New Analysis Yields Improvements in a Classic 3-D Imaging Technique

Research conducted at Curtin University in Perth has enabled significant increases in image quality in a widely used 3D printing technique that is more than 100 years old.

Anaglyph printing -- think of the red-and-blue 3D glasses used to transform 2D images to 3D images in comics, magazines, books, and newspapers -- came into being when the continuous-tone printed anaglyph was invented by French physicist Louis Ducos du Hauron in 1891.

The technique works by combining the left and right images of a stereoscopic image pair into the red and blue color channels of the output anaglyph image. With the red/blue 3D glasses, the left eye sees only the red channel of the anaglyph image, and the right sees only the blue. If the anaglyph 3D image has been constructed correctly, the viewer sees a pleasing 3D image on the printed page.

The project team, led by Curtin research engineer Andrew Woods, targeted crosstalk problems which are visible as ghost-like shadows. Their paper published recently in the SPIE journal Optical Engineering details seven recommendations for overcoming crosstalk.

"The largest reduction in crosstalk is likely be achieved by using inks which have a better spectral purity than current process inks used in color printers," Woods said. "We found that an 80% reduction in crosstalk was potentially achievable just by changing the cyan ink."

The anaglyph technique is easy to implement and the anaglyph 3D glasses are relatively cheap, so the technique is used very widely, Woods said.

However, printed anaglyph images often suffer from a number of image quality limitations. When the 3D image is viewed through the colored glasses, there is often a significant amount of crosstalk (or ghosting), an undesirable property of some 3D techniques whereby the left eye sees some of the image intended for only the right eye, and vice-versa. Crosstalk is usually visible as ghost-like shadows throughout the image. If crosstalk levels are too high, the quality of the 3D experience can be significantly reduced.

"The printed anaglyph is 121 years old, but this appears to be the first time that a detailed technical simulation of crosstalk in printed anaglyphs has been developed," Woods said. "We started by measuring the spectral characteristics of various printing inks, 3D glasses, light sources, and papers. From there we developed a simulation which models the viewing of an anaglyph 3D image, and subsequently performed an experiment to validate the accuracy of the model. We hope this work will help provide a 21st-century improvement to the 19th-century invention."

In addition to changing the cyan ink, recommendations include using high-quality anaglyph glasses, an optimized light source, and improved image processing algorithms.

The full paper is available via open access in the SPIE Digital Library: "Characterizing and reducing crosstalk in printed anaglyph stereoscopic 3D images."

Read more at Science Daily

Understanding the Past and Predicting the Future by Looking Across Space and Time

Studying complex systems like ecosystems can get messy, especially when trying to predict how they interact with other big unknowns like climate change.

In a new paper published this week (May 20) in the Proceedings of the National Academy of Sciences, researchers from the University of Wisconsin-Madison and elsewhere validate a fundamental assumption at the very heart of a popular way to predict relationships between complex variables.

To model how climate changes may impact biodiversity, researchers like Jessica Blois and John W. (Jack) Williams routinely use an approach called "space-for-time substitution." The idea behind this method is to use the information in current geographic distributions of species to build a model that can predict climate-driven ecological changes in the past or future. But does it really work?

"It's a necessary assumption, but it's generally untested," says lead study author Blois, a former postdoctoral fellow with Williams at UW-Madison. She is now an assistant professor at the University of California, Merced. "Yet we're using this every day when we make predictions about biodiversity going into the future with climate change."

Their results should give other ecologists -- and potentially others such as economists who use similar models -- more confidence in their methods.

"At these spatial and temporal scales, the space-for-time assumption does work well," says Williams, professor of geography and director of the Center for Climatic Research at the UW-Madison Nelson Institute for Environmental Studies. "Our fossil data did support the idea that you can use spatial relationships as a source of information for making these predictions for the future."

Their research focus is paleoecology, the study of ancient ecosystems. By looking at fossilized pollen trapped in cores of sediment from the bottoms of lakes, the scientists reconstructed information about the plant communities present at locations across eastern North America during the past 21,000 years.

If climate has influenced communities the same way across space and through time, Blois explains, then a model based on the spatial data should make the same predictions as a model based on their temporal data. And in fact, they did.

The space-for-time model explained about 72 percent of the variation seen in their time data, and the remainder is likely due to other biological and environmental factors that the simplified model does not include, Blois says.

Though the testing does not capture all the ways space-for-time substitutions are used in other predictive fields, she says that the results are very encouraging for questions spanning large geographic and time scales -- scales at which collecting good temporal data can be very challenging.

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Expedition to Study Ancient Continental Breakup West of Spain

An international team of scientists has embarked on a shipboard expedition to study how Earth's crust was pulled apart in an area beneath the Atlantic Ocean off the coast of Spain. The team includes geophysicists from University of Southampton Ocean and Earth Science (SOES) based at the National Oceanography Centre in Southampton, UK.

From the research vessels RV Poseidon and RV Marcus G. Langseth the team will use sound waves to create a three-dimensional picture of the rocks in the Deep Galicia Basin, located to the west of northern Spain. The new datasets will improve understanding of how continents stretch and break apart, creating new ocean basins in between.

About 250 million years ago, Spain and Newfoundland in Canada were connected as part of a larger continent. Then around 220-200 million years ago, the continental crust in between began to spread apart, exposing the mantle beneath and eventually forming new oceanic crust by volcanic activity.

Professor Tim Minshull, Head of SOES, who is leading the Southampton team aboard the German vessel RV Poseidon, says: "We first conceived this project almost nine years ago, so after many years of preparation it is exciting to finally be doing the experiment."The team will drop 78 seismic detectors onto the seabed in cooperation with colleagues from GEOMAR Helmholtz Centre for Ocean Research Kiel, NOCS' German counterpart, led by Dr Dirk Klaeschen.

Led by Professor Dale Sawyer of Rice University, scientists aboard RV Marcus G. Langseth will then image Earth's crust in three dimensions over a 64 x 22 kilometre region of the ocean floor.

Seismologists use sound waves to image structures below the sea floor in much the same way that ultrasound techniques image organs in the human body. The sophisticated seismic instruments aboard the US vessel RV Marcus G. Langseth will allow seismologists to build up a picture of the faults and continental blocks up to 15 kilometres below the sea floor. Pressure guns towed behind the ship produce sound waves that penetrate the rocks and bounce off fault planes and boundaries. The reflected sound waves are then recorded by the detectors on the sea floor as well as instruments called hydrophones that are towed behind the ship.

The scientists are particularly interested in a strongly reflective fault surface -- known as the "S reflector" -- as well as the structures above and below it. This fault is thought to have formed when the crust was pulled apart. It is the boundary between the overlying crustal blocks and the underlying mantle rocks that have been penetrated by seawater. The scientists will also use the seismic images to work out how and in what order the different blocks moved as the crust was stretched.

Read more at Science Daily

King Richard III Buried in Hasty Grave

The body of King Richard III was buried in great haste, a new study finds — perhaps because the medieval monarch's corpse had been out for three days in the summer sun.

The new research is the first academic paper published on the discovery of Richard III, which was publically announced in February 2013. A team of archaeologists from the University of Leicester found the body beneath a parking lot in Leicester that was once the site of a medieval church. The full study will be available online on Friday evening (May 24).

The archaeological analysis contains details only alluded to in the initial announcement of the findings. In particular, the archaeologists found that Richard III's grave was dug poorly and probably hastily, a sharp contrast to the neat rectangular graves otherwise found in the church where the king was laid to rest.

Richard III's journey to Leicester

Richard III ruled England from 1483 to 1485, when he was killed during the Battle of Bosworth Field, the definitive fight in the War of the Roses.

Historical records reveal that after the battle, Richard's body was stripped and brought to Leicester, where it remained on public display for three days until burial on August 25, 1485. The church where the body was interred, a Franciscan friary called Grey Friars, was eventually demolished around 1538. A former mayor of Leicester built a mansion on the site, but by the 1700s, the land had been subdivided and sold off, the location of the church lost.

With it went all memory of where one of England's most famous kings was buried. Richard III was immortalized by a Shakespeare play of the same name and made out to be a villain by the Tudor dynasty that followed his rule. Today, however, there are societies of Richard III enthusiasts called Richardians who defend the dead king's honor. One of these Richardians, a screenwriter named Philippa Langley, spearheaded the excavation that discovered Richard III's body.

Digging for Richard

The new paper, published in the journal Antiquity, outlines how archaeologists dug three trenches in a city government parking lot, hoping to hit church buildings they knew had once stood in the area. They soon found evidence of the friary they were looking for: first, a chapter house with stone benches and diamond-pattern floor tiles. This chapter house would have been used for daily monastery meetings.

South of the chapter houses, the excavation revealed a well-worn cloister walk, or covered walkway. Finally, the researchers found the church building itself. The church was about 34 feet (10.4 meters) wide. It had been demolished, but the floors (and the graves in the floor) were left intact. Among the rubble were decorated tiles and copper alloy letters that likely once marked the graves.

Brick dust suggested the outer church walls may have been covered with a brick façade, which would have created a striking red-and-white look with the church's limestone-framed windows, the researchers wrote.

A hasty grave

Most of the graves in the Grey Friars church floor are neat and orderly, with squared-off rectangle sides. Richard III's is an exception. The grave is irregularly shaped, with sloping sides. It was also too small for the 5-foot-8-inch (1.7 m) skeleton interred within: Richard's torso is twisted and his head propped up rather than laid flat. The body was also crammed against the north wall of the grave, perhaps because someone stood against the south wall to guide the body into its resting place. Whoever it was did not spend time afterward rearranging the body into a more symmetrical position.

"The haste may partially be explained by the fact that Richard’s damaged body had already been on public display for several days in the height of summer, and was thus in poor condition," the researchers wrote.

Read more at Discovery News

Pope Francis Accepts Atheists: Not the First

Being an atheist is fine, as long as you do good, Pope Francis said Wednesday, rocking the minds of less tolerant Catholics.

In his homily at the morning Mass in Rome, the leader of the world’s 1.2 billion Roman Catholics urged the faithfuls to broaden their horizon, following a principle Jesus taught his disciples. Citing the Gospel of Mark, he described how upset the disciples were at the news that someone outside their group was doing good.

“They complained: If he is not one of us, he cannot do good. If he is not of our party, he cannot do good,” Francis said.

“This was wrong,” he added, according to a report from Vatican Radio.

Labeling the disciples as “a little intolerant,” closed off by the idea that “those who do not have the truth, cannot do good,” Francis remarked the importance of the “doing good” commandment. The principle, he said, unites all humanity, beyond religions and ideologies, creating a “culture of encounter” which is at the basis of peace.

Narrow and self centered attitudes should be banned, as everyone doing good, including atheists, can be redeemed by Jesus, Francis said.

“Just do good and we’ll find a meeting point,” the pope said, referring to a hypothetical conversation in which someone told a priest: “But I don’t believe. I’m an atheist.”

Francis’s reaching out to atheists is not a completely new move. A dialogue with non believers was sought in 1964 by Pope Paul VI. In his debut encyclical Ecclesiam Suams, Paul conceded that some atheists were undoubtedly inspired by “great-hearted dreams of justice and progress.”

Adding to a number of unconventional speeches and gestures, Pope Francis’ words have sounded almost revolutionary as they are in striking contrast with the radical views of his predecessor Benedict XVI, who often described atheism as a terrible threat, harshingly attacking what he called “aggressive secularism.”

In a much criticized speech during his first papal visit to Britain in 2010, Benedict even appeared to tie atheism with the crimes of the Nazi, by stating that the “Nazi tyranny that wished to eradicate God from society” had resulted in the Holocaust.

According to Christian News, reports state that a number of atheists are favorable toward the charismatic pope, mainly because of his humanitarian goals.

“I might not believe in God, but I believe that Catholics and atheists can work together just as all of humanity can work together towards equality and justice when we put the needs of modern people first and the arcane doctrine second,” author Luis Ruuska wrote in a Huffington Post article entitled “Why This Atheist Has a New Hope in Pope Francis.”

Read more at Discovery News

Stem Cell Study Researcher Admits Mistakes

A blockbuster study in which US researchers reported that they had turned human skin cells into embryonic stem cells contained errors, its lead author has acknowledged.

Shoukhrat Mitalipov nevertheless adamantly stood by the conclusions of the study published last week in journal Cell, which reported that human stem cell lines for the first time had been created via cloning.

The journal Nature contacted Mitalipov after an anonymous online critic on PubPeer spotted four separate problems in the paper.

In an interview with Nature, Mitalipov confirmed that three errors were made in the rush to publish -- but denied the fourth issue raised was an error and said the overall conclusions were unaffected.

"The results are real, the cell lines are real, everything is real," said Mitalipov, a reproductive biology specialist at the Oregon Health and Science University in Beaverton.

"I personally made the cells," he said. "I saw them grow into colonies."

He blamed the errors on his rush to publish the research, which he hoped to present next month at the International Society for Stem Cell Research meeting. "Maybe it was rushed," he said. "It was my mistake."

Mitalipov said his research team will be issuing an erratum correcting the flaws, and hopes that other scientists will try to duplicate his findings, which will lend it even more credibility.

"The first thing we want to do is have people confirm our results," Mitalipov said. "We are not hiding these cell lines."

The scientific community was divided as to how seriously to view the errors.

Robin Lovell Badge, who heads the Division of Stem Cell Biology and Developmental Genetics at the MRC National Institute for Medical Research in London, warned against a rush to condemn.

"I expect the errors above were also due to the rush to publish. The authors should be given a chance to answer and correct mistakes," he told Nature.

Others said they were surprised that Cell accepted the paper in just days -- a time they deemed insufficient for proper peer review.

"The four-day review process was obviously inadequate," said Arnold Kriegstein, director of the stem cell program at the University of California, San Francisco.

"It's a degree of sloppiness that you wouldn't expect in a paper that was going to have this high profile," Kriegstein told the British journal.

"One worries if there is more than meets the eye and whether there are other issues with the work that are not as apparent," he said.

The cloning method written about in the article was described as an important breakthrough because it does not destroy embryos in creating the type of stem cell that can morph into any other type of cell in the body.

The technique involves transplanting an individual's DNA into an egg cell that has been stripped of genetic material, a variation of a method called somatic cell nuclear transfer.

Read more at Discovery News

What the Smallest Infectious Agents Reveal About Evolution

Radically different viruses share genes and are likely to share ancestry, according to research published in BioMed Central's open access journal Virology Journal this week. The comprehensive phylogenomic analysis compares giant viruses that infect amoeba with tiny viruses known as virophages and to several groups of transposable elements. The complex network of evolutionary relationships the authors describe suggests that viruses evolved from non-viral mobile genetic elements and vice versa, on more than one occasion.

The recent discovery of virophages inside the giant viruses, which in turn infect amoeba, has led to speculation about their origin and their relationship to other viruses and small transposable genetic elements. To try to answer this question a research team including Eugene Koonin from the NIH and Didier Raoult from URMITE compared the genetic material from virophages, such as the Mavirus, Sputnik, or OLV (which was isolated from an Antarctic organic lake), to eukaryotic self replicating transposable elements known as Polintons or Mavericks.

Eugene Koonin explains: "Between the known virophages there are six conserved genes, arranged in a similar way. Five of these have counterparts in the Polintons, but their sequence and arrangement are sufficiently different to discount suggestions that Polintons evolved directly from a Maviruse-like ancestor. Rather our data suggests that Maviruses have evolved from a fusion between a Politon/Maverick-like transposable element and an unknown virus."

Including information about other viruses and virus-like elements: adenoviruses that infect animals and are one of the causes of the common cold; certain bacteriophages that infect bacteria; transpovirons which infect giant viruses; and a Tetrahymena transposable element (Tlr1), the virus "evolutionary tree" appears as a network of swapped genes.

Read more at Science Daily

The Secret Lives (and Deaths) of Neurons

As the human body fine-tunes its neurological wiring, nerve cells often must fix a faulty connection by amputating an axon -- the "business end" of the neuron that sends electrical impulses to tissues or other neurons. It is a dance with death, however, because the molecular poison the neuron deploys to sever an axon could, if uncontained, kill the entire cell.

Researchers from the University of North Carolina School of Medicine have uncovered some surprising insights about the process of axon amputation, or "pruning," in a study published May 21 in the journal Nature Communications. Axon pruning has mystified scientists curious to know how a neuron can unleash a self -destruct mechanism within its axon, but keep it from spreading to the rest of the cell. The researchers' findings could offer clues about the processes underlying some neurological disorders.

"Aberrant axon pruning is thought to underlie some of the causes for neurodevelopmental disorders, such as schizophrenia and autism," said Mohanish Deshmukh, PhD, professor of cell biology and physiology at UNC and the study's senior author. "This study sheds light on some of the mechanisms by which neurons are able to regulate axon pruning."

Axon pruning is part of normal development and plays a key role in learning and memory. Another important process, apoptosis -- the purposeful death of an entire cell -- is also crucial because it allows the body to cull broken or incorrectly placed neurons. But both processes have been linked with disease when improperly regulated.

The research team placed mouse neurons in special devices called microfluidic chambers that allowed the researchers to independently manipulate the environments surrounding the axon and cell body to induce axon pruning or apoptosis.

They found that although the nerve cell uses the same poison -- a group of molecules known as Caspases -- whether it intends to kill the whole cell or just the axon, it deploys the Caspases in a different way depending on the context.

"People had assumed that the mechanism was the same regardless of whether the context was axon pruning or apoptosis, but we found that it's actually quite distinct," said Deshmukh. "The neuron essentially uses the same components for both cases, but tweaks them in a very elegant way so the neuron knows whether it needs to undergo apoptosis or axon pruning."

In apoptosis, the neuron deploys the deadly Caspases using an activator known as Apaf-1. In the case of axon pruning, Apaf-1 was simply not involved, despite the presence of Caspases. "This is really going to take the field by surprise," said Deshmukh. "There's very little precedent of Caspases being activated without Apaf-1. We just didn't know they could be activated through a different mechanism."

In addition, the team discovered that neurons employ other molecules as safety brakes to keep the "kill" signal contained to the axon alone. "Having this brake keeps that signal from spreading to the rest of the body," said Deshmukh. "Remarkably, just removing one brake makes the neurons more vulnerable."

Read more at Science Daily

Stephen Hawking Gets Superhero Treatment in New Comic

A new comic book gets its action from the tremendous ideas of cosmologist Stephen Hawking.

Living legend Stephen Hawking has already achieved superhero status in the eyes of many science geeks, and now his ideas are being honored in comic book form.

"Stephen Hawking: Riddles of Time & Space" (Bluewater) details the life story of the physicist, from his early days at Cambridge and struggles with a body-wrecking disease to his academic achievements and current fame.

Hawking, 71, is widely considered one of the greatest scientific minds since Albert Einstein, and he has greatly enriched our understanding of the universe over the past several decades. His work with fellow cosmologist Roger Penrose helped unite Einstein's general theory of relativity and quantum theory. Hawking also studied black holes, with a groundbreaking theory that the cosmic monsters do actually emit a faint glimmer of radiation.

But his life has been marked by physical challenges. At age 21, Hawking was diagnosed with the motor neuron disease called amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease. The disease eventually robbed him of his mobility and later his ability to speak; today, Hawking uses a speech-generating device controlled by the muscles in his cheek.

"The very concept of making an engaging comic book where the protagonist is essentially immobile is a pretty tall order, but I think the key to us keeping it exciting was being able to get inside his mind (one of the greatest of our time) and show some of his most abstract concepts in a visual and dynamic way," artist Zach Bassett said in a statement.

One page detailing Hawking's ideas about black holes puts the scientist into conversation with Einstein, picturing him as Michelangelo's Adam reaching out to Einstein as God.

"Additionally, we got several chances to tip our hat to many famous artistic icons of pop culture, as well as famous people that he's met, taken inspiration from or even inspired himself," Bassett added. Hawking has been featured on "Star Trek: The Next Generation," "The Simpsons," "Futurama" and "The Big Bang Theory."

Read more at Discovery News

Can Life's Fingerprint Be Found On Super-Earths?

NASA is preparing the TESS observatory (Transiting Exoplanet Survey Satellite) to follow-up on the successes of the planet-hunting Kepler observatory by identifying nearby exoplanets that pass in front of, or “transit,” their stars. A small sample of these worlds will be singled out for further scrutiny if they lie within the habitable zone of the parent star. The habitable zone is the distance from a star where temperatures on a world may allow liquid water to exist on the planetary surface.

Kepler showed us an incredible diversity among planetary systems, and that small planets like Earth greatly outnumber bloated Jupiter-class worlds. But the Kepler planets are typically over 1,000 light-years away, so understanding the environments of these worlds is technologically out of the question — at least for the foreseeable future.

It is a reasonable prediction that the first transiting candidate planet to look for the chemical signature of life will be a world orbiting a nearby red dwarf star. There are about 90 red dwarfs within just 20 light-years of Earth, but only seven sun-like stars.

A transiting planet will allow for measuring the fraction of starlight passing through its atmosphere as well as recording the difference in light from the system when the planet passes behind its star.

TESS’ survey should at least find a few nearby transiting worlds within reach of doing a chemical inventory with NASA’s planned James Webb Space Telescope. At the very least, Webb would have a shot at providing evidence for an ocean on a planet.  This would further narrow down the candidates for more detailed studies.

Kepler’s survey found a number of super-Earths, planets several times Earth’s mass, and therefore too small to be gassy so-called ice giants like Uranus and Neptune. But what might the spectral fingerprint of a nearby super-Earth look like? And could we unequivocally deduce the planet is inhabited to everyone’s satisfaction?

Astrobiologists are now modeling super-Earth atmospheres for planets orbiting in the habitable zone of red dwarf stars. It’s time to begin to try and understand and predict the expected signature of an alien biosphere.

A set of models developed by J. L. Grenfell of the Zentrum fur Astronomie und Astrophysik, Technische Universitat Berlin, and colleagues, start out with the assumption the planet is blanketed with life (unlike Mars where apparently nothing survives on the surface). This would likely require that the target world be several billion years old to allow for the evolution of life to expand, diversify, and significantly modify the planet’s atmosphere.

Life on any planet would use chemical reactions to extract energy, store it, and release certain gases as a byproduct of their metabolism. On Earth the biggest chemical signature of metabolism is oxygen produced by photosynthesis. Other strong signals would come from the presence of ozone and nitrous oxide. Other biotracers, carbon dioxide and methane (already detected on and exoplanets by the Hubble Space Telescope) can also be produced by non-biological processes.

The researchers find that ozone levels can vary widely given other conditions on the super-Earths. In particular ultraviolet radiation from a red dwarf star is anemic. Without UV radiation to break apart certain gasses a red dwarf planet might have a higher concentration of biosignature gasses, as well as a smoggy sky.

The model also looks at surface gravities that could be as high as three times that of Earth’s. This might inhibit the movement of biogases from the planet’s surface into the higher stratosphere. What’s missing in the models are such critical but unknown variables are whether the planet has a shielding magnetic field, or plate tectonic for recycling atmospheric gases like carbon dioxide that otherwise might build up to trigger a runaway greenhouse effect.

The bottom line is that super-Earth atmospheres will be complicated and messy and will probably not look like anything that unequivocally settles the question of habitability. This will spur the far-future goal of building interstellar probes to visit the nearest habitable planet candidates.

Read more at Discovery News