The New York Public Library Helps You Turn 100-Year-Old Photographs Into 3-D GIFs

By Dan Nosowitz

Stereogranimator, Pre-Stereogranimation NYPL

The New York Public Library has an archive of over 40,000 historical stereographs, many well over a hundred years old. Stereographs are regular photographs, except in pairs, with the perspective very slightly different. Essentially, stereographs are what you were looking at through your ViewMaster as a kid. And now the NYPL has created a pretty amazing tool they're calling the Stereogranimator that lets users create animated 3-D GIFs from the photos in the archive.

Moving the image back and forth between the two perspectives tricks the eye into seeing depth--it's kind of a lo-fi way to get around that problem of both eyes seeing the same thing. (Regular 3-D beams a different image to each eye.) Here's a recent example:

GIF made with the NYPL Labs Stereogranimator

It's especially cool that the tool, while easy to use, isn't really automatic--you still have to play around with it to get the perspective and speed just right. Go check it out!

[NYPL Stereogranimator]

Smallest-Ever Nanotube Transistors Outperform Silicon

COMPUTING

A nine-nanometer device shows that nanotubes could be a viable alternative to silicon as electronics get even tinier.

• BY KATHERINE BOURZAC

The smallest carbon-nanotube transistor ever made, a nine-nanometer device, performs better than any other transistor has at this size.

For over a decade, researchers have promised that carbon nanotubes, with their superior electrical properties, would make for better transistors at ever-tinier sizes, but that claim hadn't been tested in the lab at these extremes. Researchers at IBM who made the nanotube transistors say this is the first experimental evidence that any material is a viable potential replacement for silicon at a size smaller than 10 nanometers.

"The results really highlight the value of nanotubes in the most sophisticated type of transistors," says John Rogers, professor of materials science at the University of Illinois at Urbana-Champaign. "They suggest, very clearly, that nanotubes have the potential for doing something truly competitive with, or complementary to, silicon."

The shrinkage of silicon transistors over the past several decades has reduced the cost of electronics and led to more processing power with less energy consumption. But the downsizing of silicon electronics might hit a roadblock at around 10 nanometers, says Aaron Franklin, a researcher at the IBM Watson Research Center in Yorktown Heights, New York. "We are now reaching physical limits," he says. As transistors are made smaller, it gets more difficult to control how electrons move through the silicon channel to turn the transistor on and off. Faced with this unruly, power-draining behavior, Intel announced last year that it would switch to a new, three-dimensional transistor design for its 22-nanometer generation of chips. Other companies are working on so-called ultrathin body transistors. No matter how it's shaped, though, silicon is silicon, and dealing with it at extremely small sizes presents problems even in these new transistor designs.

Many materials have been hyped as a potential replacement for silicon, including carbon nanotubes. That material and others have shown promise in larger transistors, but until now, no one had demonstrated a carbon-nanotube transistor smaller than 10 nanometers. "If nanotubes can't go much further than silicon, then working on them is a waste of time," says Franklin. "We've made nanotube transistors at aggressively scaled dimensions, and shown they are tremendously better than the best silicon devices."

To test how the size of a nanotube transistor affected its performance, Franklin's group made multiple transistors of different sizes along a single nanotube. This enabled them to control for any variations that might occur from nanotube to nanotube. First, they had to lay down a very thin layer of insulating material for the nanotube to sit on. And they developed a two-step process for adding electrical gates to the nanotube without damaging it. These techniques are by no means ready for manufacturing, but they enabled the IBM group to make the first nanotube devices smaller than 10 nanometers to test in the lab. The work is described online in the journal Nano Letters.

The IBM group demonstrated that its nine-nanometer nanotube transistor had much lower power consumption than other transistors the same size. And it can carry more current than comparable silicon devices, which means a better signal.

Several major engineering problems remain, says Franklin. First, researchers have to come up with better methods for making pure batches of semiconducting nanotubes—metallic tubes in the mix will short out integrated circuits. Second, they must come up with a way to place large numbers of nanotubes on a surface with perfect alignment.

Aiding cancer therapy by mathematically modeling tumor-immune interactions

 by Biomechanism 

Cancer is one of the five leading causes of death. And yet, despite decades of research, there is no standardized first-line treatment for most cancers. In addition, disappointing results from predominant second-line treatments like chemotherapy have established the need for alternative methods.

Mathematical modeling of cancer usually involves describing the evolution of tumors in terms of differential equations and stochastic or agent-based models, and testing the effectiveness of various treatments within the chosen mathematical framework. Tumor progression (or regression) is evaluated by studying the dynamics of tumor cells under different treatments, such as immune therapy, chemotherapy and drug therapeutics while optimizing dosage, duration and frequencies.

In a paper published last month in the SIAM Journal on Applied Mathematics, ‘Controlled Drug Delivery in Cancer Immunotherapy: Stability, Optimization, and Monte Carlo Analysis,’ authors Andrea Minelli, Francesco Topputo, and Franco Bernelli-Zazzera propose a differential equation model to describe tumor–immune interactions. “We study the dynamics of the competition between the tumor and the immune system,” Topputo explains.

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The relationship between cancers and the immune system has been studied for many years, and immune therapy has been known to influence tumor regression. Clinically called immunotherapy, it involves using external factors to induce, enhance, or suppress a patient’s immune response for treatment of disease. In this study, the therapy consists of injecting a type of immune cells called dendritic cells, which generate tumor-specific immunity by presenting tumor-associated antigens.

“In particular, cancer immunotherapy has the purpose of identifying and killing tumor cells,” says Topputo.  “Our research considers a model that describes the interaction between the neoplasia [or tumor], the immune system, and drug administration.” Such modeling and simulation can be used to assess the impact of drugs and therapies before clinical application.

Using ordinary differential equations, the authors model the progress of different cell populations in the tumor environment as a continuous process. Within the dynamical system presented by the tumor environment, they apply the theory of optimal control—a mathematical optimization method—to design ad-hoc therapies and find an optimal treatment.

The end goal of the control policy is to minimize tumor cells while maximizing effectors, such as immune cells or immune-response chemicals. “The aim is to minimize the tumor concentration while keeping the amount of administered drug below certain thresholds, to avoid toxicity,” says Topputo. “In common practice, one searches for effective therapies; in our approach, we look for efficiency and effectiveness.”

Elaborating on a prior study where indirect methods used to solve the optimal control problem are not effective, the authors use direct methods that apply algorithms from aerospace engineering to solve the associated optimal control problem in this paper. Optimal protocols are analyzed, and the duration of optimal therapy is determined.

The robustness of the optimal therapies is then assessed. In addition, their applicability toward personalized medicine is discussed, where treatment is customized to each individual based on various factors such as genetic information, family history, social circumstances, environment and lifestyle.

“We have shown that personalized therapy is robust even with uncertain patient conditions. This is relevant as the model coefficients are characterized by uncertainties,” Topputo explains. “Further studies would include designing optimal protocols by considering personalized constraints based on individual patient conditions, such as maximum amount of drug, therapy duration, and so on.”

Other future directions would be the use of more diverse models and studying the effectiveness of treatment combinations. “More detailed approaches like agent-based models that describe tumor-immune interactions and hybrid therapies that consist of combined chemotherapy-immunotherapy treatments should also be considered,” says Topputo.

The Full study: Controlled Drug Delivery in Cancer Immunotherapy: Stability, Optimization, and Monte Carlo Analysis

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About the authors:Andrea Minelli is a researcher in the Applied Aerodynamics Department at ONERA, The French Aerospace Lab in Meudon, France. Francesco Topputo is a post-doctoral research fellow and Franco Bernelli-Zazzera a full professor in the Aerospace Engineering Department at Politecnico di Milano in Milano, Italy.

Researchers develop gene therapy that could correct a common form of blindness

 by Biomechanism 

A new gene therapy method developed by University of Florida researchers has the potential to treat a common form of blindness that strikes both youngsters and adults.

The technique works by replacing a malfunctioning gene in the eye with a normal working copy that supplies a protein necessary for light-sensitive cells in the eye to function. The findings are published in the Proceedings of the National Academy of Sciences online.

Several complex and costly steps remain before the gene therapy technique can be used in humans, but once at that stage, it has great potential to change lives.

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“Imagine that you can’t see or can just barely see, and that could be changed to function at some levels so that you could read, navigate, maybe even drive — it would change your life considerably,” said study co-author William W. Hauswirth, Ph.D., the Rybaczki-Bullard professor of ophthalmology in the UF College of Medicineand a professor and eminent scholar in department of molecular genetics and microbiology and the UF Genetics Institute. “Providing the gene that’s missing is one of the ultimate ways of treating disease and restoring significant visual function.”

The researchers tackled a condition called X-linked retinitis pigmentosa, a genetic defect that is passed from mothers to sons. Girls carry the trait, but do not have the kind of vision loss seen among boys. About 100,000 people in the U.S. have a form of retinitis pigmentosa, which is characterized by initial loss of peripheral vision and night vision, which eventually progresses to tunnel vision, then blindness. In some cases, loss of sight coincides with the appearance of dark-colored areas on the usually orange-colored retina.

The UF researchers previously had success pioneering the use of gene therapy in clinical trials to reverse a form of blindness known as Leber’s congenital amaurosis. About 5 percent of people who have retinitis pigmentosa have this form, which affects the eye’s inner lining.

“That was a great advance, which showed that gene therapy is safe and lasts for years in humans, but this new study has the potential for a bigger impact, because it is treating a form of the disease that affects many more people,” said John G. Flannery, Ph.D., a professor of neurobiology at the University of California, Berkeley who is an expert in the design of viruses for delivering replacement genes. Flannery was not involved in the current study.

The X-linked form of retinitis pigmentosa addressed in the new study is the most common, and is caused by degeneration of light-sensitive cells in the eyes known as photoreceptor cells. It starts early in life, so though affected children are often born seeing, they gradually lose their vision.

“These children often go blind in the second decade of life, which is a very crucial period,” said co-author Alfred S. Lewin, Ph.D., a professor in the UF College of Medicine department of molecular genetics and microbiology and a member of the UFGenetics Institute. “This is a compelling reason to try to develop a therapy, because this disease hinders people’s ability to fully experience their world.”

Both Lewin and Hauswirth are members of UF’s Powell Gene Therapy Center.

The UF researchers and colleagues at the University of Pennsylvania performed the technically challenging task of cloning a working copy of the affected gene into a virus that served as a delivery vehicle to transport it to the appropriate part of the eye. They also cloned a genetic “switch” that would turn on the gene once it was in place, so it could start producing a protein needed for the damaged eye cells to function.

A new gene therapy method developed by University of Florida researchers, William W. Hauswirth, Ph.D. and Alfred S. Lewin, Ph.D., has the potential to reverse a common form of blindness that strikes young children.

After laboratory tests proved successful, the researchers expanded their NIH-funded studies and were able to cure animals in which X-linked retinitis pigmentosa occurs naturally. The injected genes made their way only to the spot where they were needed, and not to any other places in the body. The study gave a good approximation of how the gene therapy might work in humans.

“The results are encouraging and the rescue of the damaged photoreceptor cells is quite convincing,” said Flannery, who is on the scientific advisory board of the Foundation Fighting Blindness, which provided some funding for the study. “Since this type of study is often the step before applying a treatment to human patients, showing that it works is critical.”

The researchers plan to repeat their studies on a larger scale over a longer term, and make a version of the virus that proves to be safe in humans. Once that is achieved, a pharmaceutical grade of the virus would have to be produced and tested before moving into clinical trials in humans. The researchers will be able to use much of the technology they have already developed and used successfully to restore vision.

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Courtesy University of Florida

Mechanism sheds light on how the brain adapts to stress

 by Biomechanism 

Scientists now have a better understanding of the way that stress impacts the brain.

New research, published by Cell Press in the January 26 issue of the journal Neuron, reveals pioneering evidence for a new mechanism of stress adaptation and may eventually lead to a better understanding of why prolonged and repeated exposure to stress can lead to anxiety disorders and depression.

Most stressful stimuli cause the release of corticotropin-releasing hormone (CRH) from neurons in the brain. This is typically followed by rapid changes in CRH gene expression. In more practical terms, as soon as the CRH-containing neurons run out of CRH, they are already receiving directions to make more. CRH controls various reactions to stress, including immediate “fight-or-flight” responses as well as more delayed adaptive responses in the brain. Regulation of CRH activity is critical for adaptation to stress, and abnormal regulation of CRH is linked with multiple human psychiatric disorders.

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“Despite the wealth of information regarding the physiological role of CRH in mediating the response to stress, the molecular mechanisms that regulate expression of the CRH gene, and thereby CRH synthesis, have remained largely elusive,” explains senior study author, Dr. Gil Levkowitz, from the Weizmann Institute of Science in Israel. “In our study, we used mouse and zebrafish model systems to identify a novel intracellular signaling pathway that controls stress-induced CRH gene expression.”

Dr. Levkowitz and colleagues discovered that the protein Orthopedia (Otp), which is expressed in parts of the brain associated with stress adaptation, modulated CRH gene expression and was required for stress adaptation. The researchers went on to show that Otp regulates production of two different receptors on the neurons’ surface. The receptors, which receive and relay CRH production instructions, essentially function as “ON” and “OFF” switches.

“This regulation of the CRH gene is critical for neuronal adaptation to stress. Failure to activate or terminate the CRH response can lead to chronic over- or under-activation of stress-related brain circuits, leading to pathological conditions,” concludes Dr. Levkowitz. “Taken together, our findings identify an evolutionarily conserved biochemical pathway that modulates adaptation to stress.”

Oldest dinosaur nest discovered

JAMES COOK UNIVERSITY

A James Cook University researcher has helped unearth a 190-million-year-old dinosaur nesting site in South Africa, the oldest nesting site for dinosaurs ever found. The discovery, of the prosauropod dinosaurMassospondylus, at an excavation site in South Africa, has revealed significant clues about the evolution of complex reproductive behaviour in early dinosaurs. Led by University of Toronto (Mississauga) palaeontologist Robert Reisz, with co-author Dr Eric Roberts from JCU and a group of international researchers, the study describes clutches of eggs, many with embryos, as well as tiny dinosaur footprints. It has provided the oldest known evidence that the hatchlings remain at the nesting site long enough to at least double in size. The eggs are approximately five centimetres wide and seven centimetres long and the embryonic dinosaur skeleton is about five to six centimetres long and an estimated four centimetres tall in the egg. They can grow up to about five metres in length and about two metres tall. According to the authors, the newly unearthed dinosaur nesting ground is more than 100 million years older than previously known nesting sites. Dr Roberts, Senior Lecturer in JCU’s Discipline of Geology, said the sediments were an incredible source of information about the life and times of early dinosaurs. “Clues recorded in the rock, such as the tracks of the hatchling dinosaurs, traces of ancient ripples and evidence desiccation cracks all suggest that these animals were nesting in a dynamic shoreline environment with fluctuating climate conditions,” he said. “Ultimately, the preservation of these exquisite fossils appears to be tied to episodic flooding that buried parts of the nesting colony multiple times over unknown generations.” Dr Roberts said more than 10 nests had been discovered at several levels at the site, each with up to 34 round eggs in tightly clustered clutches. “The distribution of the nests in the sediments indicate that these early dinosaurs returned repeatedly, known as ‘nesting site fidelity’ to this site, and likely assembled in groups or colonial nesting to lay their eggs, the oldest known evidence of such behaviour in the fossil record.” The large size of the mother, at six metres in length, the small size of the eggs, about six to seven centimetres in diameter, and the highly organised nature of the nest, suggested that the mother may have arranged them carefully after she laid them, he said. “The eggs, embryos, and nests come from the rocks of a nearly vertical road cut only 25 metres long,” said Dr Reisz, head of Vertebrate Paleontology at the University of Toronto. “Even so, we found 10 nests, suggesting that there are a lot more nests in the cliff, still covered by tonnes of rock. We predict that many more nests will be eroded out in time, as natural weathering processes continue.” The fossils were found in sedimentary rocks from the Early Jurassic Period in the Golden Gate Highlands National Park in South Africa. The site has previously yielded the oldest known embryos belonging to Massospondylus, a relative of the giant, long-necked sauropods of the Jurassic and Cretaceous periods. The study, co-authored by Drs. David Evans (Royal Ontario Museum, Canada), Eric Roberts (JCU, Australia), Hans-Dieter Sues (Smithsonian Institute, USA), and Adam Yates (University of the Witwatersrand, South Africa), was published on January 23 in the Proceedings of the National Academy of Sciences. Editor's Note: Original news release can be found here.

Space invasions: what to do when stuff falls from the sky

ALICE GORMAN, FLINDERS UNIVERSITY

Satellites have a bad habit of occasionally falling to Earth but it's no cause for alarm, writes the author. Image: cristamei/iStockphoto In the past six months, it seems something has fallen from the sky every second minute. In September, the UARS satellite re-entered the Earth’s atmosphere, causing a media frenzy. In October, the German satellite Rosat re-entered, with much less fanfare. Before Christmas, there were reports of space junk falling near Esperance in Western Australia. And skywatchers were out in droves when theQuadrantid meteor shower put on its annual display earlier this month. Last weekend, the Russian Phobos-Grunt spacecraft, the country’s 19th attempt to reach Mars, plunged back to Earth amid much speculation about the effects of its toxic fuel. Near Earth Objects We’re getting used to the idea we’re under continual bombardment from the heavens. But as well as objects from Earth orbit, there are some more sinister things to worry about: the nearly 8,000 identified Near Earth Objects (NEOs), asteroids, comets and meteoroids, whose orbits bring them close enough to Earth for collision to be a real risk. In November last year, the asteroid 2005 YU55 missed the Earth by a mere 300,000 km. So what are we doing about this? At a panel convened in January 2012 in Adelaide by theInternational Space University’s Southern Hemisphere Summer Space Program, experts noted that our knowledge about what’s “out there” has increased exponentially in recent decades. We’ve got a pretty good idea of what is roaming around in the Near Earth environment. But as they also pointed out, very little is actively being done in the Southern Hemisphere to track and prepare for events such as re-entries. It wasn’t always this way: until 1996, the Australian government funded a Spaceguard program, which was responsible for identifying one-third of all catalogued NEOs – a very impressive track record. There are currently calls to revive Spaceguard activities, bringing Australia more into line with international efforts. (And in the meantime, it looks as if Australia will participate in talks with the US and Europe to help address the space junk issue.) Australia is indeed very well placed, in terms of its location, size, expertise and availability ofradio-quiet areas, to play an important role in observing and tracking both natural and human-manufactured objects in space. It’s also one of the few countries that has direct experience in what happens when a spacecraft makes an uncontrolled re-entry over land. In 1979, Skylab, one of the largest spacecraft ever launched at that time, fell out of the sky in flaming fragments over Western Australia. No-one was hurt and there was no property damage, although the Shire of Esperance famously fined the US State Department $400 for littering. (The fine was finally paid in 2009 by public donations). Hit and miss The first thing to note is that you would have to be very unlucky indeed to have a piece of space junk fall on you. It’s only happened once that we know of. According to the Centre for Orbital and Reentry Debris Studies (CORDS), Lottie Williams of Oklahoma was hit by a small piece of a Delta II rocket as she was taking a walk one day in 1996. She was unharmed. Similarly, there are no accounts of people being injured by meteorites. There’s just so much ocean, desert and ice – and this is usually where the stuff lands. Accounts of Skylab’s re-entry, however, can be used to derive some indications about what to expect. Sonic booms typically accompany objects falling at high speed through the upper atmosphere. As with fireworks, these loud noises can upset domestic pets and livestock. Take the same precautions as you would for your pets on New Year’s Eve; there is plenty of information about this online. Falling meteorites have frequently been blamed for causing fires, and this was also a concern for people in the debris footprint of Skylab. Having an up-to-date fire plan and managing the local risk around your house in terms of available fuel are the best way to prepare for this. If spacecraft fragments fall near you, don’t rush to collect them. For a start, there may be toxic fuel residues or metals such as beryllium, or radioactive material from power sources and onboard experiments. The most common spacecraft components to survive re-entry are spherical titanium pressure vessels. Usually regarded as an inert metal, titanium is now thought to have dangerous corrosion products. There are no recorded instances of people falling ill from contact with space junk, but there’s no point taking the risk. As appealing as the idea of having a personal souvenir of space is, this is not technically junk. Under the terms of the 1967 Outer Space Treaty, the fragments belong to the country which launched the spacecraft. So don’t collect fragments and sell them on eBay – as people may well have done if the internet existed in 1979. (But, if you are really keen, you can still buy tiny pieces of Skylab encased in resin with an authentification certificate today). The pieces can be used to analyse the re-entry event, and perhaps what went wrong with the spacecraft. If you or your property have been damaged by the spacecraft, you may be entitled to compensation. It will be the responsibility of the appropriate government agency to negotiate what happens next. For most countries, this will be the national space agency. The closest Australia has at the moment is the Space Policy Unit based in Canberra. Next time you hear that a spacecraft might fall on Australia, don’t be too alarmed. Keep an eye on the predictions, bring your kittens inside, and rejoice in the fact that there is one less objectclogging up Earth’s orbit. If you are concerned about NEOs, join those lobbying for the reinstatement of Spaceguard. It’s not all doom and gloom. The stuff that falls from space reminds us we are part of the cosmos too.