Whole genome analysis speeds up: 240 full genomes in 50 hours

Although the time and cost of sequencing an entire human genome has plummeted, analyzing the resulting three billion base pairs of genetic information from a single genome can take many months.In the journal Bioinformatics, however, a University of Chicago-based team — working with Beagle, one of the world’s fastest supercomputers devoted to life sciences — reports that genome analysis can be radically accelerated. This computer, based at Argonne National Laboratory, is able to analyze 240 full genomes in about two days.”This is a resource that can change patient management and, over time, add depth to our understanding of the genetic causes of risk and disease,” said study author Elizabeth McNally, MD, PhD, the A. J. Carlson Professor of Medicine and Human Genetics and director of the Cardiovascular Genetics Clinic at the University of Chicago Medicine.”The supercomputer can process many genomes simultaneously rather than one at a time,” said first author Megan Puckelwartz, a graduate student in McNally’s laboratory. “It converts whole genome sequencing, which has primarily been used as a research tool, into something that is immediately valuable for patient care.”Because the genome is so vast, those involved in clinical genetics have turned to exome sequencing, which focuses on the two percent or less of the genome that codes for proteins. This approach is often useful. An estimated 85 percent of disease-causing mutations are located in coding regions. But the rest, about 15 percent of clinically significant mutations, come from non-coding regions, once referred to as “junk DNA” but now known to serve important functions. If not for the tremendous data-processing challenges of analysis, whole genome sequencing would be the method of choice.To test the system, McNally’s team used raw sequencing data from 61 human genomes and analyzed that data on Beagle. They used publicly available software packages and one quarter of the computer’s total capacity. …

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Rest can be best medicine but difficult for young athletes

Billy Kuhl, age 14, is no stranger to bumps and bruises having been involved in numerous sports, including football and hockey, for several years. But last fall on his way to football practice a bicycle accident made him realize how important it is to take injuries seriously. While biking to football practice, Kuhl’s football spikes caused him to lose his footing. He was thrust forward over the front of the bike. The handle bars were jammed into his upper thigh causing a deep muscle injury.”It blew up like a grapefruit, but I’ve had lots of bruises so I didn’t think anything about it. I thought I just needed to work through it, but the bruise just kept getting bigger and bigger,” said Kuhl.Though he didn’t take part in practices that week, he did play in the football game as well as three hockey games that weekend. Kuhl’s parents noticed that instead of getting better the bruise was getting worse and had become hard in the middle.”We realized it should’ve gone down by now, but it was just getting worse so we decided to take him in for an X-ray,” said William Kuhl, Billy’s father. Kuhl saw Jerold Stirling, MD, pediatric sports medicine expert at Loyola University Health System and chair of the Department of Pediatrics at Loyola University Chicago Stritch School of Medicine.”When a large muscle is injured by bruising, it may cause bleeding into the muscle itself. On occasion, as the body is healing itself from the bleeding it can calcify in the muscle causing bone to form inside the muscle. This is called myositis ossificans,” said Stirling. …

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Roadmap for implementing quality preschool

Oct. 16, 2013 — Early childhood education can yield short- and long-term educational, economic, and societal benefits, underscoring the value of expanding publicly funded preschool education, New York University Professor Hirokazu Yoshikawa outlines in a research brief released today.”Investing in Our Future: The Evidence Base on Preschool Education,” authored by Yoshikawa, a professor NYU’s Steinhardt School of Culture, Education, and Human Development, and other early childhood experts, reviews existing scholarship on why early skills matter, which children benefit from preschool, the short- and long-term effects of preschool programs on children’s school readiness and life outcomes, the importance of program quality, and the costs versus benefits of preschool education.The findings, which offer a roadmap for broad, quality implementation of preschool programs, expand upon studies that have long served as barometers for the value of early childhood education: the Abecedarian Project, which traces back to the 1970s, and the Perry Preschool Project, which commenced in the 1960s.”Scientific evidence on the impacts of early childhood education has progressed well beyond exclusive reliance on the evaluations of the Perry Preschool and Abecedarian programs,” says Yoshikawa, the Courtney Sale Ross University Professor in NYU Steinhardt’s Department of Applied Psychology and lead author of the brief. “More recent evidence tells us a great deal about what works in early education and how early education might be improved. The combination of evidence-based curricula and in-classroom coaching is particularly promising and has been implemented at scale with large positive effects on children.””The recent evidence includes evaluations of city-wide public preschool programs such as those in Tulsa and Boston,” according to Deborah Phillips, professor of psychology at Georgetown University and a co-author of the brief. “Evaluations of these programs tell us that preschool programs implemented at scale can be high quality, can benefit children from a range of socioeconomic backgrounds, and can reduce disparities.”The evaluation of the Boston preschool program was conducted by Yoshikawa and Christina Weiland of the University of Michigan and was recently published in the journal Child Development.The research brief was funded by the Foundation for Child Development and produced in collaboration with the Society for Research in Child Development.According to the authors, the current science and evidence base on early childhood education shows that:• Large-scale public preschool programs that are of high quality can have a substantial impact on children’s early learning. For example, preschool systems in Tulsa and Boston have produced gains of between half and a full year of additional learning in reading and math.• Quality preschool education is a profitable investment. Cost-benefit estimates based on older, intensive interventions, such as the Perry Preschool Program, as well as contemporary, large-scale public preschool programs, such as the Chicago Child-Parent Centers and Tulsa’s preschool program, range from three to seven dollars saved (e.g., higher earnings) for participants for every dollar spent.• Quality preschool education can benefit middle-class children as well as disadvantaged children. The evidence is clear that middle-class children can benefit substantially and that benefits outweigh the costs for children from middle-income as well as those from low-income families. However, children from low-income families benefit more and therefore universal preschool can reduce disparities in skills at school entry.• Long-term benefits occur despite convergence of test scores. As children from low-income families in preschool evaluation studies are followed into elementary school, differences between those who participated in preschool and those who did not on tests of academic achievement are reduced. …

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FDA Issues Approval for Phase 2 Clinical Trial of Potential New Mesothelioma Treatment

The FDA has issued approval for biopharmaceutical company Verastem to begin a Phase 2 clinical study of a new drug for the treatment of malignant pleural mesothelioma. VS-6063 is an orally available, small molecule inhibitor of a crucial signaling pathway inside stem cells called the Focal Adhesion Kinase (FAK) pathway.FAK is vital for tumor development and is critical for the survival of cancer stem cells. VS-6063 was well-tolerated in a Phase 1 study and demonstrated signs of clinical activity in advanced solid tumors.Dr. Dean Fennell, Chair of Thoracic Medical Oncology at the University of Leicester, incoming President of the International Mesothelioma Interest Group (iMig) and a member of the Verastem Mesothelioma Steering Committee, presented promising data at a briefing session on VS-6063 at the annual American …

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Gene regulation differences between humans, chimpanzees very complex

Oct. 17, 2013 — Changes in gene regulation have been used to study the evolutionary chasm that exists between humans and chimpanzees despite their largely identical DNA. However, scientists from the University of Chicago have discovered that mRNA expression levels, long considered a barometer for differences in gene regulation, often do not reflect differences in protein expression — and, therefore, biological function — between humans and chimpanzees. The work was published Oct. 17 in Science.”We thought that we knew how to identify patterns of mRNA expression level differences between humans and chimpanzees that would be good candidates to be of functional importance,” said Yoav Gilad, PhD, Professor of Human Genetics at the University of Chicago. “Now we see that even such mRNA patterns are not translated to the protein level. Which means that it is unlikely that they can affect a functional phenotypic difference.”For genes to be expressed, DNA must be transcribed into messenger RNA (mRNA), which then code for proteins, the biological building blocks and engines that drive cellular function. Although humans and chimpanzees share highly similar genomes, previous studies have shown that the species evolved major differences in mRNA expression levels. Many of these differences were thought to indicate areas of evolutionary divergence, thus pointing to genes important for human-specific traits.To test this, Gilad, Jonathan Pritchard, PhD, currently at Stanford University, and their team, spearheaded by postdoctoral fellow Zia Khan, PhD, used high-resolution mass spectrometry to compare the expression levels of thousands of proteins with corresponding mRNA expression data in human and chimpanzee cell lines.The team found 815 genes with differing mRNA expression levels but only 571 genes that differed in protein expression. In total, they identified an estimated 266 genes with mRNA differences that did not lead to changes in protein levels. …

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Chronic pain treatment cools hot flashes in menopausal women

Oct. 12, 2013 — Menopausal women suffer from half as many hot flashes after receiving a non-hormonal chronic pain treatment, according to a study presented at the ANESTHESIOLOGY™ 2013 annual meeting. The nerve block treatment interrupts the area of the brain that regulates body temperature, reducing moderate-to-severe hot flashes and alleviating depression in menopausal women, breast cancer patients and women in surgical menopause.”Hot flashes affect more than 80 percent of menopausal women,” said David R. Walega, M.D., chief of the Division of Pain Medicine, and program director of the Multidisciplinary Pain Medicine Fellowship Department of Anesthesiology at Northwestern University Feinberg School of Medicine, Chicago. “This is the first effective, non-hormonal treatment for hot flashes, which for many women have a serious negative effect on their lives. This treatment will also help breast cancer patients who suffer from hot flashes as a side effect of their treatments or medication. Some breast cancer patients stop taking their medication (tamoxifen) because of hot flashes.”Hot flashes are a sudden feeling of heat or warmth starting in the face and extending to the neck and chest area. Some women also experience profuse sweating and a “reddening” or flush to their skin. Hot flashes can last anywhere from one to 10 minutes and vary in strength and frequency.This prospective, randomized, controlled study included 40 patients between 30 and 65 years old who experienced at least 25 hot flashes per week. Half of the participants received a stellate ganglion blockade (SGB) injection with a local anesthetic. …

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The eyes have it: How organic mercury can interfere with vision

Sep. 11, 2013 — More than one billion people worldwide rely on fish as an important source of animal protein, states the United Nations Food and Agriculture Organization. And while fish provide slightly over 7 per cent of animal protein in North America, in Asia they represent about 23 per cent of consumption.Humans consume low levels of methylmercury by eating fish and seafood. Methylmercury compounds specifically target the central nervous system, and among the many effects of their exposure are visual disturbances, which were previously thought to be solely due to methylmercury-induced damage to the brain visual cortex. However, after combining powerful synchrotron X-rays and methylmercury-poisoned zebrafish larvae, scientists have found that methylmercury may also directly affect vision by accumulating in the retinal photoreceptors, i.e. the cells that respond to light in our eyes.Dr. Gosia Korbas, BioXAS staff scientist at the Canadian Light Source (CLS), says the results of this experiment show quite clearly that methylmercury localizes in the part of the photoreceptor cell called the outer segment, where the visual pigments that absorb light reside.”There are many reports of people affected by methylmercury claiming a constricted field of vision or abnormal colour vision,” said Korbas. “Now we know that one of the reasons for their symptoms may be that methylmercury directly targets photoreceptors in the retina.”Korbas and the team of researchers from the University of Saskatchewan including Profs. Graham George, Patrick Krone and Ingrid Pickering conducted their experiments using three X-ray fluorescence imaging beamlines (2-ID-D, 2-ID-E and 20-ID-B) at the Advanced Photon Source, Argonne National Laboratory near Chicago, US, as well as the scanning X-ray transmission beamline (STXM) at the Canadian Light Source in Saskatoon, Canada.After exposing zebrafish larvae to methylmercury chloride in water, the team was able to obtain high-resolution maps of elemental distributions, and pinpoint the localization of mercury in the outer segments of photoreceptor cells in both the retina and pineal gland of zebrafish specimens. The results of the research were published in ACS Chemical Biology under the title “Methylmercury Targets Photoreceptor Outer Segments.”Korbas said zebrafish are an excellent model for investigating the mechanisms of heavy metal toxicity in developing vertebrates. …

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Botox not just for wrinkles

Aug. 27, 2013 — Botox is best known as a cosmetic treatment for frown lines, but the drug also effectively treats the after effects of Bell’s palsy and other serious facial nerve problems.Bell’s palsy results from damage to the facial nerve that controls muscles on one side of the face. Ear-nose-throat surgeon Dr. Matthew Kircher of Loyola University Medical Center is giving patients Botox injections to treat facial nerve disorders that sometimes occur after Bell’s palsy, including unwanted facial movements known as synkinesis.Botox injections work by weakening or paralyzing certain muscles or by temporarily blocking the nerve input into the muscles.Facial synkinesis is the involuntary movement of one set of muscles when the patient tries to move another set of muscles. For example, when the patient blinks, the mouth smiles or grimaces.Botox can improve the symmetry of the face and reduce muscle contractures and spasms. Botox also is effective for platysmal banding — verticle lines that develop in the neck as a result of muscle contractions.Kircher said he starts out conservatively, treating patients with dilute doses. After seeing how well the patient does, Kircher adjusts the dose if necessary.Botox is not a cure. The drug wears off after three or four months, so patients need repeat injections.”While we can never make the face perfect, we have found Botox to be extremely effective,” Kircher said. “It can make a huge difference in patients’ lives.”Kircher is an assistant professor in the Department of Otolaryngology of Loyola University Chicago Stritch School of Medicine.

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Neurologists report unique form of musical hallucinations

Aug. 20, 2013 — One night when she was trying to fall asleep, a 60-year-old woman suddenly began hearing music, as if a radio were playing at the back of her head.The songs were popular tunes her husband recognized when she sang or hummed them. But she herself could not identify them.This is the first known case of a patient hallucinating music that was familiar to people around her, but that she herself did not recognize, according to Dr. Danilo Vitorovic and Dr. José Biller of Loyola University Medical Center. The neurologists describe the unique case in the journal Frontiers in Neurology.The case raises “intriguing questions regarding memory, forgetting and access to lost memories,” the authors write.Musical hallucinations are a form of auditory hallucinations, in which patients hear songs, instrumental music or tunes, even though no such music is actually playing. Most patients realize they are hallucinating, and find the music intrusive and occasionally unpleasant. There is no cure.Musical hallucinations usually occur in older people. Several conditions are possible causes or predisposing factors, including hearing impairment, brain damage, epilepsy, intoxications and psychiatric disorders such as depression, schizophrenia and obsessive-compulsive disorder. Hearing impairment is the most common predisposing condition, but is not by itself sufficient to cause hallucinations.Vitorovic and Biller describe a hearing-impaired patient who initially hallucinated music when she was trying to fall asleep. …

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New species of carnivore looks like a cross between a house cat and a teddy bear

Aug. 15, 2013 — Observed in the wild, tucked away in museum collections, and even exhibited in zoos around the world — there is one mysterious creature that has been a victim of mistaken identity for more than 100 years. A team of Smithsonian scientists, however, uncovered overlooked museum specimens of this remarkable animal, which took them on a journey from museum cabinets in Chicago to cloud forests in South America to genetics labs in Washington, D.C. The result: the olinguito (Bassaricyon neblina) — the first carnivore species to be discovered in the American continents in 35 years.The team’s discovery is published in the Aug. 15 issue of the journal ZooKeys.The olinguito (oh-lin-GHEE-toe) looks like a cross between a house cat and a teddy bear. It is actually the latest scientifically documented member of the family Procyonidae, which it shares with raccoons, coatis, kinkajous and olingos. The 2-pound olinguito, with its large eyes and woolly orange-brown fur, is native to the cloud forests of Colombia and Ecuador, as its scientific name, “neblina” (Spanish for “fog”), hints. In addition to being the latest described member of its family, another distinction the olinguito holds is that it is the newest species in the order Carnivora — an incredibly rare discovery in the 21st century.”The discovery of the olinguito shows us that the world is not yet completely explored, its most basic secrets not yet revealed,” said Kristofer Helgen, curator of mammals at the Smithsonian’s National Museum of Natural History and leader of the team reporting the new discovery. “If new carnivores can still be found, what other surprises await us? So many of the world’s species are not yet known to science. …

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Blocking key enzyme in cancer cells could lead to new therapy

Aug. 1, 2013 — Researchers from the University of Illinois at Chicago College of Medicine have identified a characteristic unique to cancer cells in an animal model of cancer — and they believe it could be exploited as a target to develop new treatment strategies.An enzyme that metabolizes the glucose needed for tumor growth is found in high concentrations in cancer cells, but in very few normal adult tissues. Deleting the gene for the enzyme stopped the growth of cancer in laboratory mice, with no associated adverse effects, reports Nissim Hay, UIC professor of biochemistry and molecular genetics, and his colleagues in the August 12 issue of Cancer Cell. Targeting glucose metabolism for cancer therapy — while avoiding adverse effects in other parts of the body — has been a “questionable” strategy, Hay said. But he and his coworkers showed that the glucose-metabolism enzyme hexokinase-2 can be almost completely eliminated in adult mice without affecting normal metabolic functions or lifespan.Hexokinase-2 is abundant in embryos but absent in most adult cells, where related enzymes take over its role in metabolism. One of the changes that mark a cell as cancerous is expression of the embryonic enzyme. Hay and his colleagues showed that the embryonic version is required for cancer cells to proliferate and grow, and that eliminating it halts tumor growth.They developed a mouse strain in which they could silence or delete the HK2 gene in the adult animal, and they found that these mice could not develop or sustain lung or breast cancer tumors but were otherwise normal and healthy.”We have deleted the HK2 gene systemically in these mice, and they have been living for more than two years now. Their lifespan is the same as normal mice,” Hay said. The researchers also looked at human lung and breast cancer cells in the lab, and found that if they eliminated all HK2, the cells stopped growing.”We think that the process we used to delete the HK2 gene is not absolutely perfect, so there must be some low levels of HK2 in the mice. But that seems to be enough for the cells that use HK2, and the therapeutic effects on tumors in these mice are stable.”Hay thinks the enzyme is involved in making the building-blocks for the DNA of cancer cells, which need lots of all cellular components as they rapidly divide.”Without HK2, the cancer cells don’t make enough DNA for new cells, and so tumor growth comes to a standstill,” said Hay.Krushna C. …

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A glass of milk after eating sugary cereals may prevent cavities

July 31, 2013 — Washing down sugary breakfast cereal with milk after eating reduces plaque acid levels and may prevent damage to tooth enamel that leads to cavities, according to new research at the University of Illinois at Chicago College of Dentistry.Dry ready-to-eat, sugar-added cereals combine refined sugar and starch. When those carbohydrates are consumed, bacteria in the dental plaque on tooth surfaces produce acids, says Christine Wu, professor of pediatric dentistry and director of cariology, who served as principal investigator of the study.The research is published in the July issue of the Journal of the American Dental Association.Reports have shown that eating carbohydrates four times daily, or in quantities greater than 60 grams per person per day, increases the risk of cavities.The new study, performed by Wu’s former graduate student Shilpa Naval, involved 20 adults eating 20 grams of dry Froot Loops cereal, then drinking different beverages — whole milk, 100 percent apple juice, or tap water.Plaque pH, or acidity, was measured with a touch microelectrode between the premolar teeth before eating; at two and five minutes after eating; and then two to 30 minutes after drinking a liquid.The pH in plaque dropped rapidly after consuming cereal alone, and remained acidic at pH 5.83 at 30 minutes. A pH below 7 is acidic; a pH greater than 7 is basic. Pure water has a pH close to 7.Participants who drank milk after eating sugary cereal showed the highest pH rise, from 5.75 to 6.48 at 30 minutes. Those who drank apple juice remained at pH 5.84 at 30 minutes, while water raised the pH to 6.02.Fruit juices are considered healthy food choices, but the added sugar can be a risk to dental health, Wu said.”Our study results show that only milk was able to reduce acidity of dental plaque resulting from consuming sugary Froot Loops,” said Naval, who is currently a fellow at the Centers for Disease Control and Prevention in Atlanta. “We believe that milk helped mitigate the damaging effect of fermentable carbohydrate and overcome the previously lowered plaque pH.”Milk, with a pH ranging from 6.4 to 6.7, is considered to be a functional food that fights cavities because it promotes tooth remineralization and inhibits the growth of plaque, Wu said.Wu says most consumers think that since milk is considered to be cavity-fighting, acid production by plaque bacteria can be minimized by mixing it with cereal. However, in an unpublished study in her lab, it was discovered that the combination of Froot Loops and milk became syrupy. Eating cereal combined with milk lowered plaque pH to levels similar to that obtained after rinsing with a 10 percent sugar solution.Eating sugar-added cereal with milk, followed by drinking fruit juice is thus a highly cavity-causing combination, Wu said.Diet plays an important role in oral health, Wu said. Studies of food intake and cavities have focused mainly on the sugar, or carbohydrate, content. Fewer studies have looked at how combinations of food, and the order in which they are eaten, may help fight cavities.”Results from a previous study suggested that the last food item consumed exerts the greatest influence on subsequent plaque pH,” she said. …

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Water molecules control inactivation and recovery of potassium channels

July 28, 2013 — Just 12 molecules of water cause the long post-activation recovery period required by potassium ion channels before they can function again. Using molecular simulations that modeled a potassium channel and its immediate cellular environment, atom for atom, University of Chicago scientists have revealed this new mechanism in the function of a nearly universal biological structure, with implications ranging from fundamental biology to the design of pharmaceuticals.Their findings were published online July 28 in Nature.”Our research clarifies the nature of this previously mysterious inactivation state. This gives us better understanding of fundamental biology and should improve the rational design of drugs, which often target the inactivated state of channels” said Benoît Roux, PhD, professor of biochemistry and molecular biology at the University of Chicago.Potassium channels, present in the cells of virtually living organisms, are core components in bioelectricity generation and cellular communication. Required for functions such as neural firing and muscle contraction, they serve as common targets in pharmaceutical development.These proteins act as a gated tunnel through the cell membrane, controlling the flow of small ions into and out of cells. After being activated by an external signal, potassium channels open to allow ions through. Soon after, however, they close, entering an inactive state and are unable to respond to stimuli for 10 to up to 20 seconds.The cause of this long recovery period, which is enormously slow by molecular standards, has remained a mystery, as structural changes in the protein are known to be almost negligible between the active and inactivated states — differing by a distance equivalent to the diameter of a single carbon atom.To shed light on this phenomenon, Roux and his team used supercomputers to simulate the movement and behavior of every individual atom in the potassium channel and its immediate environment. After computations corresponding to millions of core-hours, the team discovered that just 12 water molecules were responsible for the slow recovery of these channels.They found that when the potassium channel is open, water molecules quickly bind to tiny cavities within the protein structure, where they block the channel in a state that prevents the passage of ions. The water molecules are released slowly only after the external stimulus has been removed, allowing the channel to be ready for activation again. This computer simulation-based finding was then confirmed through osmolarity experiments in the laboratory.”Observing this was a complete surprise, but it made a lot of sense in retrospect,” Roux said. “Better understanding of this ubiquitous biological system will change how people think about inactivation and recovery of these channels, and has the potential to someday impact human health.”

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A warmer planetary haven around cool stars, as ice warms rather than cools

July 19, 2013 — In a bit of cosmic irony, planets orbiting cooler stars may be more likely to remain ice-free than planets around hotter stars. This is due to the interaction of a star’s light with ice and snow on the planet’s surface.Stars emit different types of light. Hotter stars emit high-energy visible and ultraviolet light, and cooler stars give off infrared and near-infrared light, which has a much lower energy.It seems logical that the warmth of terrestrial or rocky planets should depend on the amount of light they get from their stars, all other things being equal. But new climate model research led by Aomawa Shields, a doctoral student in the University of Washington astronomy department, has added a surprising new twist to the story: Planets orbiting cool stars actually may be much warmer and less icy than their counterparts orbiting much hotter stars, even though they receive the same amount of light.That’s because the ice absorbs much of the longer wavelength, near-infrared light predominantly emitted by these cooler stars. This is counter to what we experience on Earth, where ice and snow strongly reflect the visible light emitted by the Sun.Around a cooler (M-dwarf) star, the more light the ice absorbs, the warmer the planet gets. The planet’s atmospheric greenhouse gases also absorb this near-infrared light, compounding the warming effect.The researchers found that planets orbiting cooler stars, given similar amounts of light as those orbiting hotter stars, are therefore less likely to experience so-called “snowball states,” icing over from pole to equator.However, around a hotter star such as an F-dwarf, the star’s visible and ultraviolet light is reflected by planetary ice and snow in a process called ice-albedo feedback. The more light the ice reflects, the cooler the planet gets.This feedback can be so effective at cooling that terrestrial planets around hotter stars appear to be more susceptible than other planets to entering snowball states. That’s not necessarily a bad thing, in the scheme of time — Earth itself is believed to have experienced several snowball states during the course of its 4.6 billion year history.Shields and co-authors found that this interaction of starlight with a planet’s surface ice is less pronounced near the outer edge of the habitable zone, where carbon dioxide is expected to build up as temperatures decrease. The habitable zone is the swath of space around a star that’s just right to allow an orbiting planet’s surface water to be in liquid form, thus giving life a chance.That is the case because planets at that zone’s outer edge would likely have a thick atmosphere of carbon dioxide or other greenhouse gases, which blocks the absorption of radiation at the surface, causing the planet to lose any additional warming advantage due to the ice.The researchers’ findings are documented in a paper published in the August issue of the journal Astrobiology, and published online ahead of print July 15.Shields said that astronomers hunting for possible life will prioritize planets less vulnerable to that snowball state — that is, planets other than those orbiting hotter stars. But that doesn’t mean they will rule out the cooler planets.”The last snowball episode on Earth has been linked to the explosion of multicellular life on our planet,” Shields said. …

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What are fructooliogosaccharides and how do they provide digestive, immunity and bone health benefits?

July 16, 2013 — A new presentation today at the 2013 Institute of Food Technologists (IFT) Annual Meeting & Expo® in Chicago focused on the health benefits of short-chain fructooliogosaccharides (scFOS), which are low-calorie, non-digestible carbohydrates that can improve food taste and texture while aiding immunity, bone health and the growth and balance of important bacteria in the digestive track.Fructooliogosaccharides are naturally found in chicory, onions, asparagus, wheat, tomatoes and other fruits, vegetables and grains. They also can be derived from cane sugar and seaweed for use as a low-calorie (1.5 — 2 Kcal/g) food sweetener and supplement. As scFOS provides approximately 30-to-50 percent of the sweetness of regular sugar, it can be used to enhance flavor and lower the amount of sugar in a food product.In addition, scFOS are considered prebiotics. After they are consumed, fructooliogosaccharides move to the large intestine to stimulate the production of microbiota in the colon and gastrointestinal track.Microbiotas are “friendly, beneficial” bacteria, said Kelly A. Tappenden, Ph.D., Kraft Foods human nutrition endowed professor at the University of Illinois at Urbana-Champaign and editor-in-chief of the Journal of Parenteral and Enteral Nutrition. Microbiotas produce essential nutrients such as short-chain fatty acids; control epithelial cell growth (the cells that line body cavities); prevent overgrowth of infectious organisms; boost intestinal immunity; and prevent inflammation, diarrhea and other intestinal conditions. This “essential ecosystem” provides an important “balance between health and disease” in the body.Fructooliogosaccharides also increase calcium absorption in the body, an important consideration for pre- and post-menopausal women, ages 45 and older, who are losing critical bone mass that increases their risk for osteoporosis and bone fractures.The regular addition of scFOS to the diet is “ideal for maintaining mineral density and (bone) strength,” said Phillip Allsopp, Ph.D., research associate at the University of Ulster in Coleraine, Ireland. Most Americans, including many formula-fed infants and children, do not get enough scFOS, said Cristina Munteanu, senior technical service technologist at Ingredion, Inc.As an additive, scFOS is a clear, stable powder suitable for pasteurization, baking and beverages, said Munteanu. It can be found in milk, yogurts and other dairy products, as well as snacks, cereal, bars and candy.

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Findings offer alternative approach to creating a universal influenza vaccine

July 15, 2013 — A team of scientists, led by researchers at The Wistar Institute, has determined that it might be possible to stimulate the immune system against multiple strains of influenza virus by sequentially vaccinating individuals with distinct influenza strains isolated over the last century.Their results also suggest that world health experts might need to re-evaluate standard tests used for surveillance of novel influenza strains. Their findings are published in the Journal of Experimental Medicine, available online now.According to the Wistar researchers, their analysis could lead to an alternative approach to creating a “universal” flu vaccine — a vaccine that would provide resistance to seasonal and pandemic influenza strains over many years, negating the need for an annual flu shot.”Influenza vaccines are very safe and provide good protection. However, we need to continuously update seasonal flu vaccines because influenza viral proteins change over time,” said Scott Hensley, Ph.D., an assistant professor at The Wistar Institute and corresponding author on the study. “Since influenza viruses are constantly changing, we all have unique pre-exposure histories that depend on when we were born and the specific types of viruses that circulated during our childhood.”Vaccines work by stimulating the immune system to produce antibody proteins against particles (called antigens) from an infectious agent, such as bacteria or a virus. The immune system saves the cells that produce effective antibodies, which then provide immunity against future attacks by the same or similar infectious agents. Despite the availability of a vaccine, seasonal influenza typically kills 36,000 Americans, alone, and nearly a half million individuals around the world, in total.Most current efforts to create universal vaccines hinge on the idea of generating antibodies against a portion of the virus that is relatively unchanged year-to-year.”Our studies demonstrate that individuals that are infected sequentially with dramatically different influenza strains mount antibody responses against a conserved region of influenza virus,” Hensley said. “Since we now know that pre-exposure events can influence vaccine responsiveness in a predictable way, we can begin to design vaccine regiments that preferentially elicit antibody responses against conserved regions of influenza virus.”The researchers began their current work by studying human antibody responses against the 2009 pandemic H1N1 virus. The 2009 strain is antigenically distinct from recently circulating seasonal H1N1 strains, and a distant relative of the virus that caused the devastating “Spanish Flu” of the early 20th century. The most effective antibodies are those that bind to a particular portion (or “epitope”) of hemagglutinin (HA), a protein produced by the influenza virus.According to Hensley, however, their chief insight occurred when his team hit the “sort” button on a spreadsheet document, thereby arranging all samples by age of the donor. Different aged people, they found, mount vastly different antibody responses to pandemic H1N1, depending on whether or not they were exposed to a seasonal H1N1 years earlier. …

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Computer as smart as a 4-year-old? Researchers IQ test new artificial intelligence system

July 15, 2013 — Artificial and natural knowledge researchers at the University of Illinois at Chicago have IQ-tested one of the best available artificial intelligence systems to see how intelligent it really is.Turns out it’s about as smart as the average 4-year-old, they will report July 17 at the U.S. Artificial Intelligence Conference in Bellevue, Wash.The UIC team put ConceptNet 4, an artificial intelligence system developed at M.I.T., through the verbal portions of the Weschsler Preschool and Primary Scale of Intelligence Test, a standard IQ assessment for young children.They found ConceptNet 4 has the average IQ of a young child. But unlike most children, the machine’s scores were very uneven across different portions of the test.”If a child had scores that varied this much, it might be a symptom that something was wrong,” said Robert Sloan, professor and head of computer science at UIC, and lead author on the study.Sloan said ConceptNet 4 did very well on a test of vocabulary and on a test of its ability to recognize similarities.”But ConceptNet 4 did dramatically worse than average on comprehension­the ‘why’ questions,” he said.One of the hardest problems in building an artificial intelligence, Sloan said, is devising a computer program that can make sound and prudent judgment based on a simple perception of the situation or facts-the dictionary definition of commonsense.Commonsense has eluded AI engineers because it requires both a very large collection of facts and what Sloan calls implicit facts-things so obvious that we don’t know we know them. A computer may know the temperature at which water freezes, but we know that ice is cold.”All of us know a huge number of things,” said Sloan. “As babies, we crawled around and yanked on things and learned that things fall. We yanked on other things and learned that dogs and cats don’t appreciate having their tails pulled.” Life is a rich learning environment.”We’re still very far from programs with commonsense-AI that can answer comprehension questions with the skill of a child of 8,” said Sloan. He and his colleagues hope the study will help to focus attention on the “hard spots” in AI research.Study coauthors are UIC professors Stellan Ohlsson of psychology and Gyorgy Turan of mathematics, statistics and computer science; and UIC mathematical computer science undergraduate student Aaron Urasky.The study was supported by award N00014-09-1-0125 from the Office of Naval Research and grant CCF-0916708 from the National Science Foundation.

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Young job seekers, check your privacy settings

July 12, 2013 — Social media websites can be a boon for employers scoping out job applicants, and that’s bad news for certain groups of young people, according to a new Northwestern University study.Researchers found that — among young adults — men, Hispanics and those with lower Internet skills are the least likely to keep employment-related audiences in mind when it comes to their online profiles. Women, whites and those with higher Internet skills are more likely to actively manage their social media privacy settings as they seek a job or maintain employment.This is the first study to analyze how different demographics of young adults approach online reputation management strategies during a job search. It was published online in June in the journal IEEE Security & Privacy.”Young people could benefit from understanding the implications of these issues,” said Eszter Hargittai, lead author of the study. “Without adequate privacy settings, inappropriate pictures or comments posted on a social media profile could be seen by an employer and cost you a job opportunity.”Hargittai is an associate professor and Delaney Family Professor in the department of communication studies at Northwestern.”Managing the privacy of your social media profiles can be complex,” she said. “A site’s settings can change quickly, and if you are not keeping track and checking in on your settings regularly, you could inadvertently leave parts of your profile open to the public even if you had set them to more restricted access earlier.”Because a significant portion of the young people in this study seemed at risk in regard to privacy management practices, there may be a need for more formal training from career service organizations, libraries and others on best practices for maintaining self-presentation online, Hargittai said.Study highlights:34.5 percent of men and 25 percent of women never managed their privacy settings or the content of their social media profiles with respect to an employer audience. Whites were much more likely than other races to adjust social media profiles at least once in the past year in anticipation of employers searching for information about them. Hispanics were the least likely to keep an employment-related audience in mind in regards to the content of their online profiles. Women were more likely than men to manage their privacy settings for an employer-related audience and tended to do so more frequently. Those more knowledgeable about Internet privacy matters and privacy-related terms, such as “tagging,” “limited profile” and “preference settings,” were more likely to engage in managing the privacy of their social media profiles. For the study, researchers analyzed responses from a paper-and-pencil survey given to a sample of 545 diverse young adults, ages 21 or 22. …

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Cloud behavior expands habitable zone of alien planets

July 1, 2013 — A new study that calculates the influence of cloud behavior on climate doubles the number of potentially habitable planets orbiting red dwarfs, the most common type of stars in the universe. This finding means that in the Milky Way galaxy alone, 60 billion planets may be orbiting red dwarf stars in the habitable zone.Researchers at the University of Chicago and Northwestern University based their study, which appears in Astrophysical Journal Letters, on rigorous computer simulations of cloud behavior on alien planets. This cloud behavior dramatically expanded the habitable zone of red dwarfs, which are much smaller and fainter than stars like the sun.Current data from NASA’s Kepler Mission, a space observatory searching for Earth-like planets orbiting other stars, suggest there is approximately one Earth-size planet in the habitable zone of each red dwarf. The UChicago-Northwestern study now doubles that number.”Most of the planets in the Milky Way orbit red dwarfs,” said Nicolas Cowan, a postdoctoral fellow at Northwestern’s Center for Interdisciplinary Exploration and Research in Astrophysics. “A thermostat that makes such planets more clement means we don’t have to look as far to find a habitable planet.”Cowan is one of three co-authors of the study, as are UChicago’s Dorian Abbot and Jun Yang. The trio also provide astronomers with a means of verifying their conclusions with the James Webb Space Telescope, scheduled for launch in 2018.The formula for calculating the habitable zone of alien planets — where they can orbit their star while still maintaining liquid water at their surface — has remained much the same for decades. But the formula largely neglects clouds, which exert a major climatic influence.”Clouds cause warming, and they cause cooling on Earth,” said Abbot, an assistant professor in geophysical sciences at UChicago. “They reflect sunlight to cool things off, and they absorb infrared radiation from the surface to make a greenhouse effect. That’s part of what keeps the planet warm enough to sustain life.”A planet orbiting a star like the sun would have to complete an orbit approximately once a year to be far enough away to maintain water on its surface. “If you’re orbiting around a low mass or dwarf star, you have to orbit about once a month, once every two months to receive the same amount of sunlight that we receive from the sun,” Cowan said.Tightly orbiting planetsPlanets in such a tight orbit would eventually become tidally locked with their sun. …

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