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AI reveals new breast cancer types that respond differently to treatment

Scientists have used artificial intelligence to recognise patterns in breast cancer — and uncovered five new types of the disease each matched to different personalised treatments.

Their study applied AI and machine learning to gene sequences and molecular data from breast tumours, to reveal crucial differences among cancers that had previously been lumped into one type.

The new study, led by a team at The Institute of Cancer Research, London, found that two of the types were more likely to respond to immunotherapy than others, while one was more likely to relapse on tamoxifen.

The researchers are now developing tests for these types of breast cancer that will be used to select patients for different drugs in clinical trials, with the aim of making personalised therapy a standard part of treatment.

The researchers previously used AI in the same way to uncover five different types of bowel cancer and oncologists are now evaluating their application in clinical trials.

The aim is to apply the AI algorithm to many types of cancer — and to provide information for each about their sensitivity to treatment, likely paths of evolution and how to combat drug resistance.

The new research, published today (Friday) in the journal NPJ Breast Cancer, could not only help select treatments for women with breast cancer but also identify new drug targets.

The Institute of Cancer Research (ICR) — a charity and research institute — funded the study itself from its own charitable donations.

The majority of breast cancers develop in the inner cells that line the mammary ducts and are ‘fed’ by the hormones oestrogen or progesterone. These are classed as ‘luminal A’ tumours and often have the best cure rates.

However, patients within these groups respond very differently to standard-of-care treatments, such as tamoxifen, or new treatments — needed if patients relapse — such as immunotherapy.

The researchers applied the AI-trained computer software to a vast array of data available on the genetics, molecular and cellular make-up of primary luminal A breast tumours, along with data on patient survival.

Once trained, the AI was able to identify five different types of disease with particular patterns of response to treatment.

Women with a cancer type labelled ‘inflammatory’ had immune cells present in their tumours and high levels of a protein called PD-L1 — suggesting they were likely to respond to immunotherapies.

Another group of patients had ‘triple negative’ tumours — which don’t respond to standard hormone treatments — but various indicators suggesting they might also respond to immunotherapy.

Patients with tumours that contained a specific change in chromosome 8 had worse survival than other groups when treated with tamoxifen and tended to relapse much earlier — after an average of 42 months compared to 83 months in patients who had a different tumour type that contained lots of stem cells. These patients may benefit from an additional or new treatment to delay or prevent late relapse.

The markers identified in this new study do not challenge the overall classification of breast cancer — but they do find additional differences within the current sub-divisions of the disease, with important implications for treatment.

The use of AI to understand cancer’s complexity and evolution is one of the central strategies the ICR is pursuing as part of a pioneering research programme to combat the ability of cancers to adapt and become drug resistant. The ICR is raising the final £15 million of a £75 million investment in a new Centre for Cancer Drug Discovery to house a world-first programme of ‘anti-evolution’ therapies.

Study leader Dr Anguraj Sadanandam, Team Leader in Systems and Precision Cancer Medicine at The Institute of Cancer Research, London, said:

“We are at the cusp of a revolution in healthcare, as we really get to grips with the possibilities AI and machine learning can open up.

“Our new study has shown that AI is able to recognise patterns in breast cancer that are beyond the limit of the human eye, and to point us to new avenues of treatment among those who have stopped responding to standard hormone therapies. AI has the capacity to be used much more widely, and we think we will be able to apply this technique across all cancers, even opening up new possibilities for treatment in cancers that are currently without successful options.”

Dr Maggie Cheang, a pioneer in identifying different types of breast cancer and Team Leader of the Genomic Analysis Clinical Trials Team at The Institute of Cancer Research, London, said:

“Doctors have used the current classification of breast cancers as a guide for treatment for years, but it is quite crude and patients who seemingly have the same type of the disease often respond very differently to drugs.

“Our study has used AI algorithms to spot patterns within breast cancers that human analysis had up to now missed — and found additional types of the disease that respond in very particular ways to treatment.

“Among the exciting implications of this research is its ability to pick out women who might respond well to immunotherapy, even when the broad classification of their cancer would suggest that these treatments wouldn’t work for them.

“The AI used in our study could also be used to discover new drugs for those most at risk of late relapse, beyond 5 years, which is common in oestrogen-linked breast cancers and can cause considerable anxiety for patients.”

As well as ICR charity funding, the work was also supported by the NIHR Biomedical Research Centre at The Institute of Cancer Research, London, and The Royal Marsden NHS Foundation Trust.

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Hackster.io

SparkFun Artemis Unboxing // MCU Monday

Check it out – one powerful new module for AI on the edge, FOUR different ways to use it! This little powerhouse comes with 48 pins, Bluetooth 5, and tons of bells and whistles: Qwiic connector, MEMS mic, tons of power options… or mount it onto your own custom board! We’re pretty excited about this one.

// https://blog.hackster.io/say-hello-to-the-sparkfun-artemis-2af46ecfddec
// https://www.sparkfun.com/products/15376
// https://learn.sparkfun.com/tutorials/artemis-development-with-arduino
// https://github.com/sparkfun/Arduino_Apollo3
// https://learn.sparkfun.com/tutorials/designing-with-the-sparkfun-artemis
// https://github.com/uTensor/uTensor
// https://www.hackster.io/videos/164
// https://www.tensorflow.org/lite/microcontrollers/overview
// https://aiweirdness.com/post/174211306032/metal-band-or-my-little-pony

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Kennedy Christian

Wednesday 31st July 2019 Kennedy HS

Up on today’s agenda? #drones #smiles #soldering We made a raptor claw cookie cutter, golf ball prototype, broke a drone in under 4 minutes and Cole coached his mother in making a wiring harness. Another successful #makerspace at Kennedy Catholic High School.

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ScienceDaily

Clearing up the ‘dark side’ of artificial leaves

While artificial leaves hold promise as a way to take carbon dioxide — a potent greenhouse gas — out of the atmosphere, there is a “dark side to artificial leaves that has gone overlooked for more than a decade,” according to Meenesh Singh, assistant professor of chemical engineering in the University of Illinois at Chicago College of Engineering.

Artificial leaves work by converting carbon dioxide to fuel and water to oxygen using energy from the sun. The two processes take place separately and simultaneously on either side of a photovoltaic cell: the oxygen is produced on the “positive” side of the cell and fuel is produced on the “negative” side.

Singh, who is the corresponding author of a new paper in ACS Applied Energy Materials, says that current artificial leaves are wildly inefficient. They wind up converting only 15% of the carbon dioxide they take in into fuel and release 85% of it, along with oxygen gas, back to the atmosphere.

“The artificial leaves we have today aren’t really ready to fulfill their promise as carbon capture solutions because they don’t capture all that much carbon dioxide, and in fact, release the majority of the carbon dioxide gas they take in from the oxygen-evolving ‘positive’ side,” Singh said.

The reason artificial leaves release so much carbon dioxide back to the atmosphere has to do with where the carbon dioxide goes in the photoelectrochemical cell.

When carbon dioxide enters the cell, it travels through the cell’s electrolyte. In the electrolyte, the dissolved carbon dioxide turns into bicarbonate anions, which travel across the membrane to the “positive” side of the cell, where oxygen is produced. This side of the cell tends to be very acidic due to splitting of water into oxygen gas and protons. When the bicarbonate anions interact with the acidic electrolyte at the anodic side of the cell, carbon dioxide is produced and released with oxygen gas.

Singh noted that a similar phenomenon of carbon dioxide release occurring in the artificial leaf can be seen in the kitchen when baking soda (bicarbonate solution) is mixed with vinegar (acidic solution) to release a fizz of carbon dioxide bubbles.

To solve this problem, Singh, in collaboration with Caltech researchers Meng Lin, Lihao Han and Chengxiang Xiang, devised a system that uses a bipolar membrane that prevents the bicarbonate anions from reaching the “positive” side of the leaf while neutralizing the proton produced.

The membrane placed in between the two sides of the photoelectrochemical cell keeps the carbon dioxide away from the acidic side of the leaf, preventing its escape back into the atmosphere. Artificial leaves using this specialized membrane turned 60% to 70% of the carbon dioxide they took in into fuel.

“Our finding represents another step in making artificial leaves a reality by increasing utilization of carbon dioxide,” Singh said.

Earlier this year, Singh and colleagues published a paper in ACS Sustainable Chemistry & Engineering, where they proposed a solution to another problem with artificial leaves: current models use pressurized carbon dioxide from tanks, not the atmosphere.

He proposed another specialized membrane that would allow the leaves to capture carbon dioxide directly from the atmosphere. Singh explains that this idea, together with the findings reported in this current publication on using more of the carbon dioxide captures, should help make artificial leaf technology fully implementable.

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ScienceDaily

How to recognize where a volcano will erupt

Most of the times you see the eruption of a volcano on TV or the internet, the magma shoots right out of its top. However, it is not so uncommon that the magma erupts from the volcano’s flank rather than its summit. After leaving the underground magma chamber, the magma forces its way sideways by fracturing rock, sometimes for tens of kilometres. Then, when it breaches the Earth’s surface, it forms one or more vents from which it spills out, sometimes explosively. This for example occurred at Bardarbunga in Iceland in August 2014, and Kilauea in Hawaii in August 2018.

It is a big challenge for volcanologists to guess where magma is heading and where it will breach the surface. A lot of effort is spent on this task as it could help minimise the risk for villages and cities endangered by eruptions. Now, Eleonora Rivalta and her team from the GFZ German Research Centre for Geosciences in Potsdam, together with colleagues from the University Roma Tre and the Vesuvius Observatory of the Italian Istituto Nazionale di Geofisica e Vulcanologia in Naples have devised a new method to generate vent location forecasts. The study is published in the journal Science Advances.

“Previous methods were based on the statistics of the locations of past eruptions,” says Eleonora Rivalta. “Our method combines physics and statistics: we calculate the paths of least resistance for ascending magma and tune the model based on statistics.” The researchers successfully tested the new approach with data from the Campi Flegrei caldera in Italy, one of the Earth’s highest-risk volcanoes.

“Calderas often look like a lawn covered in molehills”

Vents opened at the flank of a volcano are often used by just one eruption. All volcanoes may produce such one-time vents, but some do more than others. Their flanks are punctured by tens of vents whose alignment marks the locations where subsurface magma pathways have intersected the Earth’s surface.

At calderas, that is large cauldron-like hollows that form shortly after the emptying of a magma chamber in a volcanic eruption, vents may also open inside and on its rim. That is because they lack a summit to focus eruptions. “Calderas often look like a lawn covered in molehills,” says GFZ’s Eleonora Rivalta.

Most vents at calderas have only been used once. The resulting scattered, sometimes seemingly random spatial vent distribution threatens wide areas, presenting a challenge to volcanologists who draw forecast maps for the location of future eruptions. Such maps are also necessary for accurate forecasts of lava and pyroclastic flows or the expansion of ash plumes.

Vent forecast maps have so far been mainly based on the spatial distribution of past vents: “Volcanologists often assume that the volcano will behave like it did in the past,” says Eleonora Rivalta. “The problem is that often only a few tens of vents are visible on the volcano surface as major eruptive episodes tend to cover or obliterate past eruptive patterns. Hence, as mathematically sophisticated as the procedure can be, sparse data lead to coarse maps with large uncertainties. Moreover, the dynamics of a volcano may change with time, so that vent locations will shift.”

Succesful tests at the Campi Flegrei

That is why Rivalta, a trained physicist, together with a team of geologists and statisticians, used volcano physics to improve the forecasts. “We employ the most up-to-date physical understanding of how magma fractures rock to move underground and combine it with a statistical procedure and knowledge of the volcano structure and history. We tune the parameters of the physical model until they match previous eruptive patterns. Then, we have a working model and can use it to forecast future eruption locations,” says Eleonora Rivalta.

The new approach was applied in southern Italy to the Campi Flegrei, a caldera close to Naples, which has a population of nearly one million. In the more than ten kilometres wide caldera, about eighty vents have fed explosive eruptions in the last 15,000 years. The approach performs well in retrospective tests, that is correctly forecasting the location of vents that were not used to tune the model, the researchers report.

“The most difficult part was to formulate the method in a way that works for all volcanoes and not just one — to generalise it,” Rivalta explains. “We will now perform more tests. If our method works well on other volcanoes too, it may help planning land usage in volcanic areas and forecasting the location of future eruptions with a higher certainty than previously possible.”

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You can’t squash this roach-inspired robot

If the sight of a skittering bug makes you squirm, you may want to look away — a new insect-sized robot created by researchers at the University of California, Berkeley, can scurry across the floor at nearly the speed of a darting cockroach.

And it’s nearly as hardy as a cockroach, too. Try to squash this robot under your foot, and more than likely, it will just keep going.

“Most of the robots at this particular small scale are very fragile. If you step on them, you pretty much destroy the robot,” said Liwei Lin, a professor of mechanical engineering at UC Berkeley and senior author of a new study that describes the robot. “We found that if we put weight on our robot, it still more or less functions.”

Small, durable robots like these could be advantageous in search and rescue missions, squeezing and squishing into places where dogs or humans can’t fit, or where it may be too dangerous for them to go.

“For example, if an earthquake happens, it’s very hard for the big machines, or the big dogs, to find life underneath debris, so that’s why we need a small-sized robot that is agile and robust,” said Yichuan Wu, first author of the paper, who completed the work as a graduate student in mechanical engineering at UC Berkeley through the Tsinghua-Berkeley Shenzhen Institute partnership. Wu is now an assistant professor at the University of Electronic Science and Technology of China.

The study appears today (Wednesday, July 31) in the journal Science Robotics.

The robot, which is about the size of a large postage stamp, is made of a thin sheet of a piezoelectric material called polyvinylidene fluoride, or PVDF. Piezoelectric materials are unique, in that applying electric voltage to them causes the materials to expand or contract.

The researchers coated the PVDF in a layer of an elastic polymer, which causes the entire sheet to bend, instead of to expand or contract. They then added a front leg so that, as the material bends and straightens under an electric field, the oscillations propel the device forward in a “leapfrogging” motion.

The resulting robot may be simple to look at, but it has some remarkable abilities. It can sail along the ground at a speed of 20 body lengths per second, a rate comparable to that of a cockroach and reported to be the fastest pace among insect-scale robots. It can zip through tubes, climb small slopes and carry small loads, such as a peanut.

Perhaps most impressively, the robot, which weighs less than one tenth of a gram can withstand a weight of around 60 kg — about the weight of an average human — which is approximately 1 million times the weight of the robot.

“People may have experienced that, if you step on the cockroach, you may have to grind it up a little bit, otherwise the cockroach may still survive and run away,” Lin said. “Somebody stepping on our robot is applying an extraordinarily large weight, but [the robot] still works, it still functions. So, in that particular sense, it’s very similar to a cockroach.”

The robot is currently “tethered” to a thin wire that carries an electric voltage that drives the oscillations. The team is experimenting with adding a battery so the robot can roam independently. They are also working to add gas sensors and are improving the design of the robot so it can be steered around obstacles.

This work is supported in part by the Berkeley Sensor and Actuator Center, an Industry-University Cooperation Research Center.

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Magnetic ‘springs’ break down marine microplastic pollution

Plastic waste that finds its way into oceans and rivers poses a global environmental threat with damaging health consequences for animals, humans, and ecosystems. Now, using tiny coil-shaped carbon-based magnets, researchers in Australia have developed a new approach to purging water sources of the microplastics that pollute them without harming nearby microorganisms. Their work appears July 31 in the journal Matter.

“Microplastics adsorb organic and metal contaminants as they travel through water and release these hazardous substances into aquatic organisms when eaten, causing them to accumulate all the way up the food chain” says senior author Shaobin Wang, a professor of chemical engineering at the University of Adelaide (Australia). “Carbon nanosprings are strong and stable enough to break these microplastics down into compounds that do not pose such a threat to the marine ecosystem.”

Although often invisible to the naked eye, microplastics are ubiquitous pollutants. Some, such as the exfoliating beads found in popular cosmetics, are simply too small to be filtered out during industrial water treatment. Others are produced indirectly, when larger debris like soda bottles or tires weather amid sun and sand.

To decompose the microplastics, the researchers had to generate short-lived chemicals called reactive oxygen species, which trigger chain reactions that chop the various long molecules that make up microplastics into tiny and harmless segments that dissolve in water. However, reactive oxygen species are often produced using heavy metals such as iron or cobalt, which are dangerous pollutants in their own right and thus unsuitable in an environmental context.

To get around this challenge, the researchers found a greener solution in the form of carbon nanotubes laced with nitrogen to help boost generation of reactive oxygen species. Shaped like springs, the carbon nanotube catalysts removed a significant fraction of microplastics in just eight hours while remaining stable themselves in the harsh oxidative conditions needed for microplastics breakdown. The coiled shape increases stability and maximises reactive surface area. As a bonus, by including a small amount of manganese, buried far from the surface of the nanotubes to prevent it from leaching into water, the minute springs became magnetic.

“Having magnetic nanotubes is particularly exciting because this makes it easy to collect them from real wastewater streams for repeated use in environmental remediation,” says Xiaoguang Duan, a chemical engineering research fellow at Adelaide who also co-led the project.

As no two microplastics are chemically quite the same, the researchers’ next steps will center on ensuring that the nanosprings work on microplastics of different compositions, shapes and origins. They also intend to continue to rigorously confirm the non-toxicity of any chemical compounds occurring as intermediates or by-products during microplastics decomposition.

The researchers also say that those intermediates and byproducts could be harnessed as an energy source for microorganisms that the polluting plastics currently plague. “If plastic contaminants can be repurposed as food for algae growth, it will be a triumph for using biotechnology to solve environmental problems in ways that are both green and cost efficient,” Wang says.

This work was supported by the Australian Research Council, the National Natural Science Foundation of China, and the Science and Technology Program of Guangdong Province.

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Experiments explore the mysteries of ‘magic’ angle superconductors

In spring 2018, the surprising discovery of superconductivity in a new material set the scientific community abuzz. Built by layering one carbon sheet atop another and twisting the top one at a “magic” angle, the material enabled electrons to flow without resistance, a trait that could dramatically boost energy efficient power transmission and usher in a host of new technologies.

Now, new experiments conducted at Princeton give hints at how this material — known as magic-angle twisted graphene — gives rise to superconductivity. In this week’s issue of the journal Nature, Princeton researchers provide firm evidence that the superconducting behavior arises from strong interactions between electrons, yielding insights into the rules that electrons follow when superconductivity emerges.

“This is one of the hottest topics in physics,” said Ali Yazdani, the Class of 1909 Professor of Physics and senior author of the study. “This is a material that is incredibly simple, just two sheets of carbon that you stick one on top of the other, and it shows superconductivity.”

Exactly how superconductivity arises is a mystery that laboratories around the world are racing to solve. The field even has a name, “twistronics.”

Part of the excitement is that, compared to existing superconductors, the material is quite easy to study since it only has two layers and only one type of atom — carbon.

“The main thing about this new material is that it is a playground for all these kinds of physics that people have been thinking about for the last 40 years,” said B. Andrei Bernevig, a professor of physics specializing in theories to explain complex materials.

The superconductivity in the new material appears to work by a fundamentally different mechanism from traditional superconductors, which today are used in powerful magnets and other limited applications. This new material has similarities to copper-based, high-temperature superconductors discovered in the 1980s called cuprates. The discovery of cuprates led to the Nobel Prize in Physics in 1987.

The new material consists of two atomically thin sheets of carbon known as graphene. Also the subject of a Nobel Prize in Physics, in 2010, graphene has a flat honeycomb pattern, like a sheet of chicken wire. In March 2018, Pablo Jarillo-Herrero and his team at the Massachusetts Institute of Technology placed a second layer of graphene atop the first, then rotated the top sheet by the “magic” angle of about 1.1 degrees. This angle had been predicted earlier by physicists to cause new electron interactions, but it came as a shock when MIT scientists demonstrated superconductivity.

Seen from above, the overlapping chicken-wire patterns give a flickering effect known as “moiré,” which arises when two geometrically regular patterns overlap, and which was once popular in the fabrics and fashions of 17th and 18th century royals.

These moiré patterns give rise to profoundly new properties not seen in ordinary materials. Most ordinary materials fall into a spectrum from insulating to conducting. Insulators trap electrons in energy pockets or levels that keep them stuck in place, while metals contain energy states that permit electrons to flit from atom to atom. In both cases, electrons occupy different energy levels and do not interact or engage in collective behavior.

In twisted graphene, however, the physical structure of the moiré lattice creates energy states that prevent electrons from standing apart, forcing them to interact. “It is creating a condition where the electrons can’t get out of each other’s way, and instead they all have to be in similar energy levels, which is prime condition to create highly entangled states,” Yazdani said.

The question the researchers addressed was whether this entanglement has any connection with its superconductivity. Many simple metals also superconduct, but all the high-temperature superconductors discovered to date, including the cuprates, show highly entangled states caused by mutual repulsion between electrons. The strong interaction between electrons appears to be a key to achieve higher temperature superconductivity.

To address this question, Princeton researchers used a scanning tunneling microscope that is so sensitive that it can image individual atoms on a surface. The team scanned samples of magic-angle twisted graphene in which they controlled the number of electrons by applying a voltage to a nearby electrode. The study provided microscopic information on electron behavior in twisted bilayer graphene, whereas most other studies to date have monitored only macroscopic electrical conduction.

By dialing the number of electrons to very low or very high concentrations, the researchers observed electrons behaving almost independently, as they would in simple metals. However, at the critical concentration of electrons where superconductivity was discovered in this system, the electrons suddenly displayed signs of strong interaction and entanglement.

At the concentration where superconductivity emerged, the team found that the electron energy levels became unexpectedly broad, signals that confirm strong interaction and entanglement. Still, Bernevig emphasized that while these experiments open the door to further study, more work needs to be done to understand in detail the type of entanglement that is occurring.

“There is still so much we don’t know about these systems,” he said. “We are nowhere near even scraping the surface of what can be learned through experiments and theoretical modeling.”

Contributors to the study included Kenji Watanabe and Takashi Taniguchi of the National Institute for Material Science in Japan; graduate student and first author Yonglong Xie, postdoctoral research fellow Berthold Jäck, postdoctoral research associate Xiaomeng Liu, and graduate student Cheng-Li Chiu in Yazdani’s research group; and Biao Lian in Bernevig’s research group.

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3D Printing Industry

I-Form and Gallomanor launch the ‘3D Printing a Sustainable World’ competition

I-Form, a Science Foundation Ireland (SFI) Research Centre for Advanced Manufacturing, and Gallomanor, an online science platform, have launched a 3D printing competition. Dubbed “3D Printing a Sustainable World”, this competition aims to ‘Shape the Future’ through environmentally-friendly ideas which replace conventionally made parts, pieces of art, or energy-based processes. The winning idea will be […]

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Author: Tia Vialva

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3D Printing Industry

VELO3D ships largest order of Sapphire metal 3D printers to aerospace customer

Californian metal 3D printer provider VELO3D has announced the largest order of its laser powder bed fusion (LPBF) Sapphire system. The company will deliver an additional four 3D metal printers to an undisclosed aerospace customer, bringing its installed base of Sapphire systems to a total of nine. Benny Buller, CEO of VELO3D, said, “We are excited to see […]

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Author: Tia Vialva