HZDR researchers conduct electricity using DNA-based nanowires

Tinier than the AIDS virus -- that is currently the circumference of the smallest transistors. The industry has shrunk the central elements of their computer chips to fourteen nanometers in the last sixty years. Conventional methods, however, are hitting physical boundaries. Researchers around the world are looking for alternatives. One method could be the self-organization of complex components from molecules and atoms. Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) and Paderborn University have now made an important advance: the physicists conducted a current through gold-plated nanowires, which independently assembled themselves from single DNA strands. Their results have been published in the scientific journal Langmuir.

At first glance, it resembles wormy lines in front of a black background. But what the electron microscope shows up close is that the nanometer-sized structures connect two electrical contacts. Dr. Artur Erbe from the Institute of Ion Beam Physics and Materials Research is pleased about what he sees. "Our measurements have shown that an electrical current is conducted through these tiny wires." This is not necessarily self-evident, the physicist stresses. We are, after all, dealing with components made of modified DNA. In order to produce the nanowires, the researchers combined a long single strand of genetic material with shorter DNA segments through the base pairs to form a stable double strand. Using this method, the structures independently take on the desired form.

"With the help of this approach, which resembles the Japanese paper folding technique origami and is therefore referred to as DNA-origami, we can create tiny patterns," explains the HZDR researcher. "Extremely small circuits made of molecules and atoms are also conceivable here." This strategy, which scientists call the "bottom-up" method, aims to turn conventional production of electronic components on its head. "The industry has thus far been using what is known as the 'top-down' method. Large portions are cut away from the base material until the desired structure is achieved. Soon this will no longer be possible due to continual miniaturization." The new approach is instead oriented on nature: molecules that develop complex structures through self-assembling processes.

Golden Bridges Between Electrodes

The elements that thereby develop would be substantially smaller than today's tiniest computer chip components. Smaller circuits could theoretically be produced with less effort. There is, however, a problem: "Genetic matter doesn't conduct a current particularly well," points out Erbe. He and his colleagues have therefore placed gold-plated nanoparticles on the DNA wires using chemical bonds. Using a "top-down" method - electron beam lithography -- they subsequently make contact with the individual wires electronically. "This connection between the substantially larger electrodes and the individual DNA structures have come up against technical difficulties until now. By combining the two methods, we can resolve this issue. We could thus very precisely determine the charge transport through individual wires for the first time," adds Erbe.

As the tests of the Dresden researchers have shown, a current is actually conducted through the gold-plated wires -- it is, however, dependent on the ambient temperature. "The charge transport is simultaneously reduced as the temperature decreases," describes Erbe. "At normal room temperature, the wires function well, even if the electrons must partially jump from one gold particle to the next because they haven't completely melded together. The distance, however, is so small that it currently doesn't even show up using the most advanced microscopes." In order to improve the conduction, Artur Erbe's team aims to incorporate conductive polymers between the gold particles. The physicist believes the metallization process could also still be improved.

He is, however, generally pleased with the results: "We could demonstrate that the gold-plated DNA wires conduct energy. We are actually still in the basic research phase, which is why we are using gold rather than a more cost-efficient metal. We have, nevertheless, made an important stride, which could make electronic devices based on DNA possible in the future."

Chury with his bi-lobe structure and the weakest part, the neck. © ESA/Rosetta/NAVCAM CC BY-SA IGO 3.0

Based on supercomputer simulations, Astrophysicists at the University of Bern, Switzerland, conclude that the comet Chury did not obtain its duck-like form during the formation of our solar system 4.5 billion years ago. Although it does contain primordial material, they are able to show that the comet in its present form is hardly more than a billion years old.

Based on data from the Rosetta space probe, scientists have so far assumed that the comet 67P/Churyumov–Gerasimenko originated from the initial phase of our solar system. Its peculiar, duck-shaped structure would have resulted from a gentle collision of two objects about 4.5 billion years ago.

Based on new research, Martin Jutzi and Willy Benz from NCCR PlanetS and the Center for Space and Habitability (CSH) of the University of Bern, together with colleagues, have now come to a different conclusion. As a result of two studies published in the specialist journal Astronomy & Astrophysics, Astrophysicist Martin Jutzi explains that "It is unlikely that a body like Chury has survived for such a long time without damage - our computer simulations show this. "

If the assumptions of the present “standard” model of the origin of our solar system are correct, a quiet initial phase was followed by a period in which large bodies initiated higher velocities and more violent collisions. In a first study, the scientists calculated how much energy would be needed to destroy a structure like Chury in a collision.  As it turned out, Chury has a weak point; the connection between the two parts - the neck between the head and the body. "We have found that this structure can be destroyed easily, even with low energy collisions," Martin Jutzi summarizes. Willy Benz compares the neck of the comet with the stem of a glass:  "A dishwasher has to clean very gently, so that the stem of the glass does not break," says the astrophysicist. Obviously, the solar system did not handle this aspect as carefully.

The new study shows that comets like Chury experienced a significant number of collisions over time, the energy of which would have been sufficient to destroy a bi-lobe structure. Therefore, the shape is not primordial, but has developed through collisions over billions of years. "Chury’s present shape is the result of the last major impact which probably occurred within the last billion years," says Martin Jutzi. The duck-shaped Chury is therefore much younger than previously thought. The only alternative would be that the current standard model of the early evolution of the Solar System is not correct and there were fewer small objects than previously thought. In this case there would not have been as many collisions and Chury would have had the chance to keep its primordial shape. “At the moment, we do think though that Chury’s shape is the result of many collisions, and that the standard model doesn’t need to be revised”, says Jutzi.

New shape, same content

In the second paper, Jutzi and Benz investigate exactly how Chury’s current form could have resulted from a collision. In their supercomputer models, they had small objects with a diameter of 200 to 400 meters crashing into a roughly five-kilometre, rotating body in the form of a rugby ball (see animation). The impact speed was in the range of 200 to 300 meters per second, which clearly exceeds the escape velocity for objects of this size (about 1 meter per second). However, the energy involved is still far below that of a catastrophic impact in which a large part of the body is pulverized. As a result, the target was torn in two parts, which, due to the effects of their mutual gravitational force, later merged into a structure with two parts - a structure like Chury.

Does the result of this research contradict previous knowledge that comets consist of primordial material at least as old as our solar system? "No," the researchers say. Their computer simulations show that the relatively small impact energy does not heat or compress the comet globally. The body is still porous and the volatile material which was contained in it since the beginning is retained. In connection with Chury, these properties could be measured convincingly with the space probe Rosetta. "So far, it has been assumed that comets are original building blocks - similar to Lego," says Willy Benz. "Our work shows that the Lego blocks no longer have their original form, but the plastic that they consist of is still the same as in the beginning."

Cray's revenue for the third quarter of 2016 was $77.5 million, down 60% compared with $191.4 million in the third quarter of 2015.  Net loss for the third quarter of 2016 was $23.0 million, or $0.58 per diluted share, compared to net income of $10.9 million, or $0.27 per diluted share in the third quarter of 2015.  Non-GAAP net loss was $19.5 million, or $0.49 per diluted share for the third quarter of 2016, compared to non-GAAP net income of $19.5 million, or $0.48 per diluted share for the same period of 2015.

Overall gross profit margin on a GAAP and non-GAAP basis for the third quarter of 2016 was 30% and 31%, respectively.  For the third quarter of 2015, GAAP and non-GAAP gross profit margin was 34% and 35%, respectively. 

Operating expenses for the third quarter of 2016 were $52.1 million, compared to $47.9 million for the third quarter of 2015.  Non-GAAP operating expenses for the third quarter of 2016 were $49.3 million, compared to $45.1 million for the third quarter of 2015. 

As of September 30, 2016, cash, investments and restricted cash totaled $147 million. Working capital decreased in the third quarter of 2016 to $364 million compared to $381 million at the end of the second quarter.

“Our performance in the third quarter was highlighted by a number of new installations of supercomputers and storage systems worldwide,” said Peter Ungaro, president and CEO of Cray. “While market conditions remain challenging, we are beginning to see early signs of stabilization in certain areas, including in the energy market where we recently installed an additional XC system at PGS, and in the weather and climate market with a major win in the United States.  Overall, while our visibility remains limited, our competitive position is strong and we're focused on delivering on our outlook for the rest of the year.”

New method most accurate to date

A multi-institution academic-industrial partnership of researchers led by Case Western Reserve University School of Medicine has developed a new method to broadly assess cell communication networks and identify disease-specific network anomalies. The computer-based method, called InFlo, was developed in collaboration with researchers at Philips and Princeton University and predicts how cells send signals across networks to cause cancer or other disease. Details about the new method were recently published in Oncogene.

"Cellular signaling networks are the mechanisms that cells use to transfer, process, and respond to biological information derived from their immediate surroundings," said Vinay Varadan, PhD, assistant professor at Case Western Reserve University School of Medicine, member of the Case Comprehensive Cancer Center, and senior corresponding author on the study. "InFlo can be viewed as modeling the flow of information within these signaling networks."

InFlo works by assessing gene activity levels in tissue samples and predicting corresponding protein levels. It then uses statistical probabilities and other mathematical models to build activity webs showing how the proteins interact. Researchers can use InFlo to compare diseased and healthy tissues and pinpoint signaling differences. InFlo is tissue-specific and accounts for genetic alterations associated with disease, unlike other methods. It represents a major step forward in deciphering the activities of multi-tiered signaling networks commonly used by cells.

"Complex diseases such as cancer involve the simultaneous disruptions of multiple cellular processes acting in tandem," said Varadan. "We developed InFlo to robustly integrate multiple molecular data streams and develop an integrative molecular portrait of an individual cancer sample."

InFlo incorporates data related to each level of cell communication within a single sample, including DNA, RNA, proteins, and molecules commonly attached to proteins such as chemical methyl groups. The method also includes strategies to reduce "noise" and only highlight the signaling networks most likely to cause disease.

Analisa DiFeo, PhD, senior co-corresponding author on the study, Norma C. and Al I. Geller Designated Professor of Ovarian Cancer Research at Case Western Reserve University School of Medicine, and member of the Case Comprehensive Cancer Center, validated InFlo using ovarian cancer tumor cells that were resistant to platinum-based chemotherapy. InFlo pinpointed the interaction between two proteins called cAMP and CREB1 as a key mechanism associated with platinum resistance.

"Following up on InFlo's predictions, we showed that inhibiting CREB1 potently sensitizes ovarian cancer cells to platinum therapy and is also effective in killing ovarian cancer stem cells. We are therefore excited about this discovery and are currently evaluating whether this could lead to a potential therapeutic target for the treatment of platinum-resistant ovarian cancer," said DiFeo.

InFlo is being incorporated into Philips IntelliSpace Genomics platform, and will soon be available for widespread use in basic and translational research settings. Case Western Reserve University researchers will continue to develop the IntelliSpace Genomics InFlo module and the next step will be to expand InFlo to incorporate other data streams. "We are currently collaborating with the Imaging Informatics research group in the Center for Computational Imaging and Personalized Diagnostics at Case Western Reserve University to integrate InFlo with imaging-features derived from pathology and radiology data," said Varadan. Such an addition would result in one of the most comprehensive tools available to researchers to infer mechanisms underlying complex diseases such as cancer.

Using a person's spoken or written words, new computer tools can identify with great accuracy whether that person is suicidal, mentally ill but not suicidal, or neither.

A new study shows that supercomputer technology known as machine learning is up to 93 percent accurate in correctly classifying a suicidal person and 85 percent accurate in identifying a person who is suicidal, has a mental illness but is not suicidal, or neither. These results provide strong evidence for using advanced technology as a decision-support tool to help clinicians and caregivers identify and prevent suicidal behavior, says John Pestian, PhD, professor in the divisions of Biomedical Informatics and Psychiatry at Cincinnati Children's Hospital Medical Center and the study's lead author.

"These computational approaches provide novel opportunities to apply technological innovations in suicide care and prevention, and it surely is needed," says Dr. Pestian. "When you look around health care facilities, you see tremendous support from technology, but not so much for those who care for mental illness. Only now are our algorithms capable of supporting those caregivers. This methodology easily can be extended to schools, shelters, youth clubs, juvenile justice centers, and community centers, where earlier identification may help to reduce suicide attempts and deaths."

The study is published in the journal Suicide and Life-Threatening Behavior, a leading journal for suicide research.

Dr. Pestian and his colleagues enrolled 379 patients in the study between Oct. 2013 and March 2015 from emergency departments and inpatient and outpatient centers at three sites. Those enrolled included patients who were suicidal, were diagnosed as mentally ill and not suicidal, or neither - serving as a control group.

Each patient completed standardized behavioral rating scales and participated in a semi-structured interview answering five open-ended questions to stimulate conversation, such as "Do you have hope?" "Are you angry?" and "Does it hurt emotionally?"

The researchers extracted and analyzed verbal and non-verbal language from the data. They then used machine learning algorithms to classify the patients into one of the three groups. The results showed that machine learning algorithms can tell the differences between the groups with up to 93 percent accuracy. The scientists also noticed that the control patients tended to laugh more during interviews, sigh less, and express less anger, less emotional pain and more hope.

Page 6 of 392