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Machine learning flags patients at risk of TB comeback

14 min 5 sec ago

New diagnostic tools such as machine learning and precision medicine could help identify tuberculosis patients with the highest risk of reactivation of the disease, report researchers.

The researchers are showing that identifying multiple biomarkers can provide a more accurate diagnosis for patients.

“A multi-array test can provide a more detailed, disease specific glimpse into patient’s infection and likely outcome,” says Ryan Bailey, professor of chemistry at the University of Michigan and coauthor of the study, which appears in Integrative Biology.

“Using a precision medicine approach reveals previously obscured diagnostic signatures and reactivation risk potential.”

Latent tuberculosis infection (LTBI) affects nearly 2 billion people around the world and about 10 percent of those cases result in active tuberculosis. The reactivation from latency can happen anytime and the mechanism for it is not well-understood.

Currently, doctors test for LTBI using a skin scratch test or a blood test that identifies one biomarker but cannot distinguish between memory immune response, vaccine-initiated response, and non-tuberculous mycobacteria exposure. The possibility of correctly identifying the disease through these tests is less than 5 percent.

Doctors use an antibiotic regimen to treat tuberculosis, but that can increase the risk of antibiotic resistance.

The new diagnostic tools will help identify patients with the highest risk of reactivation and who will benefit from therapy, and reduce some of the side effects of overtreatment. By introducing multiple biomarker assays in blood tests with powerful analysis tools, the chances for correctly diagnosing TB increases dramatically.

The researchers used a precision normalization approach to correct for differences in individual basal immune function that revealed a high- and low-reactivation risk.

“This high-level multiplexing, high-assay performance can be cost-effective and scalable,” Bailey says, adding that it can also be used to detect other diseases like autoimmune diseases and cancer.

Additional researchers from the University of Michigan, the University of Illinois, and the Mayo Clinic in Rochester, Minnesota contributed to the study.

Source: University of Michigan

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‘Reverse trick’ for LEDs could keep future computers cool

51 min 28 sec ago

In a finding that runs counter to a common assumption in physics, researchers ran a light emitting diode (LED) with electrodes reversed in order to cool another device mere nanometers away.

The approach could lead to new solid-state cooling technology for future microprocessors, which will have so many transistors packed into a small space that current methods can’t remove heat quickly enough.

“We have demonstrated a second method for using photons to cool devices,” says Pramod Reddy, who co-led the work with Edgar Meyhofer, both professors of mechanical engineering at the University of Michigan.

The first—known in the field as laser cooling—is based on Arthur Ashkin’s foundational work. Ashkin shared the Nobel Prize in Physics in 2018. The researchers instead harnessed the chemical potential of thermal radiation—a concept more commonly used to explain, for example, how a battery works.

The team made a calorimeter with a sensing area 80 micrometers (0.08 millimeters) across, shown in this electron microscope image. They used the calorimeter to show that an infrared photodiode running with electrodes reversed behaved as if it were at a lower temperature and cooled the calorimeter. (Credit: Linxiao Zhu)

“Even today, many assume that the chemical potential of radiation is zero,” Meyhofer says. “But theoretical work going back to the 1980s suggests that under some conditions, this is not the case.”

The chemical potential in a battery, for instance, drives an electric current when put into a device. Inside the battery, metal ions want to flow to the other side because they can get rid of some energy—chemical potential energy—and we use that energy as electricity. Electromagnetic radiation, including visible light and infrared thermal radiation, typically doesn’t have this type of potential.

“Usually for thermal radiation, the intensity only depends on temperature, but we actually have an additional knob to control this radiation, which makes the cooling we investigate possible,” says lead author Linxiao Zhu, a research fellow in mechanical engineering.

That knob is electrical. In theory, reversing the positive and negative electrical connections on an infrared LED won’t just stop it from emitting light, but will actually suppress the thermal radiation that it should be producing just because it’s at room temperature.

The researchers modified an infrared photodiode about the size of a grain of rice, shown in this electron microscope image. They smoothed its surface so that they could place it in close proximity to their custom-made calorimeter, just 55 nanometers (0.000055 millimeters) between them. The calorimeter’s measurements showed that the photodiode, when run with electrodes reversed, behaved as if it were at a lower temperature, and cooled down the calorimeter. (Credit: Linxiao Zhu)

“The LED, with this reverse bias trick, behaves as if it were at a lower temperature,” Reddy says.

However, measuring this cooling—and proving that anything interesting happened—is complicated.

To get enough infrared light to flow from an object into the LED, the two would have to be extremely close together—less than a single wavelength of infrared light. This is necessary to take advantage of “near field” or “evanescent coupling” effects, which enable more infrared photons, or particles of light, to cross from the object to be cooled into the LED.

The researchers had a leg up because they had already been heating and cooling nanoscale devices, arranging them so that they were only a few tens of nanometers apart—or less than a thousandth of a hair’s breadth. At this close proximity, a photon that would not have escaped the object to be cooled can pass into the LED, almost as if the gap between them did not exist. And the team had access to an ultra-low vibration laboratory where measurements of objects separated by nanometers become feasible because of dramatically reduced vibrations, such as those from footsteps by others in the building.

Linxiao Zhu shows the experimental platform that housed the calorimeter and photodiode. This system can damp vibrations from the room and building, steadily holding the two nanoscale objects 55 nanometers (0.000055 millimeters) apart. (Credit: Joseph Xu)

The group proved the principle by building a minuscule calorimeter, which is a device that measures changes in energy, and putting it next to a tiny LED about the size of a grain of rice. These two were constantly emitting and receiving thermal photons from each other and elsewhere in their environments.

“Any object that is at room temperature is emitting light. A night vision camera is basically capturing the infrared light that is coming from a warm body,” Meyhofer says.

But once the LED is reverse biased, it begins acting as a very low temperature object, absorbing photons from the calorimeter. At the same time, the gap prevents heat from traveling back into the calorimeter via conduction, resulting in a cooling effect.

The team demonstrated cooling of 6 watts per meter squared. Theoretically, this effect could produce cooling equivalent to 1,000 watts per meter squared, or about the power of sunshine on Earth’s surface.

This could turn out to be important for future smartphones and other computers. With more computing power in smaller and smaller devices, removing the heat from the microprocessor is beginning to limit how much power can fit into a given space.

With improvements of the efficiency and cooling rates of this new approach, the team envisions this phenomenon as a way to quickly draw heat away from microprocessors in devices. It could even stand up to the abuses endured by smartphones, as nanoscale spacers could provide the separation between microprocessor and LED.

The research appears in Nature. The Department of Energy and the Army Research Office supported the research. The researchers made the devices in the University of Michigan’s Lurie Nanofabrication Facility.

Source: University of Michigan

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Watch ‘flares’ repair leak in protective cell barrier

2 hours 4 min ago

Using a new live-imaging technique, researchers directly detected short-lived leaks in tissues that protect us from bacteria, viruses, and other disease-causing invaders.

Epithelial tissues are sheets of cells that coat our organs, creating wall-like barriers for protection. And when potentially harmful gaps between these cells emerge, a molecular switch gets flipped to call the repair crew and fix the leaks.

The researchers’ new microscopy barrier assay also allowed them to discover that the repair mechanism involves local activation of a protein called Rho.

As epithelial cells move and change shape, the junctions between these cells can develop gaps, resulting in a leaky barrier. Bursts of Rho activity (called Rho flares (white arrows)) occur at the breakage sites and signal for the repair of leaky junctions. The movie on the right is an enlargement of a Rho flare from the movie on the left. Green: a fluorescent reporter for active Rho. Magenta: fluorescently tagged ZO-1, a junction protein. (Credit: Rachel Stephenson)

The new assay could help provide insights into the mechanisms of diseases that target the epithelial barrier—ailments that microbes and allergens cause, as well as various inflammatory states, immune disorders, diabetes, and even cancers. And the assay could potentially help screen drugs to treat those afflictions, according to the researchers.

“An important unanswered question about epithelial tissues is: How are the junctions between cells able to maintain the biological barrier function even as cells change shape?” says senior author Ann Miller, an associate professor in the molecular, cellular, and developmental biology department at the University of Michigan.

In their study, the researchers used epithelial cells in live frog embryos, which have cell-cell junctions similar in structure and protein composition to those in human epithelial tissues.

Epithelial cells from a frog embryo. The junctions between the cells are highlighted in white, and cell nuclei are blue. (Credit: Rachel Stephenson)

During embryonic development, many epithelial cells work together to bend and fold tissues. Using their new microscopy assay—which is known as ZnUMBA for Zinc-based Ultrasensitive Microscopic Barrier Assay—the researchers studied what happens at the cellular level when epithelial cell-cell junctions are stretched.

They showed that leaks in barrier function happened when cell-cell junctions elongate. But the leaks are short-lived, suggesting there is an active repair mechanism.

On further investigation, the researchers discovered that the repair mechanism involves local activation of the protein Rho, in a sudden burst of activity they dubbed a Rho flare. Rho then activates proteins that contract the junction, repairing it.

“We discovered that cells are normally very proactive when it comes to maintaining the barrier,” says first author Rachel Stephenson, a research scientist in Miller’s lab who carried out the project for her doctoral dissertation.

“This repair mechanism happens quickly and is carried out very locally, affecting only a small part of the cell junction, rather than multiple cells or the whole tissue.

“We think that this proactive approach is what gives our cells the flexibility to move and change shape without compromising the barrier function of the tissue. Diseases involving a leaky barrier might be due to a faulty repair mechanism or the cells’ inability to detect leaks and flip the switch.”

The researchers are now working to determine how the switch gets flipped to turn on Rho at the right time and place and to identify other proteins that are part of the cellular repair crew to plug leaky biological barriers.

The team’s findings appear in the journal Developmental Cell. Additional coauthors are from the University of Michigan and the University of Edinburgh. The National Institutes of Health, National Science Foundation Graduate Research Fellowships, and a postdoctoral fellowship from the Japan Society for the Promotion of Science funded the research.

Source: University of Michigan

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‘Master control’ puts brakes on deadly food allergy reactions

3 hours 17 min ago

A master control mechanism on mast cells, a type of immune cell, can prevent the immune system from overreacting in times of stress, which could limit or even stop severe allergic reactions to food, researchers report.

In cases of severe, even deadly, allergic reactions to foods such as peanuts and fish, immune cells go into hyperdrive. This can trigger anaphylactic shock, which can in turn cause blood pressure to plummet and obstruct breathing.

“What we found is that the CRF2 receptor can act as an inhibitor, or a control point, in mast cells, which prevents them from becoming over-activated,” says Adam Moeser, an associate professor specializing in stress-induced diseases at Michigan State University. “Up until now, no one has really understood the exact role this particular receptor plays on these important cells.”

Protective role

Stressful situations immediately activate mast cells, according to Moeser. This can be either psychological or immunological stress—where a virus or bacteria challenges the body.

Cell receptors typically have one primary job, regulating cell function. In the case of CRF2, or corticotropin-releasing factor 2, researchers discovered its ability to control how much of a chemical substance, such as histamine mast cells release into the body. As a result, CRF2 could help reduce the onset of a severe reaction or disease.

“Histamine’s role is protective, to get rid of invading allergens and pathogens,” Moeser says. “But if a receptor like CRF2 isn’t working properly, then too much of it is released.”

When this happens, instead of fighting off the invaders, it exacerbates the immune response causing anaphylaxis or other serious health complications. The same thing happens with gastrointestinal diseases, such as irritable bowel syndrome, which can cause acute abdominal pain, Moeser says.

The researchers were able to duplicate the same result by isolating mice, pig and human mast cells.

“When we manipulated the CRF2 receptor with a drug, basically blocking its ability to function properly, it caused these mast cells to become hyperactive and increase the release of histamine,” Moeser says. “This showed us just how important this receptor is and by using these different models, we now have good supporting evidence that this is likely what happens in actual patients.”

Beyond EpiPens

Moeser notes a recent case that drew national attention in which a young boy went into anaphylactic shock and died simply by smelling cooked fish.

“Allergies and anaphylaxis are common these days, and anaphylaxis is actually on the rise,” Moeser says. “Being able to respond quickly and effectively is key. Knowing what we know now about this receptor could lead to other potential therapies beyond an EpiPen that’s more preventative than reactive.”

This could mean people with known allergies wouldn’t have to wait until a severe reaction occurred to administer treatment. Rather, they could simply take a drug that targeted this receptor to ensure normal function and stop these responses from happening.

“There’s still more we want to know, like what factors—whether a person’s sex or different types of stress—are involved in how this particular receptor works,” Moeser says.

“But now that we know the critical role it plays, a pharmaceutical company could potentially develop a drug that targets these specific cells. That would be the ultimate goal.”

The National Institutes of Health funded the work, which appears in the Journal of Allergy and Clinical Immunology.

Source: Michigan State University

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Service dogs give handlers an emotional boost

4 hours 11 min ago

Service dogs can have measurable positive effects on the health and well-being of people with physical disabilities, a new study shows.

“We found that compared to individuals on the wait list, those who had a service dog had significantly better psychosocial health including better emotional, social, and work/school functioning,” says Maggie O’Haire from the Center for the Human-Animal Bond at Purdue University.

“However, we found that having a service dog was surprisingly not related to other indicators of well-being such as anger, sleep quality, or social companionship. These findings help shed light on the fact that having a service dog may impact some areas of life more than others.”

Service dogs—more specifically, mobility and medical alert service dogs—are often placed with individuals who have a variety of different conditions or disabilities, such as seizures disorders, quadri- or paraplegia, or cerebral palsy.

Service dogs can help with mobility—including with basic tasks such as opening and closing doors—or trainers can teach them to recognize and respond to the onset of a medical emergency such as a seizure.

For the study, which appears in Disability and Rehabilitation, researchers recruited 154 individuals from the databases of Canine Assistants, a national service dog provider, to participate in a survey. A total of 97 individuals had a service dog from Canine Assistants while 57 were on a waiting list to receive one.

The findings show how service dogs may help their handler in ways that extend beyond what they are directly trained to do, the researchers say.

“Our findings are important because they empirically validate the numerous anecdotal reports from individuals with service dogs that say that these dogs really have an impact on their life,” says coauthor Kerri Rodriguez.

But if service dogs provide these sorts of benefits, what about dogs in general?

“We are still unsure how having a service dog and a pet dog may differ,” Rodriguez says. “Although these service dogs are extensively trained to provide medical or physical assistance, we know that their companionship and unconditional love are important factors in the relationship.”

Rodriguez also says future research will benefit from measuring  well-being, self-esteem, or sleep quality both before and after someone receives a service dog to measure change over time.

O’Haire has also been leading research regarding how psychiatric service dogs may help veterans with PTSD. So far, her research has revealed how service dogs might offer both psychosocial and physiological benefits to veterans. O’Haire’s research group is currently conducting a clinical trial studying veterans with and without service dogs over an extended period of time.

Elanco funded the work.

Source: Purdue University

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Fewer suicidal teens die young after caring ‘circle’

4 hours 41 min ago

Building a circle of trusted adults around a suicidal teen may have long-term effects that reduce their risk of dying young, a new study suggests.

Researchers from the University of Michigan tracked deaths among hundreds of young adults who spent time in the hospital for suicidal thoughts or attempts during their teen years, and took part in a study that the team ran in the early 2000s.

Half of the young people had been randomly assigned to receive the extra support of a few caring adults who received training in how to help the teens stick to their treatment plan and how to talk with them in ways that could encourage positive behavioral choices. The other half received the usual levels of care for the time.

The new data, published in JAMA Psychiatry, show that about 12 years later, far more of the young people who got standard care had died, compared with young adults in the group who had received the extra adult support.

The YST approach

The “Youth-Nominated Support Teams,” as the original study called them, were made up of family members, coaches, teachers, youth group leaders, and other adults. For three months following each teen’s hospitalization for suicidal behavior, these 656 “caring adults” received weekly telephone support from professional staff to address their questions and concerns and help them feel more comfortable in their role with the teens.

Although the study of hundreds of young adults cannot show cause and effect, it shows a strong association between the YST approach and a reduced overall risk of early death, and also specifically a reduced risk of death from either suicide or drug overdose of undetermined intent.

“…results suggest that caring adults in the lives of at-risk adolescents can make a difference…”

The leader of the research team is Cheryl King, professor of psychiatry and psychology, and leader of the original YST study. The researchers matched the original information about the study participants with national death records and state death certificates.

In all, 15 of the 448 study participants had died by 2016—but only two of the deaths were among those who had been assigned to the YST group. Statistically, this meant that the non-YST group had a sixfold higher rate of death.

The deaths, which occurred when the study participants were age 18 through 26, were ruled suicides in four instances, drug overdoses or an infection likely related to drug use in nine cases, and one case each of homicide and motor vehicle crash.

When the researchers looked at only the unknown intent drug deaths and suicides, there were eight in the usual-treatment group, but only one in the YST group. However, the number of suicides was too small to show a statistical difference in the number of suicides between the three in the non-YST group and the one in the YST group.

“The YST intervention may have had small and cascading positive effects that combined to have a long-term impact on the risk of dying,” says King. “Although further studies are needed to replicate findings and understand exactly how YST is helping, results suggest that caring adults in the lives of at-risk adolescents can make a difference, and this may be facilitated by education and support for these caring adults.”

Intertwined challenges

When King and her colleagues carried out the original study, they looked mainly at whether the teens stuck to their mental health treatment plans, got help for drug or alcohol problems if they had them, and expressed suicidal thoughts in the first year.

“Our aim is not to just prevent suicide but to improve the quality of life…”

The teens in the YST group were more likely to go to their therapy and medication-related appointments, and to attend substance use-related sessions during the year following their hospitalization for suicide risk.

In the first weeks after their hospitalization, the YST group had lower rates of suicidal thoughts. But when the one-year follow-up ended, the researchers found no major effect on suicidal ideation or self-harm.

The precise cause of the difference in deaths between the two groups, more than a decade later, is unknown. But King ventures that the extra support of adults—including parents, one of whom teens named to their support teams three-quarters of the time—may have helped.

“We know from other research that we need to look at all causes of early mortality that are preventable” because of the often intertwined nature of drug use and abuse, depression and other mental health disorders, and suicidal behavior, says King. “Our aim is not to just prevent suicide but to improve the quality of life for young people and prevent early mortality whenever possible.”

The intertwined nature of these disorders can even continue in death, when death certificates are vague about the cause of death and whether an overdose was intentional or unintentional.

Additional trials

King and her coauthors call on researchers to try to further examine YST and its long-term results and to examine the mortality outcomes of individuals who took part in other studies testing suicide-prevention treatments or strategies.

“The rate of suicide for adolescents in the United States is rising, and it is imperative that we identify and implement effective prevention and intervention strategies,” she says. “The YST approach, which is intended to supplement medication and psychotherapy treatments, shows promise as one such intervention.”

King notes that the team has copies of the YST manual available for researchers, clinicians, and advocates, and is willing to share them upon request.

The research team also includes representatives of Havenwyck Hospital, a private inpatient mental health facility where many of the patients originally received treatment.

Source: University of Michigan

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Sign-language translator is as portable as Chapstick

5 hours 23 min ago

A new sign language translator technology is non-invasive and as portable as a tube of Chapstick, researchers report.

“We are providing a ubiquitous solution to sign language translation,” says Mi Zhang, assistant professor of electrical and computer engineering at Michigan State University.

“Hard-of-hearing individuals who need to communicate with someone who doesn’t understand sign language can have a personalized, virtual interpreter at anytime, anywhere.”

Hundreds of thousands of hard-of-hearing people rely upon American Sign Language, or ASL, to communicate. Without an interpreter present, they don’t have the same employment opportunities and are often at a disadvantage in delicate or sensitive situations, Zhang says.

“Think about if you were in the hospital and needed to communicate with a doctor. You would have to wait for the hospital’s translator—if they have one—to arrive, connect with a toll-free service or rely on a family member to be present,” Zhang says.

The Deep ASL camera. (Credit: Michigan State U.)

“This compromises your privacy and could worsen a health emergency. This is just one example demonstrating the critical need for sign language translation technology.”

Zhang and colleagues saw an opportunity to help the hard-of-hearing population break through this communication barrier.

Zhang’s technology, called DeepASL, features a deep learning—or machine learning based on data inspired by the structure and function of the brain—algorithm that automatically translates signs into English. The technology uses a three-inch sensory device, which Leap Motion developed, that is equipped with cameras to capture hand and finger motions continuously.

“Leap Motion converts the motions of one’s hands and fingers into skeleton-like joints. Our deep learning algorithm picks up data from the skeleton-like joints and matches it to signs of ASL,” says doctoral student Biyi Fang.

“Other translators are word-for-word, requiring users to pause between signs. This limitation significantly slows down face-to-face conversations…”

Similar to setting up Siri on an iPhone, users sign certain words to familiarize their hands and joints to the technology and sensors. They also can create custom signs for their names or non-dictionary words by spelling them out, and have more ease and comfort communicating.

“One differentiating feature of DeepASL is that it can translate full sentences without needing users to pause after each sign. Other translators are word-for-word, requiring users to pause between signs. This limitation significantly slows down face-to-face conversations, making conversations difficult and awkward,” Fang says.

“Our technology is also non-intrusive, unlike other interpreter technologies that require signers to wear gloves, making them feel marginalized because you can literally see their disability.”

Beyond its ability to help the hard-of-hearing communicate to others, DeepASL can help those virtually learning ASL by giving real-time feedback on their signing. Prior technology through video tutorials had limited personal assistance, Zhang explains.

“About 90 percent of deaf children are born to hearing parents. These parents are learning sign language to communicate with their children but don’t usually have time to attend live classes,” Zhang says. “Our technology can gauge their signing to help them learn and improve.”

While the technology translates sign language to verbal conversation, Zhang says that existing, successful speech recognition technologies can help the other side of the conversation, allowing verbal communicators to speak with the hard-of-hearing.

The next step for the technology is commercialization, making it available to the hundreds of thousands of people who need a more accessible interpreter, the researchers say. Leap Motion retails for about $78. The researchers also plan to make the technology compatible with iPhones, and plan to teach it different sign languages.

Source: Michigan State University

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Many hospitals send patients home with high-risk antibiotics

Thu, 2019-02-14 16:27

Even as hospitals try to cut back on prescribing fluoroquinolones—powerful but risky antibiotics—many patients still head home with prescriptions for those same drugs, a new study shows.

In fact, the hospitals that say they are trying to reduce the use of fluoroquinolones are twice as likely to discharge patients with a new prescription for one of the drugs in that risky group.

In all, one-third of the patients researchers studied received a fluoroquinolone prescription at the end of their hospital stay, despite current guidelines calling for restricted use because of dangerous side effects.

FDA warnings

Fluoroquinolones include name brands like Cipro and Levaquin and generic antibiotics whose names end in “-floxacin.” They have been especially linked to the rise of drug-resistant organisms and potentially life-threatening gut infections with an opportunistic microbe called Clostridioides difficile.

They are also linked to ruptures of Achilles tendons, dangerously low blood sugar levels in people with diabetes, and mental health problems including disorientation and delirium.

The US Food and Drug Administration has issued several “black box” warnings about their side effects—most recently in December with a warning that fluoroquinolones could cause rupture of the aorta, the huge artery leading from the heart to the rest of the body.

That warning suggests doctors should not prescribe the drugs to the elderly, people with high blood pressure, and people with a risk or history of aneurysms.

Still, across all 48 Michigan hospitals in the study, discharge-related prescriptions accounted for two-thirds of the fluoroquinolone supply prescribed to the nearly 12,000 patients treated for pneumonia or urinary tract infections.

The drugs accounted for 42 percent of all antibiotics prescribed at discharge.

“Fluoroquinolone antibiotics are easy to use but carry a lot of risk for patients and society at large,” says Valerie Vaughn, a hospital medicine specialist at Michigan Medicine, the University of Michigan’s academic medical center, and lead author of the paper, which appears in Clinical Infectious Diseases.

“These results show we need to focus on not just their use in hospitals, but also in the prescriptions that we send patients home with,” she says. “Discharge prescribing is a big loophole.”

Choose wisely

Researchers used Michigan Hospital Medicine Safety Consortium data from patients treated for pneumonia or UTIs over a nearly two-year period ending in fall 2017. That includes the first nine months after national organizations began requiring hospitals to have a program for tracking and reducing use of antibiotics.

Called antimicrobial stewardship, such programs stem from a need to curb the rise of superbugs, or bacteria that evolve to resist treatment and threaten patients’ lives.

The new study focuses on pneumonia and UTIs because these conditions account for almost half of antibiotic use in hospitals. Hospitalists and general internists are largely the ones to care for these patients, rather than infectious diseases specialists, who mainly focus on the most serious cases.

In all, hospital personnel switched more than 10 percent of patients in the study to a fluoroquinolone antibiotic at discharge. While fluoroquinolones are just one group of antibiotics that doctors can choose, they have the advantage of being able to treat a broad spectrum of infectious organisms and can treat patients who are allergic to penicillin.

They also come in pill form rather than intravenously, which makes them much more attractive for discharge prescriptions.

But if patients are getting through their hospitalization without them, then fluoroquinolones are probably not the right choice for treatment after they leave the hospital, Vaughn says.

“When patients first come in to the hospital, doctors don’t typically have test results to show what’s causing their infection,” which could guide antibiotic choice, Vaughn says. They also may not know if the patient is allergic to penicillin.

“But by the time they’re leaving, you have more results and history—the most information you’re going to have about them,” she says. “This makes the discharge prescription a great place for stewardship programs to intervene and to make antibiotic choice more of an active thought than an afterthought.”

After discharge

The fact that hospitals that have active antimicrobial stewardship programs have higher rates of prescribing fluoroquinolones at discharge deserves more scrutiny, Vaughn says.

Fourteen hospitals in the study had measures in place to require review of fluoroquinolone prescriptions during hospitalization. In these hospitals, more than 78 percent of the supply of fluoroquinolones was prescribed at discharge, compared with 68 percent of the supply for the other 34 hospitals, nearly all of which had antimicrobial stewardship programs but no special emphasis on fluoroquinolones.

It may be that while pharmacists and infection prevention specialists are keeping an eye on in-hospital prescribing, they don’t have access to, or don’t focus on, the prescriptions written at discharge. Electronic health record systems track both inpatient and discharge medications, but they are often in separate sections of the record.

In fact, when researchers showed hospital-specific data on discharge antibiotic prescribing to the physicians in the partnership, it was the first time most had seen it.

After researchers shared the data, several hospitals in the consortium started paying special attention to discharge prescribing of fluoroquinolones, and others are preparing to. If prescribing drops, drug side effects should, too.

Special focus on appropriate fluoroquinolone prescribing in the United Kingdom resulted in a 60 percent drop in C. diff infections, the researchers say.

In the US, hospitals can face financial penalties if a high proportion of their inpatients develop C. diff infections during their stay. But those penalties don’t apply if the patients develop C. diff after they leave the hospital.

Speak up

Hospitalized patients don’t usually express a preference for which antibiotic they receive, except for saying they have a penicillin allergy if they think they do, Vaughn says.

Patients and their families can speak up about not wanting a fluoroquinolone in the hospital or at discharge, especially if they have conditions such as diabetes, high blood pressure, history of aneurysm, or tendon or muscle problems. Patients with a history of C. diff should be especially wary.

Furthermore, Vaughn says, patients often think they have a penicillin allergy when they don’t. If they tell their health care team they have a penicillin allergy, that might receive a higher-risk antibiotic instead.

Patients who have a past test confirming their penicillin allergy, or who experienced shortness of breath or hives after receiving a penicillin-containing drug, should make sure their record notes this. Patients who have an upset stomach or diarrhea after taking penicillin typically don’t have an allergy.

Less is better

Even if the doctor recommends a fluoroquinolone, patients and families can ask for the shortest course possible, to reduce the risk of side effects. Previous research shows that often short courses of the drugs are safe and effective.

“In this era of choosing wisely in medicine, our mantra should be that less is more when it comes to antibiotics,” Vaughn says.

Blue Cross Blue Shield of Michigan and Blue Care Network as part of the BCBSM Value Partnerships program funded the work.

Source: University of Michigan

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Fluorescent tags light up when proteins misfold

Thu, 2019-02-14 13:55

A new method uses fluorescence to detect potentially disease-causing forms of proteins as they unravel due to stress or mutations.

Researchers reengineered a fluorescent compound and developed a method to simultaneously light up two different proteins as they misfold and aggregate inside a living cell, highlighting forms that likely play a role in several neurodegenerative diseases including Alzheimer’s and Parkinson’s.

“In order to function properly, proteins fold into very precise structures, but environmental stress or pathogenic mutations can cause proteins to misfold and aggregate,” says Xin Zhang, assistant professor of chemistry and of biochemistry and molecular biology at Penn State and leader of the research team.

“Protein aggregation is a multi-step process, and it is believed that the intermediate form, which previous imaging techniques could not detect, is responsible for a number of diseases, including Alzheimer’s, Parkinson’s, type 2 diabetes, and cystic fibrosis. We developed the Aggregation Tag method—AggTag—to see these previously undetectable intermediates—soluble oligomers—as well the final aggregates in live cells.”

Turn on the light

Previous techniques to identify protein aggregation used fluorescent compounds that were always lit up, which made it impossible to distinguish properly folded proteins from the intermediate form because both trigger low-level diffuse fluorescence. The AggTag method uses “turn-on fluorescence,” so the compound only lights up when misfolding starts to occur.

“When the fluorescent compound has plenty of space to move, it rotates freely and remains turned off, as in the presence of a properly folded protein,” says Yu Liu, assistant research professor of chemistry at Penn State and the key developer of AggTag method. “But when the protein starts to misfold and aggregate, the compound’s movement becomes restricted and it begins to light up. Diffuse fluorescence indicates that intermediate oligomers are present, while small points of brighter fluorescence indicate that the denser insoluble aggregates are present.”

To allow for this distinction between forms, the research team reengineered the color-causing core of the green fluorescent protein (GFP), which is common in imaging studies because it fluoresces when exposed to certain wavelengths of light. The reengineered compound binds to a tag, which in turn fuses to a protein targeted for imaging.

Red and green

The research team used two different kinds of commercially available tags, Halo-tag and SNAP-tag, which when used with AggTag can induce red or green fluorescence, respectively. Because Halo-tags and SNAP-tags do not interact with each other, they can be used to simultaneously image two different proteins with the two colors. The team also engineered the tags so that the green and red colors can be reversed, giving researchers options for future imaging.

“We plan to continue developing this method so that we can signal the transition of oligomers into insoluble aggregates using a color change,” says Zhang. “This method provides a new toolbox to study protein aggregation, which is currently a highly studied topic among scientists. Hopefully this will allow us to better understand the entire process of protein aggregation and the role of each of these forms in the progression of neurodegenerative and other diseases.”

A paper describing the AggTag method appears online in the Journal of the American Chemical Society. This work had funding from the National Science Foundation, the Burroughs Wellcome Fund, Penn State, the Penn State Huck Institutes of the Life Sciences, and the National Institutes of Health.

A paper extending the method to simultaneously detect two proteins appears online in the journal ChemBioChem. The Burroughs Wellcome Fund, Penn State, the Penn State Huck Institutes of the Life Sciences, and the Sloan Research Foundation supported that work.

Source: Penn State

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Common weed killer ups risk of some cancers by 40%

Thu, 2019-02-14 13:48

Exposure to glyphosate—the world’s most widely used, broad-spectrum herbicide and the primary ingredient in the weed killer Roundup—increases the risk of some cancers by more than 40 percent, according to new research.

Various reviews and international assessments have come to different conclusions about whether glyphosate leads to cancer in humans.

Now, researchers have conducted an updated meta-analysis—a comprehensive review of existing literature—and focused on the most highly exposed groups in each study. They found that the link between glyphosate and non-Hodgkin lymphoma is stronger than previously reported.

“Our analysis focused on providing the best possible answer to the question of whether or not glyphosate is carcinogenic,” says senior author Lianne Sheppard, a professor in the environmental and occupational health sciences and biostatistics departments at the University of Washington. “As a result of this research, I am even more convinced that it is.”

By examining epidemiologic studies published between 2001 and 2018, the team determined that exposure to glyphosate may increase the risk of non-Hodgkin lymphoma by as much as 41 percent. The authors focused their review on epidemiological research in humans but also considered the evidence from laboratory animals.

“This research provides the most up-to-date analysis of glyphosate and its link with Non-Hodgkin Lymphoma, incorporating a 2018 study of more than 54,000 people who work as licensed pesticide applicators,” says coauthor Rachel Shaffer, a doctoral student in the environmental and occupational health sciences department.

“These findings are aligned with a prior assessment from the International Agency for Research on Cancer, which classified glyphosate as a ‘probable human carcinogen’ in 2015,” Shaffer says.

The agricultural industry started using glyphosate in 1974. Its use soared, particularly since the mid-2000s when the practice of “green burndown” began, in which glyphosate-based herbicides are applied to crops shortly before harvest. As a consequence, crops now are likely to have higher residues of glyphosate.

Researchers say more studies are needed to account for the effects of increased exposures from green burndown, which may not be fully captured in the existing studies reviewed in this new publication.

Their findings appear in the journal Mutation Research/Reviews in Mutation Research. Additional coauthors are from the University of California, Berkeley and the Icahn School of Medicine at Mount Sinai in New York. The National Institutes of Environmental Health Sciences and the University of Washington Retirement Association Aging Fellowship funded the research.

Source: University of Washington

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What are the laws around vaccines and kids’ rights?

Thu, 2019-02-14 13:36

The measles outbreak in the US continues to grow, with more than 100 cases reported across the country—most involving young children who have not received immunizations.

Here, Michael Wald, a professor at the Stanford University Law School and an expert on legal policy related to children, discusses the legal rights of children to receive vaccinations and how the law varies from state to state:

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Farewell: Opportunity ends 15-year mission to Mars

Thu, 2019-02-14 10:54

The Mars rover Opportunity finally ended its mission on February 13—three weeks after its 15th anniversary and long past its 90-day warranty.

Over the course of its scientific mission, Opportunity returned hundreds of thousands of images and reshaped our understanding of Mars’ surface for nearly 14 and a half years. Opportunity’s twin, Spirit, challenged by a rocky and rough terrain, officially ended its mission in 2011.

“It’s hard to put the scientific payoff yet into context, since the mission has just come to a close,” says Steve Squyres, professor of physical sciences at Cornell University and the principal scientific investigator for the Mars Exploration Rovers mission. “Both rovers together revealed that ancient Mars was a very, very different place from modern-day Mars; it was more habitable, more Earthlike than Mars is today.”

Opportunity launched just before midnight July 7, 2003, from Cape Canaveral Air Force Base, Florida. It flew 283 million miles to Mars over six months and 19 days. As the craft landed January 25, 2004, cradled in its cocoon of air bags, it bounced 26 times, traveling 220 yards on the surface, before settling in Eagle Crater on Meridiani Planum—a plains area on the red planet.

Squyres called the landing a “hole in one.”

Spherules, nicknamed “blueberries,” indicate evidence of water. (Credit: NASA/JPL Caltech/Cornell) Hints of water

Designed to travel 1,100 yards and run for 90 Martian sols (days that are 39 minutes longer than Earth days), before the dust storm hit, the golf-cart size rover had roamed more than 28 miles and logged more than 5,000 sols.

Hours after landing in Eagle Crater, Opportunity relayed panoramic images back to Earth. When researchers noted a bedrock outcrop, the rover examined it for a first mission.

“…those ‘blueberries’ are a strong indicator that this place once contained water.”

“The thing about an outcrop is its geologic truth…it is the story of what happened in that place,” Squyres says. “There was a story waiting for us.”

There, researchers found “blueberries.”

“When we drove off the lander, we saw something very strange – there was a lot of sand and gravel. Lots of gravel…grains of gravel that looked awfully round,” Squyres says. Using the rover’s microscope, the scientists found the area “littered with an uncountable number of round things, they were scattered everywhere.”

“We had no clue what they were…initially.” The scientists knew that Meridiani Planum likely contained the mineral hematite and eventually realized that the hard, gravel-like spherules were “concretions” made of hematite and formed in the sedimentary rock when water was present.

“It turns out that those blueberries are a strong indicator that this place once contained water,” he says.

‘An honorable end’

Late last spring, as Opportunity hunkered down in Perseverance Valley on the western rim of Endeavour Crater, a gigantic Martian dust storm began to envelop a large portion of the planet.

“The payoff has been immensely greater than anything ever imagined in our wildest dreams.”

NASA’s Mars Reconnaissance Orbiter first detected the storm May 30. On June 10, the Jet Propulsion Laboratory received a transmission from Opportunity, indicating that the craft had enough battery charge then to enable communication. But scientists have heard nothing since.

By June 20, the dust storm blotted out the sun and entirely blanketed Mars. The storm abated in late July, and engineers tried in vain to reach Opportunity through early February 2019. But, it never responded.

“When I saw that the storm had gone global, I thought this could be it,” says Squyres, explaining that Opportunity was a solar-powered vehicle and needed the sun for energy.

“To have Opportunity—designed for 90 days—taken out after fourteen and a half years by one of the most ferocious dust storms to hit the planet in decades, you have got to feel pretty good about it. It was an honorable end, and it came a whole lot later than any of us expected.”

Both rovers gathered a lot of science, Squyres says.

“It’s mind boggling to me. If you had told me around the time that we landed that Spirit and Opportunity were going to each accomplish one-quarter or even one-tenth of what they ultimately did, I would have been thrilled.

“It’s because of the longevity of the vehicles…that Mars just kept giving us more stuff. The payoff has been immensely greater than anything ever imagined in our wildest dreams.”

Source: Cornell University

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Will going gluten-free cause weight loss?

Thu, 2019-02-14 10:31

Although people have been eating wheat for thousands of years, one third of US adults now shun foods containing wheat in an effort to avoid gluten.

“…blaming gluten for weight gain draws a flawed conclusion.”

But what is gluten? And is it worthy of this tarnished reputation?

Thomas Campbell, family physician and medical director of the University of Rochester Medicine Weight Management & Lifestyle Center at Highland Hospital, explains:

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Falling in love boosts women’s immune genes

Thu, 2019-02-14 10:15

Falling in love may boost genes in women’s immune systems related to fighting infection, according to new research.

“What we found was that women who fell in love had increased activity of genes involved in antiviral defenses, compared to when they began the study,” says Damian Murray, an assistant professor in the School of Science and Engineering at Tulane University.

“No similar change was observed in women who did not fall in love. This could reflect a kind of a proactive response to anticipating future intimate contact, given that most viruses are spread via close physical contact. However, this increased activity of antiviral genes is also consistent with the biological preparation of the body for pregnancy. From this women-only sample, both of these interpretations remain possible,” he explains.

Participants had to report that they were not yet in love with their partners.

“A few years ago, Martie Haselton and I attended a talk by Steven Cole on the epigenetic and health consequences of being chronically lonely. Chronic inflammation is bad for health, and loneliness is one of the biggest predictors of mortality. Martie and I wondered if there could be a flipside to this ‘lonely’ epigenetics profile and we arrived at love.

“Is new romantic love the actual antithesis of loneliness? The answer depends on whom you ask, but we wanted to investigate whether new romantic love in new romantic relationships was associated with favorable health and a favorable immune-related epigenetic profile,” Murray says.

The 12-month paid study included both undergraduate and graduate students from the University of California, Los Angeles and centered on women only. A total of 47 women completed the research, which included blood draws and biweekly questionnaires. Depending upon their relationship timeline, women participated in the study for up to 24 months.

To be eligible to participate in the study, researchers only considered healthy women who were not taking drugs and were in a new romantic relationship. The researchers defined a new relationship as seeing someone less than a month, but the participants had to report that they were not yet in love with their partners.

“One of the biggest challenges was figuring out how we could access this fairly narrow population and be in the best position to make statistical inferences. We arrived at a two-year longitudinal study that would assess within-person change in gene expression over time,” Murray says.

“We put out flyers and women called or emailed us and were pre-screened. It was a challenge to recruit for this study. Over half the women we pre-screened had been seeing someone romantically for less than a month and reported already being in love with them, but by study completion we had a sample of 47 women who had completed at least two blood draws,” Murray says.

After completing a baseline blood draw, researchers gave the participants questionnaires every couple of weeks to answer specific life-event questions. One of the questions asked the participant if they had fallen in love with their partner. Reporting having fallen in love would lead to a second blood draw. When the participant reported that the relationship had broken up, they completed a third and final blood draw.

Upon completion, Murray circled back to the original thought that sparked the study and stated that new romantic love is probably not the antithesis of loneliness, subjectively speaking. There were no significant changes in self-reported loneliness or depressive symptoms between when women started the study and when they reported falling in love.

Going forward, Murray and his group hope to look at the longer-term epigenetic and health implications of love in a less acute way by analyzing people not just when they are newly in love, but also when they have been securely in love for an extended period. The follow-up study will feature both women and men.

“Ultimately, I think what we’d like to accomplish is to be able to map the physiological changes that accompany the initiation and progression of human romantic relationships and see how those have implications for both immediate and long-term health and how the epigenetic implications of love may facilitate pregnancy and reproduction,” Murray says.

The research appears in the journal Psychoneuroendocrinology.

Source: Tulane University

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These penguin parents are weirdly fair

Thu, 2019-02-14 10:12

Magellanic penguins feed their brood in a surprising way: Each chick gets an equal portion, regardless of age or size.

The finding is different from other parents across the animal kingdom, including other penguin species, that often allocate resources unequally to their chicks based on factors like offspring age, body condition, health, and behavior, researchers say.

“This is an exciting finding because, among animals, it is very unusual for parents to divide food equally among their offspring,” says P. Dee Boersma, a professor of biology at the University of Washington and director of the Center for Ecosystem Sentinels. “This makes Magellanic penguin parents stand out not just among penguins, but also animals in general.”

Dinner time

Magellanic chicks are the same size when they hatch, but eggs within a nest hatch at different times. After mating, a female lays two eggs about four days apart. One chick typically hatches at least two days before the other. Chicks grow to different sizes based on the timing of their first feedings.

By the time both chicks are at least 20 days old, one chick is on average 22 percent heavier than its sibling, researchers say. Yet despite these size differences, when Magellanic chicks are older and more mobile, parents still feed both chicks equally as well as rapidly.

“These findings raise some very interesting evolutionary questions about how and why this behavior—feeding chicks equally—arose,” Boersma says.

Parents with two chicks manage this equal division despite the rushed choreography of mealtimes, researchers say. Feedings lasted just 21 minutes on average, during which the parent used its flippers to keep one chick to its left and one to its right—turning its head to feed one and then the other.

Light and heavy chicks begged a similar number of times and each switched sides five or six times during the feeding, yet siblings didn’t act aggressively toward one other. Parents directed more non-feeding behaviors—such as opening its mouth but not regurgitating any food—to the lighter chick. Yet ultimately the lighter chick still received the same amount of food as its sibling.

Feed me now

The findings shed light on when, where, and how animals decide whether to treat their offspring equally or give preferential attention to one.

For Magellanic penguins, food supply, digestion, and the time between feedings could affect this behavior.

In other penguin species, food supply impacts feeding behaviors. Adélie penguins, for example, have a relatively stable and abundant food supply because long daylight hours in Antarctic summers allow them to feed around the clock. Adélie parents run from their chicks, and the chick that follows its parent the longest is typically fed the most.

For Magellanic penguins, food is less plentiful, and chicks typically wait three to five days between feedings. Each year, about 40 percent of chicks die at Punta Tombo due to starvation, and research indicates that a chick is most at risk of starvation when it is between 5 and 9 days old. Magellanic parents feed chicks as soon as they arrive at the nest because food that digests too long in their stomachs is less nutritious for their babies.

These factors may pressure adults to feed chicks quickly and equally. In addition, chicks may avoid direct competition because that could delay the feeding. Further, the chicks’ age might also explain the findings, Boersma says.

“This behavior may have evolved because, once both chicks reach this age, it may be advantageous for the parents to try to raise both of their chicks to fledging—the stage at which chicks leave the nest—rather than preferentially giving one more resources than the other,” she says.

Eric Wagner, who worked on the project as part of his biology doctoral degree, is lead author of the paper in Animal Behaviour.

The Chase Foundation, the Cunningham Foundation, the CGMK Foundation, the Offield Family Foundation, the Peach Foundation, the Thorne Foundation, the University of Washington Wadsworth Endowed Chair in Conservation Science, and Friends of the Penguins funded the work.

Source: University of Washington

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Newlywed brains suggest altruism is hard-wired

Thu, 2019-02-14 08:16

Thinking of the well-being of our romantic partners before our own may be hard-wired in our brains, according to new research.

Such altruism has perplexed and intrigued scientists for centuries. The new study explores how an individual’s genetics and brain activity correlate with altruistic behaviors directed toward romantic partners.

The team found that pathways related to bonding in other animals showed up in humans, and may be involved in altruism more generally.

Social survival strategy

Scientists currently think that altruism evolved in social species as a strategy for ensuring the survival of relatives. The idea is that genes that promote altruism will persist, perhaps not through an individual’s children but through those of their kin, who carry similar genetics. In this way, providing for your relatives ensures some of your own genes are passed down.

For humans, with our complex social systems, this basic premise takes on new dimensions. “It would make sense that people would be particularly invested in the well-being of their partners because they want to live long, happy, healthy lives together,” says lead author Bianca Acevedo, a research scientist at the Neuroscience Research Institute at the University of California, Santa Barbara.

“And in the case of newlyweds, some of them will want to have children. So being selfless towards their partner is an investment in their offspring.”

Altruism is an important aspect of pair bonding, but according to Acevedo, it hasn’t been examined much—especially when compared to the bond between parents and their children, where altruism is critical. “Responding to a child in a selfless way is such an important piece of care-giving,” says Acevedo.

Good chemistry

Phenomena as nuanced as love and altruism involve a lot of chemistry. Oxytocin is a neurotransmitter that has taken hold in popular consciousness as the “cuddle hormone.” And while it’s involved in a variety of processes, it’s role in trust, empathy, and bonding is well established. Less well known is the hormone vasopressin, which scientists have also connected with pair bond behaviors.

Acevedo’s team recruited newlywed couples to investigate how a person’s genetics and brain activity correlate with the empathy they show toward their romantic partner. The team tested each participant for two genetic variants, one involved in oxytocin sensitivity and another connected to vasopressin sensitivity. The researchers then had them respond to a standardized questionnaire asking about their feelings toward their partner and other individuals. This gave them a measurement of each person’s general levels of empathy and altruism toward their partner.

“It’s almost like the brain is responding in a way that signals, ‘this is important, pay attention…'”

Then the participants entered a functional magnetic resonance imaging (fMRI) machine. Though similar to the standard MRI machines doctors use to image soft tissue, fMRIs can track changes associated with blood flow. This allows researchers to see how different parts of the brain activate in response to different types of stimuli.

In this case, researchers showed participants pictures of their romantic partners, friends, and strangers with different facial expressions. The researchers explained what the person in the picture was feeling and why, in order to elicit an emotional response.

When participants felt a strong sense of empathy with the person in the picture, regions of the brain associated with emotion and emotional memory lit up. “It’s almost like the brain is responding in a way that signals, ‘this is important, pay attention,'” says Acevedo.

These areas of the brain—like the amygdala and ventral pallidum—have a particularly dense concentration of receptors for oxytocin and vasopressin, further implicating these neurotransmitters in empathy and altruism. What’s more, individuals with genetic variations that made them more sensitive to these hormones exhibited stronger emotional responses across the board.

The researchers also found that brain regions that activated specifically in response to a partner’s face were the same regions that are critical in other animals during studies of pair bonding and attachment. This suggests that our brains have pathways devoted specifically to attachment-related behaviors, pathways which may be quite old. However, some of these attachment pathways showed activity even when participants saw strangers’ faces, providing evidence of the intricate notions of empathy and altruism at play in humans.

Beyond romance

Acevedo is continuing to investigate empathy, altruism, and care-giving in different types of couples. She’s currently exploring how mind-body activities like yoga influence how individuals respond to partners struggling with memory problems.

“It’s important that we’re thinking about these systems and these behaviors beyond romance,” says Acevedo. “When people think about relationships, they tend to think of romantic love as being really important. But we’ve forgotten some of the other basic and important reasons that people are together, like to take care of each other.

“Beyond romantic love, we live long lives together. Many of us raise children together, or take care of each other into old age,” continues Acevedo. “And altruism is deeply rooted in our evolutionary, neural, and genetic framework.”

The results appear in the journal Behavioral Neuroscience.

Source: UC Santa Barbara

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Spending outpaces population in shrinking counties

Thu, 2019-02-14 08:01

Growing United States counties are increasing their total spending, but so are shrinking counties, research finds.

For the new study, researchers used US Census of Governments data to examine municipal spending aggregated to the county level nationwide from 1972 to 2012.

Because of the American Society of Civil Engineers’ failing grades for the nation’s built infrastructure, the study used three types of variables:

  • economic (median household income),
  • demographic (total population change),
  • and institutional (state and local tax expenditure limits).

The researchers studied the relationship between these variables with total municipal spending, with an emphasis on capital spending.

Super spending

“One of the things we were curious to see was how counties across the nation grew or shrunk over the last 40 years, and how total municipal expenditures and capital spending were related to that growth or decline,” says Biswa Das, assistant professor of community and regional planning at Iowa State University.

“What we found is the asymmetry is clear, but shrinking cities are spending at a high rate, both on the aggregate as well as on capital projects, which is surprising.”

The findings show that aggregate municipal spending is more responsive to population growth than decline, and the effect is most pronounced for capital spending. The findings also show that places that have implemented school finance reform tend to reduce municipal spending, though more so in growing counties than in shrinking ones.

Growing counties saw population increase by 69 percent over the study’s timeframe; municipal spending increased by more than 300 percent. Shrinking counties saw population decrease by 28 percent during this timeframe; but municipal spending still increased by 200 percent. Further, municipal spending increased at a faster rate than did median household income in both growing and shrinking counties.

Downward cycle

While increased spending on new infrastructure in growing places could be attributed to meeting the needs of a burgeoning population, increased spending in shrinking counties may be an effort to maintain infrastructure, either because of general degradation or federal mandates, the researchers say. Maintenance can be more expensive than building new infrastructure.

This puts shrinking counties in an “exacerbated” downward cycle, according to the study. Population loss means a municipality has less tax revenue, which makes it more difficult to maintain infrastructure that meets quality of life standards, which in turn triggers further population loss. And tax increases—particularly to develop new or maintain excess infrastructure—are often unpopular with residents.

“These places are forced to take a hard look at existing infrastructure and make strategic decisions about what requires reinvestment and what infrastructure does not yield positive net returns to the community; this infrastructure should be allowed to depreciate,” according to the study.

To maintain infrastructure investments in the long run, growing counties should plan carefully, the researchers say.

“Sometimes places that are growing invest way more in infrastructure than is necessary,” Das says. “Cities make long-term projections, but sometimes those aren’t realized and they’re left with extra infrastructure.”

Researchers from Michigan State University also contributed to the paper, which appears in the Journal of Regional Analysis and Policy.

Source: Iowa State University

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More crime on the route to school ups absentee risk

Wed, 2019-02-13 14:31

The more crime that occurs along a student’s way to school, the higher the likelihood that student will be absent, researchers report.

By modeling the most efficient routes to school for Baltimore students, researchers found those who commute through areas with double the average amount of crime are 6 percent more likely to miss school. Even more crime-ridden routes to school led to proportionately more absenteeism. The findings, which demonstrate yet another way urban violence effects school outcomes, appear in the journal Sociological Science.

“Having to travel through dangerous streets is leading kids to miss school…”

“Having to travel through dangerous streets is leading kids to miss school,” says lead author Julia Burdick-Will, a sociologist at Johns Hopkins University. “Not showing up for school has important academic consequences and students who must prioritize their own personal safety over attendance have a clear disadvantage.”

Researchers including Burdick-Will have shown that students exposed to violent crime have lower test scores and lower graduation rates. And chronic absenteeism has been linked to lower achievement, student disengagement, and increased risk of dropping out.

Meanwhile families, especially those living in violent and disadvantaged neighborhoods, are increasingly choosing to send their children to schools in different parts of town. But getting to these schools is often difficult. Many districts have cut back on traditional school busses and students must use public transportation. This means just showing up to school every day can mean long and difficult journeys through potentially dangerous streets, Burdick-Will says.

“What if the closest bus stop isn’t safe and you need a ride to a farther stop. Then what if what ride falls through?”

This is the first time anyone has attempted to gauge how neighborhood violence might influence school attendance.

Researchers first determined the quickest, most efficient route to school using public transportation for 4,200 first-time 9th-graders in Baltimore City public high schools. Then they linked those streets with crime data from the Baltimore Police Department.

The team found that students whose best route required walking or waiting for a bus in areas with higher violent crime rates had higher rates of absenteeism throughout the year. And the scary spots weren’t limited to certain parts of town—they were essentially all over the city.

The average student went to school in a neighborhood where 87 violent crimes were reported during the academic year, but lived in a neighborhood where 95 violent crimes happened during the same time. Students pass streets on public transit where 41 violent crimes happened and passed streets on foot where there were 27 such crimes.

The relationship between exposure to violence during the commute to school and absenteeism provides important insights into the ways urban violence links to low achievement and high school dropout, the researchers conclude. Not only does violence stress and traumatize students in their communities, they say, they’re missing school because of it.

“What if the closest bus stop isn’t safe and you need a ride to a farther stop. Then what if what ride falls through? Do you risk it or walk really far or do you just not go to school,” Burdick-Wills says. “Missing an extra day of school a year doesn’t sound like a lot but these things add up.”

The Spencer Foundation supported the research.

Source: Johns Hopkins University

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Machine learning unlocks plant gene ‘treasure chest’

Wed, 2019-02-13 14:23

Combining plant biology and machine learning let researchers sort through tens of thousands of genes to determine which make specialized metabolites.

Researchers have combined plant biology and machine learning to sort through tens of thousands of genes to determine which genes make specialized metabolites.

Some metabolites attract pollinators while others repel pests. Ever wonder why deer eat tulips and not daffodils? It’s because daffodils have metabolites to fend off the critters who’d dine on them.

“Plants are amazing—they are their own mini factories, and we wanted to recreate what they do in a lab…”

The results could potentially lead to improved plants but also to the development of plant-based pharmaceuticals and environmentally safe pesticides, says Shin-Han Shiu, a plant computational biologist at Michigan State University.

“Plants are amazing—they are their own mini factories, and we wanted to recreate what they do in a lab to produce synthetic chemicals to make drugs, disease-resistant crops and even artificial flavors,” Shiu says.

“Our research found that it is possible to pick out the right gene by automating the process since machines are more capable of picking out minute differences among thousands of genes.”

Taking a machine-learning approach, an interdisciplinary team of biochemists and computational biologists created a model that looked at more than 30,000 genes in Arabidopsis thaliana, a small flowering plant that is called the “lab rat of plant science.”

Shin-Han Shiu looks over Arabidopsis thaliana plants. (Credit: G.L. Kohuth)

The model is based on technology used by e-commerce to forecast consumer behavior and create targeted advertising, such as ads seen on a person’s Facebook page. Basically, the technology sorts through thousands of ads based on your previous online behavior to send you select ads geared toward your interests and activities.

In the plant study, scientists wrote a program that sorted through 30,000 genes to hone in on the ones related to making specialized metabolites.

“Machine learning was a novel approach for us in plant biology, a new application of tools widely used in other fields,” Shiu says.

“The model we created with machine learning can now be applied to other plant species that produce medicinally or industrially useful compounds to speed up the process of discovering the genes responsible for their production.”

“We’ve known for a long time that plants make a wealth of useful, valuable compounds, but this work really throws open that treasure chest in important new ways,” says Clifford Weil, a program director in the National Science Foundation’s Plant Genome Research Program, which funded the research. “It’s a great advance in how, and how well, we can explore nature’s most-creative biofactories.”

The research appears in Proceedings of the National Academy of Sciences. Additional researchers who contributed to the project are from Michigan State University and the University of Michigan.

Source: Michigan State University

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3 ways climate change can foster violence

Wed, 2019-02-13 13:30

New research identifies three ways climate change will increase the likelihood of violence.

Images of extensive flooding or fire-ravaged communities help us see how climate change is accelerating the severity of natural disasters. The devastation is obvious, but what is not as clear is the indirect effect of these disasters, or more generally of rapid climate change, on violence and aggression.

Study coauthor Craig Anderson, professor of psychology at Iowa State University, says the first route is the most direct: higher temperatures increase irritability and hostility, which can lead to violence.

The other two are more indirect and stem from the effects of climate change on natural disasters, failing crops, and economic instability. A natural disaster, such as a hurricane or wildfire, does not directly increase violence, but the economic disruption, displacement of families, and strain on natural resources that result are what Anderson finds problematic.

One indirect way natural disasters increase violence is through the development of babies, children, and adolescents into violence-prone adults, he says. For example, poor living conditions, disrupted families, and inadequate prenatal and child nutrition are risk factors for creating violence-prone adults.

Anderson and lead author Andreas Miles-Novelo note these risk factors will become more prevalent as a result of climate change-induced disasters, such as hurricanes, droughts, floods, water shortages, and changing agricultural practices for efficient production of food.

Another indirect effect: Some natural disasters are so extensive and long term that they force large groups of people to migrate from their homeland. Anderson says this “eco-migration” creates intergroup conflicts over resources, which may result in political violence, civil wars, or wars between nations.

“This is a global issue with very serious consequences. We need to plan for ways to reduce the negative impacts,” Anderson says. “An inadequate food supply and economic disparity make it difficult to raise healthy and productive citizens, which is one way to reduce long-term violence. We also need to plan for and devote resources to aid eco-migrants in their relocation to new lands and countries.”

Escalating conflicts

There are no data and there is no method to estimate which of the three factors will be most damaging, Anderson says. The link between heat and aggression has the potential to affect the greatest number of people, and existing research, including Anderson’s, shows hotter regions have more violent crime, poverty, and unemployment.

“We should tear down negative stereotypes and prejudices about those who will need help…”

However, Anderson fears the third effect he and Miles-Novelo identified—eco-migration and conflict—could be the most destructive. He says we are already seeing the migration of large groups in response to physical, economic, or political instability resulting from ecological disasters. The conflict in Syria is one example.

Differences between migrants and the people living in areas where migrants are relocating can be a source of tension and violence, Anderson says. As the level of such conflicts escalates, combined with the availability of weapons of mass destruction, the results could be devastating.

“Although the most extreme events, such as all-out war, are relatively unlikely, the consequences are so severe that we cannot afford to ignore them,” Anderson says. “That is why the US and other countries must make sure these regional conflicts and eco-migration problems don’t get out of hand. One way to do that is to provide appropriate aid to refugees and make it easier for them to migrate to regions where they can be productive, healthy, and happy.”

What can be done?

Anderson and Miles-Novelo, an Iowa State graduate student, say the purpose of their research is to raise awareness among the scientific community to work on prevention efforts or ways to limit harmful consequences. The long-term goal is to educate the public on the potential for increased violence.

“From past experience with natural disasters, we should be able to prepare for future problems by setting aside emergency resources and funds,” Miles-Novelo says. “We should tear down negative stereotypes and prejudices about those who will need help and humanely assist refugees and others who are displaced. By doing all these things we can reduce conflict and hostility.”

Changing attitudes and policies about immigration also will lessen the potential for conflict, Anderson says. He points to the backlash against refugees in many European countries.

“The view that citizens of wealthy countries often have about refugees needs to change—from seeing them as a threat to a view that emphasizes humanitarian values and the benefits refugees bring when they are welcomed into the community,” Anderson says.

Their research appears in the journal Current Climate Change Reports.

Source: Iowa State University

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