Big data to identify triple-negative breast and other cancers


Researchers at Case Western Reserve University and colleagues used “big data” analytics to predict if a patient is suffering from aggressive triple-negative breast cancer, slower-moving cancers or non-cancerous lesions with 95 percent accuracy.

If the tiny patterns they found in magnetic resonance images prove consistent in further studies, the technique may enable doctors to use an MRI scan to diagnose more aggressive cancers earlier and fast track these patients for therapy. Their work is published online in the journal Radiology at http://pubs.rsna.org/doi/full/10.1148/radiol.14121031?queryID=48%2F1089655.

The work comes just two months after senior author Anant Madabhushi and another group of researchers showed they can detect differences between persistent and treatable forms of head and neck cancers caused by exposure to human papillomavirus, with 87.5 percent accuracy. In that study, digital images were made from slides of patients’ tumors.

Next up, Madabhushi’s lab recently received a $534,000, 2-year grant from the Department of Defense to find the patterns of indolent versus aggressive cancer in the lungs. The goal is to diagnose the presence of aggressive lung cancers from CT scans alone.

“Literally, what we’re trying to do is squeeze out the information we’re not able to see just by looking at an image,” said Madabhushi, a professor of biomedical engineering at Case School of Engineering and director of the Center for Computational Imaging and Personalized Diagnostics.

Searching for telltale markers

Madabhushi worked with Shannon C. Agner at Rutgers University and Mark A. Rosen, MD; Sarah Englander; Mitchell D. Schnall, MD; Michael D. Feldman, MD; Paul Zhang, MD; and Carolyn Miles; MD, at the University of Pennsylvania, on the breast cancer study.

They analyzed MR images of breast lesions from 65 women. The researchers sifted through hundreds of gigabytes of image data from each patient to try to find differences that distinguish the different subtypes of breast cancers from each other.

Madabhushi and his colleagues discovered that triple-negative cancer, benign fibroadenoma that is commonly mistaken for triple-negative, and two other common types of breast cancer—estrogen-receptor positive (ER+) and human epidermal growth factor receptor type 2-postive (HER2+)—reflect different textures when images are enhanced with contrasting agents.

The scientists mathematically modeled the textures that appear as the tissues absorb contrast-enhancing dye. The model revealed that changes over just milliseconds distinguished triple-negative from benign lesions. The investigators used machine learning and pattern recognition methods to aid in diagnoses among the three types of cancers based on texture changes and other quantitative evidence.

“Today, if a woman or her doctor finds a lump, she gets a mammogram and then a biopsy for molecular analysis, which can take two weeks or up to a month,” Madabhushi said. “If we can predict the cancer is triple-negative, we can fast track the patient for biopsy and treatment. Especially in cases with triple-negative cancer, two to four weeks saved can be crucial.”

For the three types of cancers, the early diagnosis would enable quick and personalized treatments. ER+ and HER2+ respond to different therapies. An MRI could also become a regular screening device for women who have family histories of these cancers.

Other cancers

Using much the same science, Madabhushi and fellow researchers from Washington University developed a way to distinguish between recurrent and treatable forms of a specific head and neck cancer called human papillomavirus-related oropharyngeal squamous cell carcinoma. That work was published earlier this year in the American Journal of Surgical Pathology. The abstract can be found at http://www.ncbi.nlm.nih.gov/pubmed/24145650.

“Most sufferers tend to have good outcomes, but a small subset—about 10 percent—doesn’t,” he said. “There’s nothing out there to predict which.

“We developed an algorithm and found patterns that allowed us to distinguish between the two with 80 to 90 percent accuracy.”

After scanning biopsy and tumor resection slides from 160 patients into a computer, the researchers found they could use nuclei of the cancerous cells to characterize and measure cell distribution and clustering patterns.

They found where the nuclei of cells had reverted to a more primitive form, a condition called anaplasia, the cells were tightly clustered and the patient suffered recurrent cancer. They graphed the nuclei in each of the images and found there was little to no overlap between the highly clustered recurrent cancer and the comparatively disperse treatable form.

The results, if confirmed through further studies, could lead to milder treatment for patients who have the non-recurrent cancer and more aggressive treatment for those with recurrent cancer, the researchers say.

“Personalized medicine is possible using this,” Madabhushi said. “Using biopsy specimens, pathologists can’t tell one from the other, but big data analytics can.”

His lab’s newest project is to find characteristics that can identify cancer or precancerous conditions in the lungs, and distinguish among different types of lung cancers.

The majority of lung cancers are diagnosed at advanced stages, beyond the period in which surgery can be successful. Survival rate for one of the worst forms, non small-cell lung cancer, remains at 15 to 18 percent. In this study, the lab will use x-ray images taken with computed tomography scans to build their digital image library.

The Search for a New Donor: Kidneys with Small Renal Masses


The Search for a New Donor: Kidneys with Small Renal Masses
Abstract
The gap between organ demand and supply is increasing gradually for both the developed and the
developing countries. Lack of deceased donors leads to kidney transplantationfrom cardiac death and
living donors. Recently, a new organ donor is added to the above mentioned options. This is the use of the
kidneys procured from the patients with small renal tumors. Many studies showed the possibility, feasibility
and safety of utilization of the restored or tumor excised kidneys in selective cases. Here, the important
point is that the ethical principles, the balance of risk and benefit for both donor as well as recipient
should take the priority. Long-term follow-up outcomes and further multicenter studies will be guiding in
determining the future of this approach.
 
Discussion

Organ shortage is an important problem in kidney transplantation. The gap between organ demand and supply is increasing gradually. Lack of deceased donors leads to use of expended criteria, cardiac death and living donors. Recently, a new organ sourcewas added to the above mentioned options. This is the use of the kidneys procured from the patients with small renal tumors. Incidental small renal tumors are detected more frequently by using imaging methods like US, CT scan, MRI. Nephron sparing partial nephrectomy is the gold standard treatment for the patients with small renal tumors (pT1a).[1] Thermal ablation and active follow up are recommended for the patients unfit for the surgery and with comorbid disease. [1] The studies conducted in the United States and England revealed that total nephrectomy is the most common treatment modality in practice (92.5%-96%).[2,3] Although the nephron sparing partial nephrectomy lately began to take place of total nephrectomy for the treatment of small  renal masses, it is still not common. Nowadays, the factors for universality of the total nephrectomy could be summarized as potential risks of partial  nephrectomy (bleeding, urinary leak, wound infection), experience of the surgeon and the request of the patients.

There are few reports about the use of kidneys with small renal masses in kidney transplantation. Brook et al. have compared the outcomes of kidney transplantations in patients with small renal tumors (renal cell carcinoma-pT1a-grade 1-3, papillary carcinoma-grade 1-2, chromophobe carcinomagrade 2, oncocytoma), live unrelated donors and dialysis wait-listed patients.[5] In a subsequent matched cohort analysis, kidney recipients from donors with excised renal tumors had comparable graft than the patient survival with the kidney recipients from live unrelated donors. Patient survival for excised tumor kidney recipients was better than those who did not receive a transplant.[5]Mannami et al reported the results by the use of not only kidneys with small renal tumors (renal cell carcinoma, pT1a, grade 1-2) but also kidneys with ureteral cancer(transitional cell carcinoma, pT1a,2,3 grade 1-3), benign diseases (angiomyolipoma, recurrent urinary tract infections, hydronephrosis due to retroperitoneal fibrosis after radiotherapy), aneurism and severe nephrotic syndrome.[4] In this study, the graft and patient survival for 5 years and 10 years were 51.8% and 42.7%, 79.3% and 63.8, respectively. In patients of the same age group on dialysis, patient survival was 72% and 52% at 5years and 10 years, respectively.[4] Beside the graft and patient survival, the improvement of the QoL is also another prominent benefit of the kidney transplantation.

Considering the tumor recurrence, Mannami et al reported no recurrence in the small renal tumor group but showed one at 15 months in ureteral cancer group.[4] Brook et al reported only one tumor recurrence at 9 years after the transplant of the kidney with excised renal tumor.[5]Sener et al reported the results of 5 kidney transplantations after tumor excision with the median 15 months (1 month to 41 months) follow up and there was no recurrence or metastatic disease in the recipients and the donors.[6]In another study it was revealed  that no recurrence of tumor by the median 69 months(14 months to 200 months) follow up of 14recipients with tumor excised kidney transplant. [7] These successive findings support the safe use of the kidneys from the patients with small renal  tumor after excision. Availability or lack of the data for long-term follow up should be kept in mind. Transplantation of these kidneys in high risk  recipients (like age over 60, no living donor, comorbid disease, estimated live expectancy in 5 years lower than 50%, with history of un successful transplantation) may be helpful to eliminate the concerns about the tumor recurrence.

The use of kidneys with incidentally detected small renal tumors during organ procurement or patient examination doesn’t prohibit the transplantation. Furthermore, earlier mentioned studies showed the possibility, feasibility and safety of utilization of the restored or tumorexcised kidneys in selective cases. When comparing with the wait-listed dialysis patients, kidney transplant recipients have the advantage of better survival and QoL, as well. In the light of this, utilization of the restored or tumor excised kidneys in selective group recipients may be helpful to expand the donor pool. In countries where the organ shortage is still a big problem,most of the transplantations are performed using organs from healthy live donors. The balance between risk and benefit for both donor and recipient should take the priority. The legislations as well as clinic protocols should be based on objective criteria and should be free from bias. Long-term followup outcomes and multicenter studies will guide the future of this approach.

References

  1. Thomas AA, Campbell SC. Small renal masses: toward more rational treatment. Cleve Clin J Med. August 2011; 78(8): 539-547.
  2. Hollenbeck BK, Taub DA, Miller DC, Dunn RL, Wei JT. National utilization trends of partial nephrectomy for renal cell carcinoma: a case of underutilization? Urology. 2006;67:254-259.
  3. Nuttall M, Cathcart P, van der Meulen J, et al. A description of radical nephrectomy practice and outcomes in England: 1995-2002. BJU Int. 2005;96:58-61.
  4. Mannami M, Mannami R, Mitsuhata N, et al. Last resort for renal transplant recipients, ‘restored kidneys’ from living donors/patients. Am J Transplant. 2008;8(4):811-818.
  5. Brook NR, Gibbons N, Johnson DW, Nicol DL. Outcomes of the transplants from patients with small renal tumours live unrelated donors and dialysis wait-listed patients. Transplant Int. May 2010;23(5): 476-483.
  6. Sener A, Uberoi V, Bartlett ST, Kramer AC, Phelon MW. Living donor renal transplantation of grafts with incidental renal masses after exvivo partial nephrectomy. BJU Int. December 2009;104(11): 1655-1660.
  7. Buell JF, Hanawway MT, Munda R, et al. Donor kidneys with small renal cell cancers: can they be transplanted? Transplant Proc. 2005 ;37: 581-582.

 

What to Do Before Same Day Surgery .


A health reporter shares the key tips that weren’t mentioned in official pre-op instructions but had a dramatic impact on her recovery.

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Last summer, after a broken wristbone slipped too far out of place to fuse properly, I was scheduled for a minor, same-day surgery to install a plate and screws. I knew I’d have to skip breakfast that morning and arrange for someone to drive me home afterward. But along the way, I picked up a number of other little tips—from nurses, doctors, and even fellow patients—that weren’t mentioned in my official pre-op instructions but had a dramatic impact on my health and recovery. The surprising advice I learned could help people having one of the 50 million–plus outpatient surgeries this year.

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DAYS BEFORE
Drink Up
It’s vital that there’s nothing in your stomach during general anesthesia (food or drink could be a choking hazard). But if you’re well hydrated, you’ll feel better and your veins will be fully dilated—and thus more receptive to IV fluids and drugs. If your cutoff for food and water is at midnight, drink plenty of clear fluids (not alcohol) during the evening until then. The common “midnight” deadline assumes that your surgery is bright and early. If your procedure is in the afternoon, ask if the cutoff can be moved closer to the time of surgery.

Cancel Your Manicure
Skip the presurgery splurge. The anesthesiologist needs polish-free fingers to monitor your oxygen levels while you’re sedated. “The pulse oximeter must be able to send and receive light through your fingertip, and acrylics and other nail coatings interfere,” says anesthesiologist Steven Gayer, MD, chair of the American Society of Anesthesiologists committee on ambulatory surgical care.

Curb the Herbs
Tell your doctor about any supplements you take. About 70 percent of surgery patients don’t think to do so, but it’s important. Even benign-sounding substances like fish oil can increase bleeding, while others, such as kava and St.-John’s-wort, may prolong the effects of anesthesia. Your surgeon may advise you to stop taking certain supplements two weeks prior to surgery, if possible.

Wash Away Germs
Infected incisions are always a big concern—and a major source of the germs that cause them is your own skin. Shower the night before and the morning of your surgery with antibacterial soap, or, even better, use a special wash, like Hibiclens, which kills germs on contact and helps protect your skin for the next 24 hours, advises J. Wesley Alexander, MD, director of research at the Shriners Hospitals for Children in Cincinnati. (Look for a wash that contains chlorhexidine and some alcohol.) Three cautions: Don’t use chlorhexidine if you are allergic to it (if you have any allergies, ask your doctor or pharmacist if it is safe). Don’t put chlorhexidine on your head or genitals—it’s too harsh. And don’t use bleach when you wash the towel you’ll use to dry off; doing so can cause a permanent reddish-brown stain. Use an oxygen-based laundry product, such as OxiClean, instead.

THAT MORNING
Answer With a Smile
Be patient as everyone you meet asks your name and what procedure you’re having done on which body part. The Joint Commission, which accredits more than 20,000 U.S. health-care organizations, requires double-checking by everyone along the way. It’s also wise to have someone act as your second eyes, ears, and voice. Write down your medications and medical history beforehand in case you forget.

Avoid a No-Caffeine Headache For many, the worst part of having a procedure is waking up afterward with a roaring headache. This is three times more likely to occur if you would normally start your day with a mug of coffee or tea, and the risk rises with the additional cups you’d usually consume. A patient pal who loves her java and has had numerous outpatient surgeries suggested this trick: Ask your doctor if you can take a caffeine tablet (NoDoz or Vivarin; one tablet is equivalent to one cup of coffee) with a sip of water first thing in the morning on the day of your procedure. My health team gave me permission, and it worked great: Because I’d had my caffeine fix, I could cheerfully agree when asked to delay surgery for an hour.

Snuggle Up
Accept the blanket offered in pre-op. Several studies show that staying warm can lower your risk of infection. Low temperatures decrease blood flow to the skin, which reduces the number of immune cells present to fight infection.

De-stress with a Pre-Op Scent
At my hospital, a volunteer visited pre-op to offer aromatherapy. Turns out, there’s some solid science behind the pampering. When 50 pre-op patients in Minnesota inhaled a lavender scent and placed a drop of oil on their skin, their anxiety levels fell 28 percent, and they entered the operating room significantly less tense than those who got a placebo oil or no special treatment. “When you’re extremely anxious, you may need more medication, which can lead to more side effects,” says Margo Halm, RN, director of nursing research at Salem Hospital in Oregon. (But ask first before you bring your own oils. Some facilities have strict no-fragrance policies because they may irritate fellow patients.)

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BACK HOME
Have a Sleepover
You’ll be required to have someone drive you home, but it’s better if a companion is around for at least 24 hours (this is especially important for older patients). You may not be thinking clearly for a full day after anesthesia and may need help changing dressings or fetching snacks and meds.

Don’t Tough It Out
If your pain isn’t well controlled, you’re more likely to suffer nausea and vomiting, says Jan Davidson, RN, director of ambulatory surgery at the Association of Operating Room Nurses. Make sure the discomfort is under control before you go home, and don’t skip prescribed painkillers.

Postpone the Dentist
Check with your surgeon before having dental work during the first six weeks after a surgery. Depending on your procedure, you may need to reschedule your appointment or take antibiotics to avoid infection.

Can this radar spot a missing plane?


Research team test photonics-based coherent radar system
The new laser system could send live cockpit video as well as pinpoint a plane’s precise location

As the search for the missing Malaysia Airlines flight intensifies, a new advanced radar system has been unveiled by scientists. But could it spot the plane?

The world’s first photonic radar was tested at Pisa Airport in Italy and achieved “world-class” performance, according to an independent expert.

It uses lasers to produce high fidelity signals that pinpoint planes precisely.

But there are doubts over its range, say researchers in Nature journal.

Could it really have followed flight MH370 as it veered off its route from Kuala Lumpur to Beijing – possibly travelling far out over the southern Indian Ocean where search teams are now investigating sightings of possible debris?

Today’s radar networks track planes via a combination of ground stations and satellites – as this guide explains.

Normal aircraft tracking

Graphic: How planes can be tracked

The new PhoDiR (Photonics-based fully digital radar) system is a working prototype for next-generation radars – designed to let pilots and air traffic control exchange far more information in a single signal.

Photonic systems promise:

  • Higher precision – less noise (interference) in the radar transmission
  • Higher bandwidth – able to transmit cockpit data (eg critical flight systems) as well as location data, simultaneously
  • Greater flexibility – more frequencies available
  • Smaller antennas – cheaper, lighter and more portable

PhoDiR was developed by Paolo Ghelfi and colleagues at Italy’s National Laboratory of Photonic Networks.

“Start Quote

One could imagine transmitting live streaming video from the cockpit together with the radar data”

Dr Paolo Ghelfi National Laboratory of Photonic Networks, Italy

To test their radar, they put it on the roof of their lab – and pointed it at planes taking off from nearby Pisa Airport.

“It was even more precise than we expected. We detected airplanes much farther away than we expected, with even higher precision,” he told BBC Radio 4’s Inside Science.

“We’re still trying to find out exactly how much better it is than conventional radar. It’s only a prototype – we don’t have clear numbers yet.”

The compact system could potentially be installed on aircraft, and has a very large bandwidth – allowing pilots to transmit detailed information directly to ground stations within range.

“In future, we imagine a system on an airplane that can scan objects around but also communicate what’s happening in the cockpit – what has been said, movements in the airplane, everything,” Dr Ghelfi told BBC News.

“One could imagine transmitting live streaming video, together with the radar surveillance data. The advantage would be that a single system can do the entire job, instead of multiple systems.”

Map of MH370 information

Experts say photonic radar can overcome some of the limitations of current electronic systems.

A laser produces a finely-tuned digital signature, which is converted into a radio frequency wave and transmitted from the radar antenna.

The returning wave is also converted via laser into a digital signal free from “jitter”.

“Because the light is very precise, so is the radio frequency signal,” said Prof David Stupples, an expert on radar systems at City University in London.

“Currently we produce the carrier wave using electronics. But then you’ve got to transport it up to the radar head through expensive, heavy cabling – and this creates noise in the system.

“But if you use light – with fibre optics – it is cheaper, lighter and crucially – it has less interference. It’s very accurate.”

The BBC’s Richard Westcott takes a look at the gadgets used to track a plane in flight

Jason McKinney, of the US Naval Research Laboratory, said the performance of the system’s transmitter and return signal converter were “world-class with respect to those of other photonics-based devices”.

“These elements… are appealing components for future frequency-agile, software-defined radar architectures,” he wrote in a commentary in Nature.

The main limitation on the system, he says, is range. It’s not clear how a photonic ground radar could cover any greater swathe of ocean than current coastal stations.

Dr Ghelfi agrees. “Over oceans you might still depend on satellite capacity,” he told BBC News.

And for this reason, the missing Malaysia Airlines flight MH370 would likely evade PhoDiR too – assuming it has taken a path across the Indian Ocean.

Rather than hunting planes over seas, the new system would be much more useful over land – benefiting European air traffic control for instance, the researchers suggest.

In highly-congested airspaces – such as above London’s Heathrow Airport – pilots will know precisely how much breathing space they have.

But the photonic system could also have applications beyond air traffic control.

It could be used more widely in surveillance and wireless communications. Dr Stupples even suggests it could help motorway drivers to avoid collisions in fast-moving traffic.

“We are putting all these radar systems into a single small chip – low-cost with multiple functionalities,” said Dr Ghelfi.

“But it will not be something that you will see right away – we are in the range of years and not of months.”

IBM’s Watson to help fight cancer


IBM's Watson
Using Watson should speed up the treatment process for cancer patients

IBM supercomputer Watson is to help determine the best treatments for a common type of brain cancer.

Watson will analyse glioblastoma patients’ DNA and correlate the results with available relevant medical data.

New York Genome Center president Robert Darnell said tremendous progress had been made in understanding the genetic drivers of cancer in the past 10 years.

And the project would “improve outcomes for patients with deadly diseases by providing personalised treatment”.

IBM Research director John E Kelly said: “It’s like big data on steroids.

“Watson can do in seconds what would take people years. And we can get it down to a really personal level.

“This is the proverbial needle in the haystack and the haystack is enormous.”

Watson uses artificial intelligence to examine huge amounts of data and can also understand human language. Rather than being programmed to spot patterns it “learns” about connections between different types of data. It is hoped that it will continue to “learn” as it processes new patient information and new medical research.

Diagram A cancer mutation on a cell protein pathway from genome sequencing

IBM Global Technology and Analytics vice-president Stephen Harvey said: “What we’re really talking about is taking a process that takes three weeks to three months for research organisations to complete today and to boil that down, using Watson technology, in to less than three minutes.”

Watson is already being used by doctors and nurses at the Memorial Sloan-Kettering Cancer Center, in New York, to help make decisions about lung cancer treatment.

Watson has become smaller and faster over the years. What started as a system the size of an average bedroom is now the size of three stacked pizza boxes. It is also available via the cloud, meaning it can be accessed from anywhere.

It can process 500GB of information – equivalent to a million books – every second.

And it has proved its abilities. In 2011 it appeared on the Jeopardy game show answering general knowledge questions, without being connected to the internet.

Pitted against the two biggest winners of the trivia quiz show, despite a few stumbles it eventually walked away with the $1m (£605,000) prize.

New semiconductor holds promise for 2-D physics and electronics.


From super-lubricants, to solar cells, to the fledgling technology of valleytronics, there is much to be excited about with the discovery of a unique new two-dimensional semiconductor, rhenium disulfide, by researchers at Berkeley Lab’s Molecular Foundry. Rhenium disulfide, unlike molybdenum disulfide and other dichalcogenides, behaves electronically as if it were a 2D monolayer even as a 3D bulk material. This not only opens the door to 2D electronic applications with a 3D material, it also makes it possible to study 2D physics with easy-to-make 3D crystals.

“Rhenium disulfide remains a direct-bandgap semiconductor, its photoluminescence intensity increases while its Raman spectrum remains unchanged, even with the addition of increasing numbers of layers,” says Junqiao Wu, a physicist with Berkeley Lab’s Materials Sciences Division who led this discovery. “This makes bulk crystals of rhenium disulfide an ideal platform for probing 2D excitonic and lattice physics, circumventing the challenge of preparing large-area, single-crystal monolayers.”

Wu, who is also a professor with the University of California-Berkeley’s Department of Materials Science and Engineering, headed a large international team of collaborators who used the facilities at the Molecular Foundry, a U.S Department of Energy (DOE) national nanoscience center, to prepare and characterize individual monolayers of rhenium disulfide. Through a variety of spectroscopy techniques, they studied these monolayers both as stacked multilayers and as bulk materials. Their study revealed that the uniqueness of rhenium disulfide stems from a disruption in its crystal lattice symmetry called a Peierls distortion.

“Semiconducting dichalcogenides consist of monolayers held together by weak forces,” says Sefaattin Tongay, lead author of a paper describing this research in Nature Communications for which Wu was the corresponding author. The paper was titled “Monolayer behaviour in bulk ReS2 due to electronic and vibrational decoupling.”

The atomic structure of a monolayer of rhenium disulphide shows the dimerization of the rhenium atoms as a result of the Peierls, forming a rhenium chain denoted by the red zigzag line. Credit: Junqiao Wu, Berkeley Lab

“Typically the monolayers in a semiconducting transition metal dichalcogenides, such as , are relatively strongly coupled, but isolated monolayers show large changes in electronic structure and lattice vibration energies,” Tongay says. “The result is that in bulk these materials are indirect gap semiconductors and in the monolayer they are direct gap.”

What Tongay, Wu and their collaborators found in their characterization studies was that rhenium disulfide contains seven valence electrons as opposed to the six valence electrons of molybdenum disulfide and other transition metal dichalcogenides. This extra valence electron prevents strong interlayer coupling between multiple of rhenium disulfide.

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“The extra electron is eventually shared between two rhenium atoms, which causes the atoms to move closer to one another other, forming quasi-one-dimensional chains within each layer and creating the Peierls distortion in the lattice,” Tongay says. “Once the Peierls distortion takes place, interlayer registry is largely lost, resulting in weak interlayer coupling and monolayer behavior in the bulk.”

Rhenium disulfide’s weak interlayer coupling should make this material highly useful in tribology and other low-friction applications. Since rhenium disulfide also exhibits strong interactions between light and matter that are typical of monolayer semiconductors, and since the bulk rhenium disulfide behaves as if it were a monolayer, the new material should also be valuable for solar cell applications. It might also be a less expensive alternative to diamond for valleytronics.

In valleytronics, the wave quantum number of the electron in a crystalline material is used to encode information. This number is derived from the spin and momentum of an electron moving through a crystal lattice as a wave with energy peaks and valleys. Encoding information when the electrons reside in these minimum energy valleys offers a highly promising potential new route to quantum computing and ultrafast data-processing.

“Rhenium atoms have a relatively large atomic weight, which means electron spin-orbit interactions are significant,” Tongay says. “This could make rhenium disulfide an ideal material for valleytronics applications.”

The collaboration is now looking at ways to tune the properties of rhenium disulfide in both monolayer and bulk crystals through engineered defects in the lattice and selective doping. They are also looking to alloy disulfide with other members of the dichalcogenide family.

Pentagon developing combat chewing gum .


Reuters/Andrew Burton

Maintaining good dental health may not seem like it’d be a top priority for soldiers, but the US military is hard at work developing a new kind of chewing gum that can battle cavities.

Simply dubbed “Combat Gum,” the new product is currently under development at the Army Institute of Surgical Research. Featuring a synthetic collection of anti-microbial peptide – the same naturally-occurring molecules in human saliva that kill bacteria – the gum can potentially help reduce plaque and tooth decay, as well as prevent cavities.

The gum has been in development for roughly seven years, and after that much time and up to $12 million spent, the New Yorker is reporting it’s finally entered a testing phase that will last throughout the year. Not many people have tried the gum so far, but according to Domenick Zero, the director of the Indiana University School of Dentistry’s Oral Health Research Institute, the first set of human trials has been completed and “everything is going well.”

Although Zero mentioned “this is not intended to replace tooth brushing,” he told the New Yorker that the gum could reinforce the mouth’s resistance and “prevent pathogens from colonizing our skin, or our mouths, or our defenses.”

Still, if the Combat Gum is effective, at $2 a piece it could potentially save the military a significant amount of cash. The armed forces spend more than $100 million every year on dental procedures, some of which require shouldering the burden of transporting a soldier to another continent for emergency services. According to Colonel Robert Hale, the commander of the Army’s Dental and Trauma Research Detachment, 40 percent of recruits have at least three cavities.

“Oral health is essential to warriors on the battlefield and could potentially save the military countless hours and dollars in dental health,” he told the Army Times in a January report. “[And] it would save a lifetime of dental disease for a significant population.”

Originally intended for soldiers serving in territories lacking water, the Army is now looking to give the gum to those it considers to be high-risk soldiers, who make up 15 percent of all troops. That includes those with multiple cavities and anyone with decaying teeth.

Beyond that, however, there are also preliminary plans to bring the product to the consumer market, much like nicotine gum.

“If we can develop an anti-plaque chewing gum and offer it to a company like, I don’t know, Wrigley’s, and distribute that to the general population, then those kids will come and join the Armed Forces with less dental decay issues,” Hale said.

The Human Nose Can Distinguish Between One Trillion Different Smells | Science | Smithsonian


New research says our olfactory system is far more sensitive than we thought

You may have heard this one before: Humans, especially compared to animals such as dogs, have a remarkably weak sense of smell. Over and over again, it’s reported that we can only distinguish between about 10,000 different scents—a large number, but one that’s easily dwarfed by that of dogs, estimated to have a sense of smell that’s 1,000 to 10,000 times more sensitive than ours.

It may be indisputable that dogs do have a superior sense of smell, but new research suggests that our own isn’t too shabby either. And it turns out that the “10,000 different scents” figure, concocted in the 1920s, was a theoretical estimate, not based on any hard data.

When a group of researchers from the Rockefeller University sought to rigorously figure out for the first time how many scents we can distinguish, they showed the 1920s figure to be a dramatic underestimate. In a study published today in Science, they show that—at least among the 26 participants in their study—the human nose is actually capable of distinguishing between something on the order of a trillion different scents.

“The message here is that we have more sensitivity in our sense of smell than for which we give ourselves credit,” Andreas Keller, an olfactory researcher at Rockefeller and lead author of the study, said in a press statement. “We just don’t pay attention to it and don’t use it in everyday life.”

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Vials of odors used by the researchers to test participants’ sense of smell. (Photo by Zach Veilleux / The Rockefeller University)

A big part of the reason it took so long to accurately gauge our scent sensitivity is that it’s much more difficult to do so than, say, test the range of wavelengths of light the human eye can perceive, or the range of soundwaves the human ear can hear. But the researchers had a hunch that the real number was far greater than 10,000, because it was previously documented that humans have upwards of 400 different smell receptors which work in concert. For comparison, the three light receptors in the human eye allow us to see an estimated 10 million colors.

Noting that the vast majority of real-world scents are the result of many molecules mixed together—the smell of a rose, for instance, is the result of 275 unique molecules in combination—the researchers developed a method to test their hunch. They worked with a diverse set of 128 different molecules that act as odorants, mixing them in unique combinations. Although many familiar scents—such as orange, anise and spearmint—are the results of molecules used in the study, the odorants were deliberately mixed to produce unfamiliar smells (combinations that were often, the researchers note, rather “nasty and weird”).

By mixing either 10, 20 or 30 different types of molecules together in varying concentrations, the researchers could theoretically produce trillions of different scents to test on the participants. Of course, given the impracticality of asking people to stand around and sniff trillions of small glass tubes, the researchers had to come up with an expedited method.

They did so by using the same principles that political pollsters use when they call a representative sample of voters and use their responses to extrapolate to the general population. In this case, the researchers sought to determine how different two vials had to be—in terms of the percentage of different odorant molecules between them—for participants to generally tell them apart at levels greater than chance.

Then the work began: For each test, a volunteer was given three vials—two with identical substances, and one with a different mixture—and asked to identify the outlier. Each participant was exposed to about 500 different odorant combinations, and in total, a few thousand scents were sniffed.

After analyzing the test subjects’ success rates in picking the odd ones out, the authors determined that, on average, two vials had to contain at least 49 percent different odorant molecules for them to be reliably distinguished. To put this in more impressive words, two vials could be 51 percent identical, and the participants were still able to tell them apart.

Extrapolating this to the total amount of combinations possible, merely given the 128 molecules used in the experiment, indicated that the participants were able to distinguish between at least a trillion different scent combinations. The real total is probably much higher, the researchers say, because of the many more molecules that exist in the real world.

For a team of scientists that have devoted their careers to the oft-overlooked power of olfaction, this finding smells like sweet vindication. As co-author Leslie Vosshall put it, “I hope our paper will overturn this terrible reputation that humans have for not being good smellers.”

Surprised scientists find deadly Florida pythons have internal GPS.


Researchers studying a species that has invaded Florida’s Everglades made an unanticipated discovery

A California man's home was full of pythons packed tightly in plastic bins, police have said.
Each snake was fitted with a radio tracker and its position monitored by GPS one to three times per week. Photograph: Wayne Lynch/Getty Images /All Canada Photos

They are Florida’s deadliest and most unwelcome visitors, blamed for a massive decades-long decline in the population of native species in the Everglades wetlands even as their own numbers expand at an uncontrollable rate.

Now researchers have discovered one more tool in the Burmese python’s kit of survival mechanisms – a previously unknown homing instinct that enables the giant snakes to travel great distances at speed, right back to any particular spot where the hunting was good.

“We found that Burmese pythons have navigational map and compass senses,” said Shannon Pitman of North Carolina’s Davidson College, the lead researcher of a team of scientists that released six captured snakes back into the wild, then tracked them through the Everglades National Park for up to nine months.

“It wasn’t what we expected. We thought we’d see a kind of aimless, wandering behaviour, but the pythons made their way pretty quickly back to where to where they were captured. It was more sophisticated in terms of movement than we’ve seen in other species of snake.”

What makes the discovery more remarkable is that it was completely accidental. Pitman’s team originally wanted to release the snakes closer to their capture points within the Everglades, as they were more interested in studying the habitat through which they were moving than the actual distances they travelled.

But wildlife officials, whose efforts to eradicate or contain the up to 100,000 non-native snakes estimated to have spread through the park’s 1.5m acres, refused permission.

That led to the team releasing the snakes at more remote locations between 13 and 23 miles away, outside the National Park’s boundaries, and then watching in amazement as one python after another made its way back “home”.

Each snake was fitted with a radio tracker and its position monitored by GPS one to three times per week. All six moved in a near-straight line towards their capture points and five ended up within a couple of miles. The snake with the longest journey took nine months to reach its destination.

Recent studies have exposed the devastating impact pythons have had on native species in the Everglades. In 2012, a National Parks report described the decline in mammal populations in the wetlands as “severe and dramatic”, with marsh rabbits and foxes having completely vanished, along with 99% of the area’s raccoons, in the time since the pythons gained a foothold. Two years earlier, researchers found 25 different bird species, including the endangered wood stork, in the digestive tracts of several snakes.

The Florida Fish and Wildlife Commission (FWC) believes the first pythons, which can grow up to 5.2 metres (17 feet) in length, were probably released into the Everglades as exotic pets that grew too big for their owners, or escaped into the wild from homes or pet shops when Hurricane Andrew devastated a large area of South Florida in 1992. Since then, the agency has been fighting a losing battle to control their numbers.

A well-publicised public “bounty hunt” last year attracted about 1,500 keen hunters but resulted in the capture of only 68 pythons, and FWC has no immediate plans to repeat the exercise, spokesperson Carli Segelson said.

Instead, eradication and control efforts have included an exotic pet amnesty, which has seen 70 Burmese pythons turned in since 2006; the Python Patrol, an educational programme for anyone working in or near the Everglades about how to identify and humanely remove the creatures; an exotic species hotline and those with hunting licences being encouraged to visit a handful of wildlife management areas where pythons are known to be prevalent.

“Pythons are well camouflaged and notoriously difficult to find, so it’s hard to estimate their numbers,” Segelson said. “Any research that helps us better understand them is beneficial.”

Pitman, one of eight scientists who worked on the study, said more research was needed. “It’s impossible to draw a straight line from this to a new management strategy but we hope more information can lead to better efforts to eradicate them,” she said.

Stool DNA Test Beats Existing Noninvasive Screen for Colorectal Cancer


In a side-by-side comparison, a noninvasive, multitarget stool DNA test proved to be more sensitive than a fecal immunochemical test (FIT). This result, published March 19 in the New England Journal of Medicine, suggests that the DNA test, which includes quantitative molecular assays for genetic abnormalities related to cancer, could significantly improve the effectiveness of colon cancer screening.

The FIT test detects hidden blood in the stool, a potential signal for cancer. In contrast, the DNA test includes quantitative molecular assays for KRAS mutations, aberrant NDRG4 and BMP3 methylation, and β-actin, plus a hemoglobin immunoassay.

The effectiveness of the DNA test was established in a study that evaluated nearly 10,000 asymptomatic patients who were deemed to be at average risk of developing colorectal cancer. It turned out that 65 (0.7%) of these patients had colorectal cancer, and 757 (7.6%) had advanced precancerous lesions. When these patients were screened, the study determined that the sensitivity for detecting colorectal cancer was 92.3% with DNA testing and 73.8% with FIT.

The investigators who evaluated the DNA and FIT tests published their results in an article entitled “Multitarget Stool DNA Testing for Colorectal-Cancer Screening,” which indicated that “sensitivity is the most important characteristic for screening tests because the primary role of such testing is to rule out diseases such as cancer.”

Other results related to sensitivity were as follows: “The sensitivity for detecting advanced precancerous lesions was 42.4% with DNA testing and 23.8% with FIT. The rate of detection of polyps with high-grade dysplasia was 69.2% with DNA testing and 46.2% with FIT.”

The study added that although high sensitivity is the most important attribute of cancer-screening tests, specificity is also important, since it affects the number of persons who have positive test results, a majority of whom will have false-positive results because of the low prevalence of cancer: “The specificity of FIT (94.9 to 96.4%) was superior to that of the DNA test (86.6 to 89.8%), with false positive rates of 3.6 to 5.1% and 10.2 to 13.4%, respectively.”

The authors of the study represented Indiana University School of Medicine, the University of North Carolina, Icahn School of Medicine at Mount Sinai, Kaiser Permanente Medical Center, the Boston Biostatistics Research Foundation, Exact Sciences (which funded the study), and the Mayo Clinic.
One of the authors, David Ransohoff, M.D., professor of medicine at the University of North Carolina, said, “Detection of 92% of colon cancer is extremely high for a noninvasive test, so that a negative test result means that no further evaluation, like colonoscopy, is needed at that time. Having such a sensitive, noninvasive option could have an important effect on screening rates for colorectal cancer.”

The article was accompanied by an editorial entitled “Stool DNA and Colorectal-Cancer Screening.” It took note of the specificity issue and raised a couple of additional caveats: “First, the number of participants who were excluded from the study because of problems with sample collection or assay application was far greater in the stool DNA group. Given that colorectal cancer was detected in nearly 1 of 154 participants on colonoscopy, it is possible that four cancers would have been missed simply because of the complexity of the test. Second, this study compared only the one-time sensitivity of these two tests. Given the lower specificity and greater expense of stool DNA testing as compared with FIT, it is unlikely that the test would be performed annually in the way that FIT testing is recommended.”

Stool DNA Test Beats Existing Noninvasive Screen for Colorectal Cancer

Nonetheless, the editorial (by a pair of authors affiliated with the Veterans Administration) concluded that the “new multitarget stool DNA test is clearly an improvement over its predecessors, and the results of this study will help to inform the current effort of the U.S. Preventive Services Task Force to reevaluate screening tests.”

A press release issued by the Mayo Clinic emphasized the development of the DNA test, which is called Cologuard. “Cologuard detection rates of early-stage cancer and high-risk precancerous polyps validated in this large study were outstanding and have not been achieved by other noninvasive approaches,” said David Ahlquist, M.D., a Mayo Clinic gastroenterologist, co-inventor of the Cologuard test, and one of the study’s authors. “It is our hope that this accurate and user-friendly test will expand screening effectiveness and help curb colorectal cancer rates in much the same way as regular Pap smear screening has done for cervical cancer.”

Exact Sciences, the co-developer of Cologuard, is in the process of seeking approval from the FDA for the use of the DNA test for colorectal cancer screening.