New technology may identify tiny strains in body tissues before injuries occur

The top image shows how the new algorithm is able to identify an area (in red) where stress has created a weak spot in a small piece of plastic wrap. The older method (shown in the bottom half of the picture) is unable to pinpoint the place where the plastic wrap is weakening.
Credit: John Boyle, © The Royal Society (used with permission)

Researchers at Washington University in St. Louis have developed algorithms to identify weak spots in tendons, muscles and bones prone to tearing or breaking. The technology, which needs to be refined before it is used in patients, one day may help pinpoint minor strains and tiny injuries in the body's tissues long before bigger problems occur.

The research is available online Aug. 27 in the Journal of the Royal Society Interface, which publishes research at the nexus of the physical and life sciences.

"Tendons are constantly stretching as muscles pull on them, and bones also bend or compress as we carry out everyday activities," said senior investigator Stavros Thomopoulos, PhD, professor of orthopaedic surgery. "Small cracks or tears can result from these loads and lead to major injuries. Understanding how these tears and cracks develop over time therefore is important for diagnosing and tracking injuries."

To that end, Thomopoulos and his colleagues developed a way to visualize and even predict spots where tissues are weakened. To accomplish this, they stretched tissues and tracked what happened as their shapes changed or became distorted.

The paper's first author, John J. Boyle, a graduate student in biomedical engineering, combined mechanical engineering fundamentals with image-analysis techniques to create the algorithms, which were tested in different materials and in animal models.

"If you imagine stretching Silly Putty or a swimming cap with a picture on it, as you pull, the picture becomes distorted," Boyle said. "This allows us to track how the material responds to an external force."

In one of the experiments described in the paper, Boyle sprayed a pattern of dots on plastic wrap, stretched it and tracked the dots.

"As you pull and stretch the plastic wrap, eventually tears begin to emerge," he explained. 

"The new algorithm allowed us to find the places where the tears were beginning to form and to track them as they extended. Older algorithms are not as good at finding and tracking localized strains as the material stretches."

In fact, one of the two new algorithms is 1,000 times more accurate than older methods at quantifying very large stretches near tiny cracks and tears, the research showed. And a second algorithm has the ability to predict where cracks and failures are likely to form.

"This extra accuracy is critical for quantifying large strains," said Guy Genin, PhD, professor of mechanical engineering and co-senior investigator on the study. "Commercial algorithms that estimate strain often are much less sensitive, and they are prone to detecting noise that can arise from the algorithm itself rather than from the material being examined. The new algorithms can distinguish the noise from true regions of large strains."

Thomopoulos, who also is a professor of biomedical engineering and of mechanical engineering, works with Genin to study the shoulder's rotator cuff, a group of tendons and muscles that connect the upper arm to the shoulder blade. They want to learn why some surgeries to repair rotator cuff injuries ultimately fail. Their goal is to increase the odds that the tissue in the shoulder will heal following surgery, and they believe the new algorithms could help them get closer to that goal.

How soon the new algorithms could be used in patients depends on getting better images of the body's tissues. Current imaging techniques, such as MRI and ultrasound, lack the required clarity and resolution.

Genin also explained that although the goal of the current study is to better understand how forces at work on human tissue cause injury and stress, the algorithms also could help engineers identify vulnerable parts of buildings and other structures. Our muscles and bones, he said, are influenced by the same strains that affect those structures.

"Whether it's a bridge or a tendon, it's vital to understand the ways that physical forces cause structures and tissues to deform so that we can identify the onset of failures and eventually predict them," he said.

In the long run, they want to use the algorithms to prevent additional injuries following surgery to repair knees, shoulders and other tissues. They also said it may be possible some day to predict problems before they occur.

The group, which applied for a provisional patent earlier this year, hopes the algorithms will be useful to researchers in the medical and engineering fields.

As a piece of plastic wrap is stretched, the new algorithms identify the location (in red) where it is weakening, which is where the material eventually breaks.

Source: Washington University in St. Louis

Sculpting costumes with 3-D printers is 'the way theater is headed,' say theater education experts

Baylor junior Mackenzie Dobbs, a theatre performance major, in a witch's costume decorated with beans and mushrooms produced from a 3D printer. Credit: Drapers: Sylvia Fuhrken and Ryan Schapp, Photo by Jared Tseng

Three-dimensional printers, which already have churned out jewelry, prosthetic limbs and one fully functioning car, are taking the stage -- literally -- in another arena: live theater.

They allow greater speed, flexilibity, creativity -- and can appease directors who change their minds mid-rehearsal.

Synthetic beans and mushrooms -- accessories for the cursed, hump-backed witch in a Baylor University production of the musical "Into the Woods" -- recently emerged from a little machine tucked away in a corner of the costume shop at Baylor. And that's only the beginning for the new printer, says former Disneyland costume designer/wardrobe coordinator Joe Kucharski, assistant professor of theatre arts at Baylor.

Using his computer mouse and some free software, Kucharski tugged, flattened and pinched a digital "ball of clay" into the desired shapes: rotting vegetables, including two dozen beans and a dozen mushrooms. That done, the 3D printer heated and spun plastic cord into the delicate thread to create the costume elements for the witchy wardrobe.

Depending on the size and how complicated a design is, 3D printing may take 20 minutes to a couple hours.

"You can set a few buttons and walk away during printing," Kucharski said. "You can customize and print multiples, and you can use colors that are the whole range of the rainbow.

"Designers are always thinking, 'How can we design quickly but keep it adjustable so we're ready if the director says, 'Well, we're kinda there. . .'? We can go back and tweak quickly."

The printers have been used in film and fashion, and "it's a great application for scenic design in theater, too," he said. "You can use miniatures created on a small-scale model and save time instead of carving little details."

The 3D printer is rapidly becoming part of the "designer tool bag." While students still need to learn traditional drawing and creating, incorporating 3D technology into curriculum for costume and prop design can give them an edge in the job market.

"This is the way theatre is going," said Stan Denman, Ph.D., chair and professor of theatre arts at Baylor. "This even lets us create items that are no longer being produced -- like brooches or hatpins -- for period plays. Otherwise, because those things are antiques, the cost is prohibitive.

"This also can be helpful if you have an item that has to be broken in a scene," he said. "You can have multiple items to replace it for repeat performances."

Source: Baylor University

A mobile app for conducting opinion polls

Opiner is an open source tool for opinion polling. Credit: Image courtesy of KTH The Royal Institute of Technology

Soon anyone can conduct public opinion polls to drive issues that are important to them, using a new open source tool being developed at Sweden's KTH Royal Institute of Technology.

Researcher Konrad Tollmar and his colleagues intend for the mobile app, Opiner, to be used as a tool for direct democracy. Tollmar says that once Opiner is publicly available, it will enable anyone to conduct surveys, drive public opinion and influence political decisions.

"This will be an alternative to services that can cost millions to use," says Tollmar. "It gives people an opportunity that historically only large organisations have had."

Public opinion polls are an important tool for interest groups, which regularly hire commercial firms to conduct polls for them. The ability to take stock of -- and present -- public opinion enables interest groups to control the narrative around their issues, establish their communications themes and influence how the media and policymakers grasp a given subject.

"Polling can be expensive," he says. "But Opiner enables anyone to drive public opinion or conduct surveys."

Opiner could also have the benefit of energising more people to become politically involved. And it's not just for activists. Media organisations big and small can use the tool for their own purposes.

"We're working on a form of direct democracy. That people can have a voice in society," he says.

"But Opiner can be used for just about anything, large or small," he says, noting that one of the strengths of Opiner is that it can be context-specific.

Targeting mobile devices means that Opiner pollsters can make use of both space and time 

to find out what people think, and ask relevant questions based on these two parameters. For example, what do people think about public transportation when they are riding on the subway? What do students think about the quality of lunch while they're sitting in the school cafeteria?

"There is evidence in behavioral science and what is called "Experience Sampling," that surveys get a more true result when people are asked what they think in the moment, instead of afterward," he says.

Opiner also offers transparency. In addition to implementing polls, users can analyse the performance and freely share it. The system includes a toolkit to easily visualise the results in an understandable way.

"There are a lot of great tools on the web for public polling, but they are closed and commercial. Opiner is fully open and works on all types of newer phones. The system is open source, so anyone can download the software and set up their own Opiner," he says.

But it's not just the political benefit that Tollmar hopes to spread. In beta tests with teachers and students, the research team found that the act of surveying itself serves an educational purpose: as a way of developing students understanding of politics and language.

"First, we talked with their teachers about which questions should be asked. That worked so-so," he says. "The students didn't think the questions were always relevant. It was much better when the students themselves had to formulate their questions."

Opiner is part of the European research project, FlashPoll. Flashpoll has a mature Android app available, but what makes Opiner stand-out, Tollmar says, is its truly open platform -- from the establishment of questions, running the polls and analysis, to the sharing of results. "You should rather see Opiner as a research prototype of the next generation of Flashpoll tools," he says.

Tollmar is among a group of researchers at KTH who have worked with various digital tools over the last several years to help people make their voices heard, including Måns Wrange, Patrik Hernwall, Igor Isaksson och Mats Gustavsson.

Source: KTH The Royal Institute of Technology

New tool for exploring cells in 3D created

The new software can generate editable models of mid-size biological structures such as this one of HIV. Credit: Image created by Graham Johnson and Ludovic Autin of The Scripps Research Institute

Researchers can now explore viruses, bacteria and components of the human body in more detail than ever before with software developed at The Scripps Research Institute (TSRI).

In a study published online ahead of print December 1 by the journal Nature Methods, the researchers demonstrated how the software, called cellPACK, can be used to model viruses such as HIV.

"We hope to ultimately increase scientists' ability to target any disease," said Art Olson, professor and Anderson Research Chair at TSRI who is senior author of the new study.

Putting cellPACK to the Test

The cellPACK software solves a major problem in structural biology. Although scientists have developed techniques to study relatively large structures, such as cells, and very small structures, such as proteins, it has been harder to visualize structures in the medium "mesoscale" range.

With cellPACK, researchers can quickly and efficiently process the data they've collected on smaller structures to assemble models in this mid-size range. Previously, researchers had to create these models by hand, which took weeks or months compared with just hours in cellPACK.

As a demonstration of the software's power, the authors of the new study created a model of HIV showing how outer "spike" proteins are distributed on the surface of the immature virus.

The new model put to the test a conclusion made by HIV researchers from super-resolution microscopic studies -- that the distribution of the spike proteins on the surface of the immature virus is random. But by using cellPACK to generate thousands of models, testing alternative hypotheses, the researchers found that the distribution was not random. "We demonstrated that their interpretation of the distribution did not match that hypothesis," said Olson.

A Team Effort

The cellPACK software began as the thesis project of a TSRI graduate student, Graham Johnson, now a QB3 faculty fellow at the University of California, San Francisco (UCSF) who continues to contribute to the project. Johnson had more 15 years' experience as a medical illustrator, and he wanted to create an easy way to visualize mesoscale structures. cellPACK is an expansion of Johnson's autoPACK software, which maps out the density of materials -- from concrete in a building to red blood cells in an artery.

The researchers see cellPACK as a community effort, and they have made the autoPACK and cellPACK software free and open source. Thousands of people have already downloaded the software from http://www.autopack.org.

"With the creation of cellPACK, Dr. Olson and his colleagues have addressed the challenge of integrating biological data from different sources and across multiple scales into virtual models that can simulate biologically relevant molecular interactions within a cell," said Veersamy Ravichandran, PhD, of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research. "This user-friendly tool provides a new platform for data analysis and simulation in a collaborative manner between laboratories."

As new information comes in from the scientific community, researchers will tweak the software so it can model new shapes. "Making it open source makes it more powerful," said Olson. "The software right now is usable and very useful, but it's really a tool for the future."

Source: Scripps Research Institute

Self-repairing software tackles malware

Eric Eide, University of Utah research assistant professor of computer science, stands in the computer science department's "Machine Room" where racks of web servers sit. It is on these computers that Eide, U computer science associate professor John Regehr, and their research team created and tested A3, a suite of computer applications that defeat malware and automatically repair the damage it causes. The project could help lead to better consumer software defenses.
Credit: Dan Hixson/University of Utah College of Engineering

University of Utah computer scientists have developed software that not only detects and eradicates never-before-seen viruses and other malware, but also automatically repairs damage caused by them. The software then prevents the invader from ever infecting the computer again.

A3 is a software suite that works with a virtual machine -- a virtual computer that emulates the operations of a computer without dedicated hardware. The A3 software is designed to watch over the virtual machine's operating system and applications, says Eric Eide, University of Utah research assistant professor of computer science leading the university's A3 team with U computer science associate professor John Regehr. A3 is designed to protect servers or similar business-grade computers that run on the Linux operating system. It also has been demonstrated to protect military applications.

The new software called A3, or Advanced Adaptive Applications, was co-developed by Massachusetts-based defense contractor, Raytheon BBN, and was funded by Clean-Slate Design of Resilient, Adaptive, Secure Hosts, a program of the Defense Advanced Research Projects Agency (DARPA). The four-year project was completed in late September.

There are no plans to adapt A3 for home computers or laptops, but Eide says this could be possible in the future.

"A3 technologies could find their way into consumer products someday, which would help consumer devices protect themselves against fast-spreading malware or internal corruption of software components. But we haven't tried those experiments yet," he says.

U computer scientists have created "stackable debuggers," multiple de-bugging applications that run on top of each other and look inside the virtual machine while it is running, constantly monitoring for any out-of-the-ordinary behavior in the computer.

Unlike a normal virus scanner on consumer PCs that compares a catalog of known viruses to something that has infected the computer, A3 can detect new, unknown viruses or malware automatically by sensing that something is occurring in the computer's operation that is not correct. It then can stop the virus, approximate a repair for the damaged software code, and then learn to never let that bug enter the machine again.

While the military has an interest in A3 to enhance cybersecurity for its mission-critical systems, A3 also potentially could be used in the consumer space, such as in web services like Amazon. If a virus or attack stops the service, A3 could repair it in minutes without having to take the servers down.

To test A3's effectiveness, the team from the U and Raytheon BBN used the infamous software bug called Shellshock for a demonstration to DARPA officials in Jacksonville, Florida, in September. A3 discovered the Shellshock attack on a Web server and repaired the damage in four minutes, Eide says. The team also tested A3 successfully on another half-dozen pieces of malware.

Shellshock was a software vulnerability in UNIX-based computers (which include many web servers and most Apple laptops and desktop computers) that would allow a hacker to take control of the computer. It was first discovered in late September. Within the first 24 hours of the disclosure of Shellshock, security researchers reported that more than 17,000 attacks 

by hackers had been made with the bug.

"It is a pretty big deal that a computer system could automatically, and in a short amount of time, find an acceptable fix to a widespread and important security vulnerability," Eide says. 

"It's pretty cool when you can pick the Bug of the Week and it works."

Now that the team's project into A3 is completed and proves their concept, Eide says the U team would like to build on the research and figure out a way to use A3 in cloud computing, a way of harnessing far-flung computer networks to deliver storage, software applications and servers to a local user via the Internet.

The A3 software is open source, meaning it is free for anyone to use, but Eide believes many of the A3 technologies could be incorporated into commercial products.

Other U members of the A3 team include research associate David M. Johnson, systems programmer Mike Hibler and former graduate student Prashanth Nayak.

Source: University of Utah

Software to automatically outline bones in x-rays

An image from the Bone Finder software. Credit: Image courtesy of Manchester University

Research into disorders such as arthritis is to be helped by new software developed at the University of Manchester which automatically outlines bones -- saving thousands of hours of manual work.

Amidst a national shortage of radiographers in the UK and an increasing requirement for researchers to work with large databases of radiograph images, the software which is being funded by the Engineering and Physical Sciences Research Council, is being designed to automatically pick out the shapes of bones in the images, rather than relying on individual researchers.

The system can already identify hips, but the researchers from the University's Institute of Population Health will now adapt it to map out knees and hands and to be able to learn to identify other bones and structures within the body.

The funding will allow further development to ensure the system is accurate enough that it can be used in hospitals to help provide faster diagnosis of problems in patients.

Professor of Computer Vision, Tim Cootes said: "Mapping the outlines of bones from radiographs is hard work that takes time and skill. When researchers into conditions like arthritis are working with hundreds of images, it's a very inefficient way of obtaining data.

"The idea of this software is to take the routine tasks out of human hands, so scientists can 

focus on drawing conclusions and developing treatments."

The funding of £300,000 lasts for three years and builds on earlier work which developed software, called Bonefinder, to identify problems and find the outlines of hips. This free software has been adopted by a number of research groups, including some based in Oxford and California.

Professor Cootes added: "We have a growing problem with arthritis which affects more than 30% of over 65s and costs around £30 billion to the UK economy year.

"Ultimately we want to get this technology into hospitals where it can save time and resources for the benefit of patients."

Source: Manchester University

Software models more detailed evolutionary networks from genetic data

Phylogenetic networks depict the movement of genetic sequences from one species to another as a means of showing where horizontal gene transfer may have taken place. Software by scientists at Rice University aims to reveal far more about species’ evolutionary histories than traditional tree models are able to. Credit: Luay Nakhleh/Rice University

The tree has been an effective model of evolution for 150 years, but a Rice University computer scientist believes it's far too simple to illustrate the breadth of current knowledge.

Rice researcher Luay Nakhleh and his group have developed PhyloNet, an open-source software package that accounts for horizontal as well as vertical inheritance of genetic material among genomes. His "maximum likelihood" method, detailed this month in the Proceedings of the National Academy of Sciences, allows PhyloNet to infer network models that better describe the evolution of certain groups of species than do tree models.

"Inferring" in this case means analyzing genes to determine their evolutionary history with the highest probability -- the maximum likelihood -- of connections between species. Nakhleh and Rice colleague Christopher Jermaine recently won a $1.1 million National Science Foundation grant to analyze evolutionary patterns using Bayesian inference, a statistics-based technique to estimate probabilities based on a data set.

To build networks that account for all of the genetic connections between species, the software infers the probability of variations that phylogenetic trees can't illustrate, such as horizontal gene transfers. These transfers circumvent simple parent-to-offspring evolution and allow genetic variations to move from one species to another by means other than reproduction.

Biologists want to know when and how these transfers happened, but tree structures conceal such information. "When horizontal transfer occurs, as with the hybridization of two species, the tree model becomes inadequate to describe the evolutionary history, and networks that incorporate horizontal gene transfer become the more appropriate model," Nakhleh said.

Nakhleh's Java-based software accounts for incomplete lineage sorting, in which clues to gene evolution that don't match the established lineage of species appear in the genetic record.

"We are the first group to develop a general model that will allow biologists to estimate hybridization while accounting for all these complexities in evolution," Nakhleh said.

Most existing programs for phylogenetics (the study of evolutionary relationships) ignore such complexities. "They end up overestimating the amount of hybridization," Nakhleh said. 

"They start seeing lots of complexities in the data and say, 'Oh, it's complex here; it must be hybridization,' and end up inferring too much. Our method acknowledges that part of the complexity has nothing to do with hybridization; it has to do with other random processes that happened during evolution."

The Rice researchers used two data sets to test the new program. One, a computer-generated set of data that mimics a realistic model of evolution, allowed them to evaluate the accuracy of the program. The second involved multiple genomes of mice found across Europe and Asia. "There have been stories about mice hybridizing," Nakhleh said. "Now that we have the first method to allow for systematic analysis, we ran it on a very large amount of data from five mouse samples and we detected hybridization" -- most notably in the presence of a genetic signal from a mouse in Kazakhstan that found its way to mice in France and Germany, he said.

Nakhleh hopes evolutionary biologists will use PhyloNet to take a fresh look at the massive amount of genomic data collected over the past few decades. "The exciting thing for me about this is that biologists can now systematically go through lots of data they have generated and check to see if there has been hybridization."

Source: Rice University

Researchers develop a system to reconstruct grape clusters in 3D, assess quality

Antonio José Sánchez Salmerón, researcher at the Instituto ai2 of the UPV, explains that, today, grape classification is based on an inspection by a panel of experts, that award it score depending on a series of parameters that determine its quality. Credit: Image courtesy of Asociación RUVID

Researchers of the Universitat Politècnica de València (UPV) have developed software to help reconstruct grape clusters with three-dimensional computer vision techniques. The system helps to automatically assess different parameters that define the quality of the wine grape during harvest time.

During the work, the researchers of the UPV collaborated with the Research Centre of Vine and Wine related Sciences of the University of La Rioja, the Spanish National Research Council (CSIC, in Spanish) and the Government of La Rioja. The results of this work were released last September in the journal Food Control.

Antonio José Sánchez Salmerón, researcher at the Instituto ai2 of the UPV, explains that, today, grape classification is based on an inspection by a panel of experts, that award it score depending on a series of parameters that determine its quality. Moreover, different tests are performed in the laboratory in order to estimate the quantity of sugar, the pH, the total acidity and the phenolic quality.

"Among the factors that define the quality of a wine, one of the most important is the quality of the grape as the raw material, but this concept is difficult to assess, due to problems such as subjective parameters, the short period of time available in the field to do the analysis during harvest time, the lack of measuring instruments and their high price, as well as the mixing of good quality and bad quality grape in the trucks. The introduction of this 3D grape reconstruction system helps assess different quality parameters for a wine grape cluster avoiding these problems. One of these parameters is the average size of the grape, which is a very important factor as it establishes the ratio between the quantity of skin and pulp," explains the researcher.

"Increasing the objectivity and automating the grape quality monitoring tasks would be a technological breakthrough with regard to the traditional evaluation system of the grape, based on the knowledge of an expert, and it would have a great impact on the wine industry," adds Sánchez.

Source: Asociación RUVID

The Earthquake simulation tops one petaflop mark

Visualization of vibrations inside the Merapi volcano. Credit: Alex Breuer/Christian Pelties

A team of computer scientists, mathematicians and geophysicists at Technische Universitaet Muenchen (TUM) and Ludwig-Maximillians Universitaet Muenchen (LMU) have -- with the support of the Leibniz Supercomputing Center of the Bavarian Academy of Sciences and Humanities (LRZ) -- optimized the SeisSol earthquake simulation software on the SuperMUC high performance computer at the LRZ to push its performance beyond the "magical" one petaflop/s mark -- one quadrillion floating point operations per second.

Geophysicists use the SeisSol earthquake simulation software to investigate rupture processes and seismic waves beneath Earth's surface. Their goal is to simulate earthquakes as accurately as possible to be better prepared for future events and to better understand the fundamental underlying mechanisms. However, the calculations involved in this kind of simulation are so complex that they push even super computers to their limits.

In a collaborative effort, the workgroups led by Dr. Christian Pelties at the Department of Geo and Environmental Sciences at LMU and Professor Michael Bader at the Department of Informatics at TUM have optimized the SeisSol program for the parallel architecture of the Garching supercomputer "SuperMUC," thereby speeding up calculations by a factor of five.

Using a virtual experiment they achieved a new record on the SuperMUC: To simulate the vibrations inside the geometrically complex Merapi volcano on the island of Java, the supercomputer executed 1.09 quadrillion floating point operations per second. SeisSol maintained this unusually high performance level throughout the entire three hour simulation run using all of SuperMUC's 147,456 processor cores.

Complete parallelization
This was possible only following the extensive optimization and the complete parallelization of the 70,000 lines of SeisSol code, allowing a peak performance of up to 1.42 petaflops. This corresponds to 44.5 percent of Super MUC's theoretically available capacity, making SeisSol one of the most efficient simulation programs of its kind worldwide.

"Thanks to the extreme performance now achievable, we can run five times as many models or models that are five times as large to achieve significantly more accurate results. Our simulations are thus inching ever closer to reality," says the geophysicist Dr. Christian Pelties. "This will allow us to better understand many fundamental mechanisms of earthquakes and hopefully be better prepared for future events."

The next steps are earthquake simulations that include rupture processes on the meter scale as well as the resultant destructive seismic waves that propagate across hundreds of kilometers. The results will improve the understanding of earthquakes and allow a better assessment of potential future events.
"Speeding up the simulation software by a factor of five is not only an important step for geophysical research," says Professor Michael Bader of the Department of Informatics at TUM. "We are, at the same time, preparing the applied methodologies and software packages for the next generation of supercomputers that will routinely host the respective simulations for diverse geoscience applications."
Besides Michael Bader and Christian Pelties also Alexander Breuer, Dr. Alexander Heinecke and Sebastian Rettenberger (TUM) as well as Dr. Alice Agnes Gabriel and Stefan Wenk (LMU) worked on the project. In June the results will be presented at the International Supercomputing Conference in Leipzig (ISC'14, Leipzig, 22-June 26, 2014; title: Sustained Petascale Performance of Seismic Simulation with SeisSol on SuperMUC)

Source: Technische Universitaet Muenchen