii, as they report in the journalPNAS. Study authors Hernando Martínez Vergara and Detlev Arendt explain.

 

The researchers are interested in the evolution of animals and in particular the evolution of the nervous system. Ultimately they would like to understand how simple nervous systems gave rise to the complexity of the human brain. An important step in answering this question is identifying all the types of cells that are present in various organisms. The scientists can then make comparisons to infer whether certain cell types in different organisms were inherited from a common ancestor, and at what point in the history of life they evolved. To be able to do this, they need to construct comprehensive atlases of cell types that exist in a range of organisms. That’s a huge technical challenge but they have now succeeded in creating one such atlas for Platynereis, focusing on gene expression. An international project is currently under way to create a human cell atlas, which is likely to take many years.

 

The technique used is called "whole mount in situ hybridization", in which a whole Platynereis larva is taken and label molecules are added. These labels then enter its cells and reveal where a particular gene is active. Separate observations in different larvae are carried out for each gene, and the researchers then use a computer to superimpose all the resulting images. This allows them to see which genes are active in different parts of the animal.

 

In this study they investigated about 100 genes that are known to be important for defining cell types.

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Blue Brain team discovers a multi-dimensional universe of brain networks

Blue Brain team discovers a multi-dimensional universe of brain networks | Amazing Science | Scoop.it

For most people, it is a stretch of the imagination to understand the world in four dimensions but a new study has discovered structures in the brain with up to eleven dimensions - ground-breaking work that is beginning to reveal the brain's deepest architectural secrets. Using algebraic topology in a way that it has never been used before in neuroscience, a team from the Blue Brain Project has uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.

 

The research, published today in Frontiers in Computational Neuroscience, shows that these structures arise when a group of neurons forms a clique: each neuron connects to every other neuron in the group in a very specific way that generates a precise geometric object. The more neurons there are in a clique, the higher the dimension of the geometric object.

 

"We found a world that we had never imagined," says neuroscientist Henry Markram, director of Blue Brain Project and professor at the EPFL in Lausanne, Switzerland, "there are tens of millions of these objects even in a small speck of the brain, up through seven dimensions. In some networks, we even found structures with up to eleven dimensions."

 

Markram suggests this may explain why it has been so hard to understand the brain. "The mathematics usually applied to study networks cannot detect the high-dimensional structures and spaces that we now see clearly."

 

If 4D worlds stretch our imagination, worlds with 5, 6 or more dimensions are too complex for most of us to comprehend. This is where algebraic topology comes in: a branch of mathematics that can describe systems with any number of dimensions. The mathematicians who brought algebraic topology to the study of brain networks in the Blue Brain Project were Kathryn Hess from EPFL and Ran Levi from Aberdeen University.

 

"Algebraic topology is like a telescope and microscope at the same time. It can zoom into networks to find hidden structures - the trees in the forest - and see the empty spaces - the clearings - all at the same time," explains Hess.

 

In 2015, Blue Brain published the first digital copy of a piece of the neocortex - the most evolved part of the brain and the seat of our sensations, actions, and consciousness. In this latest research, using algebraic topology, multiple tests were performed on the virtual brain tissue to show that the multi-dimensional brain structures discovered could never be produced by chance.

 

Experiments were then performed on real brain tissue in the Blue Brain's wet lab in Lausanne confirming that the earlier discoveries in the virtual tissue are biologically relevant and also suggesting that the brain constantly rewires during development to build a network with as many high-dimensional structures as possible.


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Eye-opening picture of the fetal immune system finally emerges

Eye-opening picture of the fetal immune system finally emerges | Amazing Science | Scoop.it

A human fetus in its second trimester is extraordinarily busy. It is developing skin and bones, the ability to hear and swallow, and working on its first bowel movement. Now, a study published on 14 June in Nature finds that fetuses are also acquiring a functioning immune system — one that can recognize foreign proteins, but is less inclined than a mature immune system to go on the attack (N. McGovern et al. Naturehttp://dx.doi.org/10.1038/nature22795; 2017).

 

The results add to a growing body of literature showing that the fetal immune system is more active than previously appreciated. “In general textbooks, you see this concept of a non-responsive fetus is still prevailing,” says immunologist Jakob Michaelsson at the Karolinska Institute in Stockholm. But the fetal immune system is unique, he says. “It’s not just immature, it’s special.”

 

A developing fetus is constantly exposed to foreign proteins and cells, which are transferred from the mother through the placenta. In humans, this exposure is more extensive than in many other mammals, says immunologist Mike McCune at the University of California, San Francisco. As a result, laboratory mice have proved a poor model for studying the developing human fetal immune system.

 

But fully understanding that development could reveal the reasons for some miscarriages, as well as explain conditions such as pre-eclampsia, which is associated with abnormal immune responses to pregnancy and causes up to 40% of premature births. And organ-transplant surgeons have long been interested in how a developing fetus and its mother tolerate one another without either of them launching an immune attack — the hope is to find ways to suppress the immune system’s response to transplanted organs. 

 

For Jerry Chan, an obstetrician and gynaecologist at the KK Women’s and Children’s Hospital in Singapore, understanding the fetal immune system was important for his goal of developing stem-cell treatments and gene therapies for genetic disorders in developing fetuses. Chan and his colleagues wanted to know whether there was a developmental stage at which such treatments could be given without the risk of the therapies themselves being attacked by the immune system. 

 

To do this, Chan teamed up with immunologist Florent Ginhoux at the Agency for Science, Technology and Research in Singapore to study dendritic cells, immune cells that break down foreign material and present fragments of it to other immune cells called T cells. Some T cells are then activated to target the foreign material for destruction. The team found that human fetuses have functional dendritic cells by 13 weeks of gestation. But although the cells behave much like the adult versions, their response to foreign human proteins differs: rather than mark the foreign material for annihilation, fetal dendritic cells are more likely to activate a special category of T cell called regulatory T cells, which suppress immune responses.

 

This could reflect a need to avoid a catastrophic immune response against a mother’s cells. “You don’t want too much immune response in a developing fetus,” says Ginhoux. “It is very dangerous — this is a critical point in development.” Previous studies had found specialized immune cells — including T cells and natural killer cells — in fetuses as young as nine weeks, says Ginhoux. But the dendritic-cell findings are particularly important because these cells orchestrate immune responses, says Michaelsson. Without them, he says, the body can’t target specific foreign material for destruction.

 

The results highlight the fact that the fetal immune system is not merely an immature, less-active version of its adult counterpart, but one that has its own distinct function, says transplant immunologist William Burlingham at the University of Wisconsin in Madison.

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Despite setbacks, Google's drone delivery project is moving forward rapidly

Despite setbacks, Google's drone delivery project is moving forward rapidly | Amazing Science | Scoop.it

Project Wing, the delivery drone initiative under development at Google-parent Alphabet, felt another jolt of turbulence as more members of the team were officially cut loose. But even as sources inside the high-profile group report ongoing challenges, the drone unit is preparing an important update to demonstrate progress that's expected in a matter of weeks.

Business Insider has heard from multiple people that a group of employees left the team this week. And despite getting a big shout-out from Alphabet CEO Larry Page in a recent public letter, Project Wing is still not close to being ready to launch, according to a person familiar with the matter.

Our sources are calling the latest job reductions at Wing a layoff, however an X spokesperson explains that these cuts are not new but rather the final part of the reorganization that began in January, shortly after the departure of the unit's leader Dave Vos in the fall.

Employees were informed back then that their jobs were going away and they had until mid-April to land another one elsewhere including within Google. Some of the affected employees managed to get hired into new groups, while others are no longer employed by Alphabet.

"X (and Alphabet generally) typically gives people time and support to find new roles when there are changes in teams/projects," a spokesperson told Business Insider.

Ambitious initiatives like Project Wing, which is trying to invent a drone that can deliver packages, is by definition a risky undertaking with no guarantee of success. 

Wing is part of X, formerly known as Google X, which is the company's R&D unit working on far-out "moonshot" projects, racing against Amazon and drone makers like DJI to usher in what may one day be a massive new market, delivering everything from food to medicine straight to people's doorsteps.

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HAL: An Artificial Intelligence Developed Its Own Non-Human Language

HAL: An Artificial Intelligence Developed Its Own Non-Human Language | Amazing Science | Scoop.it
When Facebook designed chatbots to negotiate with one another, the bots made up their own way of communicating.

 

A buried line in a new Facebook report about chatbots’ conversations with one another offers a remarkable glimpse at the future of language. In the report, researchers at the Facebook Artificial Intelligence Research lab describe using machine learning to train their “dialog agents” to negotiate. (And it turns out bots are actually quite good at dealmaking.) At one point, the researchers write, they had to tweak one of their models because otherwise the bot-to-bot conversation “led to divergence from human language as the agents developed their own language for negotiating.” They had to use what’s called a fixed supervised model instead.

 

In other words, the model that allowed two bots to have a conversation—and use machine learning to constantly iterate strategies for that conversation along the way—led to those bots communicating in their own non-human language. If this doesn’t fill you with a sense of wonder and awe about the future of machines and humanity then, I don’t know, go watch Blade Runner or something.

 

The larger point of the report is that bots can be pretty decent negotiators—they even use strategies like feigning interest in something valueless, so that it can later appear to “compromise” by conceding it. But the detail about language is, asone tech entrepreneur put it, a mind-boggling “sign of what’s to come.”

 

To be clear, Facebook’s chatty bots aren’t evidence of the singularity’s arrival. Not even close. But they do demonstrate how machines are redefining people’s understanding of so many realms once believed to be exclusively human—like language.

 

Already, there’s a good deal of guesswork involved in machine learning research, which often involves feeding a neural net a huge pile of data then examining the output to try to understand how the machine thinks. But the fact that machines will make up their own non-human ways of conversing is an astonishing reminder of just how little we know, even when people are the ones designing these systems.


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Blood-red ‘zombie’ worms that suck at the bone marrow of dead whales found in abyss off Australian coast

Blood-red ‘zombie’ worms that suck at the bone marrow of dead whales found in abyss off Australian coast | Amazing Science | Scoop.it

Blood-red zombie worms that suck on the bone marrow of dead whales have been found in Australian waters for the first time.

After hauling up the skeleton of a pilot whale lying four kilometers underwater just off the northern seaside town of Byron Bay, scientists discovered the worms burrowed deep inside the mammal’s bones and sucking on the marrow.

The one-centimetre long worms have previously been found in parts of the Pacific and Atlantic oceans, but never off the Australian coast.

 

Scientists believe the animals been around for millions of years and once feasted on the bones of aquatic dinosaurs.

The worms were among hundreds of new and rarely seen marine creatures discovered by the team of 58 scientists, technicians and crew during a month-long voyage, which ended in Brisbane yesterday.

 

Dr Tim O'Hara, the chief scientist on board and Museum Victoria's senior curator of marine invertebrates, described the worms as an “exciting find” given their unusual way of feeding.


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A Theory of Reality is More Than Just the Sum of Its Parts

A Theory of Reality is More Than Just the Sum of Its Parts | Amazing Science | Scoop.it
New math shows how, contrary to conventional scientific wisdom, conscious beings and other macroscopic entities might have greater influence over the future than does the sum of their microscopic components.

Via Complexity Digest, Bernard Ryefield
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Mammals Seem to Have a 12-Hour Clock in Addition to the 24-Hour Circadian Clock

Mammals Seem to Have a 12-Hour Clock in Addition to the 24-Hour Circadian Clock | Amazing Science | Scoop.it

Along with their standard 24-hour circadian cycle, mammals may also harbor a distinct 12-hour clock, scientists report in Cell Metabolism.

 

Researchers led by Bert O’Malley of Baylor College of Medicine in Houston, Texas, identified a set of metabolism and stress genes in mouse liver cells that followed a pattern of expression on a 12-hour cycle—starting in the morning and again in the evening. O’Malley’s team also found that a 12-hour clock, distinct from the 24-hour circadian clock, drives this morning-evening rhythm in gene expression.

 

The clock’s origin, the scientists suggest, may be rooted in organisms’ initial evolution in the ocean millions of years ago. “It’s a provocative argument,” Cambridge University biologist Michael Hastings tells The Scientist in a phone interview. He is cautious about the claim of an evolutionary connection between the 12-hour clock in sea creatures and the 12-hour cycles seen in mammals. Still, he commends the team on taking a “cross-biology” approach toward exploring 12-hour gene-expression rhythms in a range of animals.

 

In past studies, researchers have shown that coastal sea animals, such as the crustacean Eurydice pulchra have a dominant body clock driven by the 12-hour ebb and flow of the tides. Rhythms of gene expression every 12-hours have also been found in mammals, such as mice. Whether mammals’ 12-hour rhythms are driven by the body’s circadian clock or something else, however, has remained a mystery.

 

Interested in that question and also observations that the time of day can affect humans’ ability to think clearly, handle stress, and respond to medicine, O’Malley and colleagues began to look more closely at mammals’ 12-hour gene-expression rhythms. In the new study, they analyzed gene-expression data of 18,108 mouse liver genes. Using a mathematical technique developed by researchers at Rice University, the team identified 3,652 genes that had 12-hour rhythms that didn’t appear to be associated with the mouse’s circadian clock.

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Severe pollution ‘devastating’ China’s vital ecosystem, research study shows

Severe pollution ‘devastating’ China’s vital ecosystem, research study shows | Amazing Science | Scoop.it

The startling extent to which man-made pollution is devastating China’s vital ecosystem’s ability to offset damaging carbon emissions has been revealed.

 

The study found that the Net Primary Productivity (NPP) – or the amount of carbon plants in an ecosystem can take in – is significantly reduced when the amount of surface ozone increases. Crucially, this reduction is significantly greater than the effect aerosol particles have in encouraging plants to increase carbon intake through reducing canopy temperatures and increasing the scattering of light.

 

Professor Unger added: “Essentially, our results reveal a strong ‘dampening effect’ of air pollution on the land carbon uptake in China today. “This is significant for a number of reasons, not least because the increase in surface ozone produced by man-made pollution in the region will continue to grow over the next 15 years unless something is done. “If – and it is of course a big ‘if’ – China reduce their pollution to the maximum levels, we could reduce the amount of damage to the ecosystems by up to 70 per cent - offering protection of this critical ecosystem service and the mitigation of long-term global warming.”

 

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Intriguing oscillatory back-and-forth motion of a quantum particle

Intriguing oscillatory back-and-forth motion of a quantum particle | Amazing Science | Scoop.it

In the quantum world, our intuition for the motion of objects is strongly challenged and may sometimes even completely fail. What about imagining a marble falling through water oscillating up and down rather than just moving straight downwards? Sounds strange. Yet, that's what experimental physicist from Innsbruck in collaboration with theorists from Munich, Paris and Cambridge have discovered for a quantum particle. At the heart of this surprising behavior is what physicists call 'quantum interference', the fact that quantum mechanics allows particles to behave like waves, which can add up or cancel each other.

 

To observe the quantum particle oscillating back and forth the team had to cool a gas of Cesium atoms just above absolute zero temperature and to confine it to an arrangement of very thin tubes realized by high-power laser beams. By means of a special trick, the atoms were made to interact strongly with each other. At such extreme conditions the atoms form a quantum fluid whose motion is restricted to the direction of the tubes. The physicists then accelerated an impurity atom, which is an atom in a different spin state, through the gas. As this quantum particle moved, it was observed to scatter off the gas particles and to reflect backwards. This led to an oscillatory motion, in contrast to what a marble would do when falling in water. The experiment demonstrates that Newton's laws cannot be used in the quantum realm.

 

The fact that a quantum-wave may get reflected into certain directions has been known since the early days of the development of the theory of quantum mechanics. For example, electrons reflect at the regular pattern of solid crystals, such as a piece of metal. This effect is termed 'Bragg-scattering'. However, the surprise in the experiment performed in Innsbruck was that no such crystal was present for the impurity to reflect off. Instead, it was the gas of atoms itself that provided a type of hidden order in its arrangement, a property that physicist dub 'correlations'.

 

The Innsbruck work has demonstrated how these correlations in combination with the wave-nature of matter determine the motion of particles in the quantum world and lead to novel and exciting phenomena that counteract the experiences from our daily life.

Understanding the oddity of quantum mechanics may also be relevant in a broader scope, and help to understand and optimize fundamental processes in electronics components, or even transport processes in complex biological systems.

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Harnessing solar energy from semi-transparent glass walls

Harnessing solar energy from semi-transparent glass walls | Amazing Science | Scoop.it
A Korean research team has developed semi-transparent perovskite solar cells that could be great candidates for solar windows.

 

A Korean research team has developed semi-transparent perovskite solar cells that could be great candidates for solar windows. Scientists are exploring ways to develop transparent or semi-transparent solar cells as a substitute for glass walls in modern buildings with the aim of harnessing solar energy. But this has proven challenging, because transparency in solar cells reduces their efficiency in absorbing the sunlight they need to generate electricity.

 

Typical solar cells today are made of crystalline silicon, which is difficult to make translucent. By contrast, semi-transparent solar cells use, for example, organic or dye-sensitized materials. But compared to crystalline silicon-based cells, their power-conversion efficiencies are relatively low. Perovskites are hybrid organic-inorganic photovoltaic materials, which are cheap to produce and easy to manufacture. They have recently received much attention, as the efficiency of perovskite solar cells has rapidly increased to the level of silicon technologies in the past few years.

 

Using perovskites, a Korean research team, led by Professor Seunghyup Yoo of the Korea Advanced Institute of Science and Technology and Professor Nam-Gyu Park of Sungkyunkwan University, has developed a semi-transparent solar cell that is highly efficient and functions very effectively as a thermal mirror. One key to achieving efficient semitransparent solar cells is to develop a transparent electrode for the cell's uppermost layer that is compatible with the photoactive material. The Korean team developed a 'top transparent electrode' (TTE) that works well with perovskite solar cells. The TTE is based on a multilayer stack consisting of a metal film sandwiched between a high refractive index layer and an interfacial buffer layer. This TTE, placed as a solar cell's top-most layer, can be prepared without damaging ingredients used in the development f perovskite solar cells. Unlike conventional transparent electrodes that only transmit visible light, the team's TTE plays the dual role of allowing visible light to pass through while at the same time reflecting infrared rays.

 

The semi-transparent solar cells made with the TTEs exhibited an average power conversion efficiency as high as 13.3%, reflecting 85.5% of incoming infrared light. Currently available crystalline silicon solar cells have up to 25% efficiency but are opaque.

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