Software could determine where a video was shot, based on scenery and ambient sound

Sometimes, a posted video is the only clue to the whereabouts of a missing person, or a terrorist group. Unfortunately, unless that video has already been geo-tagged, it can often be very difficult to tell where it was shot. Now, however, scientists have created algorithms that can determine a video’s location by comparing its background imagery and audio to that of thousands of other videos.

The researchers, from Spain’s Ramón Llull University, utilized the existing MediaEval Placing Task database. It’s a collection of videos and photos from known locations, used for developing geolocation software.

Given that the videos being scrutinized presumably wouldn’t show well-known landmarks, the algorithms instead look for distinct images in seemingly generic scenes (such as streets or wilderness areas) that have a match in the database.

Random ambient audio also plays a key role. “The acoustic information can be as valid as the visual and, on occasions, even more so when it comes to geolocating a video,” said researcher Xavier Sevillano. “In this field we use some physics and mathematical vectors taken from the field of recognition of acoustic sources, because they have already demonstrated positive results.”

So far, the system has been tested by comparing sample videos to approximately 10,000 other clips already in the MediaEval database. It was able to geolocate three percent of those samples to within a 10-km (6.2-mile) radius of where they were actually shot, and one percent to within one kilometer (0.6 mile).

While those figures obviously leave a lot of videos still unlocated, the scientists believe that the success rate should be much higher if the database is expanded to include many more clips. Additionally, even in its present form, the technology is claimed to be more accurate than other approaches used on the database.

Source: FECYT
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Software analyzes human genome in as little as 90 minutes

New software developed at Nationwide Children’s Hospital in Ohio can take raw sequence data on a person’s genome and search it for disease-causing variations in a matter of hours, which its creators claim puts it ahead of the pack as the fastest genome analysis software around. They believe that this makes it now feasible to do large-scale analysis across entire populations.

Whereas it took 13 years and cost US$3 billion to sequence a human genome for the first time, senior author Peter White notes that now “even the smallest research groups can complete genomic sequencing in a matter of days.” The chokepoint lies in the next step: calibrating and analyzing the billions of generated data points for genetic variants that could lead to diseases.

White and his team tackled the problem by automating the analytical process in a computational pipeline they called Churchill. Churchill spreads each analysis step across multiple computing instances – a process its creators call balanced regional parallelization – with special care taken to preserve data integrity so that results are “100 per cent reproducible.”

Tests showed that Churchill can analyze a whole genome sequence in as little as 90 minutes from a raw FASTQ text-based format through to identifying variant cells at high confidence. An exome, which contains the bulk of disease-causing variants despite being a mere one per cent of the whole genome, can be analyzed in less than an hour. Churchill’s performance was validated against the National Institute of Standards and Technology’s benchmarks, with scores of 99.7 per cent on sensitivity, 99.99 per cent on accuracy, and 99.66 per cent on diagnostic effectiveness.

While the goal of the research was to create an ultra-fast analysis pipeline, White and his team found an unexpected benefit. Churchill scales efficiently across many servers, which makes it possible to perform population-scale analysis.

They took the first phase of the raw data generated by the 1000 Genomes Project – an international research collaboration started in 2008 to establish an extensive public catalog of human genetic variation across the globe – and put Churchill to task on all 1,088 whole genome samples across a cluster of computers in Amazon Web Services’ Elastic Compute Cloud. Churchill averaged a mere nine minutes per genome in its week-long analysis, which the researchers note compares favorably to a similar analysis performed in 2013 on a Cray XE6 supercomputer.

The Cray supercomputer test analyzed 61 whole genomes in two days, at an average of 50 minutes per genome – around five times longer than Churchill required in its cloud test.

“Given that several population-scale genomic studies are underway, we believe that Churchill may be an optimal approach to tackle the data analysis challenges these studies are presenting,” White says.

The Churchill algorithm has been licensed to a company calledGenomeNext, which adapted the technology for use in a commercial setting. People can get their genome sequenced in a local lab or clinic and then upload the raw data to the GenomeNext system for analysis.

A paper describing the Churchill algorithms and research was published in the journal Genome Biology. The Churchill software is also available, for research purposes only, via its project page.

Source: Nationwide Children’s Hospital.                        

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Scuba diver discovers 10,000-year-old forest underwater

A diving enthusiast in the UK has uncovered an ancient forest that has been trapped underwater for thousands of years. 

 

Remnants of 10,000-year-old forest that once spanned thousands of acres and connected Great Britain with continental Europe have been discovered by British divers. 

Dawn Watson was diving in the North Sea off the Norfolk coast in the UK – about 200 km northeast of London – when she made the unexpected discovery. 

After being forced off her normal course by rough water, Watson continued swimming, and was eventually in the midst of large oak trees, some with branches measuring eight-metres-long, lying on the sea floor.  

“To start with I actually thought it was a piece of wreck,” Watson told the BBC . “It just looked like a piece of hull. It wasn’t until I had a really close look that I realised it was actually solid wood.”

Watson, whose air tank was nearing empty, had to turn around very quickly, and told the BBC she was very lucky to make the find: “If I’d been three or four metres to the right we’d never have seen it at all.”  

Watson runs a marine conservation program called Seasearch with her partner Rob Spray. The organisation’s objective is to “map out the various types of sea bed found in the near-shore zone around the whole of Britain and Ireland.” 

Of course, it’s unlikely they expected to find a prehistoric forest.

The pair, who have both returned to photograph and explore their ruined forest, say it likely became exposed after a big storm hit the coast in December 2013.  

“You can see the damage it did on the surface, and underwater you have that on a grander scale,” Spray told the BBC. “Thousands of tonnes of sand and gravel can just be sort of shuffled… it’s no surprise that after an event like that you see sand stripped away.” 

The forest is believed to be part of an ancient land mass known as Doggerland, which once linked Great Britain to the rest of Europe, and disappeared under rising sea levels about 6,000 years ago.  

For decades, fisherman in the North Sea have been dragging up bones and artifactsfrom that long-vanished world . 

Once thought to be uninhabited, it is now suspected that Doggerland was settled by Mesolithic hunter-gatherers, probably in great numbers. 

As the BBC reported, “by around 10,000 years ago, the area would still have been one of the richest areas for hunting, fishing and fowling in Europe.”

Watson and Spray are now in the process of surveying the ancient forest, which has evolved into a kind of natural reef, and is home to all kinds of marine life. 

SOURCES: Reuters, BBC              via:http://www.sciencealert.com/

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Hydrogen sulfide offers clue to how reducing calories lengthens lives

Tapping into an ancient cellular energy source may help stave off the rigors of surgery and the ravages of age.
Hydrogen sulfide, a foul-smelling poisonous gas that microbes have been munching for eons, may be responsible for the health benefits and life-extending effects of reduced-calorie diets, scientists propose December 23 in Cell. Caloric restriction is a proven method for lengthening life span of a wide variety of organisms, but scientists still don’t know exactly how it works. The new work, by James Mitchell at the Harvard School of Public Health and colleagues, suggests that holding back calories causes cells to produce hydrogen sulfide, which somehow makes tissues more resilient and prolongs the life of laboratory organisms.
                                                                                                                        Source:www.sciencenews.org

                                                                                  

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How to unboil an egg

A team of scientists led by UC Irvine has shown that you can unboil an egg, or at least egg whites … but it isn’t easy. Far more than a breakfast table trick, the feat is designed to demonstrate a new technique for recovering valuable molecular proteins quickly and cheaply that could have important biochemical applications.

Boiling an egg may seem like the simplest part of breakfast, but it involves some interesting chemistry. An egg is 90 percent water and ten percent protein, which is what gives egg whites their gloppy appearance. These proteins are in the form of long chains of amino acids tangled and folded in upon themselves like microscopic piles of yarn held together by weak atomic bonds. When the egg is dropped into boiling water, the heat breaks these bonds and the chains start to unravel and break. The chains then bond with other amino acids and capture water inside the new folds, causing the whites to turn white and gelatinous. Cook them too long, and the chains curl in on themselves; forcing the water out and turning the whites hard and rubbery.

This is what the UC Irvine team did when they boiled their eggs. In fact, they boiled the heck out them for 20 minutes at 90 degrees C (194 degrees F), so they were very hard indeed. They then set out to reverse the process and turn the hard whites into a clear protein called lysozyme by adding urea, which breaks down the chemical bonds that cause the coagulated chains to misfold on one another. The rather unpalatable liquid mass was then run through a vortex fluid device designed by Professor Colin Raston at South Australia’s Flinders University. This set up shear stresses that caused the chains to untangle into their previous uncooked form.

Thankfully, unboiled eggs won’t be added to breakfast menus anytime soon. The purpose behind all this is to demonstrate a new technique for recovering molecular proteins. Where conventional techniques take up to four days to recover the proteins, the UC Irvine process takes only minutes.

“It’s not so much that we’re interested in processing the eggs; that’s just demonstrating how powerful this process is,” says Gregory Weiss, UCI professor of chemistry and molecular biology and biochemistry. “The real problem is there are lots of cases of gummy proteins that you spend way too much time scraping off your test tubes, and you want some means of recovering that material.”

The team says that the process has valuable applications in producing proteins for science and industry, such as a cheaper, faster way of making antibodies for cancer treatments or using recombinant proteins for cheesemakers.

The team’s results were published in ChemBioChem.

Source: UC Irvine

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