Shake The Fake

The WVU Reed College of Media, in collaboration with computer science students and faculty at the WVU Benjamin M. Statler College of Engineering and Mineral Resources, is hosting an artificial intelligence (AI) course at its Media Innovation Center that includes two projects focused on using AI to detect and combat fake news articles.

Students in the senior-level computer science elective course are working in teams to develop and implement their own AI programs under the instruction of Don McLaughlin, research associate and retired faculty member of the Lane Department of Computer Science and Electrical Engineering.

Stephen Woerner, a computer science senior, is on one of the teams charged with creating a system that detects fake news articles. His team’s approach utilizes a machine learning system to analyze text and generate a score that represents each article’s likeliness that it is fake news. Woerner added that this score is accompanied by a breakdown that explains the rating and provides transparency.

“Artificial intelligence can have all the same information as people, but it can address the volume of news and decipher validity without getting tired,” Woerner said. “People tend to get political or emotional, but AI doesn’t. It just addresses the problem it’s trained to combat.”

This collaboration with the computer science course serves as an example of the Media Innovation Center’s mission to support initiatives, projects, research and curriculum innovations that intersect its work in technology, media and information networks.

“Fake news isn’t just a media problem,” said the Center’s Creative Director Dana Coester. “It’s also a social and political problem with roots in technology. Solving that problem requires collaborating across disciplines.”

McLaughlin says working at the Center has helped his students this semester, as it suggests a more creative atmosphere than classrooms he’s used in the past.

“I’ve taught this course before, but the students seem to be more enthused this time. We appreciate the space and the breakout areas available for team collaboration here at the Center,” said McLaughlin. “Those amenities are valuable in a university environment.”

Each team will demonstrate their completed AI project during the last week of classes at the Media Innovation Center located in the Evansdale Crossing building.

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Plastic Waste

Of the 78 million tons of plastic used for packaging, just 2 percent actually gets recycled and re-used in a similar way.

Nearly a third is leaked into the environment, around 14 percent is used in incineration and/or energy recovery, and about 40 percent winds up in landfills.

One of the problems: Polyethylene (PE) and polypropylene (PP), which account for two-thirds of the world’s plastics, have different chemical structures and thus cannot be repurposed together. Or, at least, an efficient technology to meld these two materials into one hasn’t been available in the 60 years they’ve both been on the market.

That could change with a discovery out of Coates’ lab. Geoffrey Coates, a professor of chemistry and chemical biology at Cornell University and his group have collaborated with a group from the University of Minnesota to develop a multiblock polymer that, when added in small measure to a mix of the two otherwise incompatible materials, create a new and mechanically tough polymer.

The two groups’ work is detailed in a paper, “Combining polyethylene and polypropylene: Enhanced performance with PE/iPP multiblock polymers,” published online in Science.

James Eagan, a postdoctoral researcher in Coates’ group, is lead author of the paper. Other collaborators included researcher Anne LaPointe and former visiting scientist Rocco DiGirolamo.

Scientists for years have tried to develop a polymer that does what Coates, LaPointe and Eagan have achieved. By adding a miniscule amount of their tetrablock (four-block) polymer, with alternating polyethylene and polypropylene segments, the resultant material has strength superior to diblock (two-block) polymers they tested.

In their test, two strips of plastic were welded together using different multi-block polymers as adhesives, then mechanically pulled apart. While the welds made with diblock polymers failed relatively quickly, the weld made of the group’s tetrablock additive held so well that the plastic strips broke instead.

“People have done things like this before,” Coates said, “but they’ll typically put 10 percent of a soft material, so you don’t get the nice plastic properties, you get something that’s not quite as good as the original material.”

“What’s exciting about this,” he said, “is we can go to as low as 1 percent of our additive, and you get a plastic alloy that really has super-great properties.”

Not only does this tetrablock polymer show promise for improving recycling, Eagan said, it could spawn a whole new class of mechanically tough polymer blends.

“If you could make a milk jug with 30 percent less material because it’s mechanically better, think of the sustainability of that,” he said. “You’re using less plastic, less oil, you have less stuff to recycle, you have a lighter product that uses less fossil fuel to transport it.”

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Tomato Flavour

Consumers say supermarket tomatoes lack flavour, so a University of Florida researcher led a global team on a mission to identify the important factors that have been lost and put them back into modern tomatoes.

In a study published in the journal Science, Harry Klee, a professor of horticultural sciences with UF’s Institute of Food and Agricultural Sciences, identifies the chemical combinations for better tomato flavour.

“We’re just fixing what has been damaged over the last half century to push them back to where they were a century ago, taste-wise,” said Klee, stressing that this technique involves classical genetics, not genetic modification. “We can make the supermarket tomato taste noticeably better.”

Step one was to find out which of the hundreds of chemicals in a tomato contribute the most to taste.

Modern tomatoes lack sufficient sugars and volatile chemicals critical to better flavour, Klee said. Those traits have been lost during the past 50 years because breeders have not had the tools to routinely screen for flavour, he said.

To help, researchers studied what they call “alleles,” the versions of DNA in a tomato gene that give it its specific traits. Klee likened the concept to DNA in humans. Everyone has the same number of genes in their DNA, but a particular version of each gene determines traits such as height, weight and hair colour.

“We wanted to identify why modern tomato varieties are deficient in those flavour chemicals,” Klee said. “It’s because they have lost the more desirable alleles of a number of genes.”

Scientists then identified the locations of the good alleles in the tomato genome, he said. That required what’s called a genome-wide assessment study. There, scientists mapped genes that control synthesis of all the important chemicals. Once they found them, they used genetic analysis to replace bad alleles in modern tomato varieties with the good alleles, Klee said.

The U.S. is second only to China in worldwide tomato production, according to the U.S. Department of Agriculture. Florida and California account for two-thirds to three-fourths of all commercially produced fresh-market tomatoes in the U.S. Florida growers produce 33,000 acres of tomatoes worth $437 million annually as of 2014, according to UF/IFAS economic research.

Because breeding takes time, and the scientists are studying five or more genes, Klee said the genetic traits from his latest study may take three to four years to produce in new tomato varieties.

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What Goes In

Scientists have developed a urine test that measures the health of a person’s diet.

The five-minute test measures biological markers in urine created by the breakdown of foods such as red meat, chicken, fish and fruit and vegetables.

The analysis, developed by researchers from Imperial College London, Newcastle University and Aberystwyth University, also gives an indication of how much fat, sugar, fibre and protein a person has eaten.

Although the work is at an early stage, the team hope that with future development the test will be able to track patients’ diets. It could even be used in weight loss programmes to monitor food intake.

Evidence suggests people inaccurately record their own diets, and under-report unhealthy food while over-reporting fruit and vegetable intake and that the likelihood of inaccuracies in food diaries increases if a person is overweight or obese.

Professor Gary Frost, senior author of the study from the Department of Medicine at Imperial said: “A major weakness in all nutrition and diet studies is that we have no true measure of what people eat. We rely solely on people keeping logs of their daily diets, but studies suggest around 60 per cent of people misreport what they eat to some extent. This test could be the first independent indicator of the quality of a person’s diet and what they are really eating.”

In the study, published in the journal Lancet Diabetes and Endocrinology and conducted at the MRC-NIHR National Phenome Centre, the researchers asked 19 volunteers to follow four different diets, ranging from very healthy to very unhealthy. These were formulated using World Health Organisation dietary guidelines, which advise on the best diets to prevent conditions such as obesity, diabetes and heart disease.

The volunteers strictly followed these diets for three days while in a London research facility, throughout which the scientists collected urine samples in the morning, afternoon and evening.

The research team then assessed the urine for hundreds of compounds, called metabolites, produced when certain foods are broken down in the body.

These included compounds that indicate red meat, chicken, fish, fruit and vegetables, as well as giving a picture of the amount of protein, fat, fibre and sugar eaten. They also included compounds that point to specific foods such as citrus fruits, grapes and green leafy vegetables.

From this information the researchers were able to develop a urine metabolite profile that indicated a healthy, balanced diet with a good intake of fruit and vegetables. The idea is this ‘healthy diet’ profile could be compared to the diet profile from an individual’s urine, to provide an instant indicator of whether they are eating healthily.

The scientists then tested the accuracy of the test on data from a previous study. This included 225 UK volunteers as well as 66 people from Denmark. All of the volunteers had provided urine samples, and kept information on their daily diets.

Analysis of these urine samples enabled the researchers in the current study to accurately predict the diet of the 291 volunteers.

Professor John Mathers, co-author from the Human Nutrition Research Centre at Newcastle University, said: “For the first time, this research offers an objective way of assessing the overall healthiness of people’s diets without all the hassles, biases and errors of recording what they’ve eaten.”

The team now hope to refine the technology by testing it on larger numbers of people. They also need to further assess the accuracy of the test on an average person’s diet, outside of a research setting.

Dr Isabel Garcia-Perez, co-author from the Faculty of Medicine at Imperial explained: “We need to develop the test further so we can monitor the diet based on a single urine sample, as well as increase the sensitivity. This will eventually provide a tool for personalised dietary monitoring to help maintain a healthy lifestyle. We’re not at the stage yet where the test can tell us a person ate 15 chips yesterday and two sausages, but it’s on the way.”

The team added the technology may one day be used alongside weight loss programmes, as well as patient rehabilitation, for instance to help heart attack patients follow a healthy diet.

Professor Elaine Holmes, co-author from the Department of Surgery and Cancer at Imperial added: “We are hoping to make this test available to the public within the next two years. The idea would be to collect a urine sample at home and deliver it to a local centre for analysis. We envisage the tool being used by dieticians to help guide their patients’ dietary needs, or even by individuals who are interested in finding out more about the relationship between diet and their health”

Dr Des Walsh, head of population and systems medicine at the Medical Research Council said: “Though this research is still in its early stages, it’s grappling with essential methods in food and diet studies where advances are really needed. Measuring what we eat and drink more accurately will widen the benefits of nutrition research, developing better evidence-based interventions to improve individual’s health and reduce obesity.”

Professor John Draper, co-author from Aberystwyth University added: “The future challenge is to apply the technology developed in this laboratory study in a community setting and objectively monitor diet in the home. The teams in Aberystwyth and Newcastle have been doing just this and the results are looking very promising.”

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Scleroderma And Melanoma

Michigan State University researchers have discovered that a chemical compound, and potential new drug, reduces the spread of melanoma cells by up to 90 percent.

The human-made, small-molecule drug compound goes after a gene’s ability to produce RNA molecules and certain proteins in melanoma tumours. This gene activity, or transcription process, causes the disease to spread but the compound can shut it down. Up until now, few other compounds of this kind have been able to accomplish this.

“It’s been a challenge developing small-molecule drugs that can block this gene activity that works as a signaling mechanism known to be important in melanoma progression,” said Richard Neubig, a pharmacology professor and co-author of the study. “Our chemical compound is actually the same one that we’ve been working on to potentially treat the disease scleroderma, which now we’ve found works effectively on this type of cancer.”

Scleroderma is a rare and often fatal autoimmune disease that causes the hardening of skin tissue, as well as organs such as the lungs, heart and kidneys. The same mechanisms that produce fibrosis, or skin thickening, in scleroderma also contribute to the spread of cancer.

Small-molecule drugs make up over 90 percent of the drugs on the market today and Neubig’s co-author Kate Appleton, a postdoctoral student, said the findings are an early discovery that could be highly effective in battling the deadly skin cancer. It’s estimated about 10,000 people die each year from the disease.

Their findings are published in  Molecular Cancer Therapeutics.

“Melanoma is the most dangerous form of skin cancer with around 76,000 new cases a year in the United States,” Appleton said. “One reason the disease is so fatal is that it can spread throughout the body very quickly and attack distant organs such as the brain and lungs.”

Through their research, Neubig and Appleton, along with their collaborators, found that the compounds were able to stop proteins, known as Myocardin-related transcription factors, or MRTFs, from initiating the gene transcription process in melanoma cells. These triggering proteins are initially turned on by another protein called RhoC, or Ras homology C, which is found in a signaling pathway that can cause the disease to aggressively spread in the body.

The compound reduced the migration of melanoma cells by 85 to 90 percent. The team also discovered that the potential drug greatly reduced tumours specifically in the lungs of mice that had been injected with human melanoma cells.

“We used intact melanoma cells to screen for our chemical inhibitors,” Neubig said. “This allowed us to find compounds that could block anywhere along this RhoC pathway.”

Being able to block along this entire path allowed the researchers to find the MRTF signaling protein as a new target.

Appleton said figuring out which patients have this pathway turned on is an important next step in the development of their compound because it would help them determine which patients would benefit the most.

“The effect of our compounds on turning off this melanoma cell growth and progression is much stronger when the pathway is activated,” she said. “We could look for the activation of the MRTF proteins as a biomarker to determine risk, especially for those in early-stage melanoma.”

According to Neubig, if the disease is caught early, chance of death is only 2 percent. If caught late, that figure rises to 84 percent.

“The majority of people die from melanoma because of the disease spreading,” he said. “Our compounds can block cancer migration and potentially increase patient survival.”

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No Thanks For The Memory

Researchers from Schepens Eye Research Institute of Massachusetts Eye and Ear have uncovered two factors responsible for the chronic, lifelong nature of autoimmune disorders, which tend to “flare up” intermittently in affected patients. These two factors are cell-signaling proteins called cytokines, specifically Interleukin-7 and -15 (IL-7 and IL-15), that are secreted by cells of the immune system and help modulate memory Th17 cells, a subset of T cells which are known to contribute to autoimmune disorders. Until now, it was unclear how Th17 cells maintained memory; the study results show that IL-7 and IL-15 signal the Th17 cells to chronically reside in the body. These findings, published online in the Journal of Autoimmunity, may lead to the development of new therapies to address a variety of chronic autoimmune disorders.

“We wanted to know the precise factors that maintain memory in Th17 cells so that we can better understand what is causing chronic autoimmune disorders,” said senior author Reza Dana, M.D., M.Sc., MPH, Director of the Cornea and Refractive Surgery Service at Mass. Eye and Ear and the Claes H. Dohlman Professor of Ophthalmology at Harvard Medical School. “By selectively targeting the production and expression of IL-7 and IL-15, we may be able to prevent the development of chronic autoimmune disorders.”

Affecting up to 50 million Americans, autoimmune disorders develop when the body’s immune system attacks its own healthy tissue. Many autoimmune disorders are chronic, and patients may experience “flare-ups,” in which symptoms worsen temporarily and then enter a period of remission.

Previous research studies have linked Th17 cells to a variety of autoimmune disorders, including multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, and chronic inflammatory eye disorders such as uveitis and dry eye disease. When Th17 cells are activated, a subset of them become memory cells, causing them to reside in the body for long periods of time. These memory Th17 cells can become reactivated and cause flare-ups of the autoimmune condition. However, the underlying mechanisms that promote the maintenance of Th17 memory were previously unknown.

Using a mouse model for dry eye disease, an autoimmune condition affecting the surface of the eye, the study authors set out to determine what molecular factors are critical for the maintenance of Th17 memory. They identified IL-7 and -15 as playing a crucial role in the survival and homeostatic proliferation of memory Th17 cells and when they neutralised IL-7 and IL-15, they saw a substantial reduction of memory Th17 cells.

While further studies are needed to determine ways to block these factors, the findings suggest that targeting IL-7 and IL-15 in order to remove the memory Th17 cells may be an effective treatment strategy for autoimmune diseases.

“In the case of dry eye disease, many of the treatments are showing limited efficacy in patients that do not have a highly inflamed eye,” said Dr. Dana. “Targeting the chronic, immune nature of autoimmune diseases may be a better strategy for controlling these conditions.”

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Silk Drum

The Humble Silkworm.
A team with researchers based in Perth and Melbourne is moving towards clinical trials of a device that incorporates silkworm silk in an ear implant.
Named “ClearDrum”, it looks like a contact lens, but is instead a device on which the patient’s cells can grow.
Australian Perth-based surgeon Professor Marcus Atlas, said silk was the preferred choice because it was flexible.
“We felt that it had shown previously to support cell growth and proliferation, and the ability to be able to change into various forms was a really appealing thing for us, particularly when we started to mix it with other products to create different mechanical and acoustic criteria,” Professor Atlas said.
“The skin cells are there, it’s getting them to come across and heal, so it’s sort of a scaffold.”
The silk is degummed by removing sericin (the sticky stuff).
The derivative fibroin (the protein present in the silk) is then heated into a liquid and combined with other materials including glycerol and polyurethane to create the “scaffold”.
Silkworm Ear Drum

Chief Executive of the Ear Science Institute Sandra Bellekom said ClearDrum was the first implant which actually mimicked a human ear drum.
“What we find is that the cells, which are called keratinocytes, they love to thrive and migrate and move across this scaffold which helps the healing process,” she said.
“That’s why we want to use silk because we know that it works.”
She said it needed to be strong and flexible with acoustic properties and preferably transparent.
“The middle ear space is a very noxious environment, particularly when there’s disease present, there’s a lot of pressure changes occurring, it’s a very moist environment.
“So it’s not the easiest place to create an implant that’s going to be effective in the long term.”
The implant is placed under the eardrum.
For a “simple” or small perforation, it is expected it would dissolve over time, while for more complex or larger perforations, the implant would remain.
There would be a need for no more than one operation.
Ms Bellekom said surgeons around the world had been harvesting tissue for patches for eardrum perforations, and many organisations have been trying to develop a suitable device.
“We have extensively researched our technology over the past decade, and we’ve been able to produce 34 peer-reviewed journal articles which attest to the quality of our science. But the real truth of the matter is in translating that into human patients.”
That is set to happen with the grant of nearly $4 million from the UK-based charity, the Wellcome Trust.
“We are looking at recruiting patients that have chronic middle ear disease, active and inactive, so patients who have more simple perforations and also patients that have far more complex perforations with disease state present,” Ms Bellekom said.
Recruiting was expected to take place across Australia, but probably not until 2018.
The not-for-profit Ear Science Institute has been working on the project with Deakin University’s Future Fibres Hub.
Professor Atlas and Deakin’s Professor Xungai Wang had gone to London to present to the Wellcome Trust.
Professor Atlas said it has been a very rewarding joint effort.
“We saw that silk had this ability to become a really strong biological membrane that would support cell growth. And then we made contact with Deakin who had this really extensive experience in silk and silk fibroin and it grew from there, it grew from that relationship,” Professor Atlas said.
“Geography has made absolutely no difference, it’s just because the people really want to work together, it’s been very productive.
“It’s one of the best collaborations in science that I’ve worked in and I think it’s because the people are right and they want it to work.”

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