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MRI Fingerprinting: The 12-second scan that fingerprints tissues and diseases

MRI Fingerprinting: The 12-second scan that fingerprints tissues and diseases | Amazing Science | Scoop.it

Getting an MRI can be an uncomfortable experience, particularly for a 40-minute or longer scan. In the US at least, it is also quite expensive—the same kind of scan costing just over $100 in France, for example, would undoubtedly cost over $1,000 here. If the whole scan could be done in say, 12 seconds, the call to "make the patient the customer again" might be heard a little clearer. A new technique developed by a collaborative effort at Case Western University and Siemens, known as MRI Fingerprinting (MRF), promises to do just that.

While MRI is in principle a quantitative instrument, in practice, the results are typically best described as qualitative. If it were really quantitative, caregivers would probably discuss features of the scan more in terms of absolutes, ideally suffixed with appropriate units. Instead, we usually settle for the familiar, regions of hyper, or hypointensity to describe regions of anomaly.

 

MRF would be performed using the standard MRI hardware, but it draws on a set of new signal processing techniques falling under the rubric of compressive sampling. Engineers have been hammering out a novel approach to a broad class of problems arising in everything from telecommunications, to image acquisition and processing. Most recently in medicine, compressive sampling, or random sampling as it is sometimes called, has been applied to create high resolution endoscopic images.

 

To analogize how these new methods might actually work, let's imagine acquiring a natural image. It can be shown that if the image is acquired through a psuedo-random mask of sorts, much greater efficiency can generally be achieved. Intuitively we might expect that if the first 300 pixels of a seascape, for example, are all highly correlated blue sky, perhaps structuring the pixel acquisition in some other way could be more efficient.

 

The metaphor is obviously a simplification, but the key for MRF is rather than using rigidly defined and error-prone scans on the front end, all the data can be acquired up front using compressive sampling. Afterwards, pattern recognition techniques can be used in the post processing. While the fingerprint is not to be understood literally as a kind of DNA fingerprinting as used in forensic science, the process resembles matching a person's fingerprint to a database that can then draw up additional related information.

 

Following acquisition of the imaging data, a so-called "dictionary" containing the realistic range of standard MRI parameters (like relaxation times and off-resonance frequency) can be obtained with relatively modest computing resource. Other properties often obtained from MRI data such as diffusion and magnetization transfer can also be measured. These are the parameters behind the techniques now at our disposal for tracing the paths of axon tracts in the brain, in particular diffusion tractoctagraphy. The authors of the study conclude that in using MRF, the traditional imaging routine will be greatly simplified into an all-in-one scan. The dozens of parameters under operator control in current MRI machines could be replaced with a simple scan button, making MRI more routine, patient-friendly, and affordable.

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The List: 25 Up and Coming Gene Therapies

The List: 25 Up and Coming Gene Therapies | Amazing Science | Scoop.it
 

Gene therapy’s numbers look promising. In a year full of biopharmaceutical mergers and acquisitions, one of the biggest deals has been Novartis’ planned $8.7 billion purchase of AveXis, whose lead candidate AVXS-101 has advanced into a pivotal trial following positive Phase I data published in November inThe New England Journal of Medicine.

 

Additional figures by Informa show the extent of gene-therapy development: Informa Pharma Intelligence’s Trialtrove database records 729 gene therapies as having been developed, of which nearly two-thirds (461) were preclinical. Those therapies have been assessed in 1,855 clinical trials, most in early phases: 657 in Phase I, 509 in Phase I/II, and 455 in Phase II. As for later development, 89 have reached Phase III, 32 are in Phase II/III, and 28 in Phase IV.

By far the most crowded therapeutic area is oncology, accounting for two-thirds or 1,254 of the 1,855 trials. The next-largest indication is cardiovascular with 214 trials (11.5%), followed by infectious disease (6.5%).

 

Clinical activity is expected to increase, in part due to the FDA’s Regenerative Medicine Advanced Therapy (RMAT) designation, created through the 21st Century Cures Act. “There are a lot of incentives for sponsors who get RMAT, including early and frequent interactions with the FDA, as well as the ability to discuss early on any potential surrogate or intermediate endpoints in their clinical trials,” Amanda Micklus, principal analyst with Informa Pharma Intelligence, told GEN. “The RMAT designation potentially could really advance the progress of these therapies through the pipeline.”


Via Krishan Maggon
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Hide Nessie Hide: Genome Scientists Hunt for DNA Traces of the Loch Ness Monster

Hide Nessie Hide: Genome Scientists Hunt for DNA Traces of the Loch Ness Monster | Amazing Science | Scoop.it

 

 

The idea of a large lake monster living in Scotland’s Loch Ness has fascinated people for decades. But no concrete evidence has ever been found for “Nessie”’s existence. Could a plesiosaur be hiding in the depth of the lake?

 

Now, an international team of scientists led by Neil Gemmell from the University of Otago, New Zealand, will conduct an investigation into the waters of the famous loch which could help settle the mystery once and for all. The scientists will sample the water using so-called environmental DNA (eDNA), which will enable them to identify tiny remnants of genetic material left behind by any life in the loch. This technique will allow them to create a detailed list of all the organisms living in the waters and determine whether anything unusual—a larger marine monster, for example—resides there.

 

Gemmell maintains that finding traces of such an animal would be extremely unlikely, but he is nevertheless intrigued by what his team might find.

 

"Large fish, like catfish and sturgeons, have been suggested as possible explanations for the monster myth, and we can very much test that idea and others," he said in a statement. Looking for traces of a mythological monster is not the only goal of the upcoming research, though.

 

"While the prospect of looking for evidence of the Loch Ness monster is the hook to this project, there is an extraordinary amount of new knowledge that we will gain from the work about organisms that inhabit Loch Ness, the U.K.'s largest freshwater body,” Gemmell said.

 

The project will help researchers to understand more about both native and invasive species in the loch, such as the Pacific pink salmon. Gemmell predicted that the team would uncover never-before-documented species, bacteria in particular.

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Temperature-controlled turtle sex gene found – it is Kdm6b

Temperature-controlled turtle sex gene found – it is Kdm6b | Amazing Science | Scoop.it
Scientists have isolated the gene responsible for temperature-controlled sex determination in turtles.

 

Red-eared slider turtles, a common household pet, develop into male or female embryos according to their egg incubation temperature. This little understood process is also at work in the eggs of crocodiles, alligators and some lizards. Researchers are now one step closer to solving a mystery which has persisted for over 50 years.

 

An international team from China and the United States used a recently refined process to "knock out" the gene they suspected to be responsible for sex determination in the turtles - known as Kdm6b.

 

"Knockouts come in several flavors," explained Prof Blanche Capel from Duke University, an author on the study. "It usually means a genetic manipulation that deletes a gene from the genome or blocks its function." With Kdm6b blocked, over 80% of turtles incubated at the (usually male-producing) temperature of 26C shifted their development to female. Females usually only develop when eggs are incubated at 32C.

 

Dr Nicole Valenzuela from Iowa State University, who was not involved in the study, noted that the findings confirmed earlier predictions that such genes "are themselves turned on at a temperature that produces one sex and turned off at a temperature that produces the opposite sex".

Uncertain future

Other recent studies have suggested that rising temperatures due to climate change could be causing a female skew in turtle populations in the wild.Hatchling mortality could also increase if nests remain at high temperatures for long periods of time.Prof Capel points out that "if you're incubating at low temperature, males take almost twice as long to incubate as females."

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Machine Learning in Robotics - 5 Modern Applications

Machine Learning in Robotics - 5 Modern Applications | Amazing Science | Scoop.it

As the term “machine learning” has heated up, interest in “robotics” (as expressed in Google Trends) has not altered much over the last three years. So how much of a place is there for machine learning in robotics?

 

Most robots are not, and will likely not, be humanoids 10 years from now; as robots are designed for a range of behaviors in a plethora of environments, their bodies and physical abilities will reflect a best fit for those characteristics. An exception will likely be robots that provide medical or other care or companionship for humans, and perhaps service robots that are meant to establish a more personal and ‘humanized’ relationship.

 

Like many innovative technological fields today, robotics has and is being influenced and in some directions steered by machine learning technologies. According to a recent survey published by the Evans Data Corporation Global Development, machine learning and robotics is at the top of developers’ priorities for 2016, with 56.4 percent of participants stating that they’re building robotics apps and 24.7 percent of all developers indicating the use of machine learning in their projects.

 

The following overview of machine learning applications in robotics highlights five key areas where machine learning has had a significant impact on robotic technologies, both at present and in the development stages for future uses. Though by no means inclusive, the purpose of the summary is to give readers a taste for the types of machine learning applications that exist in robotics and stimulate the desire for further research in these and other areas.

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How Artificial Intelligence Can Detect, Create and Fake News

How Artificial Intelligence Can Detect, Create and Fake News | Amazing Science | Scoop.it

When Mark Zuckerberg told Congress that Facebook would use artificial intelligence to detect fake news posted on the social media site, he wasn’t particularly specific about what that meant. Given my own work using image and video analytics, I suggest the company should be careful. Despite some basic potential flaws, AI can be a useful tool for spotting online propaganda — but it can also be startlingly good at creating misleading material.

 

Researchers already know that online fake news spreads much more quickly and more widely than real news. My research has similarly found that online posts withfake medical information get more views, comments, and likes than those with accurate medical content. In an online world where viewers have limited attention and are saturated with content choices, it often appears as though fake information is more appealing or engaging to viewers.

 

The problem is getting worse: By 2022, people in developed economies could be encountering more fake news than real information. This could bring about a phenomenon that researchers have dubbed “reality vertigo” — in which computers can generate such convincing content that regular people may have a hard time figuring out what’s true anymore.

 

Machine learning algorithms, one type of AI, have been successful for decades fighting spam email, by analyzing messages’ text and determining how likely it is that a particular message is a real communication from an actual person or a mass-distributed solicitation for pharmaceuticals or claim of a long-lost fortune.

 

Building on this type of text analysis in spam-fighting, AI systems can evaluate how well a post’s text, or a headline, compares with the actual content of an article someone is sharing online. Another method could examine similar articles to see whether other news media have differing facts. Similar systems can identify specific accounts and source websites that spread fake news.

 

However, those methods assume the people who spread fake news don’t change their approaches. They often shift tactics, manipulating the content of fake posts in efforts to make them look more authentic.

 

Using AI to evaluate information can also expose and amplify certain biases in society. This can relate to gender, racial background, or neighborhood stereotypes. It can even have political consequences, potentially restricting expression of particular viewpoints. For example, YouTube has cut off advertising from certain types of video channels, costing their creators money.

 

Context is also key. Words’ meanings can change over time. And the same word can mean different things on liberal sites and conservative ones. For example, a post with the terms “WikiLeaks” and “DNC” on a more liberal site could be more likely to be news while on a conservative site it could refer to a particular set of conspiracy theories.

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AI's deep impact: why learning from massive data sets will fuel a fourth industrial revolution

AI's deep impact: why learning from massive data sets will fuel a fourth industrial revolution | Amazing Science | Scoop.it

Deep inside a cloud data center, a cluster of computers compares a critically-ill patient's symptoms, lab results, and medical history against a vast data set gleaned from thousands of medical journals and patient records. In seconds, the cluster produces a life-saving diagnosis that might have taken doctors and specialists weeks to figure out — too late for the patient with the mystery illness.

 

Such a feat would have been inconceivable not so long ago; but thanks to progress in the field of machine learning, this kind of capability is approaching reality, as advances like cloud computing provide both ready access to vast data sets and the compute power that machine-learning algorithms need to crunch them. For instance, algorithms trained on hundreds of thousands of medical images are already spotting some types of cancer in less than a second, while others detect heart conditions and lung cancers. Still another AI-based system, highlighted by Scientific American, crowdsources opinions from thousands of physicians so that machine learning algorithms can improve the diagnostic accuracy of individual doctors.


Behind all this is the recent resurgence in AI's capabilities thanks to advances in the speed of graphics processing units (GPUs), a type of microprocessor normally used for image processing that, it turns out, is  great for building massively-parallel neural networks. When installed in data center computers, these GPUs allow AI algorithms to run in the cloud — democratizing AI and making it available to all, even from smartphones.  The neural networks let deep machine learning (ML) algorithms recognize and learn from previously indiscernible patterns in data sets too large for humans to cope with. It's this powerful combination of cloud-based GPUs and deep learning networks that, after many false starts over the decades, is finally allowing AI to take off big time.

 

Diagnosing diseases with the same ease as Netflix recommends movies, or Amazon's Alexa answers a question, is only one arena in which AI's effects will be felt. A dizzying array of industries are going to be hugely impacted by AI, from agriculture to hospitality, retail, manufacturing, aviation, shipping, automotive, energy, finance, and logistics.

 

Fueling AI's rise are a clutch of key technologies that are on the march at the same time: big data, global connectivity, robotics, the Internet of Things and cloud computing. These will help amplify the impact of AI and ML and produce what Klaus Schwab, founder of the World Economic Forum, is calling the Fourth Industrial Revolution.  Following the steam-driven mechanical revolution of James Watt, the electrical revolution of Thomas Edison and Nikola Tesla, and the digital revolution of Alan Turing and John von Neumann, the fourth will bring about a transformation based on machines that appear to mimic human thinking.

 

This begs the question: What will human-competitive, or cognitive, machines mean for our futures — and, in particular, for human employment — in coming decades? Well, there are some useful clues in those previous industrial revolutions, says the London-based business consultancy Deloitte. In a novel type of study, the firm analyzed the job roles people admitted to working in in every British census since 1871. While they found that, as expected, technology eliminated some jobs — such as weavers replaced by automated looms, and telephone operators supplanted by automatic phone exchanges — they found that, over time, new technologies generated far more jobs than they destroyed.

 

"The last 144 years demonstrate that when a machine replaces a human, the result, paradoxically, is faster growth and, in time, rising employment," states Deloitte in a summary of its report. 

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ChroMorphous fabric can change its color on demand

ChroMorphous fabric can change its color on demand | Amazing Science | Scoop.it

Fashion and textiles may be among the last places you’d expect to see innovation. But college researchers in Florida have figured out a revolutionary fabric that can alter its color with a mild change in temperature.

 

Now fashion designers will be able to modify your handbag or scarf to match the rest of your outfit, thanks to a new fabric dubbed ChroMorphous.

 

Dr. Ayman Abouraddy, professor of optics and photonics at the College of Optics & Photonics at the University of Central Florida (CREOL), said in an interview with VentureBeat that the age of user-controlled color-changing fabric is here. “Our goal is to bring this technology to the market to make an impact on the textile industry,” he said.

 

With ChroMorphous, each woven thread is equipped with a micro-wire and a color-altering pigment. You can use your smartphone to change the color or pattern of the fabric on demand, as the wire can alter the temperature of the fabric in a quick and uniform way. The change in temperature is barely noticeable by touch, Abouraddy said.

 

Abouraddy and Josh Kaufman worked on optical technology for more than a decade at CREOL, but in the past couple of years they have veered away from that work to produce this new kind of fabric.

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Scientists Find ‘Fastest-Growing’ Supermassive Black Hole Known in the Universe

Scientists Find ‘Fastest-Growing’ Supermassive Black Hole Known in the Universe | Amazing Science | Scoop.it

A supermassive black hole in the center of the ultra-luminous quasar SMSS J215728.21-360215.1 (J2157-3602 for short) devours a mass equivalent to our Sun every two days and has a total mass of roughly about 20 billion solar masses, according to new research.

 

The newly-discovered black hole, which is located approximately 12.5 billion light-years from Earth, is growing so rapidly that it’s shining thousands of times more brightly than an entire galaxy, due to all of the gases it sucks in daily that cause lots of friction and heat. The image from the VISTA Hemispheric Survey shows the ultra-luminous quasar SMSS J215728.21-360215.1 (center). Image credit: Wolf et al.

 

“If we had this monster sitting at the center of our Milky Way Galaxy, it would appear 10 times brighter than a full moon,” said lead author Dr. Christian Wolf, from the Research School of Astronomy and Astrophysics at the Australian National University (ANU) and the ARC Centre of Excellence for All-sky Astrophysics (CAASTRO). “It would appear as an incredibly bright pin-point star that would almost wash out all of the stars in the sky. The energy emitted from this supermassive black hole was mostly UV light, but also radiated X-rays. Again, if this monster was at the center of the Milky Way it would likely make life on Earth impossible with the huge amounts of X-rays emanating from it.”

 

The J2157-3602 black hole was found by combining data from the recent Gaia data release 2 with data from the SkyMapper telescope at the ANU Siding Spring Observatory and NASA’s Wide-field Infrared Survey Explorer (WISE). “Large and rapidly-growing black holes are exceedingly rare, and we have been searching for them with SkyMapper for several months now,” Dr. Wolf said. “ESA’s Gaia satellite, which measures tiny motions of celestial objects, helped us find this supermassive black hole.”

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NASA’s Neutron Star Interior Composition Explorer Finds Pulsar in Ultracompact Orbit

NASA’s Neutron Star Interior Composition Explorer Finds Pulsar in Ultracompact Orbit | Amazing Science | Scoop.it

Astronomers using NASA’s Neutron star Interior Composition Explorer(NICER) have found evidence that an accreting millisecond X-ray pulsar called IGR J17062–6143 (J17062 for short) resides in an ultracompact binary system. In this system, J17062 and its companion white dwarf star orbit the common center of mass in only 38 minutes.

 

J17062, also classified as SWIFT J1706.6−6146, is about 16,300 light-years from Earth. The white dwarf star in the system is a ‘lightweight,’ only around 1.5% of our Sun’s mass. The pulsar is much heavier, around 1.4 solar masses.

 

The data from NICER show that J17062’s stars revolve around each other in a circular orbit, which is common for accreting millisecond X-ray pulsars.  The stars are only about 186,000 miles (300,000 km) apart, less than the distance between Earth and the Moon. “The distance between us and the pulsar is not constant. It’s varying by this orbital motion,” said team leader Dr. Tod Strohmayer, an astrophysicist at NASA’s Goddard Space Flight Center. "When the pulsar is closer, the X-ray emission takes a little less time to reach us than when it’s further away. This time delay is small, only about 8 milliseconds for J17062’s orbit, but it’s well within the capabilities of a sensitive pulsar machine like NICER.”

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Images of 3D objects appear on nanostructured surface

Images of 3D objects appear on nanostructured surface | Amazing Science | Scoop.it

A new nanostructured flat surface that appears like a 3D object – complete with realistic light shading and shadows – has been developed by Alexander Minovich, Anatoly Zayats and colleagues at Kings College London and the Rheinische Friedrich-Wilhelms-Universität Bonn. The optical illusion relies on a computer-graphics technique called “normal mapping”, which creates 3D objects with realistic lighting effects on a 2D display. The surface comprises a gold film 180 nm thick that is covered with a 105 nm layer of magnesium fluoride. Squat rectangular pillars of gold 30 nm tall are arranged in an array on the surface of the magnesium fluoride, which acts as a transparent spacer between the gold film and the pillars.

Shadow and contrast

Normal mapping was then used to compute the orientation of each pillar so that light reflecting from the surface appears as a cube (see figure). What is more, when the surface is illuminated or viewed from different angles, the cube appears to have the appropriate shadow and contrast.

 

Potential applications of the surface include optical security features on banknotes and other objects prone to counterfeiting. “The normal mapping demonstrated with our metasurface is a completely new concept, but it could have very important implications for a wide range of optical industries, both in introducing new functionality and making products smaller and lighter,” says Minovich.

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FontCode: Hiding information in plain text, unobtrusively and across file types

FontCode: Hiding information in plain text, unobtrusively and across file types | Amazing Science | Scoop.it

Computer scientists at Columbia Engineering have invented FontCode, a new way to embed hidden information in ordinary text by imperceptibly changing, or perturbing, the shapes of fonts in text. FontCode creates font perturbations, using them to encode a message that can later be decoded to recover the message. The method works with most fonts and, unlike other text and document methods that hide embedded information, works with most document types, even maintaining the hidden information when the document is printed on paper or converted to another file type. The paper will be presented at SIGGRAPH in Vancouver, British Columbia, August 12-16.

 

"While there are obvious applications for espionage, we think FontCode has even more practical uses for companies wanting to prevent document tampering or protect copyrights, and for retailers and artists wanting to embed QR codes and other metadata without altering the look or layout of a document," says Changxi Zheng, associate professor of computer science and the paper's senior author.

 

Zheng created FontCode with his students Chang Xiao (PhD student) and Cheng Zhang MS'17 (now a PhD student at UC Irvine) as a text steganographic method that can embed text, metadata, a URL, or a digital signature into a text document or image, whether it's digitally stored or printed on paper. It works with common font families, such as Times Roman, Helvetica, and Calibri, and is compatible with most word processing programs, including Word and FrameMaker, as well as image-editing and drawing programs, such as Photoshop and Illustrator. Since each letter can be perturbed, the amount of information conveyed secretly is limited only by the length of the regular text. Information is encoded using minute font perturbations -- changing the stroke width, adjusting the height of ascenders and descenders, or tightening or loosening the curves in serifs and the bowls of letters like o, p, and b.

 

"Changing any letter, punctuation mark, or symbol into a slightly different form allows you to change the meaning of the document," says Xiao, the paper's lead author. "This hidden information, though not visible to humans, is machine-readable just as barcodes and QR codes are instantly readable by computers. However, unlike barcodes and QR codes, FontCode doesn't mar the visual aesthetics of the printed material, and its presence can remain secret."

 

Data hidden using FontCode can be extremely difficult to detect. Even if an attacker detects font changes between two texts -- highly unlikely given the subtlety of the perturbations -- it simply isn't practical to scan every file going and coming within a company.

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Could a Multiverse be hospitable to life? - Durham University

Could a Multiverse be hospitable to life? - Durham University | Amazing Science | Scoop.it

A Multiverse – where our Universe is only one of many – might not be as inhospitable to life as previously thought, according to new research. Questions about whether other universes might exist as part of a larger Multiverse, and if they could harbor life, are burning issues in modern cosmology.

 

Now new research led by Durham University, UK, and Australia’s University of Sydney, Western Sydney University and the University of Western Australia, has shown that life could potentially be common throughout the Multiverse, if it exists. The key to this, the researchers say, is dark energy, a mysterious “force” that is accelerating the expansion of the Universe.

 

Multiverse theory

Scientists say that current theories of the origin of the Universe predict much more dark energy in our Universe than is observed. Adding larger amounts would cause such a rapid expansion that it would dilute matter before any stars, planets or life could form.

The Multiverse theory, introduced in the 1980s, can explain the “luckily small” amount of dark energy in our Universe that enabled it to host life, among many universes that could not.

 

Using huge computer simulations of the cosmos, the new research has found that adding dark energy, up to a few hundred times the amount observed in our Universe, would actually have a modest impact upon star and planet formation. This opens up the prospect that life could be possible throughout a wider range of other universes, if they exist, the researchers said.

 

The findings are published in two related papers in the journal Monthly Notices of the Royal Astronomical Society. The Durham University led paper can be read here and the University of Sydney led paper is here.

 

The simulations were produced under the EAGLE (Evolution and Assembly of GaLaxies and their Environments)project - one of the most realistic simulations of the observed Universe.

 

Star formation

Jaime Salcido, a postgraduate student in Durham University’s Institute for Computational Cosmology, said: “For many physicists, the unexplained but seemingly special amount of dark energy in our Universe is a frustrating puzzle. “Our simulations show that even if there was much more dark energy or even very little in the Universe then it would only have a minimal effect on star and planet formation, raising the prospect that life could exist throughout the Multiverse.”

 

Dr Luke Barnes, a John Templeton Research Fellow at Western Sydney University, said: “The Multiverse was previously thought to explain the observed value of dark energy as a lottery - we have a lucky ticket and live in the Universe that forms beautiful galaxies which permit life as we know it. Our work shows that our ticket seems a little too lucky, so to speak. It’s more special than it needs to be for life. This is a problem for the Multiverse; a puzzle remains.”

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Physicists present new method: 3-D images of cancer cells within the body

Physicists present new method: 3-D images of cancer cells within the body | Amazing Science | Scoop.it

Medical physicists at Martin Luther University Halle-Wittenberg (MLU) have developed a new method that can generate detailed three-dimensional images of the body's interior. These can be used to more closely investigate the development of cancer cells. The research group published its findings in Communication Physics.

 

Clinicians and scientists seek to better understand cancer cells and their properties in order to provide targeted cancer treatment. Individual cancer cells are often examined in test tubes before the findings are tested in living organisms. "Our aim is to visualise cancer cells inside the living body to find out how they function, how they spread and how they react to new therapies," says medical physicist Professor Jan Laufer from MLU. He specializes in the field of photoacoustic imaging, a process that uses ultrasound waves generated by laser beams to produce high-resolution, three-dimensional images of the body's interior.

 

"The problem is that tumur cells are transparent. This makes it difficult to use optical methods to examine tumors in the body," explains Laufer, whose research group has developed a new method to solve this problem. First, the scientists introduce a specific gene into the genome of the cancer cells.  "Once inside the cells, the gene produces a phytochrome protein, which originates from plants and bacteria. There it serves as a light sensor," Laufer says. In the next step, the researchers illuminate the tissue with short pulses of light at two different wavelengths using a laser. Inside the body, the light pulses are absorbed and converted into ultrasonic waves . These waves can then be measured outside the organism, and two images of the body's interior can be reconstructed based on this data.

 

"The special feature of phytochrome proteins is that they alter their structure and thus also their absorption properties, depending on the wavelength of the laser beams. This results in changes to the amplitude of the ultrasound waves that are generated in the tumor cells. None of the other tissue components, for example, blood vessels, have this property—their signal remains constant," Laufer says. By calculating the difference between the two images, a high-resolution, three-dimensional image of the tumor cells is created, which is free of the otherwise overwhelming background contrast.

 

The development of Halle's medical physicists can be applied to a wide range of applications in the preclinical research and the life sciences. In addition to cancer research, the method can be used to observe cellular and genetic processes in living organisms.



Read more at: https://phys.org/news/2018-05-d-images-cancer-cells-body.html#jCp


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Bird and Reptile DNA Sequences Used to Reconstruct Genome of Dinosaur Ancestor

Bird and Reptile DNA Sequences Used to Reconstruct Genome of Dinosaur Ancestor | Amazing Science | Scoop.it

Using genome sequences from present-day birds and reptiles, a research team has attempted to reconstruct the genome for an ancestral group of four-limbed amniotes known as diapsids from which birds, reptiles, and dinosaurs descended. 

The researchers brought together chromosome-level genome assemblies for four birds and reptiles, using bioinformatic analyses and new cytogenetic data to reconstruct ancestral genome organization patterns, adaptive genetic changes, and conserved sequences in the lineage with the help of evolutionary breakpoint region (EBR) and homologous synteny blocks (HSBs) gleaned from the extant genome data. With these data, the team was able to reach back some 260 million years, predicting the chromosome structure of the diapsid Eunotosaurus ancestor of birds, reptiles, dinosaurs, and pterosaurs. The findings are being published in Nature Communications.

 

"It is fascinating to see how the knowledge we collect about extant species' genomes coupled with smart computation technologies allow us to go back in time and learn about the genomes and biology of species that existed long before humans appeared and for which we would never have a biological sample," co-senior author Denis Larkin, a comparative biomedical sciences researcher at the University of London's Royal Veterinary College, said in a statement.

 

Building on a prior chromosomal reconstruction study based on half a dozen extant bird genomes, the team used a "multiple-genome rearrangement and analysis" (MGRA2) analytical tool to retrace karyotypic patterns in the diapsid ancestral genome using genome assemblies for the chicken, zebra finch, mallard, Carolina anole lizard, and the grey short-tailed opossum, which represents a mammalian outgroup. The search uncovered nearly 400 multi-species HSBs, making it possible to reconstruct 19 chromosome-like "contiguous ancestral regions" with MGRA2 analyses.

 

The researchers also evaluated genome assemblies for several other extant species such as the turkey, budgerigar, and ostrich, but did not include those genomes in their subsequent analyses due to sequence fragmentation or genome misassembly issues that cropped up when they assessed the genomes cytogenetically using fluorescence in situ hybridization.

 

In addition to the bioinformatic look at the genomes, the team used cross-species molecular cytogenetics approaches to profile and compare chromosomal patterns in the chicken, Caroline anole lizard, red-eared slider turtle, and spiny soft-shelled turtle. It also did pairwise genome alignments with the Evolution Highway chromosome browser to look at HSB positions across species.

 

Together, these data provided a peek at ancestral diapsid genomes, as well as the within- and between-chromosome rearrangements that occurred in the diverse dinosaur, reptile, and bird descendants of the diapsids.

 
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Doctors 'Grow' Ear for Transplant in Patient's Forearm

Doctors 'Grow' Ear for Transplant in Patient's Forearm | Amazing Science | Scoop.it

The procedure is rare, but could potentially help many more patients who experience similar bodily damage.

 

To successfully reconstruct a patient’s lost ear, Doctors at William Beaumont Army Medical Center in El Paso, Texas sculpted a new one from rib cartilage and implanted it under the tissues of the patient’s forearm to foster blood vessel growth.

 

The patient is Army private Shamika Burrage, who lost her ear in a car accident two years ago, reports Neel V. Patel for Popular Science. Burrage was returning from leave when her car’s front tire blew, sending the vehicle flipping across the road and ejecting her from her seat.

 

Burrage, now 21, spent several months in rehabilitation after the accident but sought counseling when she continued to suffer from insecurities about her appearance. “I didn’t feel comfortable with the way I looked so the provider referred me to plastic surgery,” Burrage says.

 

During the reconstruction process, surgeons reopened Burrage’s hearing canal to restore her hearing and implanted the vascularized ear in its rightful place. She will require two more surgeries to complete the process, but is currently faring well, according to a U.S. Army statement on the procedure.

 

“The whole goal is that by the time she’s done with all this, it looks good, it’s sensate, and in five years if somebody doesn’t know her they won’t notice,” says Lt. Col. Owen Johnson III, the chief of plastic and reconstructive surgery at the facility, in the statement.

 

Though a first for Army plastic surgeons, the procedure has long roots in medical practices, Patel reports. Since the early 20th century, doctors have reconstructed parts of ears in people suffering from congenital deformities using a technique that involves harvesting rib cartilage from the chest, sculpting it into the shape of and implanting it under the skin where the ear is normally placed.

 

As Patel writes, the second stage of the latest ear transplant, known as microvascular free tissue transfer, only became popular in the late 1990s. By stitching the implanted tissue to blood vessels, doctors can help it develop into “healthy, functioning tissue in a new area,” Patrick Byrne, the director of the Division of Facial Plastic and Reconstructive Surgery at Johns Hopkins University School of Medicine who pioneered this method, tells Patel.

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10 Breakthrough Technologies Making Promising Progress in 2018

10 Breakthrough Technologies Making Promising Progress in 2018 | Amazing Science | Scoop.it
Dueling neural networks. Artificial embryos. AI in the cloud. Welcome to our annual list of the 10 technology advances we think will shape the way we work and live now and for years to come.

 

Every year since 2001 the people at Technology Review have picked what they call the 10 Breakthrough Technologies. People often ask, what exactly is meant by “breakthrough”? It’s a reasonable question—some of the picks haven’t yet reached widespread use, while others may be on the cusp of becoming commercially available. What Technology Review is really looking for is a technology, or perhaps even a collection of technologies, that will have a profound effect on our lives.

 

For 2018, a new technique in artificial intelligence called GANs is giving machines imagination; artificial embryos, despite some thorny ethical constraints, are redefining how life can be created and are opening a research window into the early moments of a human life; and a pilot plant in the heart of Texas’s petrochemical industry is attempting to create completely clean power from natural gas—probably a major energy source for the foreseeable future.

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Google wants to push quantum computing mainstream with ‘Bristlecone’ chip

Google wants to push quantum computing mainstream with ‘Bristlecone’ chip | Amazing Science | Scoop.it

The goal of the Google Quantum AI lab is to build a quantum computer that can be used to solve real-world problems. This strategy is designed to explore near-term applications using systems that are forward compatible to a large-scale universal error-corrected quantum computer. In order for a quantum processor to be able to run algorithms beyond the scope of classical simulations, it requires not only a large number of qubits. Crucially, the processor must also have low error rates on readout and logical operations, such as single and two-qubit gates.

 

Google presented Bristlecone, their new quantum processor, at the annual American Physical Society meeting in Los Angeles (2018). The purpose of this gate-based superconducting system is to provide a testbed for research into system error rates and scalability of Google's qubit technology, as well as applications in quantum simulation, optimization, and machine learning.

 

Google states: "The guiding design principle for this device is to preserve the underlying physics of our previous 9-qubit linear array technology1, 2, which demonstrated low error rates for readout (1%), single-qubit gates (0.1%) and most importantly two-qubit gates (0.6%) as our best result. This device uses the same scheme for coupling, control, and readout, but is scaled to a square array of 72 qubits. We chose a device of this size to be able to demonstrate quantum supremacy in the future, investigate first and second order error-correction using the surface code, and to facilitate quantum algorithm development on actual hardware."

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This Nuclear Explosion Simulator Shows The Disaster Caused If Russia Dropped Another Tsar Bomb

This Nuclear Explosion Simulator Shows The Disaster Caused If Russia Dropped Another Tsar Bomb | Amazing Science | Scoop.it

There's a new nuclear simulator on the internet, and it's here to emphasize just how awful a 50,000KT blast would be.

 

For years, one of the more perversely interesting things on the internet has been Alex Wellerstein's NUKEMAP, which — true to its name — shows you the estimated damage if you dropped a nuclear weapon anywhere in the world. Now the Outrider Foundation has released its own, rather more elegant version, and we're back to blowing up our backyards. 

 

Outrider's simulator lets you enter any location and select from a number of bomb strengths, from the 15KT Little Boy (the first nuke used in war) to the 50,000KT Tsar Bomba, which Russia tested in 1961. The simulator estimates the number of casualties and describes what would happen within the various reaches of the blast (radiation, shock wave, etc). To illustrate, we dropped a 300KT W-87, which is a current part of the US nuclear arsenal. And while much of Brooklyn is destroyed, the damage stretches into lower Manhattan and across to New Jersey as well.

 

So that brings us to Tsar Bomba. If the USSR were to build another Tsar Bomba and detonated the 50,000KT behemoth over the Digg offices in lower Manhattan, how bad would that be? Reader, it would be extremely bad. The simulator estimates that Tsar Bomba would kill over 7.5 million people if it were detonated in an air burst over lower Manhattan, with the heat wave reaching well into New Jersey, Connecticut and Long Island.

 

You can play with the simulator here and pray that this remains a thought experiment forever.


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Gene-based test for urine detects, monitors bladder cancer

Gene-based test for urine detects, monitors bladder cancer | Amazing Science | Scoop.it
Researchers at The Johns Hopkins Kimmel Cancer Center have developed a test for urine, gathered during a routine procedure, to detect DNA mutations identified with urothelial cancers.

 

UroSEEK uses urine samples to seek out mutations in 11 genes or the presence of abnormal numbers of chromosomes that would indicate the presence of DNA associated with bladder cancer or upper tract urothelial cancer (UTUC). The researchers said the test, when combined with cytology, the gold standard noninvasive test currently used for detection, significantly enhanced early detection for patients who are considered at risk for bladder cancer and surveillance of patients who had already been treated for bladder cancer.

 

These findings were published online on March 20 in eLife.

"There were nearly 80,000 new cases of bladder cancer and more than 18,000 deaths in 2017," said George Netto, M.D., a senior author on the UroSEEK paper, formerly at The Johns Hopkins University and currently chair of pathology at the University of Alabama-Birmingham. "This is about using the urine to detect the cancer. UroSEEK is a method of detection that many people have tried to find that is noninvasive."

 

Most cancers are curable if they are detected early, and the researchers are exploring ways to use cancer gene discoveries to develop cancer screening tests to improve cancer survival. They announced the development of CancerSEEK, a single blood test that screens for eight cancer types, and PapSEEK, a test that uses cervical fluid samples to screen for endometrial and ovarian cancers.

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Non-Human Animals Can Mentally Replay Past Events, Study Finds

Non-Human Animals Can Mentally Replay Past Events, Study Finds | Amazing Science | Scoop.it
A team of Indiana University researchers has reported the first evidence that non-human animals (rats) can replay a stream of multiple episodic memories. The study was published in the journal Current Biology.

 

Episodic memory is the ability to remember specific events. For example, if a person loses their car keys, they might try to recall every single step — or ‘episode’ — in their trip from the car to their current location. The ability to replay these events in order is known as ‘episodic memory replay.’

 

“People wouldn’t be able to make sense of most scenarios if they couldn’t remember the order in which they occurred,” said Professor Jonathon Crystal, senior author on the study.

 

To assess animals’ ability to replay past events from memory, Professor Crystal and colleagues spent nearly a year working with 13 rats, which they trained to memorize a list of up to 12 different odors. The rats were placed inside an ‘arena’ with different odors and rewarded when they identified the second-to-last odor or fourth-to-last odor in the list.

 

The scientists changed the number of odors in the list before each test to confirm the odors were identified based upon their position in the list, not by scent alone, proving the animals were relying on their ability to recall the whole list in order. Arenas with different patterns were used to communicate to the rats which of the two options was sought.

 

“After their training, the animals successfully completed their task about 87% of the time across all trials,” Professor Crystal said. “The results are strong evidence the animals were employing episodic memory replay.” Additional experiments confirmed the rats’ memories were long-lasting and resistant to ‘interference’ from other memories, both hallmarks of episodic memory.

 

The team also ran tests that temporarily suppressed activity in the hippocampus — the site of episodic memory — to confirm the rats were using this part of their brain to perform their tasks.

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Viruses can evolve in parallel in related species of hosts

Viruses can evolve in parallel in related species of hosts | Amazing Science | Scoop.it
Viruses are more likely to evolve in similar ways in related species—raising the risk that they will "jump" from one species to another, new research shows.

 

 

Scientists from the universities of Exeter and Cambridge compared viruses that evolved in different species and found "parallel genetic changes" were more likely if two host species were closely related. The findings suggest that when a new virus appears in a species such as chimpanzees, closely related species like humans may become vulnerable too. Such jumps, also known as host shifts, are a major source of infectious disease, with viruses such as HIV, Ebola and SARS coronavirus all thought to have jumped into humans from other species.

 

The researchers used deep sequencing of genomes to track the evolution of viruses in 19 species of flies. "Our findings show that when a virus adapts to one host, it might also become better adapted to closely related host species," said Dr Ben Longdon, of the University of Exeter. "This may explain in part why host shifts tend to occur between related species. However, we sometimes see the same mutations occurring in distantly related host species, and this may help explain why viruses may sometimes jump between distantly related host species. At present we know very little about how viruses shift from one host species to another, so research like this is important if we want to understand and ultimately predict emerging viral diseases."

 

The fruit flies used in the study were 19 species from the Drosophilidae family, which shared a common ancestor 40 million years ago.

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Interacting lasers shed light on topological defects

Interacting lasers shed light on topological defects | Amazing Science | Scoop.it

A new way of using a laser cavity to study the emergence of topological defects has been unveiled by researchers in Israel.

Topological defects emerge when a system makes a rapid transition from a disordered to an ordered phase – a process called quenching because it often involves rapid cooling. In the case of magnetic order, quenched magnetic moments form small domains in which the moments point in the same direction. Moments in neighboring domains can point in different directions and the interfaces between domains are called topological defects. These defects can occur in a wide range of systems, from atomic gases to the rapidly cooling early universe. Understanding how to eliminate topological defects could even be exploited to solve hard computational problems.

Multiple lasers

How topological defects emerge can be very tricky to study in the laboratory because controlling the rapidly changing temperature throughout a sample can be very difficult. In this latest study, Vishwa Pal, Nir Davidson and colleagues at the Weizmann Institute in Israel have used a set of up to 30 coupled laser beams to create a system with topological defects that can be studied more easily.

Their system comprises a laser cavity containing a mask with a number of holes arranged in a circular pattern. Each hole produces its own laser beam, which overlaps a bit with its two neighbours – leading to an interaction between beams.

 

The laser cavity is pumped by an external light pulse and the interaction causes the laser beams to undergo rapid phase oscillations before settling into a steady state that is then measured by the team. The laser cavity contains about 1000 modes and this provides the system with a large number of initial phase relationships between the laser beams. In most cases the beams synchronize, but occasionally the system gets locked into a state in which there are phase differences between the beams. These states can be described as topological defects, and the team found that their number increased as the number of holes is increased from 10 to 30 – and also when the intensity of the pump pulse is increased.

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Scientists to grow 'mini-brains' organoids using Neanderthal DNA

Scientists to grow 'mini-brains' organoids using Neanderthal DNA | Amazing Science | Scoop.it

Scientists are preparing to create “miniature brains” that have been genetically engineered to contain Neanderthal DNA, in an unprecedented attempt to understand how humans differ from our closest relatives.

In the next few months the small blobs of tissue, known as brain organoids, will be grown from human stem cells that have been edited to contain “Neanderthalized” versions of several genes.

The lentil-sized organoids, which are incapable of thoughts or feelings, replicate some of the basic structures of an adult brain. They could demonstrate for the first time if there were meaningful differences between human and Neanderthal brain biology.

“Neanderthals are the closest relatives to everyday humans, so if we should define ourselves as a group or a species it is really them that we should compare ourselves to,” said Prof Svante Pääbo, director of the genetics department at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where the experiments are being performed.

Pääbo previously led the successful international effort to crack the Neanderthal genome, and his lab is now focused on bringing Neanderthal traits back to life in the laboratory through sophisticated gene-editing techniques.

The lab has already inserted Neanderthal genes for craniofacial development into mice (heavy-browed rodents are not anticipated), and Neanderthal pain perception genes into frogs’ eggs, which could hint at whether they had a different pain threshold to humans. Now the lab is turning its attention to the brain.

“We’re seeing if we can find basic differences in how nerve cells function that may be a basis for why humans seem to be cognitively so special,” said Pääbo.

The research comes as the longstanding stereotype of Neanderthals as gormless and thuggish is being rewritten by emerging evidence that they buried their dead, produced cave art and had brains that were larger than our own.

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World's fastest water heater - 100,000 degrees in 0.000 000 000 000 075 seconds

World's fastest water heater - 100,000 degrees in 0.000 000 000 000 075 seconds | Amazing Science | Scoop.it

Scientists have used a powerful X-ray laser to heat water from room temperature to 100,000 degrees Celsius in less than a tenth of a picosecond (millionth of a millionth of a second). The experimental set-up, that can be seen as the world's fastest water heater, produced an exotic state of water, from which researchers hope to learn more about the peculiar characteristics of Earth's most important liquid. The observations also have practical use for the probing biological and many other samples with X-ray lasers. The team of Carl Caleman from the Center for Free-Electron Laser Science (CFEL) at DESY and Uppsala University (Sweden) reports its findings in the journalProceedings of the National Academy of Sciences(PNAS).

 

The researchers used the X-ray free-electron laser Linac Coherent Light Source LCLS at the SLAC National Accelerator Laboratory in the U.S. to shoot extremely intense and ultra-short flashes of X-rays at a jet of water. "It is not the usual way to boil your water," said Caleman. "Normally, when you heat water, the molecules will just be shaken stronger and stronger." On the molecular level, heat is motion -- the hotter, the faster the motion of the molecules. This can be achieved, for example, via heat transfer from a stove, or more directly with microwaves that make the water molecules swing back and forth ever faster in step with the electromagnetic field.

 

"Our heating is fundamentally different," explained Caleman. "The energetic X-rays punch electrons out of the water molecules, thereby destroying the balance of electric charges. So, suddenly the atoms feel a strong repulsive force and start to move violently." In less than 75 femtoseconds, that's 75 millionths of a billionth of a second or 0.000 000 000 000 075 seconds, the water goes through a phase transition from liquid to plasma. A plasma is a state of matter where the electrons have been removed from the atoms, leading to a sort of electrically charged gas.

 

"But while the water transforms from liquid to plasma, it still remains at the density of liquid water, as the atoms didn't have time to move significantly yet," said co-author Olof Jönsson from Uppsala University. This exotic state of matter is nothing that can be found naturally on Earth. "It has similar characteristics as some plasmas in the sun and the gas giant Jupiter, but has a lower density. Meanwhile, it is hotter than Earth's core."

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PARP inhibitor resistance gene identified using CRISPR screen

PARP inhibitor resistance gene identified using CRISPR screen | Amazing Science | Scoop.it

Although PARP inhibitors (PARPi) target homologous recombination defective tumors, drug resistance frequently emerges, often via poorly understood mechanisms. Here, using genome-wide and high-density CRISPR-Cas9 “tag-mutate-enrich” mutagenesis screens, a group of scientists identify close to full-length mutant forms of PARP1 that cause in vitro and in vivo PARPi resistance. Mutations both within and outside of the PARP1 DNA-binding zinc-finger domains cause PARPi resistance and alter PARP1 trapping, as does a PARP1 mutation found in a clinical case of PARPi resistance. This reinforces the importance of trapped PARP1 as a cytotoxic DNA lesion and suggests that PARP1 intramolecular interactions might influence PARPi-mediated cytotoxicity. PARP1mutations are also tolerated in cells with a pathogenic BRCA1 mutation where they result in distinct sensitivities to chemotherapeutic drugs compared to other mechanisms of PARPi resistance (BRCA1 reversion,53BP1, REV7 (MAD2L2) mutation), suggesting that the underlying mechanism of PARPi resistance that emerges could influence the success of subsequent therapies.

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