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SciFrye
the science behind our environments & the changing environments of science
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Neonics present in most honey samples

Neonics present in most honey samples | SciFrye | Scoop.it
A new study finds traces of neonicotinoid chemicals in 75% of honey samples from across the world.
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Stunning 100-Million-Year-Old Flowers Found Perfectly Preserved In Amber

Stunning 100-Million-Year-Old Flowers Found Perfectly Preserved In Amber | SciFrye | Scoop.it

Seven flowers have been found perfectly preserved in amber, from 100 million years ago. The flowers, discovered in Myanmar, were encased in amber in the Cretaceous period in what would have been a pine forest.

 

The authors of a paper studying the flowers, which are in stunning condition, speculated that they could have been dislodged from their trees by a passing dinosaur. “Dinosaurs may have knocked the branches that dropped the flowers into resin deposits on the bark of an araucaria tree, which is thought to have produced the resin that fossilized into the amber." George Poinar Jr, professor emeritus of Oregon State University’s College of Science said in a statement.

 

"Araucaria trees are related to kauri pines found today in New Zealand and Australia, and kauri pines produce a special resin that resists weathering.”


Via Neelima Sinha, Dr. Stefan Gruenwald
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A breakthrough new method for 3D-printing living tissues

A breakthrough new method for 3D-printing living tissues | SciFrye | Scoop.it

Scientists at the University of Oxford have developed a radical new method of 3D-printing laboratory-grown cells that can form complex living tissues and cartilage to potentially support, repair, or augment diseased and damaged areas of the body.

 

Printing high-resolution living tissues is currently difficult because the cells often move within printed structures and can collapse on themselves. So the team devised a new way to produce tissues in protective nanoliter droplets wrapped in a lipid (oil-compatible) coating that is assembled, layer-by-layer, into living cellular structures.

 

This new method improves the survival rate of the individual cells and allows for building each tissue one drop at a time to mimic the behaviors and functions of the human body. The patterned cellular constructs, once fully grown, can mimic or potentially enhance natural tissues.

 

“We were aiming to fabricate three-dimensional living tissues that could display the basic behaviors and physiology found in natural organisms,” explained Alexander Graham, PhD, lead author and 3D Bioprinting Scientist at OxSyBio (Oxford Synthetic Biology).

 

“To date, there are limited examples of printed tissues [that] have the complex cellular architecture of native tissues. Hence, we focused on designing a high-resolution cell printing platform, from relatively inexpensive components, that could be used to reproducibly produce artificial tissues with appropriate complexity from a range of cells, including stem cells.”

 

The researchers hope that with further development, the materials could have a wide impact on healthcare worldwide and bypass clinical animal testing. The scientists plan to develop new complementary printing techniques that allow for a wider range of living and hybrid materials, producing tissues at industrial scale.


Via Dr. Stefan Gruenwald
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How cells hack their own genes

How cells hack their own genes | SciFrye | Scoop.it

Researchers at IMBA—Institute of Molecular Biotechnology of the Austrian Academy of Sciences—unveil novel mechanism for gene expression.


Via Integrated DNA Technologies
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Estimating corn grain yield prior to harvest

Estimating corn grain yield prior to harvest | SciFrye | Scoop.it
Check out the 5 tips to estimating corn yields through the Yield Component Method.
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Memories of fear could be permanently erased, study shows

Memories of fear could be permanently erased, study shows | SciFrye | Scoop.it
Research in mice reveals a new approach to wiping memories from the brain, demonstrating that specific memories can be weakened or strengthened
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Moon had magnetic field at least a billion years longer than thought – study

Moon had magnetic field at least a billion years longer than thought – study | SciFrye | Scoop.it
Even small planets could have long-lived magnetic fields, crucial for atmosphere and water, raising fresh possibilities in the hunt for new worlds
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A danger to public health? Uproar as scientist urges us to eat more salt

A danger to public health? Uproar as scientist urges us to eat more salt | SciFrye | Scoop.it
Exclusive: In a new book a US scientist claims eating more salt will make us healthier. But UK experts have condemned the advice as potentially dangerous
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Speedup of Machine Learning of up to 100 fold using Bayesian Program Synthesis

Speedup of Machine Learning of up to 100 fold using Bayesian Program Synthesis | SciFrye | Scoop.it

Ben Vigoda, Gamalon’s CEO, spoke recently at MIT Technology Review EmTech along with Pedro Domingos from University of Washington, Noah Goodman from Stanford, Ruslan Salakhutdinov from Apple/CMU, Ilya Sutskever from OpenAI, Maya Gupta from Google, and Eric Horvitz from Microsoft. He describes how deep learning and other state-of-the art machine learning is like training a dog to provide a desired response to a stimulus – ‘ring the bell, give some food’ , ‘ring the bell, give some food’, and so forth, except that with today’s machine learning you typically need to repeat this kind of labeled input/output pair 10,000 times.

 

By contrast, to teach a human we would just say, ‘This is a dinner bell, when I ring it I am going to serve you some food’ – you would insert that idea directly into their mind in between where the stimulus comes in and the response goes out – by talking to them. The person can still learn from stimulus-response experiences, but you can also teach them by communicating ideas to them. This is how Gamalon’s Idea Learning works.

 

TED video is here

 

Astronomers shared stories through the ages, enabling them to contradict and learn from each other. They broke stories apart and put them together in better ways—readjusting and reconsidering beliefs—to present new ideas that are more compelling and more accurate. Machines can do that too. "When we build stories into machine intelligence systems, we should enable them to attach probabilities to their stories" says Ben Vigoda.

Ben Vigoda is Founder, CEO/CTO of Gamalon Machine Intelligence. Before founding Gamalon, Ben was technical co-founder and CEO of Lyric Semiconductor, a startup that created the first integrated circuits and processor architectures for statistical machine learning and signal processing. He currently serves on the DARPA Information Science and Technology (ISAT) steering committee. Ben also co-founded Design That Matters, a not-for-profit that for the past decade has helped solve engineering and design problems in under-served communities and has saved thousands of infant lives by developing low-cost, easy-to-use medical technology such as infant incubators, UV therapy, pulse oximeters, and IV drip systems that have been fielded in 20 countries. Ben completed his PhD at MIT developing circuits for implementing machine learning algorithms natively in hardware.


Via Dr. Stefan Gruenwald
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The explanation of the capillary in the soil

The explanation of the capillary in the soil | SciFrye | Scoop.it
Trees do not 'drink' from ground water.
Trees 'drink' from capillary water.  Their instrument to drink from the capillary water is the primary root.  In this photo you can see the primary roots going downwards to the dark soil.  This

Via Giri Kumar
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Humans speak 7,000 languages, but why?

Humans speak 7,000 languages, but why? | SciFrye | Scoop.it

The thatched roof held back the sun’s rays, but it could not keep the tropical heat at bay. As everyone at the research workshop headed outside for a break, small groups splintered off to gather in the shade of coconut trees and enjoy a breeze. I wandered from group to group, joining in the discussions. Each time, I noticed that the language of the conversation would change from an indigenous language to something they knew I could understand, Bislama or English. I was amazed by the ease with which the meeting’s participants switched between languages, but I was even more astonished by the number of different indigenous languages.

 

Thirty people had gathered for the workshop on this island in the South Pacific, and all except for me came from the island, called Makelua, in the nation of Vanuatu. They lived in 16 different communities and spoke 16 distinct languages. In many cases, you could stand at the edge of one village and see the outskirts of the next community. Yet the residents of each village spoke completely different languages. According to recent work by my colleagues at the Max Planck Institute for the Science of Human History, this island, just 100 kilometers long and 20 kilometers wide, is home to speakers of perhaps 40 different indigenous languages. Why so many?

 

We could ask this same question of the entire globe. People don’t speak one universal language, or even a handful. Instead, today our species collectively speaks over 7,000 distinct languages. And these languages are not spread randomly across the planet. For example, far more languages are found in tropical regions than in the temperate zones. The tropical island of New Guinea is home to over 900 languages. Russia, 20 times larger, has 105 indigenous languages. Even within the tropics, language diversity varies widely. For example, the 250,000 people who live on Vanuatu’s 80 islands speak 110 different languages, but in Bangladesh, a population 600 times greater speaks only 41 languages.

 

Why is it that humans speak so many languages? And why are they so unevenly spread across the planet? As it turns out, we have few clear answers to these fundamental questions about how humanity communicates.


Via Fernando Gil, Dr. Stefan Gruenwald
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Geologists offer new clues to what caused one of world's greatest mass extinctions

Geologists offer new clues to what caused one of world's greatest mass extinctions | SciFrye | Scoop.it

A study by a researcher in the Syracuse University College of Arts and Sciences offers new clues to what may have triggered the world's most catastrophic extinction, nearly 252 million years ago.

 

James Muirhead, a research associate in the Department of Earth Sciences, is the co-author of an article in Nature Communications (Macmillan Publishers Limited, 2017) titled "Initial Pulse of Siberian Traps Sills as the Trigger of the End-Permian Mass Extinction."

His research involves Seth Burgess, the article's lead author and a geologist at the U.S. Geological Survey, and Samuel Bowring, the Robert R. Shock Professor of Geology at the Massachusetts Institute of Technology.

 

Their findings suggest that the formation of intrusive igneous rock, known as sills, sparked a chain of events that brought the Permian geological period to a close. In the process, more than 95 percent of marine species and 70 percent of land species vanished.

 

"There have been five major mass extinctions, since life originated on Earth more than 600 million years ago," says Burgess, who works at the nexus of volcanic and tectonic processes. "Most of these events have been blamed, at various times, on volcanic eruptions and asteroids impacts. By reexamining the timing and connection between magmatism [the movement of magma], climate change and extinction, we've created a model that explains what triggered the end-Permian mass extinction."

 

Central to their study is a large igneous province (LIP) in Russia called the Siberian Traps. Spanning more than 500,000 square miles, this rocky outpost was the site of nearly a million years of epic volcanic activity. Broad, flat volcanoes likely dispelled significant volumes of lava, ashes and gas, while pushing sulfur dioxide, carbon dioxide and methane to dangerous levels in the environment.


Via Dr. Stefan Gruenwald
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Plant Physiology: Sequence exchange between R genes converts virus resistance into nematode resistance, and vice versa (2017)

Plant Physiology: Sequence exchange between R genes converts virus resistance into nematode resistance, and vice versa (2017) | SciFrye | Scoop.it

Plants have evolved a limited repertoire of NB-LRR disease resistance (R) genes to protect themselves against a myriad of pathogens. This limitation is thought to be counterbalanced by the rapid evolution of NB-LRR proteins, as only few sequence changes have been shown to be sufficient to alter resistance specificities towards novel strains of a pathogen. However, little is known about the flexibility of NB-LRR genes to switch resistance specificities between phylogenetically unrelated pathogens. To investigate this, we created domain swaps between the close homologs Gpa2 and Rx1, which confer resistance in potato to the cyst nematode Globodera pallida and Potato virus X (PVX), respectively. The genetic fusion of the CC-NB-ARC of Gpa2 with the LRR of Rx1 (Gpa2CN/Rx1L) resulted in autoactivity, but lowering the protein levels restored its specific activation response including extreme resistance to PVX in potato shoots. The reciprocal construct (Rx1CN/Gpa2L) showed a loss-of-function phenotype, but exchange of the first 3 LRR repeats of Rx1 was sufficient to regain a wild type resistance response to G. pallida in the roots. These data demonstrate that exchanging the recognition moiety in the LRR is sufficient to convert extreme virus resistance in the leaves into mild nematode resistance in the roots, and vice versa. In addition, we show that the CC-NB-ARC can operate independently of the recognition specificities defined by the LRR domain, either above or belowground. These data show the versatility of NB-LRR genes to generate resistances to unrelated pathogens with completely different lifestyles and routes of invasion.


Via Kamoun Lab @ TSL
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Scientists Develop Blood Test That Spots Tumor-Derived DNA in People With Early-Stage Cancers 

Scientists Develop Blood Test That Spots Tumor-Derived DNA in People With Early-Stage Cancers  | SciFrye | Scoop.it

In a bid to detect cancers early and in a noninvasive way, scientists at the Johns Hopkins Kimmel Cancer Center report they have developed a test that spots tiny amounts of cancer-specific DNA in blood and have used it to accurately identify more than half of 138 people with relatively early-stage colorectal, breast, lung and ovarian cancers. The test, the scientists say, is novel in that it can distinguish between DNA shed from tumors and other altered DNA that can be mistaken for cancer biomarkers.


Via Integrated DNA Technologies, Dr. Stefan Gruenwald
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Astrophysicists explain the mysterious behavior of cosmic rays

Astrophysicists explain the mysterious behavior of cosmic rays | SciFrye | Scoop.it
A team of scientists from Russia and China has developed a model explaining the nature of high-energy cosmic rays (CRs) in our galaxy. These CRs have energies exceeding those produced by supernova explosions by one or two orders of magnitude. The model focuses mainly on the recent discovery of giant structures called Fermi bubbles.

One of the key problems in the theory of the origin of cosmic rays, which consist of high-energy protons and atomic nuclei, is their acceleration mechanism. The issue was addressed by Vitaly Ginzburg and Sergei Syrovatsky in the 1960s when they suggested that CRs are generated during supernova (SN) explosions in the galaxy. A specific mechanism of charged particle acceleration by SN shock waves was proposed by Germogen Krymsky and others in 1977. Due to the limited lifetime of the shocks, it is estimated that the maximum energy of the accelerated particles cannot exceed 1014-1015 eV.

Explaining the nature of particles with energies above 1015 eV is key. A major breakthrough in researching the acceleration processes of such particles came when the Fermi Gamma Ray Space Telescope detected two gigantic structures emitting radiation in the gamma-ray band in the central area of the galaxy in November 2010. The structures are elongated and symmetrically located in the galactic plane perpendicular to its center, extending 50,000 light-years, or roughly half of the diameter of the Milky Way disk. These structures became known as Fermi bubbles. Later, the Planck telescope team discovered their emission in the microwave band.

Via Mariaschnee
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Fishing for DNA during breeding season could help control invasive species

Fishing for DNA during breeding season could help control invasive species | SciFrye | Scoop.it

Research reveals that an invasive crayfish species is easier to detect in water samples during breeding, which could lead to better control.


Via Integrated DNA Technologies
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Do-it-yourself laboratories democratize science

Do-it-yourself laboratories democratize science | SciFrye | Scoop.it

In the era of social media and online tutorials, do-it-yourself (DIY) projects are more popular than ever. This trend is making its way into community laboratories, providing opportunities for the public to “do science” in ways that were previously within the exclusive realm of highly credentialed scientists and shrouded in the mystery of peer-reviewed journals.


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Crop conditions remain steady

Crop conditions remain steady | SciFrye | Scoop.it
In the Midwest, Illinois leads with 91%of the corn in the dough stage.
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Scientists reveal why whisky tastes better with water

Scientists reveal why whisky tastes better with water | SciFrye | Scoop.it
How best to enjoy whisky has long been debated, but two chemists say they have discovered why diluting your dram might make it taste better
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Why we fell for clean eating

Why we fell for clean eating | SciFrye | Scoop.it
The long read: The oh-so-Instagrammable food movement has been thoroughly debunked – but it shows no signs of going away. The real question is why we were so desperate to believe it
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Scientists reveal source of human heartbeat in 3D

Scientists reveal source of human heartbeat in 3D | SciFrye | Scoop.it

A pioneering new study is set to help surgeons repair hearts without damaging precious tissue.

 

A team of scientists from Liverpool John Moores University (LJMU), The University of Manchester, Aarhus University and Newcastle University, have developed a way of producing 3D data to show the cardiac conduction system -- the special cells that enable our hearts to beat -- in unprecedented detail. The findings were published in Scientific Reports.

 

The new data in this study gives them a much more accurate framework than previously available for computer models of the heartbeat and should improve our ability to make sense of troublesome heart rhythms like atrial fibrillation that affects 1.4 million people in the UK. The data reveals exactly where the cardiac conduction system is in a normal heart. For example, it shows just how close it runs to the aortic valve.

 

Professor Jonathan Jarvis who is based at the LJMU School of Sport and Exercise Sciences explained: "The 3D data makes it much easier to understand the complex relationships between the cardiac conduction system and the rest of the heart. We also use the data to make 3D printed models that are really useful in our discussions with heart doctors, other researchers and patients with heart problems.

 

"New strategies to repair or replace the aortic valve must therefore make sure that they do not damage or compress this precious tissue. In future work we will be able to see where the cardiac conduction system runs in hearts that have not formed properly. This will help the surgeons who repair such hearts to design operations that have the least risk of damaging the cardiac conduction system."

 

Co-author Dr Halina Dobrzynski, who is based in The University of Manchester's Cardiovascular Division, has been working on the anatomy of the cardiac conduction system for 20 years. She says: "This is just the beginning. The British Heart Foundation is supporting my group to visualize this system in 3D from aged and failing hearts. With my research assistant Andrew Atkinson and working with Professor Jonathan Jarvis, Robert Stephenson and others, we will produce families of data from aged and failing hearts in 3D."


Via Dr. Stefan Gruenwald, Mariaschnee
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The race to reveal antimatter’s secrets

The race to reveal antimatter’s secrets | SciFrye | Scoop.it
In the shadow of the Large Hadron Collider, six teams are competing to answer one of the Universe’s deepest existential questions.

 

In a high-ceilinged hangar at CERN, six rival experiments are racing to understand the nature of one of the Universe's most elusive materials. They sit just meters apart. In places, they are literally on top of one another: the metallic beam of one criss-crosses another like a shopping-centre escalator, its multi-ton concrete support hanging ominously overhead.

 

“We're constantly reminded of each other,” says physicist Michael Doser, who leads AEGIS, an experiment that is vying to be the first to discover how antimatter — matter's rare mirror image — responds to gravity.

 

Doser and his competitors have little choice but to get cosy. CERN, Europe's particle-physics laboratory near Geneva, Switzerland, boasts the world's only source of antiprotons — particles that seem identical to protons in every way except for their opposite charge and spin. The lab's Antiproton Decelerator is a ring, 182 meters around, that feeds from the same accelerators as the lab's bigger and more famous sibling, the Large Hadron Collider (LHC).

 

Antiprotons enter the machine traveling close to the speed of light. As the name implies, the decelerator slows the particles down, providing a stream of antiprotons from which experiments must take turns to sip. All this must be done carefully; upon meeting matter, the antiparticles vanish in a puff of energy.

 

Via Dr. Stefan Gruenwald
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Yatakemycin: Deciphering a DNA toxin's secrets

Yatakemycin: Deciphering a DNA toxin's secrets | SciFrye | Scoop.it
A team of Vanderbilt University researchers have worked out the molecular details that explain how one of the most potent bacterial toxins known -- yatakemycin (YTM) -- kills cells by preventing their DNA from replicating.

 

One of the most potent toxins known acts by welding the two strands of the famous double helix together in a unique fashion which foils the standard repair mechanisms cells use to protect their DNA. A team of Vanderbilt University researchers have worked out the molecular details that explain how this bacterial toxin -- yatakemycin (YTM) -- prevents DNA replication. Their results, described in a paper published online July 24 by Nature Chemical Biology, explain YTM's extraordinary toxicity and could be used to fine-tune the compound's impressive antimicrobial and antifungal properties.

 

YTM is produced by some members of the Streptomyces family of soil bacteria to kill competing strains of bacteria. It belongs to a class of bacterial compounds that are currently being tested for cancer chemotherapy because their toxicity is extremely effective against tumor cells.

 

"In the past, we have thought about DNA repair in terms of protecting DNA against different kinds of chemical insults," said Professor of Biological Sciences Brandt Eichman. "Now, toxins like YTM are forcing us to consider their role as part of the ongoing chemical warfare that exists among bacteria, which can have important side effects on human health."

 

Cells have developed several basic types of DNA repair, including base excision repair (BER) and nucleotide excision repair (NER). BER generally fixes small lesions and NER removes large, bulky lesions.

 

A number of DNA toxins create bulky lesions that destabilize the double helix. However, some of the most toxic lesions bond to both strands of DNA, thereby preventing the cell's elaborate replication machinery from separating the DNA strands so they can be copied. Normally, this distorts the DNA's structure, which allows NER enzymes to locate the lesion and excise it.

 

"YTM is different," said postdoctoral fellow Elwood Mullins. "Instead of attaching to DNA with multiple strong covalent bonds, it forms a single covalent bond and a large number of weaker, polar interactions. As a result, it stabilizes the DNA instead of destabilizing it, and it does so without distorting the DNA structure so NER enzymes can't find it."

 

"We were shocked by how much it stabilizes DNA," Eichman added. "Normally, the DNA strands that we used in our experiments separate when they are heated to about 40 degrees [Celsius] but, with YTM added, they don't come apart until 85 degrees."

 

The Streptomyces bacteria that produce YTM have also evolved a special enzyme to protect their own DNA from the toxin. Surprisingly, this is a base excision repair enzyme -- called a DNA glycosylase -- that is normally limited to repairing small lesions, not the bulky adducts caused by YTM. Nevertheless, studies have shown that it is extremely effective.

 

It so happens that one of Streptomyces' competitors, Bacillus cereus, has managed to co-opt the gene that produces this particular enzyme. In Bacillus, however, the enzyme it produces -- called AlkD -- provides only limited protection.


Via Dr. Stefan Gruenwald
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Soybeans improve slightly; corn falls again

Soybeans improve slightly; corn falls again | SciFrye | Scoop.it
The USDA NASS crop report shows soybean conditions improved two points and corn fell one point.
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Scientists genetically engineer the world’s first blue chrysanthemum

Scientists genetically engineer the world’s first blue chrysanthemum | SciFrye | Scoop.it

True blue flowers are a rarity in nature—they occur only in select species like morning glories and delphiniums. Now, researchers have created a genuinely blue chrysanthemum by adding two genes to the normally pink or reddish flower. The advance could be applied to other species—and it may mean that florists wanting to hawk blooms of blue will no longer have to dye them.


Via Integrated DNA Technologies
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