Sunday, November 27, 2011

Interesting Possibilities and Impossibilities

"...Some men see things as they are and say why - I dream things that never were and say why not..." Attributed to George Bernard Shaw

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Rebuilding the brain’s circuitry using embryonic neurons

Harvard researchers and colleagues have repaired brain circuitry and substantially normalized function in mice with a brain disorder using neuron transplants, an advance indicating that key areas of the mammalian brain are more reparable than was widely believed.

Collaborators from Harvard University, Massachusetts General Hospital (MGH), Beth Israel Deaconess Medical Center (BIDMC), and Harvard Medical School (HMS) transplanted normally functioning embryonic mouse neurons at a carefully selected stage of their development into the hypothalamus of mice unable to respond to leptin (a hormone that regulates metabolism and controls body weight).

These mutant mice usually become morbidly obese, but the neuron transplants repaired defective brain circuits, enabling them to respond to leptin and thus experience substantially less weight gain.

Repair at the cellular-level of the hypothalamus — a critical and complex region of the brain that regulates phenomena such as hunger, metabolism, body temperature, and basic behaviors such as sex and aggression — indicates the possibility of new therapeutic approaches to even higher-level conditions, such as spinal cord injury, autism, epilepsy, ALS (Lou Gehrig’s disease), Parkinson’s disease, and Huntington’s disease.

“There are only two areas of the brain that are known to normally undergo ongoing large-scale neuronal replacement (neurogenesis) during adulthood on a cellular level: in the olfactory bulb and the subregion of the hippocampus called the dentate gyrus … and in the hypothalamus,” said Jeffrey Macklis, Harvard University professor of stem cell and regenerative biology and HMS professor of neurology at MGH, and one of three corresponding authors on the paper.

“The neurons that are added during adulthood in both regions are generally smallish and are thought to act a bit like volume controls over specific signaling. Here we’ve rewired a high-level system of brain circuitry that does not naturally experience neurogenesis, and this restored substantially normal function.”

The two other senior authors on the paper are Jeffrey Flier, dean of Harvard Medical School, and Matthew Anderson, HMS professor of pathology at BIDMC.

In 2005, Flier, then the George C. Reisman professor of medicine at BIDMC, published a landmark study showing that an experimental drug spurred the addition of new neurons in the hypothalamus and offered a potential treatment for obesity. But while the finding was striking, the researchers were unsure whether the new cells functioned like natural neurons.

Macklis’ laboratory had for several years developed approaches to successfully transplanting developing neurons into circuitry of the cerebral cortex of mice with neurodegeneration or neuronal injury. In a landmark 2000 Nature study, the researchers demonstrated induction of neurogenesis in the cerebral cortex of adult mice, where it does not normally occur. While these and follow-up experiments appeared to rebuild brain circuitry anatomically, the new neurons’ level of function remained uncertain.

To learn more, Flier, an expert in the biology of obesity, teamed up with Macklis, an expert in central nervous system development and repair, and Anderson, an expert in neuronal circuitries and mouse neurological disease models.

The groups used a mouse model in which the brain lacks the ability to respond to leptin. Flier and his lab have long studied this hormone, which is mediated by the hypothalamus. Deaf to leptin’s signaling, these mice become dangerously overweight.

Prior research had suggested that four main classes of neurons enabled the brain to process leptin signaling. Postdocs Artur Czupryn and Maggie Chen, from Macklis’ and Flier’s labs, respectively, transplanted and studied the cellular development and integration of progenitor cells and very immature neurons from normal embryos into the hypothalamus of the mutant mice using multiple types of cellular and molecular analysis. To place the transplanted cells in exactly the correct and microscopic region of the recipient hypothalamus, they used a technique called high-resolution ultrasound microscopy, creating what Macklis called a “chimeric hypothalamus” — like the animals with mixed features from Greek mythology.

Postdoc Yu-Dong Zhou, from Anderson’s lab, performed in-depth electrophysiological analysis of the transplanted neurons and their function in the recipient circuitry, taking advantage of the neurons’ glowing green from a fluorescent jellyfish protein carried as a marker.

These nascent neurons survived the transplantation process and developed structurally, molecularly, and electrophysiologically into the four cardinal types of neurons central to leptin signaling. The new neurons integrated functionally into the circuitry, responding to leptin, insulin, and glucose. Treated mice matured and weighed approximately 30 percent less than their untreated siblings or siblings treated in multiple alternate ways.

The researchers then investigated the precise extent to which these new neurons had become wired into the brain’s circuitry using molecular assays, electron microscopy for visualizing the finest details of circuits, and patch-clamp electrophysiology, a technique in which researchers use small electrodes to investigate the characteristics of individual neurons and pairs of neurons in fine detail. Because the new cells were labeled with fluorescent tags, postdocs Czupryn, Zhou, and Chen could easily locate them.

The Zhou and Anderson team found that the newly developed neurons communicated to recipient neurons through normal synaptic contacts, and that the brain, in turn, signaled back. Responding to leptin, insulin and glucose, these neurons had effectively joined the brain’s network and rewired the damaged circuitry.

“It’s interesting to note that these embryonic neurons were wired in with less precision than one might think,” Flier said. “But that didn’t seem to matter. In a sense, these neurons are like antennas that were immediately able to pick up the leptin signal. From an energy-balance perspective, I’m struck that a relatively small number of genetically normal neurons can so efficiently repair the circuitry.”

“The finding that these embryonic cells are so efficient at integrating with the native neuronal circuitry makes us quite excited about the possibility of applying similar techniques to other neurological and psychiatric diseases of particular interest to our laboratory,” said Anderson.

The researchers call their findings a proof of concept for the broader idea that new neurons can integrate specifically to modify complex circuits that are defective in a mammalian brain.

The researchers are interested in further investigating controlled neurogenesis — directing growth of new neurons in the brain from within — the subject of much of Macklis’ research as well as Flier’s 2005 paper, and a potential route to new therapies.

“The next step for us is to ask parallel questions of other parts of the brain and spinal cord, those involved in ALS and with spinal cord injuries,” Macklis said. “In these cases, can we rebuild circuitry in the mammalian brain? I suspect that we can.”

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Lab-grown implanted neurons fuse with brain circuitry

Neurons generated in the lab from blank-slate human embryonic stem cells (hESC) and implanted into the brains of mice can successfully fuse with the brain’s wiring and both send and receive signals, scientists st University of Wisconsin-Madison have found — a crucial step toward deploying customized cells to repair damaged or diseased brains.

“The big question was, can these cells integrate in a functional way?” says Jason P. Weick, the lead author of the new study and a staff scientist at the University of Wisconsin-Madison’s Waisman Center. “We show for the first time that these transplanted cells can both listen and talk to surrounding neurons of the adult brain.”

The Wisconsin team tested this by transplanting the human-derived neurons into the adult mouse hippocampus, an area of the brain that plays a key role in processing memory and spatial navigation. The capacity of the human cells to integrate into the mouse brain was observed in live tissue taken from the animals that received the cell transplants.

Weick and colleagues also reported that the human neurons adopted the rhythmic firing behavior of many brain cells talking to one another in unison. And, perhaps more importantly, that the human cells could modify the way the neural network behaved.

Specifically, the study demonstrated that hESC-derived neurons adopt the bursting behavior of a preexisting neural network, can modulate the mouse network activity via synaptic output, and can elicit spontaneous postsynaptic currents in hippocampal pyramidal neurons in slices taken from transplanted mouse brains. It also demonstrated that human neurons can make both excitatory and inhibitory synaptic connections with individual mouse neurons.

Optogenetics allows for precise, noninvasive stimulation

A critical tool that allowed the UW group to answer this question was optogenetics, where light instead of electric current is used to noninvasively stimulate only the transplanted human cells.

Weick explains that the capacity to modulate the implanted cells was a necessary step in determining the function of implanted cells, because previous technologies were too imprecise and unreliable to accurately determine what transplanted neurons were doing.

The appeal of human embryonic stem cells and induced pluripotent cells is the potential to manufacture limitless supplies of healthy, specialized cells to replace diseased or damaged cells. Brain disorders such as Parkinson’s disease and amyotrophic lateral sclerosis, more widely known as Lou Gehrig’s disease, are conditions that scientists think may be alleviated by using healthy lab grown cells to replace faulty ones. Multiple studies over the past decade have shown that both embryonic stem cells and induced cells can alleviate deficits of these disorders in animal models.

The new study opens the door to the potential for clinicians to deploy light-based stimulation technology to manipulate transplanted tissue and cells. “The marriage between stem cells and optogenetics has the potential to assist in the treatment of a number of debilitating neurodegenerative disorders,” notes Su-Chun Zhang, a UW-Madison professor of neuroscience. “You can imagine that if the transplanted cells don’t behave as they should, you could use this system to modulate them using light.”

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 A fluorescent test for antioxidant drugs

A study by UC San Diego School of Medicine, with colleagues in Australia, to visualize accumulation of oxidized LDL in genetically modified zebrafish could lead to a rapid test for the potential effectiveness of new antioxidant and dietary therapies for human atherosclerosis.

Atherosclerosis is a process of lipid deposition and inflammation in the artery walls. Low-density lipoprotein (LDL) that carries “bad” cholesterol in blood is easily oxidized, and oxidized LDL promotes inflammatory responses by vascular cells. Inflamed atherosclerotic plaque can often rupture; this results in a blood clot, obstruction of blood flow to the heart or brain, and heart attack or stroke.

The zebrafish were fed a diet high in cholesterol. Because young zebrafish are transparent, the researchers were able to study vascular lipid accumulation, lipid oxidation, and uptake of oxidized LDL by macrophages, all in live animals.

To be able to see oxidized LDL, the researchers inserted into the zebrafish genome a gene that codes for an antibody that recognizes oxidized LDL, conjugated with green fluorescent protein (GFP).

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 Spectrum clash builds around bionic implants

Next week, the U.S. Federal Communications Commission will consider whether four sets of frequencies between 413MHz and 457MHz can be used by networks of sensors implanted in patients who suffer from various forms of paralysis.

One intended purpose of these MMNS (medical micropower network systems) is to transmit movement commands from a sensor on a patient’s spinal cord, through a wearable MCU (master control unit), to implants that electrically stimulate nerves. The same wireless technology might be used in devices to restore sight or hearing.

The use of wireless networks between implants and MCUs could eliminate the need to implant trouble-prone networks of wires underneath a patient’s skin, said Alfred Mann Foundation CEO David Hankin. Because of its greater precision, the new technology can also gather more accurate input about how the patient wants to move and communicate that to specific nerves.

However, broadcast engineers are fighting the proposed rule, which would allow this, saying TV and radio stations already use one of the bands to broadcast live from news events and this might interfere with the body networks.

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 Fluorescent spray tags cancer cells

Japanese researchers have developed a probe for ovarian cancer that can be sprayed onto tissue during surgery, fluorescing where malignant cells are present — allowing surgeons to identify and remove scattered bits of tumor within seconds or minutes, Nature News Blog reports.

Ovarian cancer has a tendency to spread, leaving small tumors of less than a millimeter in diameter throughout the abdominal cavity, which can be hard for surgeons to spot and remove. Being able to find all the malignant cells is crucial for a good survival outcome.

Next step: evaluate the probe using fresh tumor specimens from human patients, rather than in vitro cell lines, and working towards using it with gastric, colon, liver and uterine cancers.

Previous probes were administered through injection, which can take hours for effects to appear.

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 Malls track shoppers’ cell phones on Black Friday

Starting on Black Friday (11/25) and running through New Year’s Day, two U.S. malls — Promenade Temecula in southern California and Short Pump Town Center in Richmond, Va. — will track guests’ movements by monitoring the signals from their cell phones.

The tracking system, called FootPath Technology, works through a series of antennas positioned throughout the shopping center that anonymously capture the unique identification number assigned to each phone (similar to a computer’s IP address), and tracks its movement throughout the stores.

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A Terminator-style contact-lens display

Bringing us a step closer to a Terminator-style augmented-reality display, University of Washington engineers have constructed an experimental contact lens with a single-pixel embedded light-emitting diode (LED) and tested it in a rabbit.

The LED lights up when it receives energy from a remote radio frequency transmission, picked up by an antenna around the edge and collected via a silicon power harvesting and radio integrated circuit.

But the ultimate future concept would be to display multipixel data — from a cell phone, for example, no eyeglasses required. Here’s how the engineers say it will work:

A light emitting diode (LED) chip (1) with 100 pixels projects virtual images (6, b). Power-harvesting/control circuitry (2) uses wireless power from an external source, picked up by an antenna (3), an connects (4) to the LED. Emitted light is reimaged using planar Fresnel lenses (c).

“In the future, contact lens systems may receive data from external platforms (e.g., mobile phones) and provide real-time notification of important events,” the engineers say. “As contact lens-based biosensors advance, they may alert the wearer of physiological anomalies, such as irregular glucose or lactate levels. With more colors and increased resolution, contact lenses may display text, be used with gaming devices, or offer cues from navigation systems.

“Although high resolution, full-color, stand-alone contact lens displays might be many years away, the technological demonstrations to date depict a clear path containing a number of useful intermediate devices that can be feasibly produced in the near to medium future.”

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 Next-generation robot operated using Kinect

Yaskawa Electric has developed an upgrade to its SmartPal robot that can be operated remotely using a Kinect motion capture system, DigInfo TV reports.

SmartPal VII”s head now has a stereo camera that can pan and tilt and an infrared sensor, while the moving parts have gyro sensors.

These new features allow the robot to assist people with everyday tasks (even remotely) by bending down and picking things up, for example (the user can control it with arm motions).

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 Femtotech: computing at the femtometer scale using quarks and gluons

By Hugo de Garis

How the properties of quarks and gluons can be used (in principle) to perform computation at the femtometer (10^-15 meter) scale.

I’ve been thinking on and off for two decades about the possibility of a femtotech. Now that nanotech is well established, and well funded, I feel that the time is right to start thinking about the possibility of a femtotech.

You may ask, “What about picotech?” — technology at the picometer (10-12m) scale. The simple answer to this question is that nature provides nothing at the picometer scale. An atom is about 10-10 m in size.

The next smallest thing in nature is the nucleus, which is about 100,000 times smaller, i.e., 10-15 m in size — a femtometer, or “fermi.” A nucleus is composed of protons and neutrons (i.e., “nucleons”), which we now know are composed of 3 quarks, which are bound (“glued”) together by massless (photon-like) particles called “gluons.”

Hence if one wanted to start thinking about a possible femtotech, one would probably need to start looking at how quarks and gluons behave, and see if these behaviors might be manipulated in such a way as to create a technology, i.e., computation and engineering (building stuff).

In this essay, I concentrate on the computation side, since my background is in computer science. Before I started ARCing (After Retirement Careering), I was a computer science professor who gave himself zero chance of getting a grant from conservative NSF or military funders in the U.S. to speculate on the possibilities of a femtotech. But now that I’m no longer a “wager,” I’m free to do what I like, and can join the billion strong “army” of ARCers, to pursue my own passions.

So I started studying QCD (quantum chromodynamics), the mathematical physics theory of the strong force, or as it is known in more modern terms, the “color force.”

Since I have a computer science background, I knew what to look for when sniffing through QCD text books, to be able to map computer science concepts to QCD phenomena.

Bits and logic gates : the heart of computation

If you want to compute at the femto level, how do you do that? What would you need? To me, the essential ingredients of (digital) computing are bits and logic gates.

A bit is a two-state system (e.g., voltage or no voltage, a closed or open switch, etc.) that can be switched from one state to another. It is usual to represent one of these states as “1” and the other as “0,” i.e., as binary digits. A logic gate is a device that can take bits as input and use their states (their 0 or 1 values) to calculate its output.

The three most famous gates, are the NOT gate, the OR gate, and the AND gate. The NOT gate switches a 1 to a 0, and a 0 to a 1. An OR gate outputs a 1 if one or more of its two inputs is a 1, else outputs a 0. An AND gate outputs a 1 only if the first AND second inputs are both 1, else outputs a 0.

There is a famous theorem in theoretical computer science, that says that the set of 3 logic gates {NOT, OR, AND} are “computationally universal,” i.e., using them, you can build any Boolean logic gate to detect any Boolean expression (e.g. (~X & Y) OR (W & Z)).

So if I can find a one to one mapping between these 3 logic gates and phenomena in QCD, I can compute anything in QCD. I would have femtometer-scale computation. That was the big prize I was after.

So, I set out to find phenomena in QCD that I could map bits and logic gates to. I was quickly rewarded. It was a case of “low hanging fruit.” I just happened to be the first person (as far as I know) wandering around the QCD orchard with a very specific type of cherry picking in mind.

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Tuesday, November 22, 2011

What Newton, Leonardo, Shakespeare, Brunelleschi, Einstein, Bonaparte, Socrates, Plank, Aristotle won’t ever never teach you about misoneism in Century 21st? 

What are those decisive (notwithstanding), yet critically unanswered questions in today’s Society of Knowledge, while said “knowledge” is amplifying gargantuanly nonlinearly?

1.- Did Newton transform physics because he never stop practicing misoneism?

2.- Did Leonardo transform art and science because he always adhere to his own static mind, preemptively rejecting the dynamic one?

3.- Did Shakespeare reform literature because he never wished to fully embrace the complexity of his craftsmanship? Accordingly so because he was madly in love with so-called “simplicity”?

4.- Did Brunelleschi enrich architecture and engineering because all of his actions abide by the “rigors” of misoneism?

5.- Did Einstein refine modern physics because he worshipped misoneism and deeply believed that humankind did not deserve the advance and progression of science and technology?

6.- Did Planck renovated physics and incorporate quantum theory to physic’s body of knowledge because he founded the misoneism movement?

7.- Did Feynman redefined quantum mechanics because his mind had a great view only to misoneism?

8.- Did Bonaparte overhaul logistics management and systems methodology subjecting all of his belief system to misoneism?

9.- Did Churchill create an unheard-of methodology of statesmanship by self-discipline himself ─ both in though and deed ─ into maximum misoneism?

10.- Did Immanuel Kant make a breakthrough discovery to overhauling philosophy and anthropology through a mentality hijacked by outright misoneism?

11.- Did Francis Bacon profoundly enlightened philosophy, jurisprudence, and science by being a subject of the misoneism “Kingdom”?

12.- Did Nietzsche acculturate classical philology by a full immersion into misoneism?

13.- Did Socrates came up with his Socratic method (his pervasively disruptive innovation) by mindfully embracing a dogma, a dogma termed “misoneism”?

14.- Did Aristotle revolutionize Western philosophy by believing that the only and ultimate truth where posited by misoneism?

15.- Did Plato communicate a breakthrough modality of Western philosophy and science by exercising his mind and deeds in accordance to the doctrines of misoneism?

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Monday, November 21, 2011

NASA, Google, and Most Serious Futurology

NASA’ and Google’s joint FUTUROLOGY-DRIVEN University on NASA Ames Research Center. The Singularity University at

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Thursday, November 17, 2011

 Yesterday, Today, Success, Balance, as per Stephen Covey

Dr. Stephen Covey argues: “…Yesterday’s meal [knowledge] will not satisfy today’s hunger [desire and crystallization of accomplishment] …. We defined success as long- and sort-term balance and accomplishment...”

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How Change Operates as per Shakespeare and Bacon:

“...There is a tide in the affairs of men,
Which taken at the flood, leads on to fortune;
Omitted, all the voyage of their life
Is bound in shallows and in miseries.
On such a full sea are we now afloat,
And we must take the current when it serves,
Or lose our ventures...”

(William Shakespeare)

“... He that will not apply new remedies
must expect new evils,
for time is the greatest innovator ...”

(Sir Francis Bacon)

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 A touchscreen you can really feel

A new user interface with tactile surfaces — users can feel actual raised keys under their fingertips — has been developed by researchers at the Integrated Actuators Laboratory (LAI) of the École Polytechnique Fédérale de Lausanne (EPFL).

The technology could be used to enrich online texts, drawing the reader’s attention to certain elements on the page, or to make video games even more entertaining, by adding an additional sensory dimension. And for the visually impaired, it could open up access to smartphones and other electronic devices.

To obtain this tactile effect, the scientists used a piezoelectric material that vibrates when a voltage is applied to it. These vibrations create a very thin layer of air between the surface and a user’s finger, giving him or her the feeling that there’s something raised underneath it.

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 Geron halts pioneering stem cell research

The dream of using stem cells to treat people paralysed by spinal injury has been dealt a major blow. Biotech giant Geron has called a halt to its entire stem cell programme, the largest of its kind in the world. That includes a trial to treat 11 people with spinal injuries, which began a year ago.

"Geron is a pioneer and it is very disappointing that the company has had to change direction. The public will need reassurance that this is not the end of an era," says Dusko Ilic of King's College London.

The firm based in Menlo Park, California, says its decision is purely financial and not based on moral reasons or negative results from the four paralysed patients treated so far . The company will now focus all its resources on developing anti-cancer drugs.

The company had to choose between stem cells and cancer, and saw cancer as the better bet. "By narrowing our focus to the oncology therapeutic area, we anticipate having sufficient financial resources to reach these important [targets] without the necessity of raising additional capital," says John Scarlett, Geron's chief executive officer. "This would not be possible if we continue to fund the stem cell programmes at the current levels."

Controversial research

It took years and countless setbacks for Geron to win consent from the US Food and Drug Administration to begin the spinal trial. Geron's programme caused controversy because its cell lines come from human embryonic stem cells (hESCs) obtained through destruction of embryos. Anti-abortion and some evangelical groups have opposed the research because of this.

Most other treatments are based on adult stem cells but some based on hESCs are continuing, including a treatment for a form of blindness called Stargardt's macular dystrophy. "It leaves us holding the flag," says Robert Lanza at Advanced Cell Technology of Worcester, Massachusetts. "There's lots of pressure on us to deliver a success to keep the field alive, but of course it's the second mouse that often gets the cheese."

Too much, too soon?

Lanza questions whether Geron was wise to have chosen such a difficult condition as its first treatment. "Many experts were surprised when they selected spinal cord injury. We knew it was going to be very difficult to show a biological effect," he says.

Others agree: "Making superman walk would have been great for business, but was an ambitious target for a serious problem, and maybe not the best start scientifically or clinically for stem cell therapies," says Alison Murdoch at Newcastle University, UK.

"I have said publically that the Geron trial had no real chance of success because of the design and the [disorder] targeted," says John Martin, professor of cardiovascular medicine at University College London. "It was intrinsically flawed," says Martin, whose own trials are focussing on treating damaged hearts with adult stem cells.

Apart from cells for spinal injuries, Geron has also coaxed hESCs into cells for treating several other conditions, including heart disease, diabetes, arthritis and ligament damage.

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 Ionized plasmas as cheap sterilizers for developing world

University of California, Berkeley, scientists have shown that ionized plasmas like those in neon lights and plasma TVs not only can sterilize water, but make it antimicrobial – able to kill bacteria – for as long as a week after treatment.

Devices able to produce such plasmas are cheap, which means they could be life-savers in developing countries, disaster areas or on the battlefield where sterile water for medical use – whether delivering babies or major surgery – is in short supply and expensive to produce.

“We know plasmas will kill bacteria in water, but there are so many other possible applications, such as sterilizing medical instruments or enhancing wound healing,” said chemical engineer David Graves, the Lam Research Distinguished Professor in Semiconductor Processing at UC Berkeley. “We could come up with a device to use in the home or in remote areas to replace bleach or surgical antibiotics.”

Low-temperature plasmas as disinfectants are “an extraordinary innovation with tremendous potential to improve health treatments in developing and disaster-stricken regions,” said Phillip Denny, chief administrative officer of UC Berkeley’s Blum Center for Developing Economies, which helped fund Graves’ research and has a mission of addressing the needs of the poor worldwide.

“One of the most difficult problems associated with medical facilities in low-resource countries is infection control,” added Graves. “It is estimated that infections in these countries are a factor of three-to-five times more widespread than in the developed world.”

Graves and his UC Berkeley colleagues published a paper in the November issue of the Journal of Physics D: Applied Physics, reporting that water treated with plasma killed essentially all the E. coli bacteria dumped in within a few hours of treatment and still killed 99.9 percent of bacteria added after it sat for seven days. Mutant strains of E. coli have caused outbreaks of intestinal upset and even death when they have contaminated meat, cheese and vegetables.

Based on other experiments, Graves and colleagues at the University of Maryland in College Park reported Oct. 31 at the annual meeting of the American Vacuum Society that plasma can also “kill” dangerous proteins and lipids – including prions, the infectious agents that cause mad cow disease – that standard sterilization processes leave behind.

In 2009, one of Graves’ collaborators from the Max Planck Institute for Extraterrestrial Physics built a device capable of safely disinfecting human skin within seconds, killing even drug-resistant bacteria.

“The field of low-temperature plasmas is booming, and this is not just hype. It’s real!” Graves said.

In the study published this month, Graves and his UC Berkeley colleagues showed that plasmas generated by brief sparks in air next to a container of water turned the water about as acidic as vinegar and created a cocktail of highly reactive, ionized molecules – molecules that have lost one or more electrons and thus are eager to react with other molecules. They identified the reactive molecules as hydrogen peroxide and various nitrates and nitrites, all well-known antimicrobials. Nitrates and nitrites have been used for millennia to cure meat, for example.

Graves was puzzled to see, however, that the water was still antimicrobial a week later, even though the peroxide and nitrite concentrations had dropped to nil. This indicated that some other reactive chemical – perhaps a nitrate – remained in the water to kill microbes, he said.

Plasma discharges have been used since the late 1800s to generate ozone for water purification, and some hospitals use low-pressure plasmas to generate hydrogen peroxide to decontaminate surgical instruments. Plasma devices also are used as surgical instruments to remove tissue or coagulate blood. Only recently, however, have low-temperature plasmas been used as disinfectants and for direct medical therapy, said Graves.

Graves recently focused on medical applications of plasmas after working for more than 20 years on low-temperature plasmas of the kind used to etch semiconductors. While sparks in air typically create hot plasmas of partially ionized and dissociated oxygen and nitrogen, a very brief spark creates similar molecules without heating the air. The reactive oxygen and nitrogen created by the plasma will diffuse into nearby liquids or skin, where they can kill microbes similar to the way some drugs and immune cells kill microbes by generating very similar or even identical reactive chemicals.

Despite the widespread use of plasmas, however, they are still not well characterized, Graves said. Plasma created in air, for example, produces different molecules than plasma in helium or argon. Much needs to be learned about different ways of producing plasmas, including plasma needles and jets, and how to maximize exposure against skin or liquid, such as by confining the plasma-generated chemicals near the surface of the treated object.

“I’m a chemical engineer who applies physics and chemistry to understanding plasmas,” Graves said. “It’s exciting to now look for ways to apply plasmas in medicine.”

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 New material can enhance energy, computer, lighting technologies

Arizona State University researchers have created a new crystal nanowire material that promises advances in a range of scientific and technological pursuits.

ASU electrical engineering professor Cun-Zheng Ning  says the material, called erbium chloride silicate, can be used to develop the next generations of computers, improve the capabilities of the Internet, increase the efficiency of silicon-based photovoltaic cells to convert sunlight into electrical energy, and enhance the quality of solid-state lighting and sensor technology.

Erbium is one of the most important members of the rare earth family in the periodic table of chemical elements. It emits photons in the wavelength range of 1.5 micrometers, which are used in the optical fibers essential to high-quality performance of the Internet and telephones.

Erbium is used in doping optical fibers to amplify the signal of the Internet and telephones in telecommunications systems. Doping is the term used to describe the process of inserting low concentrations of various elements into other substances as a way to alter the electrical or optical properties of the substances to produce desired results. The elements used in such processes are referred to as dopants.

“With the new erbium compound, 1,000 times more erbium atoms are contained in the compound. This means many devices can be integrated into a chip-scale system,” he says. “Thus the new compound materials containing erbium can be integrated with silicon to combine computing and communication functionalities on the same inexpensive silicon platform to increase the speed of computing and Internet operation at the same time.”

More efficient solar cells

Erbium materials can also be used to increase the energy-conversion efficiency of silicon solar cells. Silicon does not absorb solar radiation with wavelengths longer than 1.1 microns, which results in waste of energy, making solar cells less efficient.

Erbium materials can remedy the situation by converting two or more photons carrying small amounts of energy into one photon that is carrying a larger amount of energy. The single, more powerful photon can then be absorbed by silicon, thus increasing the efficiency of solar cells.

Erbium materials also help absorb ultraviolet light from the sun and convert it into photons carrying small amounts of energy, which can then be more efficiently converted into electricity by silicon cells.  This color-conversion function of turning ultraviolet light into other visible colors of light is also important in generating white light for solid-state lighting devices.

What is unique about the new erbium material synthesized by Ning’s group is that erbium is no longer randomly introduced as a dopant. Instead, erbium is part of a uniform compound and the number of erbium atoms is a factor of 1,000 more than the maximum amount that can be introduced in other erbium-doped materials.

Increasing the number of erbium atoms provides more optical activity to produce stronger lighting. It also enhances the conversion of different colors of light into white light to produce higher-quality solid-state lighting and enables solar cells to more efficiently convert sunlight in electrical energy.

In addition, since erbium atoms are organized in a periodic array, they do not cluster in this new compound.  The fact that the material has been produced in a high-quality single-crystal form makes the optical quality superior to the other doped materials, Ning says.

Ning and his team are now trying to use the new erbium compound for various applications, such as increasing silicon solar cell efficiency and making miniaturized optical amplifiers for chip-scale photonic systems for computers and high-speed Internet.

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 Using cells’ chemical signaling to control cancer or detect toxins

MIT researchers have found that cells’ chemical signaling mechanisms can tell whether their signals are being received, and then adjust the volume of their messages as needed.

Cells use these chemical signaling systems to control many basic functions. For example, signaling can control how genes are turned on and off in response to external or internal cues, how cells grow and organize their internal structures, and even how and when cells trigger their own death, a process known as apoptosis.

The new finding could be useful for everything from synthetic biology to slowing the spread of cancer cells, or to engineer cells that can respond — perhaps by changing color — to certain disease-causing substances or toxins, thus producing very sensitive biologically based detectors.

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 Creation of the largest human-designed protein boosts protein engineering efforts

Vanderbilt chemists have built the largest human-designed protein.

They designed and successfully synthesized a variant of a protein that nature uses to manufacture the essential amino acid histidine. It is more than twice the size of the previous record holder, a protein created by researchers at the University of Washington in 2003.

The synthetic protein, designated FLR, validates a new approach that the Vanderbilt scientists have developed that allows them to design functional artificial proteins substantially larger than previously possible.

“We now have the algorithms we need to engineer large proteins with shapes that you don’t see in nature. This gives us the tools we need to create new, more effective antibodies and other beneficial proteins,” said Jens Meiler, the associate professor of chemistry at Vanderbilt who led the effort.

Recently, protein engineers have verified a potential treatment strategy for HIV by using designed protein vaccines in mice and have designed artificial proteins that mimic antibodies in broadly neutralizing flu infections. The technique developed at Vanderbilt promises to expand the scope of these efforts substantially.

That is important because proteins are the most important molecules in living cells. They perform most of the vital tasks that take place within a living organism. There are hundreds of thousands of different proteins. They come in a variety of shapes and sizes. They can be round or long and thin, rigid or flexible. But they are all made out of linear chains of 20 amino acids encoded in the genome of the organism.

Proteins assume this variety of shapes and sizes by the manner in which they bunch and fold. This complex process takes two steps. First, small numbers of adjacent amino acids form what scientists call secondary structures: the most common of which are a rod-like spiral shape called the alpha-helix and a flat, pleated shape called the beta-sheet. These secondary structures, in turn, interact, fold and coil to form the protein’s three-dimensional shape, which is the key to its function.

Over the past 10 years, an increasing number of proteins that don’t exist in nature have been designed “in silico” (in a computer). Scientists use sophisticated protein modeling software that incorporates the relevant laws of physics and chemistry to find amino acid sequences that fold into stable forms and have specific functions.

For a protein of a given size, the modeling software creates millions of versions by putting each amino acid in every position and evaluating the stability of the resulting molecule. This takes a tremendous amount of computing power, which skyrockets as the length of the protein increases.

“The current limit of this approach, even using the fastest supercomputers, is about 120 amino acids,” said Meiler. The previous record holder contained 106 amino acids. The newly designed protein contains 242 amino acids. The Vanderbilt group got around this limit by modifying the widely used protein engineering platform called ROSETTA so that it can incorporate symmetry in the design process.

Their success provides new support for a controversial theory about protein evolution called the gene duplication and fusion hypothesis. The advantage of small proteins is that they can evolve rapidly in response to changing conditions, but larger proteins can perform more complex functions. Nature found a way to get both advantages by selecting small proteins that can interact with other copies of themselves to form larger proteins, which are called dimers. Once useful dimers have been created the gene that coded for the original protein is duplicated and fused to form a new gene that can directly produce the dimer. After it is created, the dimer gene is gradually modified by natural selection to make it more efficient or develop new functions.

Because they have two identical halves, dimers have a large degree of symmetry. By taking these symmetries into account, the Vanderbilt group was able to substantially reduce the amount of computing time required to create the FLR protein. Using 400 processors of the supercomputer at Vanderbilt’s Advanced Computing Center for Research and Education, it took 10 days of continuous processing to find the most stable configuration.

To check the accuracy of their design, the researchers synthesized the DNA sequence that produces the protein, inserted it in E.coli bacteria and determined that they produced the protein and it folded properly.

The FLR protein assumes a 3-D shape called a TIM barrel, which is found in 10 percent of proteins and is particularly prevalent among enzymes. It is formed from eight beta strands that are surrounded by eight alpha helices arranged in a hexagonal shape like a tiny barrel.

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 New ‘smart’ material could help tap medical potential of tissue-penetrating light

Scientists at the University of California, San Diego Skaggs School Pharmacy and Pharmaceutical Sciences report development and successful initial testing of the first practical “smart” material to use a form of light that can penetrate four inches into the human body, for use in diagnosing diseases and engineering new human tissues in the lab.

They used near-infrared (NIR) light (just beyond what humans can see), which penetrates through the skin and almost four inches into the body. Low-power NIR does not damage body tissues. However, current NIR-responsive smart materials require high-power NIR light, which could damage cells and tissues.

So they developed a new smart polymer (plastic). Hit with low-power NIR, the material breaks apart into small pieces that appear to be nontoxic to surrounding tissue. They could put the polymer in an implantable hydrogel, which is a water-containing flexible material used for tissue engineering and drug delivery. A hydrogel with the new polymer could release medications or imaging agents when hit with NIR. “To the best of our knowledge, this is the first example of a polymeric material capable of disassembly into small molecules in response to harmless levels of irradiation,” say the researchers.

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A common cortical organization among mammals

A new study by researchers at the University of California, San Diego School of Medicine and colleagues using magnetic resonance imaging data of 406 adult human twins affirms the long-standing idea that the genetic basis of human cortical regionalization — the organization of the outer brain into specific functional areas — is similar to and consistent with patterns found in other mammals, indicating a common conservation mechanism in evolution.

Past animal studies, primarily in rodents, have shown that development of distinct areas of the cortex — the outer layer of the brain — is influenced by genes exhibiting highly regionalized expression patterns. The new study is among the first to confirm these findings using data from human subjects. As in other mammals, the researchers found that that genetic influences in human brain development progress along a graduating scale anterior-to-posterior (front-to-back) in a bilateral, symmetric pattern.

There were, of course, differences based upon the particular needs and functions of each species.

“For example, humans have very high-level thinking abilities. Mice don’t engage in abstract thinking, but they do make extensive use of their whiskers to negotiate the sensory environment,” said William S. Kremen, PhD, professor of clinical psychology and corresponding author of the study. “Consistent with these species-specific features, we found that genetic influences resulted in greatly expanded frontal regions in humans — the area of the brain responsible for higher level functions — but much-expanded somatosensory regions in the mouse brain.”

The scientists conducted their study by mapping genetic correlations in area growth between targeted brain regions and other cortical locations. By studying twins, they were able to expand the scope of the inquiry. “In non-twin studies,” Kremen said, “researchers have been able to examine the effects of a small number of individual genes. By comparing identical and fraternal twins, we can account for the total of all genetic influences on the patterns of expansion and contraction of different brain regions.”

The researchers selected targets called “seed points” in the brain to look for patterns to how each point was related to all other points. They double-checked the validity of these seed points by also examining “marching seeds” — lines of seed points from one brain region to another. “If the results are meaningful, the patterns should remain similar within a region and then change when the seed point enters a new region,” said Kremen.

Anders M. Dale, PhD, professor of radiology and neurosciences at UC San Diego and a co-author of the study, said the study’s findings have both basic and clinical implications. “We know that genetics are important in determining brain structure Increasing our understanding of genetics is a key step toward understanding normal brain development, but it is also crucial for understanding the development of brain abnormalities. Eventually, it may provide clues to the treatment of developmental brain anomalies that occur early or late in life. Also, because the study identified regions of the brain based on their genetic similarity, it may well improve the ability of researchers to find the specific individual genes that control the size of those regions.”

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A realistic look at the promises and perils of nanomedicine

Is the emerging field of nanomedicine a breathtaking technological revolution that promises remarkable new ways of diagnosing and treating diseases, or does it portend the release of dangerous nanoparticles, nanorobots, or nanoelectronic devices that will wreak havoc in the body?

A new review of more than 500 studies on the topic by Centro de Investigación Príncipe Felipe in Spain concludes that neither scenario is likely.

The authors say about 40 nanotechnology health care products are actually in use and nano-sized drugs, drug delivery devices, imaging agents, and other products are on the horizon.

The authors offer suggestions for how best to move a nanomedicine through the drug development process with risks and benefits in mind, and identify key factors critical for development of practical nanomedical technology that is safe and effective.

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The rootkit of all evil — CIQ

CarrierIQ (CIQ), hidden surveillance software, is embedded into most mobile devices, including Android, Nokia, Blackberry, and likely many more, with root access (a vendor or hacker could take over the device), xdadevelopers reports.

A developer discovered that this hidden software, normally used to provide feedback and relevant data, is given root rights over the device, which means that it can do everything it pleases, without the user’s knowledge or control.

For example, if Google’s vision of Android@Home comes true, manufacturers will know how long you spend in each room of your house, based on when you flip the light switch, and so on. There is the very real possibility of exploits that could also give criminals all this information, xdadevelopers reports in a follow-up article.

At the moment, the only people with Android phones who are able to escape CarrierIQ are users who are brave enough to root their own phones and flash a ROM that does not have the CarrierIQ software integrated with the operating system, like CyanogenMod, reports.

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 Can Intel and DreamWorks cross the uncanny valley?

A collaboration between Intel and DreamWorks is leading to near-real-time rendering that is 50 to 70 times faster than anything being used today, Forbes blogger E.D. Kain reports.

According to DreamWorks CEO Jeffrey Katzenberg, it takes an experienced 3D animator a week to animate three seconds of finished product, much of which is rendering time. That’s OK for film, but rendering time makes video games sluggish, and  lacking in realism. Solving that could cross the “uncanny valley” — or make it worse.

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 Robot controls a person’s arm using electrodes

A robot that can control both its own arm and a person’s arm to manipulate objects in a collaborative manner has been developed by Montpellier Laboratory of Informatics, Robotics, and Microelectronics (LIRMM) researchers, IEEE Spectrum Automation reports.

The robot controls the human limb by sending small electrical currents to electrodes taped to the person’s forearm and biceps, which allows the robot to command the elbow and hand to move. In the experiment, the person holds a ball, and the robot holds a hoop; the robot, a small humanoid, has to coordinate the movement of both human and robot arms to successfully drop the ball through the hoop.

The researchers say their goal is to develop robotic technologies that can help people suffering from paralysis and other disabilities to regain some of their motor skills.

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Improved quantum-dot LED design

Harvard School of Engineering and Applied Sciences (SEAS) researchers have demonstrated a robust new architecture for quantum-dot light-emitting devices (QD-LEDs) by nestling quantum dots in an insulating egg-crate structure.

Quantum dots are crystals, each only 6 nanometers in diameter, that glow with bright, rich colors when stimulated by an electric current. QD-LEDs are expected to find applications in television and computer screens, general light sources, and lasers.

Previous work in the field had been complicated by organic molecules called ligands that dangle from the surface of the quantum dots. The ligands play an essential role in quantum dot formation, but they can interfere with current conduction, and attempts to modify them can cause the quantum dots to fuse together, destroying the properties that make them useful. Organic molecules can also degrade over time when exposed to UV rays.

Thanks to an inventive change in technique devised by the Harvard team, the once-troublesome ligands can now be used to build a more versatile QD-LED structure. The new single-layer design can withstand the use of chemical treatments to optimize the device’s performance for diverse applications. The new QD-LED resembles a sandwich, with a single active layer of quantum dots nestled in insulation and trapped between two ceramic electrodes.

To create light, current must be funneled through the quantum dots, but the dots also have to be kept apart from one another in order to function. The researchers used atomic layer deposition (ALD) — a technique that involves jets of water. ALD takes advantage of the water-resistant ligands on the quantum dots, so when aluminum oxide insulation is applied to the surface, it selectively fills the gaps between the dots, producing a flat surface on the top. The new structure allows more effective control over the flow of electrical current, and essentially creates a structure that acts as an “egg crate” for quantum dots.

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 Recipe for cooking a cancer cell: add 2 million nanorods, heat with laser

Chemists at Rice University have found a way to load more than 2 million tiny gold particles called nanorods into a single cancer cell. The breakthrough could speed development of cancer treatments that would use nanorods like tiny heating elements to cook tumors from the inside.

The strategy is to deliver nontoxic particles that become deadly only when they are activated by a laser, according to study leader Eugene Zubarev, associate professor of chemistry at Rice. The nanorods, which are about the size of a small virus, can convert otherwise harmless light into heat.

“Ideally, you’d like to use a low-power laser to minimize the risks to healthy tissue, and the more particles you can load inside the cell, the lower you can set the power level and irradiation time,” said Zubarev, an investigator at Rice’s BioScience Research Collaborative (BRC).

Unfortunately, scientists who study gold nanorods have found it difficult to load large numbers of particles into living cells. Nanorods are pure gold, which means they won’t dissolve in solution unless they are combined with some kind of polymer or surfactant. The most commonly used of these is cetyltrimethylammonium bromide (CTAB), a soapy chemical often used in hair conditioner.

But CTAB is toxic, so the researchers replaced it with a closely related molecule called MTAB. Two additional atoms (sulfur and hydrogen) allow MTAB to form a permanent chemical bond with gold nanorods. (CTAB also binds more weakly to nanorods and has a tendency to leak into surrounding media from time to time, which is believed to be the underlying cause of CTAB-encased nanorod toxicity.)

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