Gauging materials’ physical properties from video

Last summer (2014), Massachusetts Institute of Technology (MIT) researchers published a paper describing an algorithm that can recover intelligible speech from the analysis of the minute vibrations of objects in video captured through soundproof glass.

In June, at the Conference on Computer Vision and Pattern Recognition, researchers from the same groups will describe how the technique can be adapted to infer material properties of physical objects, such as stiffness and weight, from video.

The technique could have application in the field of “nondestructive testing,” or determining materials’ physical properties without extracting samples from them or subjecting them to damaging physical tests. It might be possible, for instance, to identify structural defects in an airplane’s wing by analyzing video of its vibration during flight.

Freshly squeezed vaccines

Massachusetts Institute of Technology (MIT) researchers have shown that they can use a microfluidic cell-squeezing device to introduce specific antigens inside the immune system’s B cells, providing a new approach to developing and implementing antigen-presenting cell vaccines.

Such vaccines, created by reprogramming a patient’s own immune cells to fight invaders, hold great promise for treating cancer and other diseases. However, several inefficiencies have limited their translation to the clinic, and only one therapy has been approved by the Food and Drug Administration.

While most of these vaccines are created with dendritic cells, a class of antigen-presenting cells with broad functionality in the immune system, the researchers demonstrate in a study published in Scientific Reports that B cells can be engineered to serve as an alternative.

Advance in quantum error correction

Quantum computers are largely theoretical devices that could perform some computations exponentially faster than conventional computers can. Crucial to most designs for quantum computers is quantum error correction, which helps preserve the fragile quantum states on which quantum computation depends.

The ideal quantum error correction code would correct any errors in quantum data, and it would require measurement of only a few quantum bits, or qubits, at a time. But until now, codes that could make do with limited measurements could correct only a limited number of errors—one roughly equal to the square root of the total number of qubits. So they could correct eight errors in a 64-qubit quantum computer, for instance, but not 10.

Report: Photosynthesis hack needed to feed world by 2050

Using high-performance computing and genetic engineering to boost the photosynthetic efficiency of plants offers the best hope of increasing crop yields enough to feed a planet expected to have 9.5 billion people on it by 2050, researchers report in Cell.

There has never been a better time to try this, said Univ. of Illinois plant biology professor Stephen P. Long, who wrote the report with colleagues from Illinois and the CAS-MPG Partner Institute of Computational Biology in Shanghai.

“We now know every step in the processes that drive photosynthesis in C3 crop plants such as soybeans and C4 plants such as maize,” Long said. “We have unprecedented computational resources that allow us to model every stage of photosynthesis and determine where the bottlenecks are, and advances in genetic engineering will help us augment or circumvent those steps that impede efficiency.”

Substantial progress has already been made in the lab and in computer models of photosynthesis, Long said.

“Our lab and others have put a gene from cyanobacteria into crop plants and found that it boosts the photosynthetic rate by 30%,” he said.

Photosynthetic microbes offer other clues to improving photosynthesis in plants, the researchers report. For example, some bacteria and algae contain pigments that utilize more of the solar spectrum than plant pigments do. If added to plants, those pigments could bolster the plants’ access to solar energy.

Some scientists are trying to engineer C4 photosynthesis in C3 plants, but this means altering plant anatomy, changing the expression of many genes and inserting new genes from C4 plants, Long said.

“Another, possibly simpler approach is to add to the C3 chloroplast the system used by blue-green algae,” he said. This would increase the activity of Rubisco, an enzyme that catalyzes a vital step of the conversion of atmospheric carbon dioxide into plant biomass. Computer models suggest adding this system would increase photosynthesis as much as 60%, Long said.

Computer analyses of the way plant leaves intercept sunlight have revealed other ways to improve photosynthesis. Many plants intercept too much light in their topmost leaves and too little in lower leaves; this probably allows them to outcompete their neighbors, but in a farmer’s field such competition is counterproductive, Long said.

Studies headed by U. of I. plant biology professor Donald Ort aim to make plants’ upper leaves lighter, allowing more sunlight to penetrate to the light-starved lower leaves.

Computer modeling of photosynthesis also shows researchers where the traffic jams occur—the steps that slow the process down and reduce efficiency.

“The computer model predicts that by altering this system by up-regulating some genes and down-regulating others, a 60% improvement could be achieved without any additional resource—so 60% more carbon could be assimilated for no more nitrogen,” Long said.

“The next step is to create an in silico plant to virtually simulate the amazingly complex interactions among biological scales,” said U. of I. plant biology professor Amy Marshall-Colon, a co-author on the report. “This type of model is essential to fill current gaps in knowledge and better direct our engineering efforts.”

While many scientific, political and regulatory hurdles remain for plants engineered to do a better job of converting the sun’s energy into biomass, the work should be undertaken now, Long said.

“If we have a success today, it won’t appear in farmers’ fields for 15 years at the very earliest,” he said. “We have to be doing today what we may need in 30 years.”

Roll up your screen and stow it away?

From smartphones and tablets to computer monitors and interactive TV screens, electronic displays are everywhere. As the demand for instant, constant communication grows, so too does the urgency for more convenient portable devices—especially devices, like computer displays, that can be easily rolled up and put away, rather than requiring a flat surface for storage and transportation.

A new Tel Aviv Univ. study, published in Nature Nanotechnology, suggests that a novel DNA-peptide structure can be used to produce thin, transparent and flexible screens. The research, conducted by Prof. Ehud Gazit and doctoral student Or Berger of the Dept. of Molecular Microbiology and Biotechnology at TAU's George S. Wise Faculty of Life Sciences, in collaboration with Dr. Yuval Ebenstein and Prof. Fernando Patolsky of the School of Chemistry at TAU's Faculty of Exact Sciences, harnesses bionanotechnology to emit a full range of colors in one pliable pixel layer—as opposed to the several rigid layers that constitute today's screens.

"Our material is light, organic and environmentally friendly," said Prof. Gazit. "It is flexible, and a single layer emits the same range of light that requires several layers today. By using only one layer, you can minimize production costs dramatically, which will lead to lower prices for consumers as well."

From genes to screens
For the purpose of the study, a part of Berger's graudate thesis, the researchers tested different combinations of peptides: short protein fragments, embedded with DNA elements which facilitate the self-assembly of a unique molecular architecture.

Peptides and DNA are two of the most basic building blocks of life. Each cell of every life form is composed of such building blocks. In the field of bionanotechnology, scientists utilize these building blocks to develop novel technologies with properties not available for inorganic materials such as plastic and metal.

"Our lab has been working on peptide nanotechnology for over a decade, but DNA nanotechnology is a distinct and fascinating field as well. When I started my doctoral studies, I wanted to try and converge the two approaches," said Berger. "In this study, we focused on PNA—peptide nucleic acid, a synthetic hybrid molecule of peptides and DNA. We designed and synthesized different PNA sequences, and tried to build nano-metric architectures with them."

Using methods such as electron microscopy and x-ray crystallography, the researchers discovered that three of the molecules they synthesized could self-assemble, in a few minutes, into ordered structures. The structures resembled the natural double-helix form of DNA, but also exhibited peptide characteristics. This resulted in a very unique molecular arrangement that reflects the duality of the new material.

"Once we discovered the DNA-like organization, we tested the ability of the structures to bind to DNA-specific fluorescent dyes," said Berger. "To our surprise, the control sample, with no added dye, emitted the same fluorescence as the variable. This proved that the organic structure is itself naturally fluorescent."

Over the rainbow
The structures were found to emit light in every color, as opposed to other fluorescent materials that shine only in one specific color. Moreover, light emission was observed also in response to electric voltage—which make it a perfect candidate for opto-electronic devices like display screens.

The study was funded by the Momentum Fund of Ramot, TAU's technology transfer company, which also patented the new technology. The researchers are currently building a prototype of the screen and are in talks with major consumer electronics companies regarding the technology.

Diagnosis by keyboard

Analyzing people’s keystrokes as they type on a computer keyboard can reveal a great deal of information about the state of their motor function, according to a new study from Massachusetts Institute of Technology (MIT).

In a paper appearing in Scientific Reports, the researchers found that their algorithm for analyzing keystrokes could distinguish between typing done in the middle of the night, when sleep deprivation impairs motor skills, and typing performed when fully rested.
The study, which grew out of the Madrid-MIT M+Vision Consortium, is based on the premise that “there might be hidden information in the way that we type,” says Ian Butterworth, one of the authors and an M+Vision fellow. “At the moment, pretty much all of the other information in typing is thrown out. We just pay attention to what keys are being pressed, not when or for how long.”

Forecasting future flooding

The Pacific Northwest is dotted by small, low-lying, coastal cities where populations tend to cluster. These communities can be isolated and are susceptible to devastation from major storms that bring substantial wind, waves and storm surge. With climate change, it is anticipated that storms will only become more frequent and intense, signifying a need to understand how the areas will be affected.

David Hill, a researcher at Oregon State Univ., is focused on the hydrology and hydrodynamics in coastal areas, which represent the boundary between terrestrial and marine environments. His research on future levels of flooding in Tillamook Bay was published in the Journal of Geophysical Research.

"This particular project is a blending of our interests in estuarine and coastal hydrodynamics and our interests in climate change," Hill said. "We're interested in getting a good quantitative understanding of the extreme water levels we can expect from coastal flooding."

Unlike the South or East coast of the United States, coastal flooding in the Pacific Northwest comes primarily from large waves generated by major storms instead of hurricanes.