星空女人频道: 2013-06-16

2013年6月22日星期六

Bacterial DNA may integrate into human genome more readily in tumor tissue

Scientists have already shown that bacteria can transfer DNA to the genome of an animal. The researchers at the University of Maryland Institute for Genome Sciences found evidence that lateral gene transfer is possible from bacteria to the cells of the human body, known as human somatic cells. They found the bacterial DNA was more likely to integrate in the genome in tumor samples than in normal, healthy somatic cells. The phenomenon might play a role in cancer and other diseases associated with DNA damage. The paper was published in PLOS Computational Biology on June 20.

"LGT from bacteria to animals was only described recently, and it is exciting to find that such transfers can be found in the genome of human somatic cells and particularly in cancer genomes," says Julie C. Dunning Hotopp, Ph.D., Assistant Professor of Microbiology and Immunology at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine and lead author on the paper. Dr. Hotopp also is a research scientist with the University of Maryland Marlene and Stewart Greenebaum Cancer Center. "Studies applying this approach to additional cancer genome projects could be fruitful, leading us to a better understanding of the mechanisms of cancer."

In the research, a team of interdisciplinary scientists and bioinformatics researchers found that while only 63.5% of TCGA samples analyzed were from tumors, the tumor samples contained 99.9% of reads supporting bacterial integration. The data presented a compelling case that LGT occurs in the human somatic genome and that it could have an important role in cancer and other human diseases associated with mutations. It is possible that LGT mutations play a role in carcinogenesis, yet it is also possible that they could simply be passenger mutations.

The investigators suggest several competing ideas to explain the results, though more research is needed for definitive answers. One possibility is that the mutations are part of carcinogenesis, the process by which normal cells turn into cancer cells. Alternatively, tumor cells are so very rapidly proliferating that they may be more permissive to lateral gene transfer. It is also possible that the bacteria are causing these mutations because they benefit the bacteria.

The study was funded by the National Institutes of Health's Director's New Innovator Award Program (1-DP2-OD007372) and the NSF Microbial Sequencing Program (EF-0826732).

"This is the type of basic science research, conducted using the analysis of much publicly available genomic data, that makes us leaders in the cutting edge field of genomic science and personalized medicine," says E. Albert Reece, M.D., Ph.D., M.B.A., Vice President for Medical Affairs at the University of Maryland and the John Z. and Akiko K. Bowers Distinguished Professor and Dean of the University of Maryland School of Medicine. "It is just this type of research that will lead us to a new world of personalized medicine, in which doctors can use each patient's genomic make-up to determine care and preventive measures. We are excited to be a part of this future with the outstanding work of our Institute for Genome Sciences."

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TI power management chipsets use fast-charge technology

TI said its MaxLife technology uses a degradation modeling system based on a proprietary algorithm to minimize charge time while extending battery life as much as 30 percent in lab tests. The algorithm predicts and avoids charge conditions that could degrade the battery.

Some researchers concerned about potential fire hazards are working to come up with new designs and alternative chemistries for lithium-ion batteries. In the meantime, battery management systems are one option for getting more out of batteries. Unlike traditional software-controlled systems, the new chipsets give designers gauge control over the charger directly, according to the company. This allows them to predict battery capacity more accurately and translate that information into run time.

The autonomous battery management system can reduce software overhead and improve battery safety and security and a better thermal management system, TI said. Its chipsets also let designers adapt the charging algorithm to the platform and to newer, high-capacity batteries.

To read full article, go to Design News.

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Fighting infectious disease the modern way - with robots

"Loyola is a world leader in infection control and now the addition of automated room disinfection reinforces our ongoing commitment to patient safety," says Jorge Parada, MD, MPH, FACP, FIDSA, medical director, Infection Control Program, Loyola University Health System. "Loyola is doing everything humanly possible to control disease and that includes robotics."

According to studies, the disinfection robots eliminate Clostridium difficile (C. diff) in less than 4 minutes and Methicillin-resistant Staphylococcus Aureus (MRSA) in less than 2 minutes. "The robots are used for further disinfection in the operating suites and patient rooms including isolation, burn and transplant," says

Alex Tomich, DNP, RN, CIC, manager, infection prevention and control at Loyola. "Loyola takes very seriously its responsibility to protect patients, visitors and our hospital staff from infections and we are early adopters of proven technology as well as best practices."

The hospital housekeeping staff cleans the rooms and then uses the robots for additional sterilization. The pulsed UV light destroys viruses, bacteria and bacterial spores without human contact or use of chemicals.

Hospital infections are linked to approximately 100,000 deaths each year and add as much as $30 billion a year in medical costs, according to the Centers for Disease Control and Prevention.

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Beyond silicon: Transistors without semiconductors

June 21, 2013 — For decades, electronic devices have been getting smaller, and smaller, and smaller. It's now possible -- even routine -- to place millions of transistors on a single silicon chip.

But transistors based on semiconductors can only get so small. "At the rate the current technology is progressing, in 10 or 20 years, they won't be able to get any smaller," said physicist Yoke Khin Yap of Michigan Technological University. "Also, semiconductors have another disadvantage: they waste a lot of energy in the form of heat."

Scientists have experimented with different materials and designs for transistors to address these issues, always using semiconductors like silicon. Back in 2007, Yap wanted to try something different that might open the door to a new age of electronics.

"The idea was to make a transistor using a nanoscale insulator with nanoscale metals on top," he said. "In principle, you could get a piece of plastic and spread a handful of metal powders on top to make the devices, if you do it right. But we were trying to create it in nanoscale, so we chose a nanoscale insulator, boron nitride nanotubes, or BNNTs for the substrate."

Yap's team had figured out how to make virtual carpets of BNNTs,which happen to be insulators and thus highly resistant to electrical charge. Using lasers, the team then placed quantum dots (QDs) of gold as small as three nanometers across on the tops of the BNNTs, forming QDs-BNNTs. BNNTs are the perfect substrates for these quantum dots due to their small, controllable, and uniform diameters, as well as their insulating nature. BNNTs confine the size of the dots that can be deposited.

In collaboration with scientists at Oak Ridge National Laboratory (ORNL), they fired up electrodes on both ends of the QDs-BNNTs at room temperature, and something interesting happened. Electrons jumped very precisely from gold dot to gold dot, a phenomenon known as quantum tunneling.

"Imagine that the nanotubes are a river, with an electrode on each bank. Now imagine some very tiny stepping stones across the river," said Yap. "The electrons hopped between the gold stepping stones. The stones are so small, you can only get one electron on the stone at a time. Every electron is passing the same way, so the device is always stable."

Yap's team had made a transistor without a semiconductor. When sufficient voltage was applied, it switched to a conducting state. When the voltage was low or turned off, it reverted to its natural state as an insulator.

Furthermore, there was no "leakage": no electrons from the gold dots escaped into the insulating BNNTs, thus keeping the tunneling channel cool. In contrast, silicon is subject to leakage, which wastes energy in electronic devices and generates a lot of heat.

Other people have made transistors that exploit quantum tunneling, says Michigan Tech physicist John Jaszczak, who has developed the theoretical framework for Yap's experimental research. However, those tunneling devices have only worked in conditions that would discourage the typical cellphone user.

"They only operate at liquid-helium temperatures," said Jaszczak.

The secret to Yap's gold-and-nanotube device is its submicroscopic size: one micron long and about 20 nanometers wide. "The gold islands have to be on the order of nanometers across to control the electrons at room temperature," Jaszczak said. "If they are too big, too many electrons can flow." In this case, smaller is truly better: "Working with nanotubes and quantum dots gets you to the scale you want for electronic devices."

"Theoretically, these tunneling channels can be miniaturized into virtually zero dimension when the distance between electrodes is reduced to a small fraction of a micron," said Yap.

Yap has filed for a full international patent on the technology.

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Scientists solve riddle of strangely behaving magnetic material

June 21, 2013 — Materials scientists at the U.S. Department of Energy's (DOE) Ames Laboratory have found an accurate way to explain the magnetic properties of a compound that has mystified the scientific community for decades.

The compound of lanthanum, cobalt and oxygen (LaCoO₃) has been a puzzle for over 50 years, due to its strange behavior. While most materials tend to lose magnetism at higher temperatures, pure LaCoO₃ is a non-magnetic semiconductor at low temperatures, but as the temperature is raised, it becomes magnetic. With the addition of strontium on the La sites the magnetic properties become even more prominent until, at 18 percent strontium, the compound becomes metallic and ferromagnetic, like iron.

"They knew that we could calculate x-ray absorption and magnetic dichroism, so we started doing that. It is a case where we fell into doing what we thought was a routine calculation, and it turned out we discovered a totally different explanation," said Harmon. "We found we could explain pretty much everything in really nice detail, but without explicitly invoking that local model," said Harmon.

The scientists found that a small rhombohedral distortion of the LaCoO₃ lattice structure, which had largely been ignored, was key.

"We found that the total electronic energy of the lattice depends sensitively on that distortion," explained Harmon. "If the distortion becomes smaller (the crystal moves closer to becoming cubic), the magnetic state of the crystal switches from non-magnetic to a state with 1.3 Bohr magnetons per Co atom."

Ames Laboratory scientists Bruce Harmon and Yongbin Lee partnered with the researchers at the Argonne National Laboratory and the University of California, Santa Cruz to publish a paper in Physical Review Letters, "Evolution of Magnetic Oxygen States in Sr-Doped LaCO₃."

This new understanding may help the further development of these materials, which are easily reduced to nanoparticles; these are finding use in catalytic oxidation and reduction reactions associated with regulation of noxious emissions from motor vehicles.

The research is supported by the U.S. Department of Energy Office of Science through the Ames Laboratory.

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IMEC helps scale NAND flash below 20-nm

Researchers from IMEC (Leuven, Belgium) have created a nano-scale hafnium aluminum oxide dieleletric (HfAlO/Al2O3/HfAlO) stack as an inter-gate dielectric with a silicon/titanium-nitride hybrid floating gate in a planar NAND Flash structure.

IMEC said the three-layer structure that is high-k/low-k/high-k provides "excellent retention and endurance" of data. IMEC did not quantify this but endurance of 10^5 cycles is considered a practical lower limit for NAND memory. Retention of 10 years is the standard in most shipping non-volatile memories.

NAND flash memory has migrated to a planar structure at around 20-nm. The tightness of the memory cell pitch makes this necessary to avoid the wrapping the control gate round the floating gate. However, the planar cell therefore also demonstrates reduced coupling between control and floating gates making programming and reading harder.

The three-layer inter-gate dielectric has allowed an opening up of the program/erase window up to 18 volts. The dielectric is scalable in thickness making the material promising for further scaling of 2-D NAND flash memory below 20-nm, IMEC said.

Using a 25-nm thick stack (10-5-10) with an amorphous Al2O3 middle layer IMEC produced a large improvement over single Al2O3 dielectric layer. Retention tests showed little loss of charge at temperatures of 125 degrees C.

Click on image to enlarge.
Transmission electron microscopy pictures of the gate stack featuring a HfAlO/Al2O3/HfAlO inter-gate dielectric between the thin TiN from the hybrid floating gate and the TiN from the control gate. Source: IMEC.

The results were presented at the 2013 International Memory Workshop held in Monterey, Calif. from May 27 to 29.

Related links and articles:

www.imec.be

News articles:

London Calling: Moore's Law fails at NAND flash node

Intel outlines 3-D NAND transition

Intel pushes for more research beyond 10-nm

Globalfoundries joins Qualcomm in MRAM research

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2013年6月21日星期五

A cheaper drive to 'cool' fuels

Working in his lab in UD's Department of Chemistry and Biochemistry, Rosenthal and doctoral student John DiMeglio have developed an inexpensive catalyst that uses the electricity generated from solar energy to convert carbon dioxide, a major greenhouse gas, into synthetic fuels for powering cars, homes and businesses.

The research is published in the June 19 issue of the Journal of the American Chemical Society.

Gold and silver represent the "gold standard" in the world of electrocatalysts for conversion of carbon dioxide to carbon monoxide. But Rosenthal and his research team have pioneered the development of a much cheaper alternative to these pricey, precious metals. It's bismuth, a silvery metal with a pink hue that's a key ingredient in Pepto-Bismol, the famous pink elixir for settling an upset stomach.

An ounce of bismuth is 50 to 100 times cheaper than an ounce of silver, and 2,000 times cheaper than an ounce of gold, Rosenthal says. Bismuth is more plentiful than gold and silver, it is well distributed globally and is a byproduct in the refining of lead, tin and copper.

Moreover, Rosenthal says his UD-patented catalyst offers other important advantages: selectivity and efficiency in converting carbon dioxide to fuel.

"Most catalysts do not selectively make one compound when combined with carbon dioxide -- they make a whole slew," Rosenthal explains. "Our goal was to develop a catalyst that was extremely selective in producing carbon monoxide and to power the reaction using solar energy."

Many of us hear '"carbon monoxide" and think "poison."

"It's true that you do not want to be in a closed room with carbon monoxide," Rosenthal says. "But carbon monoxide is very valuable as a commodity chemical because it's extremely energy rich and has many uses."

Carbon monoxide is used industrially in the water-gas shift reaction to make hydrogen gas. It also is a prime feedstock for the Fischer-Tropsch process, which allows for the production of synthetic petroleum, gasoline and diesel.

Commercial production of synthetic petroleum is under way or in development in a number of countries, including Australia and New Zealand, China and Japan, South Africa and Qatar.

Rosenthal says that if carbon dioxide emissions become taxed in the future due to continuing concerns about global warming, his solar-driven catalyst for making synthetic fuel will compete even better economically with fossil fuels.

"This catalyst is a critically important linchpin," Rosenthal says. "Using solar energy to drive the production of liquid fuels such as gasoline from CO2 is one of the holy grails in renewable energy research. In order to do this on a practical scale, inexpensive catalysts that can convert carbon dioxide to energy-rich compounds are needed. Our discovery is important in this regard, and demonstrates that development of new catalysts and materials can solve this problem. Chemists have a big role to play in this area."

Rosenthal credits a scientific article published during America's first energy crisis in the 1970s for piquing his interest in bismuth. At that time, many researchers were examining the conversion of carbon dioxide to carbon monoxide using electricity and metal electrodes. The research went bust in the early 1980s when federal funding dried up. Rosenthal picked up the trail and blazed a new one.

"With this advance, there are at least a dozen things we need to follow up on," Rosenthal notes. "One successful study usually leads to more questions and possibilities, not final answers."

Rosenthal's lab will be operating at full tilt this summer, exploring some of those questions. And his research team of seven will have some company. Through the American Chemical Society's Project SEED summer research program, budding scientists from nearby Newark High School will join Rosenthal's team for further study of this bismuth-based catalyst.

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Are Dogs 'Kids?': Owner-dog relationships share striking similarities to parent-child relationships

June 21, 2013 — People have an innate need to establish close relationships with other people. But this natural bonding behaviour is not confined to humans: many animals also seem to need relationships with others of their kind. For domesticated animals the situation is even more complex and pets may enter deep relationships not only with conspecifics but also with their owners. Scientists at the University of Veterinary Medicine, Vienna (Vetmeduni Vienna) have investigated the bond between dogs and their owners and have found striking similarities to the parent-child relationship in humans.

Their findings are published in the journal PLOS ONE.

Domestic dogs have been closely associated with humans for about 15,000 years. The animals are so well adapted to living with human beings that in many cases the owner replaces conspecifics and assumes the role of the dog's main social partner. The relationship between pet owners and dogs turns out to be highly similar to the deep connection between young children and their parents.

The importance of the owner to the dog

One aspect of the bond between humans and dogs is the so-called "secure base effect." This effect is also found in parent-child bonding: human infants use their caregivers as a secure base when it comes to interacting with the environment. Until recently the "secure base effect" had not been well examined in dogs. Lisa Horn from the Vetmeduni's Messerli Research Institute therefore decided to take a closer look at the behaviour of dogs and their owners. She examined the dogs' reactions under three different conditions: "absent owner," "silent owner" and "encouraging owner." The dogs could earn a food reward, by manipulating interactive dog toys. Surprisingly, they seemed much less keen on working for food, when their caregivers were not there than when they were. Whether an owner additionally encouraged the dog during the task or remained silent, had little influence on the animal's level of motivation.

When the owner is replaced by a stranger

In a follow-up experiment, Horn and her colleagues replaced the owner with an unfamiliar person. The scientists observed that dogs hardly interacted with the strangers and were not much more interested in trying to get the food reward than when this person was not there. The dogs were much more motivated only when their owner was present. The researchers concluded that the owner's presence is important for the animal to behave in a confident manner.

Why do adult dogs behave like human children?

The study provides the first evidence for the similarity between the "secure base effect" found in dog-owner and child-caregiver relationships. This striking parallel will be further investigated in direct comparative studies on dogs and children. As Horn says, "One of the things that really surprised us is, that adult dogs behave towards their caregivers like human children do. It will be really interesting to try to find out how this behaviour evolved in the dogs with direct comparisons."

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Chip inventory moves point to second-half growth

The value of ICs held in inventory by chip suppliers at the end of the first quarter of 2013 was $37.6 billion, down 4.6 percent from $38.4 billion at the end of the fourth quarter of 2012, according to market analytics company IHS.

The decline is due to a resumption of demand from distributors, OEMs and contract manufacturers in anticipation of better equipment sales in the second half of 2013.

The decline in inventory in 1Q13 paralleled a sequential contraction in semiconductor revenues of 5.1 percent in line with normal seasonal demand.

However, just the chip suppliers ran down stocks so equipment companies started to ramp them. Mobile phone makers expanded their inventories by 7.2 percent during the quarter and PC OEMs expanded their backlog of notebook and desktop computers by 6 percent.

Semiconductor inventory levels at chip suppliers are expected to rise in the second quarter as they respond to positive order rates from electronics equipment manufacturers. Stockpiles for consumers of semiconductors likely will remain fairly flat, IHS said.

Quarterly inventory held by semiconductor suppliers. Source: IHS.

"The rise in inventories among the various segments of the supply chain [other than chip suppliers] indicates the electronics industry is preparing for an increase in demand during the second half of 2013," Sharon Stiefel, analyst for semiconductor market intelligence for IHS, in a statement posted at the IHS website.

Related links and posts:

www.ihs.com

News articles:

Intel leads surprise inventory decline

Indian chip market set to jump 20 percent in 2013

Memory markets to grow up to 30 percent in 2013

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Qualcomm responds to low-end smartphone threat

Fabless communications chip giant Qualcomm has upgraded its Snapdragon 200 processor range aimed at entry-level smartphones with the introduction of a dual- and quad-core devices in 28-nm manufacturing process technology.

Although Qualcomm is recognized as the market leader in smartphone application processors with more than 40 percent market share, it is thought to be hurting under competition from the likes of MediaTek and Spreadtrum at the low end.

Qualcomm's profit fell below expectations in its second quarter financial results and this was thought to be due to intense competition in China and emerging markets that are rapidly adopting smartphones but at lower price points than prestige models.

The original Snapdragon 200s were implemented in 45-nm CMOS and based on quad-core Cortex-A5 cores licensed from ARM and specified to operate at up to 1.4-GHz clock frequency. The 28-nm upgrade is based on Cortex-A7 "little" processors specified to operate at up to 1.2-GHz. Qualcomm said the 28-nm upgrade feature key modem technologies that are important in China and emerging regions, including support for HSPA+ at up to 21 Mbps download speed and TD-SCDMA.

Qualcomm has also upgraded the graphics from Adreno 203 to Adreno 302 although it supports the same 720p display resolution. The processors will have support for dual cameras, with an 8 megapixel rear-facing camera and up to a 5 megapixel front-facing one, as well as feature a single platform for all SIM variants Qualcomm will be release Qualcomm Reference Designs which provide the basics of a mobile phone with customization options, support for testing and acceptance by regional operators and for access to hardware components suppliers and application developers.

To date more than 40 equipment makers have used the Qualcomm QRD program to launch more than 250 products in 17 countries, Qualcomm said.

"We are excited to offer our customers the broadest range of 3G technologies and superior performance and power-efficiency, enabling them to deliver a wide range of innovative smartphones for the high-volume segment," said Jeff Lorbeck, senior vice president of product management, Qualcomm Technologies Inc., in a statement.

Related links and articles:

www.qualcomm.com

News articles:

Qualcomm's profits hurt by competition in China

Qualcomm leads smartphone processor market

Snapdragon processor comes on pico-ITX board

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Cities are a new kind of complex system: Part social reactor, part network

New research by Santa Fe Institute Professor Luis Bettencourt suggests a city is something new in nature -- a sort of social reactor that is part star and part network, he says.

"It's an entirely new kind of complex system that we humans have created," he says. "We have intuitively invented the best way to create vast social networks embedded in space and time, and keep them growing and evolving without having to stop. When that is possible, a social species can sustain ways of being incredibly inventive and productive."

In a paper published this week in Science, Bettencourt derives a series of mathematical formulas that describe how cities' properties vary in relation to their population size, and then posits a novel unified, quantitative framework for understanding how cities function and grow.

His resulting theoretical framework predicts very closely dozens of statistical relationships observed in thousands of real cities around the world for which reliable data are available.

"As more people lead urban lives and the number and size of cities expand everywhere, understanding more quantitatively how cities function is increasingly important," Bettencourt says. "Only with a much better understanding of what cities are will we be able to seize the opportunities that cities create and try to avoid some of the immense problems they present. This framework is a step toward a better grasp of the functioning of cities everywhere."

What has made this new view of cities possible is the growing opportunities in recent years to collect and share data on many aspects of urban life. With so much new data, says Bettencourt, it's easier than ever to study the basic properties of cities in terms of general statistical patterns of such variables as land use, urban infrastructure, and rates of socioeconomic activity.

For more than a decade, Bettencourt and members of SFI's Cities & Urbanization research team have used this data to painstakingly lay the foundation for a quantitative theory of cities. Its bricks and mortar are the statistical "scaling" relationships that seem to predict, based on a city's size, the average numerical characteristics of a city, from the number of patents it produces to the total length of its roads or the number of social interactions its inhabitants enjoy.

Those relationships and the related equations, models, network analyses, and methods provide the basis for Bettencourt's theoretical framework.

So what is a city? Bettencourt thinks the only metaphor that comes close to capturing a city's function is from stellar physics: "A city is first and foremost a social reactor," Bettencourt explains. "It works like a star, attracting people and accelerating social interaction and social outputs in a way that is analogous to how stars compress matter and burn brighter and faster the bigger they are."

This, too, is an analogy though, because the math of cities is very different from that of stars, he says.

Cities are also massive social networks, made not so much of people but more precisely of their contacts and interactions. These social interactions happen, in turn, inside other networks -- social, spatial, and infrastructural -- which together allow people, things, and information to meet across urban space.

Ultimately, cities achieve something very special as they grow. They balance the creation of larger and denser social webs that encourage people to learn, specialize, and depend on each other in new and deeper ways, with an increase in the extent and quality of infrastructure. Remarkably they do this in such a way that the level of effort each person must make to interact within these growing networks does not need to grow.

How these networks fit together, and the tensions and tradeoffs among them, often determines how productive or prosperous a city is, or whether it fissions into smaller 'burbs, or if people want to live in them or don't, Bettencourt says.

His framework has practical implications for planners and policy makers, he says. To keep these social reactors working optimally, planners need to think in terms of urban policies that create positive social interactions at low costs in terms of mobility and energy use, for example. The paper shows how obstacles to socialization, such as crime or segregation, and enablers that promote the ability of people to connect, such as transportation and electricity, all become part of the same equation.

It even names a couple of U.S. cities that appear to suboptimal in terms of their social interactivity. Brownsville, Texas, and Riverside, Calif., for example, might benefit from policies to improve citywide connectivity. Bridgeport, Conn., which includes Connecticut's "Gold Coast," could be a victim of its own socioeconomic success, as high mobility costs suggest more compact urban living or more efficient transportation might be in order.

The framework is a first theoretical step, Bettencourt says, and much more needs to be done. In the coming years, more and better data from cities in developing nations will become available, which will provide new opportunities to test the theory in places where understanding urbanization is most critical.

"Rapid urbanization is the fastest, most intense social phenomenon that ever happened to humankind, perhaps to biology on Earth," says Bettencourt. "I think we can now start to understand in new and better ways why this is happening everywhere and ultimately what it means for our species and for our planet."

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