Visualising the genome: researchers create first 3D structures of active DNA

For the first time, scientists have been able to model the physical structure of mammalian genomes from individual cells, giving us a unique 3D perspective on how DNA packages itself inside our cells.

Through the new technique, scientists can see how the arrangement of cell chromosomes (DNA strands) are designed to keep some cells active or inactive at any one time.

“Knowing where all the genes and control elements are at a given moment will help us understand the molecular mechanisms that control and maintain their expression,” says one of the researchers, Ernest Laue from the University of Cambridge in the UK.

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Google’s new AI system unscrambles pixelated faces

On the left, 8×8 images; in the middle, the images generated by Google; and on the right, the original 32×32 faces. Photograph: Google

Google’s neural networks have achieved the dream of CSI viewers everywhere: the company has revealed a new AI system capable of “enhancing” an eight-pixel square image, increasing the resolution 16-fold and effectively restoring lost data.

The neural network could be used to increase the resolution of blurred or pixelated faces, in a way previously thought impossible; a similar system was demonstrated for enhancing images of bedrooms, again creating a 32×32 pixel image from an 8×8 one.

Google’s researchers describe the neural network as “hallucinating” the extra information. The system was trained by being shown innumerable images of faces, so that it learns typical facial features. A second portion of the system, meanwhile, focuses on comparing 8×8 pixel images with all the possible 32×32 pixel images they could be shrunken versions of.

The two networks working in harmony effectively redraw their best guess of what the original facial image would be. The system allows for a huge improvement over old-fashioned methods of up-sampling: where an older system might simply look at a block of red in the middle of a face, make it 16 times bigger and blur the edges, Google’s system is capable of recognising it is likely to be a pair of lips, and draw the image accordingly. Source – Gaurdian

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Scientists Need You to Solve This Chess Problem and Find the Key to Human Consciousness

… Sir Roger Penrose wants to figure out if we’ve been looking at consciousness the wrong way all this time. Our brains are so often compared to computers, but in his 1989 book, The Emperor’s New Mind, Sir Penrose argues that not even quantum computers – which we haven’t even built yet – could rival what’s in our heads.

A deeper understanding of the quantum weirdness of physics might be the only thing that could explain consciousness, he says, and while that’s a pretty controversial view, it’s not like we’ve got a whole lot to go on when it comes to the mysterious force that suddenly makes us self-aware. We’ve found quantum effects in photosynthesis and bird migration, Sir Penrose argues, so why not the human mind?

One way of narrowing down the variables in the search for human consciousness is to figure out what separates us from the greatest processors ever built – supercomputers.

If our minds can figure out a solution that even the most advanced problem-solving machines can’t, it could be the lead scientists need to figure out what makes us so unique. To that end, Sir Penrose has come up with this chess problem. You need to figure out how to legally get the white player to either draw with the black – or win:

chess-probPenrose Institute

As Sarah Knapton at The Telegraph explains, a computer will always assume the black player will win in this scenario, because seeing those three bishops will force it to perform a massive search of possible positions “that will rapidly expand to something that exceeds all the computational power on planet Earth”. But Sir Penrose says it should be “easy” for humans, given you know your chess rules back to front.

If you do decide to solve this riddle, and succeed, you need to email your work to puzzles@penroseinstitute.com. In particular, the Penrose Institute researchers are interested in the thought process that led you to the solution – was it a sudden moment of genius, or the result of days of consternation? Source – ScienceAlert

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Genome Editing with CRISPR-Cas9

This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease. Feng Zhang, a leader in the development of this technology, is a faculty member at MIT, an investigator at the McGovern Institute for Brain Research, and a core member of the Broad Institute. Further information can be found on Prof. Zhang’s website at http://zlab.mit.edu .

Images and footage courtesy of Sputnik Animation, the Broad Institute of MIT and Harvard, Justin Knight and pond5.

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As Moore’s law ends, brain-like computers begin

Professor Kwabena Boahen has written “A Neuromorph’s Prospectus” outlining how to build computers that directly mimic in silicon what the brain does in flesh and blood. Credit: L.A. Cicero

For five decades, Moore’s law held up pretty well: Roughly every two years, the number of transistors one could fit on a chip doubled, all while costs steadily declined. Today, however, transistors and other electronic components are so small they’re beginning to bump up against fundamental physical limits on their size. Moore’s law has reached its end, and it’s going to take something different to meet the need for computing that is ever faster, cheaper and more efficient.

As it happens, Kwabena Boahen, a professor of bioengineering and of electrical engineering, has a pretty good idea what that something more is: brain-like, or neuromorphic, computers that are vastly more efficient than the conventional digital computers we’ve grown accustomed to. This is not a vision of the future, Boahen said. As he lays out in the latest issue of Computing in Science and Engineering, the future is now.

“We’ve gotten to the point where we need to do something different,” said Boahen, who is also a member of Stanford Bio-X and the Stanford Neurosciences Institute. “Our lab’s three decades of experience has put us in a position where we can do something different, something competitive.”

It’s a moment Boahen has been working toward his entire adult life, and then some. He first got interested in computers as a teenager growing up in Ghana. But the more he learned, the more traditional computers looked like a giant, inelegant mess of memory chips and processors connected by weirdly complicated wiring.

Both the need for something new and the first ideas for what that would look like crystalized in the mid-1980s. Even then, Boahen said, some researchers could see the end of Moore’s law on the horizon. As transistors continued to shrink, they would bump up against fundamental physical limits on their size. Eventually, they’d get so small that only a single lane of electron traffic could get through under the best circumstances. What had once been electron superfreeways would soon be tiny mountain roads, and while that meant engineers could fit more components on a chip, those chips would become more and more unreliable.

At around the same time, Boahen and others came to understand that the brain had enormous computing power – orders of magnitude more than what people have built, even today – even though it used vastly less energy and remarkably unreliable components, neurons. More Here – TechExplore

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Thank you Neil Turock for the inspiration

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Unlucky for some?

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Neanderthals ‘self-medicated’ for pain

Neanderthals dosed themselves with painkillers and possibly penicillin, according to a study of their teeth. One sick Neanderthal chewed the bark of the poplar tree, which contains a chemical related to aspirin. He may also have been using penicillin, long before antibiotics were developed.

The evidence comes from ancient DNA found in the dental tartar of Neanderthals living about 40,000 years ago in central Europe. Microbes and food stuck to the teeth of the ancient hominins gives scientists a window into the past. By sequencing DNA preserved in dental tartar, international researchers have found out new details of the diet, lifestyle and health of our closest extinct relatives.

“Their behaviour and their diet looks a lot more sophisticated and a lot more like us in many ways,” said Prof Alan Cooper, director of the University of Adelaide’s Australian Centre for Ancient DNA. “You know, we’ve got a guy self-medicating either because he’s got a dental abscess, which was bad, or a nasty gastrointestinal parasite, which was also bad, either way he wasn’t a happy guy. “And, here he is eating aspirin and we’re finding penicillin mould in him.”

The Neanderthal’s abscess left a trace on his jawbone. The intestinal parasite was identified through studying DNA in dental tartar. It appears the Neanderthals had a good knowledge of medicinal plants and how these might relieve the pain of toothache or stomach ache. They might also have used antibiotics, long before the medicines were developed in modern times.

“The use of antibiotics would be very surprising, as this is more than 40,000 years before we developed penicillin,” said Prof Cooper. “Certainly our findings contrast markedly with the rather simplistic view of our ancient relatives in popular imagination.” More here – BBC

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Gray’s Anatomy

Title page of American 20th edition (1918)

Gray’s Anatomy is an English-language textbook of human anatomy originally written by Henry Gray and illustrated by Henry Vandyke Carter. Earlier editions were called Anatomy: Descriptive and Surgical and Gray’s Anatomy: Descriptive and Applied, but the book’s name is commonly shortened to, and later editions are titled, Gray’s Anatomy. The book is widely regarded as an extremely influential work on the subject, and has continued to be revised and republished from its initial publication in 1858 to the present day. The latest edition of the book, the 41st, was published in September 2015.

The English anatomist Henry Gray was born in 1827. He studied the development of the endocrine glands and spleen and in 1853 was appointed Lecturer on Anatomy at St George’s Hospital Medical School in London. In 1855, he approached his colleague Henry Vandyke Carter with his idea to produce an inexpensive and accessible anatomy textbook for medical students. Dissecting unclaimed bodies from workhouse and hospital mortuaries through the Anatomy Act of 1832, the two worked for 18 months on what would form the basis of the book. Their work was first published in 1858 by John William Parker in London. It was dedicated by Gray to Sir Benjamin Collins Brodie, 1st Baronet. An imprint of this English first edition was published in the United States in 1859, with slight alterations. Gray prepared a second, revised edition, which was published in the United Kingdom in 1860, also by J.W. Parker. However, Gray died the following year, at the age of 34, having contracted smallpox while treating his nephew (who survived). His death had come just three years after the initial publication of his Anatomy Descriptive and Surgical. Even so, the work on his much-praised book was continued by others. Longman’s publication reportedly began in 1863, after their acquisition of the J.W. Parker publishing business. This coincided with the publication date of the third British edition of Gray’s Anatomy. Successive British editions of Gray’s Anatomy continued to be published under the Longman, and more recently Churchill Livingstone/Elsevier imprints, reflecting further changes in ownership of the publishing companies over the years.

The newest, 41st edition of Gray’s Anatomy was published on 25 September 2015 by Elsevier in both print and on-line versions, and is the first edition to have enhanced on-line content including anatomical videos and a bonus Gray’s imaging library. The latest edition also has 24 specially invited on-line commentaries on controversial anatomical topics as diverse as advances in electron microscopy and fluorescence microscopy; the neurovascular bundles of the prostate; stem cells in regenerative medicine; the anatomy of facial ageing; and technical aspects and applications of diagnostic radiology. Via Wiki

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How Fast a Rocket Has to Launch From Each Planet in the Solar System

Gravity makes it possible for us to live on Earth, but it also makes it pretty hard to leave. Satellites fight gravity by going just fast enough to free-fall around the planet indefinitely, like the International Space Station, with many travelling at speeds of more than 17,500 mph (28,200 km/h). But if you want to leave this planet, you have to go faster. This speed is called the escape velocity.

How fast you’d have to go to leave every planet in the solar system – in one tidy, animated GIF above: Via SciencAlert

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Skeleton Typogram

Image may contain: text

Very creative skeleton typogram by Aaron Kuehn

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The True Story of a Man Who Survived Without Any Food for 382 Days

Most people can survive without food for at least a few weeks, maybe a bit longer. Eventually, however, starvation kills. Yet the limits on how long people can go without eating are complicated; without water people are unlikely to last a week, but the amount of time starvation takes can vary drastically. Take the story of Angus Barbieri – for 382 days, ending 11 July 1966, the then-27-year-old Scotsman ate nothing.

There’s limited documentation of Barbieri’s fast: there are a few old newspaper stories recounting his ordeal and more convincingly, there’s a case report describing the experience that his doctors published in the Postgraduate Medical Journal in 1973.

According to that report, Barbieri had walked into the University Department of Medicine at the Royal Infirmary of Dundee, Scotland, more than a year before, looking for help.

He was “grossly obese” at the time, according to his doctors, weighing 456 pounds (207 kg). The doctors put him on a short fast, thinking it would help him lose some weight, though they didn’t expect him to keep it off. But as days without food turned into weeks, Barbieri felt eager to continue the program.

Absurd and risky as his goal sounded – fasts over 40 days were and still are considered dangerous – he wanted to reach his “ideal weight,” 180 pounds (49 kg). So he kept going.

In what was a surprise to his doctors, he lived his daily life mostly from home during the fast, coming into the hospital for frequent checkups and overnight stays.

Regular blood-sugar tests – intended to demonstrate that he was somehow able to function while very hypoglycemic – assured doctors that he really wasn’t eating. Weeks turned into months. Barbieri took vitamins on various occasions throughout the fast, including potassium and sodium supplements.

He was allowed to drink coffee, tea, and sparkling water, all of which are naturally calorie-free. He said there was the occasional time that he’d have a touch of sugar or milk in tea, especially in his final few weeks of fasting. At the end of his ordeal, Barbieri tipped the scales at 180 pounds. Five years later, he’d still kept almost all the weight he’d lost off, weighing in at 196 (89 kg). More here – Sciencealert

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More Hidden Paintings in Books

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Creating An Inverted Aquarium For Pond

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Embryo in the eye of a needle

Embryo in needle’s eye, by Yorkos Nikas

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Gut bacteria could be affecting the body’s response to a new type of cancer treatment

Cancer immunotherapy – treatments that harness the body’s immune system to fight cancer – has been gaining traction in recent years as a new approach to treating the disease. But one of its major drawbacks is its variability: for some cancer patients, the drugs have led to remarkable remissions with few side effects. Others have tried them only to find little benefit and a lot of discomfort

.It’s something researchers have been trying to understand, exploring whether there are other drugs that could be used to boost the response in some people, or if genetics could be playing an underlying role in making it more effective in others. And they may finally be onto something.

A team of researchers has recently discovered a link between people’s responses to immunotherapy treatments and the microbes that live in their gut. Having a more diverse gut microbiome, they found, is linked to a better response. The research, which will be presented at an upcoming medical conference, is the first study to make this link in people. Previous studies have however found similar results in mice. Source: Gut bacteria could be affecting the body’s response to a new type of cancer treatment

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Neural networks promise sharpest ever images

Telescopes, the workhorse instruments of astronomy, are limited by the size of the mirror or lens they use. Using ‘neural nets’, a form of artificial intelligence, a group of Swiss researchers now have a way to push past that limit, offering scientists the prospect of the sharpest ever images in optical astronomy. The new work appears in a paper in Monthly Notices of the Royal Astronomical Society.

The diameter of its lens or mirror, the so-called aperture, fundamentally limits any telescope. In simple terms, the bigger the mirror or lens, the more light it gathers, allowing astronomers to detect fainter objects, and to observe them more clearly. A statistical concept known as ‘Nyquist sampling theorem’ describes the resolution limit, and hence how much detail can be seen.

The Swiss study, led by Prof Kevin Schawinski of ETH Zurich, uses the latest in machine learning technology to challenge this limit. They teach a neural network, a computational approach that simulates the neurons in a brain, what galaxies look like, and then ask it to automatically recover a blurred image and turn it into a sharp one. Just like a human, the neural net needs examples – in this case a blurred and a sharp image of the same galaxy – to learn the technique. Source: Neural networks promise sharpest ever images

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3D gif of IC410

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Ruptured venule under the scanning electron microscope

Magnification x2300, by Steve Gschmeissner

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Archaeologists just made the “find of a lifetime” buried beneath Scotland

A bronze sword, a gold-decorated spearhead, well-preserved sheath fittings, and fur skins – all thought to date back to around 3,000 years – are some of the remarkable finds uncovered at a dig currently underway in the UK. Archaeologists on the site have described it as the “find of a lifetime” and continue to uncover the remains of dwellings, pots, and other artefacts, so there could be more to come from this treasure trove of ancient relics.

The items have been uncovered near the town of Carnoustie, in the council area of Angus on the east coast of Scotland.Experts from GUARD Archaeology, commissioned to carry out the dig, say that it’s a “rare and internationally significant hoard” that can teach us a lot more about Bronze Age living (and fighting) in the area. “It is very unusual to recover such artefacts in a modern archaeological excavation, which can reveal so much about the context of its burial,” project officer Alan Hunter Blair from GUARD Archaeology told BBC News.

The sword is very well preserved, according to archaeologists, but it’s the accompanying spearhead that’s really exciting – only a handful of such gold-marked spearheads have ever been uncovered in Britain. Source: Archaeologists just made the “find of a lifetime” buried beneath Scotland

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