Culture

London: As opposed to making you happy, eating ice cream may cause you a headache. Cephalalgia, the official journal of the International Headache Society, published the article entitled "Prevalence and characteristics of headache attributed to ingestion or inhalation of a cold stimulus (HICS): A cross-sectional study", by Torsten Kraya and colleagues from the Department of Neurology, at Martin-Luther-University Halle-Wittenberg, and St. Georg Hospital, Leipzig, Germany.

The authors investigated 618 adults, students and staff from the university, who filled a questionnaire about headaches. Half of the population had a headache after the ingestion of a cold stimulus, regardless of having a diagnosis of migraine or tension-type headache.

The pain was referred to as moderate, lasted less than 30 seconds and occurred in frontal and temporal areas in most individuals. Associated symptoms happened in half of the headaches (tearing, seeing flashing light dots, eye redness, and running nose).

The pleasure of eating ice cream or drinking a cold drink may be decreased by a painful headache.

PITTSBURGH--Carnegie Mellon University computer scientists have taken a deep learning method that has revolutionized face recognition and other image-based applications in recent years and redirected its power to explore the relationship between genes.

The trick, they say, is to transform massive amounts of gene expression data into something more image-like. Convolutional neural networks (CNNs), which are adept at analyzing visual imagery, can then infer which genes are interacting with each other. The CNNs outperform existing methods at this task.

The researchers' report on how CNNs can help identify disease-related genes and developmental and genetic pathways that might be targets for drugs is being published today in the Proceedings of the National Academy of Science. But Ziv Bar-Joseph, professor of computational biology and machine learning, said the applications for the new method, called CNNC, could go far beyond gene interactions.

The new insight described in the paper suggests that CNNC could be similarly deployed to investigate causality in a wide variety of phenomena, including financial data and social networking, said Bar-Joseph, who co-authored the paper with Ye Yuan, a post-doctoral researcher in CMU's Machine Learning Department.

"CNNs, which were developed a decade ago, are revolutionary," Bar-Joseph said. "I'm still in awe of Google Photos, which uses them for facial recognition," he added as he scrolled through photos on his smartphone, showing how the app could identify his son at different ages, or identify his father based on an image of the rear right side of his head. "We sometimes take this technology for granted because we use it all the time. But it's incredibly powerful and is not restricted to images. It's all a matter of how you represent your data."

In this case, he and Yuan were looking at gene relationships. The approximately 20,000 genes in humans work in concert, so it's necessary to know how genes work together in complexes or networks to understand human development or diseases.

One way to infer these relationships is to look at gene expression -- which represents the activity levels of genes in cells. Generally, if gene A is active at the same time gene B is active, that's a clue that the two are interacting, Yuan said. Still, it's possible that this is a coincidence or that both are activated by a third gene C. Several previous methods have been developed to tease out these relationships.

To employ CNNs to help analyze gene relationships, Yuan and Bar-Joseph used single-cell expression data -- experiments that can determine the level of every gene in a single cell. The results of hundreds of thousands of these single-cell analyses were then arranged in the form of a matrix or histogram so that each cell of the matrix represented a different level of co-expression for a pair of genes.

Presenting the data in this way added a spatial aspect that made the data more image-like and, thus, more accessible to CNNs. By using data from genes whose interactions already had been established, the researchers were able to train the CNNs to recognize which genes were interacting and which weren't based on the visual patterns in the data matrix, Yuan said.

"It's very, very hard to distinguish between causality and correlation," Yuan said, but the CNNC method proved statistically more accurate than existing methods. He and Bar-Joseph anticipate CNNC will be one of several techniques that researchers will eventually deploy in analyzing large datasets.

"This is a very general method that could be applied to a number of analyses," Bar-Joseph said. The main limitation is data -- the more data there is, the better CNNs work. Cell biology is well-suited for using CNNC, as a typical experiment can involve tens of thousands of cells and generate a massive amount of data.

ITHACA, N.Y.- Some problems are best solved with new tech or a flashy app. But sometimes adapting existing technology works best of all.

A new system developed by Cornell Tech researchers will allow thousands of patients of community health care workers in rural Africa to use a basic tool on their mobile phones - one that doesn't even require an internet connection - to provide feedback on their care anonymously, easily and inexpensively.

"Technological interventions, when designed in the right way, can help address some of the complex health problems we have in the world," said Fabian Okeke, doctoral student in information science at Cornell Tech and first author of "Including the Voice of Health Care Recipients in Community Health Feedback Loops in Rural Kenya," presented at the Association for Computing Machinery Conference on Computer-Supported Cooperative Work and Social Computing, Nov. 9-13 in Austin, Texas.

The system showed promising results in a recent study and will soon be expanded by Medic Mobile, a nonprofit health tech company that collaborated on the research and works with more than 20,000 health care workers across 14 African countries.

In remote areas in Africa and India, where a single doctor might serve 10,000 people, many rely on community health care workers, who visit their homes and act as intermediaries between doctors and care recipients. While this model is considered effective and has been adopted around the world, there have been cases of mistreatment. A 2016 study found that 70% of women who gave birth at a referral hospital in Tanzania experienced one form of abuse or disrespect.

Until now, efforts to improve care and accountability have focused on collecting data from caregivers. In this study, the researchers sought to create a system allowing care recipients to offer feedback of their own.

"If you're providing services for a pregnant mother in rural Kenya, how is the pregnant mother going to say whether the service is helping her?" Okeke said. "We wanted to somehow bridge this gap - not just in the research literature but in community health. So we started thinking about ways to integrate the voices of care recipients and to do it in a way that is scalable."

The researchers chose an unstructured supplementary service data (USSD) system - commonly used by owners of prepaid mobile phones to check their balances. They chose USSD because it offered anonymity, unlike short message service texting; and because it is far less expensive than a call-based system.

With USSD, users enter a series of numbers into their phones, prompting questions about their experiences at the health care centers. Since most Kenyans already own mobile phones and are familiar with USSD, it was easy for them to adopt, the researchers said.

"Often when people think about interventions in developing nations, they think, 'Let's go build an app from scratch or a completely new tool,' but many times you can go back and tap into existing infrastructures," Okeke said. "People are already used to placing calls and texting - I think the innovation here is that you can go back to those mundane technologies and transform them into something else."

The researchers deployed the tool for seven weeks, training five care workers who, in turn, trained care recipients. For example, users who were visited by health care workers could dial *384*888# on their phones to provide feedback, which took less than two minutes. Users who visited community health care centers could dial a different series of numbers to offer feedback.

Users dialed in to answer a series of questions 495 times, with an error rate of less than 1%. Around 70% of the responses were positive, 17% negative and 13% neutral.

The researchers also conducted focus groups with patients and caregivers to gauge their opinions.

"We found that people were pretty enthusiastic about using USSD for providing feedback," Okeke said. "It was a way to empower them to communicate how they felt about the services they received."

Even the health care workers - who at first feared the feedback could be used maliciously against them - seemed pleased with the results, the researchers found.

"Initially, when we started the design process, health workers said this could be a tool that becomes a punishment," Okeke said. "But most of the feedback was positive, so it's validating the hard work that they're doing, but it's also holding them accountable. We heard things from care workers like, 'Now it's on me to combine both the positive and the negative to understand where I can improve my services.'"

Medic Mobile is in the process of incorporating the USSD system into its software toolkit, which is used by health care organizations across Africa. "The potential impact is thrilling," Okeke said.

Children with Type 1 diabetes show subtle but important differences in brain function compared with those who don't have the disease, a study led by researchers at the Stanford University School of Medicine has shown.

The study, publishing online Dec. 9 in PLOS Medicine, is the first to evaluate what happens in the brains of children with diabetes during a cognitive task. On functional magnetic resonance imaging scans, when their brains were at work, children with diabetes displayed a set of abnormal brain-activity patterns that has been seen in many other disorders, including cognitive decline in aging, concussion, attention-deficit hyperactivity disorder and multiple sclerosis.

The study also reported that the abnormal brain-activity patterns were more pronounced in children who had had diabetes longer.

"Our findings suggest that, in children with Type 1 diabetes, the brain isn't being as efficient as it could," said Lara Foland-Ross, PhD, senior research associate at the Center for Interdisciplinary Brain Sciences Research at Stanford. Foland-Ross shares lead authorship of the paper with Bruce Buckingham, MD, professor emeritus of pediatrics at Stanford.

"The takeaway from our study is that, despite a lot of attention from endocrinologists to this group of patients, and real improvements in clinical guidelines, children with diabetes are still at risk of having learning and behavioral issues that are likely associated with their disease," said the study's senior author, Allan Reiss, MD, professor of psychiatry and behavioral sciences at Stanford.

Blood sugar affects brain development

Type 1 diabetes occurs when the pancreas fails to make insulin, a hormone that helps regulate blood sugar. Patients are given insulin via injections or an insulin pump. But even with treatment, their blood levels of glucose, the main sugar in blood, fluctuate much more than in healthy individuals.

"Kids with diabetes have chronic swings in blood-glucose levels, and glucose is important for brain development," Foland-Ross said. Brain cells need a steady supply of glucose for fuel. Earlier work revealed brain-structure changes and mild performance impairment on cognitive tasks in children with Type 1 diabetes, but the mechanism had never been studied. "It was important to capture what is going on in the brains of these kids functionally," she said.

The researchers conducted fMRI brain scans on 93 children with Type 1 diabetes recruited at five sites: Nemours Children's Health System in Jacksonville, Florida; Stanford; Washington University in St Louis; the University of Iowa; and Yale. An additional 57 children who did not have the disease composed the control group. All participants were 7-14 years old. Standard behavioral and cognitive tests were given to all the children before brain scanning.

Then, in the fMRI scanner, the children performed a cognitive task called "go/no-go": Different letters of the alphabet were shown in random order, and participants were asked to press a button in response to every letter except "X." The task is often used in brain-scanning studies to evaluate what is happening in the brain while participants are concentrating.

The study found that, although the children with diabetes performed the task as accurately as those in the control group, their brains were behaving differently. In children with diabetes, the default-mode network, which is the brain's "idle" system, was not shutting off during the task. To compensate for the abnormal activation of the default-mode network, the brain's executive control networks, responsible for aspects of self-regulation and concentration, were working harder than normal in the children with diabetes.

These abnormalities were more pronounced in children who had been diagnosed with diabetes at younger ages, suggesting that the problem may worsen with time.

"The longer the exposure you have to dynamic changes in blood-glucose levels, the greater the alterations in brain function with respect to the default-mode network," Foland-Ross said. Studies in adults with diabetes suggest that in the later stages of the disease, the brain eventually loses its ability to compensate for this problem, she added.

Next: Testing effects of devices

Next, scientists want to study whether achieving better blood glucose concentrations through treatment with a closed-loop artificial pancreas benefits children's brain function. These devices electronically couple a blood glucose sensor to an insulin pump that automatically adjusts insulin delivery.

"We hope that with improvements in devices for diabetes treatment, these findings will either decrease in severity or go away," Reiss said, adding that with better blood sugar control, children's brains might be able to recover normal activity. "Young brains have the most potential for plasticity and repair," he said. "But children also have a long time to live with the consequences if problems with brain function persist."

New England has a proud tradition of commercial fishing. But will it survive as the planet warms?

For decades the biggest threat to the industry has been overfishing, but it is no longer the only threat. According to new research at the University of Delaware, fluctuations in the climate have already cost some New England fishermen their jobs.

UD's Kimberly Oremus, assistant professor of marine policy, makes the direct link, for the first time, between large-scale climate variability and fishing job losses in a study published Dec. 9 in the Proceedings of the National Academy of Sciences.

By correlating the North Atlantic Oscillation (NAO)--New England's dominant climate signal--with labor numbers, Oremus determined that New England's coastal counties have, on average, lost 16% of their fishing jobs due to climate variation from 1996 to 2017.

This specific effect of climate is distinct from the overall job losses and gains caused by other factors, such as changes in market demand, regulatory changes to curb overfishing, and broader economic trends. Currently, 34,000 commercial marine fishermen are employed in New England's industry.

"As we see more warm winters off the New England coast, historic fisheries decline and fewer fishermen stay in business," Oremus said. "This has important implications for fisheries management in New England, which employs 20% of U.S. commercial harvesters."

The North Atlantic Oscillation

While other studies have used temperature projections as a proxy for climate change, Oremus chose the North Atlantic Oscillation, a climate index based on the difference in sea-surface pressure between two points in the Atlantic Ocean--at the Azores and near Iceland.

When the oscillation signal is positive, that means the subtropical high near the Azores and the subpolar low near Greenland are strong, allowing for a warmer winter pattern in the northeastern U.S. That creates difficult conditions for many of the commercial species in the region. When the oscillation signal is negative, the pressure gradient between the two points is weaker, and colder air can surge south from Canada.

"New England waters are among the fastest-warming in the world," Oremus said. "Warmer-than-average sea-surface temperatures have been shown to impact the productivity of lobsters, sea scallops, groundfish and other fisheries important to the region, especially when they are most vulnerable, from spawning through their first year of life."

That effect shows up in catch and labor data a few years later, once the affected fish reach the size at which they're allowed to be caught. In order to understand this, Oremus had to gather catch-size restrictions for 56 commercial fisheries. Squid and some shrimp, for example, typically are caught in their first year of life, while most groundfish, such as haddock, are caught between 2-4 years old. A majority of fish are caught by age 6.

In her study, Oremus connected the pathways between the North Atlantic Oscillation, its effects on aggregated catch from multiple fisheries and the resulting impacts on sales revenue, wages and fishermen's jobs. Her analysis showed that increases in the North Atlantic Oscillation signal initially reduce total catch in New England by 2%, a reduction that persists for five years, to a 10% decline. The impact on regional revenue followed the same pattern. A 1-unit increase in the oscillation reduced commercial fishing revenue by 1% initially, accumulating to a 13% decline six years later.

Over time, this supply shock measurably reduces the labor demand, with a 1-unit increase in the North Atlantic Oscillation index reducing fishing employment by 13% and wages by 35%, with effects that persist for several years.

Coping with change

But as commercial fishermen leave the industry, where do they go?

Oremus said finer resolution data would need to be gathered on a business level to determine if fishermen are being pushed into unemployment or into retirement, being reallocated into other jobs such as the extraction industry (oil, gas, minerals) or some other sector, or moving away from the East Coast entirely.

She did examine vessel permit data for all federal, commercial permits on the U.S. Atlantic coast and found no evidence that fishermen are moving farther south, where fish stocks are more stable due to a mix of warm- and cold-water species.

"The science on this particular climate variability--the North Atlantic Oscillation--is very well established," Oremus said. "But how will it change in the future? There are two predictions: some say it is moving more into the positive phase, and some are predicting it will be more variable." Her findings suggest that the region's fish populations might be impacted either way.

Understanding the links between climate, catch and labor could help regulators better manage resources to preserve New England's remaining stocks and fishing communities, Oremus added. While her findings are specific to New England, her study points the way toward considering climate's impacts on fisheries around the world.

"This is an important signal to incorporate into the fisheries management process," Oremus said. "We need to figure out what climate is doing to fisheries in order to cope with it."

Saturn's tiny, frozen moon Enceladus is a strange place. Just 300 miles across, the moon is thought to have an outer shell of ice covering a global ocean 20 miles deep, encasing a rocky core. Slashed across Enceladus' south pole are four straight, parallel fissures or "tiger stripes" from which water erupts. These fissures aren't quite like anything else in the Solar System.

"We want to know why the eruptions are located at the south pole as opposed to some other place on Enceladus, how these eruptions can be sustained over long periods of time and finally why these eruptions are emanating from regularly spaced cracks," said Max Rudolph, assistant professor of earth and planetary sciences at the University of California, Davis.

Rudolph and colleagues Douglas Hemingway of the Carnegie Institution for Science, Washington D.C. and Michael Manga of UC Berkeley now think they have a good explanation for Enceladus' erupting stripes. They used numerical modeling to understand the forces acting on Enceladus' icy shell.

Saturn's gravity exerts tidal forces on Enceladus, which cause heating and cooling of the tiny world. Those forces are strongest at the poles. As liquid water solidifies into ice under the outer ice shell, it expands in volume, putting pressure on the ice until it cracks.

Enceladus' surface temperature is about negative 200 degrees Celsius, so if a crack formed in the ice, you would expect it to freeze shut pretty quickly. Yet the south polar fissures remain open, and in fact reach all the way to the liquid ocean below.

That's because liquid water within the fissure is sloshed around by tidal forces produced by Saturn's gravity, releasing energy as heat, Rudolph said. That stops the crack from freezing shut.

The release of pressure from the fissures stops new cracks from forming elsewhere on the moon, such as at the north pole. But at the same time, water vented from the crack falls back as ice, building up the edges of the fissure and weighing it down a bit. That causes the ice sheet to flex, the researchers calculate, just enough to set off a parallel crack about 20 miles away.

"Our model explains the regular spacing of the cracks," Rudolph said.

Many of the characteristics that make people so different from each other, are often the result of small differences in the DNA between individuals. Variation in just a single base in our DNA can cause significant variation in traits like sleep length, weight, height etc. And, unfortunately, they can also become a source of disease.

To confidently connect variation within a gene or genome (what biologists call "genotypes") and variation in traits ("phenotypes"), scientists ideally need standardized genetic tools. One of these is the Drosophila Genetic Reference Panel (DGRP), which consists of >200 lines of the fruit fly Drosophila melanogaster. Each line in the DGRP has had its genome fully sequenced so that scientists can spot differences between genotypes and then connect these to differences between phenotypes of interest.

Most of the DNA in eukaryotic cells - the cells that make up higher organisms like fruit flies and humans - sits tightly packed inside the cell's nucleus. But almost all eukaryotic cells also have mitochondria, an organelle often referred to as the "powerhouse of the cell". Mitochondria are unique in that they have their own DNA with its own distinct set of genes.

Studies have hinted that variation in mitochondrial genes is associated with diseases like obesity, type-2 diabetes, multiple sclerosis, and schizophrenia. The problem is that, unlike "regular" genes in nuclear genomes, we actually know very little about how variation in mitochondrial genes relates to variation in phenotypes.

This is what Roel Bevers and Maria Litovchenko from the lab of Bart Deplancke at EPFL have addressed in a paper published in Nature Metabolism. The researchers carried out a comprehensive study connecting variation in mitochondrial DNA with various traits in DGRP fruit-fly lines. The findings can be incorporated into future genome-wide association studies (GWAS) to gain more detailed information about how variation in genes - nuclear and mitochondrial, and their interactions - affect various traits and diseases.

"So far, DGRP studies have mostly focused on genetic variants in the nucleus because of low mitochondrial DNA coverage," says Deplancke. "In this study, we wanted to investigate the impact of mitochondrial DNA variation on traits in these fly lines."

His team re-sequenced mitochondrial genomes of 169 DGRP fruit-fly lines, which allowed them to identify 231 gene variants. They then looked at "mitochondrial DNA haplotypes", which are groups of variants which are always inherited together, identifying 12 distinct haplotypes among the studied fly lines.

Interestingly, these haplotypes were found to be associated with a range of metabolic phenotypes and diseases. "We found many links to stress- and metabolism-related traits, including food intake in males," says Deplancke. To confirm this, the researchers swapped mitochondrial genomes between fruit fly lines, which actually changed the eating behavior of males: the mitochondrial haplotype associated with high food intake could increase food intake in fly lines that initially displayed a low food-intake.

The work can help future studies by providing a higher resolution to connect genes and traits, e.g. feeding behavior. "There is important mitochondrial haplotype-specific metabolic variation in the DGRP," conclude the authors. "This demonstrates the importance of incorporating such haplotypes in genotype-phenotype relationship studies."

Hamilton, ON (December 9, 2019) - Researchers at McMaster University have unlocked one of the secrets behind the many benefits of metformin.

One of the most widely used medications in the world; metformin is commonly prescribed for Type 2 diabetes. However, in addition to its effects on lowering blood sugar, in preclinical models, metformin shows benefits on aging and a number of diverse diseases such as cognitive disorders, cancer and cardiovascular disease.

One question researchers have been asking is how this is being achieved.

A multi-year study led by a collaboration of McMaster's basic science and clinical researchers has found that metformin induces the expression and secretion of a protein called growth differentiating factor 15, or GDF15.

The results were published today in Nature Metabolism.

"Studies over the past two decades have shown that metformin does more than lower glucose, but we haven't understood why," said Gregory Steinberg, senior author and professor of medicine at McMaster. He is also co-director of the Centre for Metabolism, Obesity and Diabetes Research at McMaster.

"We went into this study with the idea that metformin might communicate with other tissues in the body by causing the secretion of a protein from the liver. We were totally surprised when we found out that metformin caused the secretion of GDF15, a protein which is known to suppress appetite."

The study team took that knowledge and applied it to mice to better understand the science behind the outcome. Scientists deleted the gene that makes GDF15 in mice, then treated them with metformin. The results showed that mice without GDF15 did not eat less or lose weight, despite being administered metformin, establishing GDF15 as the connection between metformin and weight loss.

The researchers say the findings open a number of avenues of research. There are currently over 1,500 registered clinical trials to test the effects of metformin in aging and different diseases.

"The possibility that GDF15 has a role in multiple beneficial effects of metformin treatment on aging or diseases like cancer needs to be studied," Steinberg said.

In the waves offshore of Southern California, germ warfare occurs in a struggle as old as life itself.

It's where USC marine biologists completed a comprehensive new study that shows the tactics bacteria and viruses employ to gain advantages against each other. What they found is that an unlikely standoff occurs, regardless of time, season or location -- proof of the evolutionary principle of the "Red Queen."

"The Red Queen concept in biology means a species running fast in place just to keep even, and that's what we found in these microbial communities," said Jed Fuhrman, lead author of the study and marine biologist at the USC Dornsife College of Letters, Arts and Sciences. "This is one of the modern tenets of evolutionary biology, and our observations fit nicely within the framework."

The research was published today in Nature Microbiology.

The battleground for this clash of microscopic organisms is a sliver of the Pacific Ocean between Los Angeles and Catalina Island. Those waters are immediately adjacent to some of the most popular beaches in the United States.

Oceans are full of viruses and bacteria; they are the oldest and most diverse creatures on Earth. Though small, if taken together in one lump they comprise 90% of the weight of all living creatures in the ocean. They perform essential functions in the ecosystem, recycle nutrients and influence the planet's climate. They've been in the ocean since the beginning of life, and they mostly don't bother swimmers and bathers. But they are not nice to each other.

Viruses are constantly trying to infect algae and bacteria. At first glance, the fight appears lopsided, because viruses vastly outnumber other marine organisms. A cup of ocean water can hold 1 billion virus particles. Yet, bacteria rely on countermeasures to protect themselves.

The USC scientists sought to explain why the struggle is a stalemate.

"It has been a puzzle how marine viruses, which are astoundingly abundant at about 10 million per milliliter of seawater, persist at such high abundances despite the ability of their hosts -- mostly bacteria -- to defend themselves," Fuhrman said.

The researchers sampled surface seawater almost every month for five years between the summers of 2009 and 2014. They analyzed more than 1 billion genetic sequences to sort the different types of viruses. They compared those findings to weather and ocean conditions and to bacteria populations.

Two key findings emerged:

- The virus communities remained stable. Some 95% of the same virus species were identified in nearly all the samples. The stability persisted over time and location. While similar findings have been reported previously, the new study is unique because no other study showed this extent of stability over such a long period.

- Within each virus species, there was constant churning of mutants, each of which dominated the populations for only a few months. The scientists say this churn allowed the viruses to stay one step ahead of host defenses, which means they need to keep changing in order to survive.

The dynamic occurring among microbes in the ocean "strongly resembles Red Queen dynamics, which are rapid changes of genotypes within a population from ecological and evolutionary mechanisms," the study says.

The Red Queen hypothesis proposes that organisms must constantly adapt to spread or else die in a changing environment of competitors. The USC study is one of but a few to show this evolutionary dynamic anywhere in nature.

Leipzig/Halle/Arlington. In a rapidly urbanizing world, the conversion of natural habitats into urban areas leads to a significant loss of biodiversity in cities. However, these direct effects of urban growth seem to be much smaller than the indirect effects outside of cities, such as the urban release of greenhouse gases causing climate change globally or the increasing demand for food and resources in cities leading to land-use change in rural areas. Both climate and land-use change are key drivers of global biodiversity loss. An international team of researchers including researchers from The Nature Conservancy (TNC), the German Centre for Integrative Biodiversity Research (iDiv), Martin Luther University Halle-Wittenberg (MLU) and other institutions assessed the direct and indirect effects on a global scale. The results have been published in the journal Nature Sustainability.

We are living in the period of fastest urban growth in human history, with more than 2 billion additional people expected in cities by 2030 - a pace that is the equivalent to building a city the size of New York City every 6 weeks. But what do scientists know and not know about how urban growth is affecting biodiversity? To answer this question, an international team of researchers reviewed more than 900 studies. The work of the highly international synthesis working group was funded and supported by sDiv, the synthesis centre of German Centre for Integrative Biodiversity Research (iDiv).

The researchers found that the direct effects of cities on natural habitat and biodiversity are large and straightforward to map using satellite data. Direct effects occur when urban areas expand, converting natural habitat into cities. Direct effects are cumulatively significant, with 290,000 km2 of nature habitat forecast to be converted to urban land uses between 2000 and 2030. This is equal to an area larger than the entire United Kingdom. Urban areas are causing the most destruction of high-biodiversity habitat in places like coastal China, Brazil, and Nigeria. This adds up to a big loss of biodiversity, because species richness (number of species) at a site is globally on average 50% lower at urban sites than in intact natural habitat.

However, the indirect effect of urban growth on biodiversity is likely far greater than the direct effect. Indirect effects include the biodiversity impacts of resources consumed within the city as well as the impacts of pollution released from cities. The researchers estimate that just the area required to feed the world's cities is 36 times greater than the urban area of cities. "In other words, the food urban dwellers eat turns out to be more important for global biodiversity than the direct environmental impact of the urban areas", said co-author Dr Andressa Vianna Mansur, postdoctoral researcher at iDiv. Similar conclusions can be made for other indirect effects, including the role of greenhouse gas emissions from cities in making climate change worse.

To date, much research has been done on the direct effects of urban expansion in particular cities or places - out of 900 studies, more than 600 dealt with the direct effects of urban growth. However, the effects of urban growth are not studied in the regions where the satellite data suggests the most intense effects. "Most studies are in developed countries like the United States and the European Union. Relatively few papers are from developing countries, where cities are expanding the most rapidly into high-biodiversity habitat", commented first author Robert McDonald from The Nature Conservancy. "As a result, we don't know much about the way ecosystems change in these habitats in response to urbanization."

In contrast to the direct effects, little research has been done on the indirect effects of urban growth - only 34% of all studies of urban impacts on biodiversity consider indirect effects. "In other words, we are spending about twice as much effort to study direct effects than indirect effects, even though indirect effects seem to be far more important in magnitude", said Robert McDonald.

This gap in the literature may have an effect on policymaking: "The lack of data on the significance of urban biodiversity loss in middle- and low-income countries could lead policymakers to underestimate the importance of the issue", said Prof Henrique Pereira, research group head at iDiv and MLU. Moreover, there is a lack of information on how unique socioeconomic processes in developing countries, such as informal settlements (slums), affect biodiversity. "Only by closing these research gaps will society be able to make smart and informed decisions about how to protect biodiversity in an increasingly urban world."

A research team in the Department of Electrical and EIIRIS at Toyohashi University of Technology has developed a donut-shaped kirigami device for EMG recordings. The proposed device reduces device displacement on a large deformable muscle surface. Accurate and robust EMG recordings offer EMG signal-based human-machine interfaces that allow prosthesis control for amputees. The results of their research were published in an issue of Advanced Healthcare Materials on December 5, 2019. The article also appeared on the inside back cover.

An accurate and robust EMG signal recording is necessary in EMG signal-based human-machine interfaces to allow prosthesis control for amputees using their residual muscle. In 2017, the same research team previously proposed an electrode device using the kirigami structure for the intimate integration of the electronic device and biological tissues. (Y. Morikawa et al., 10.1002/adhm.201701100). The remarkable potential of the kirigami structure stems from its high stretchability, including its high strain ratio and small force necessary to be applied during device stretches. The kirigami structure can be stretched with a low strain force and its mechanical characteristics are similar to soft biological tissues, such as in the brain and muscles. However, it is challenging to obtain an accurate and robust bio-signal recording without displacement of the electrode. Device displacement occurs when the kirigami device is applied to biological tissues, such as the heart and muscles, which undergo large deformation.

A research team in the Department of Electrical and Electronic Information Engineering and the EIIRIS at Toyohashi University of Technology has developed donut-shaped kirigami device for EMG recording to solve the issue of device displacement during muscle deformation.

The donut-shaped kirigami structure is able to transform from a 2D donut shape to a 3D cylindrical shape. The cylindrical shape is suitable for numerous spherically or columnar-shaped deformable biological tissues (e.g. upper limb, lower limb, finger, abdomen, and heart). The donut-shaped kirigami device carries out the fixation mechanism to the target tissues and reduces the device displacement during tissue deformation with minimized stress to the biological tissue. The recording capability of the proposed device was confirmed through the EMG signal recording from the hind limb of a mouse, indicating the prospect of using the device for an EMG-based human-machine-interface.

"The first demonstration using our conventional sheet-shaped kirigami device could not follow the deformation of a beating heart. We discussed the device structure, which enables the device to follow deformable tissues. In the preliminary experiment, we used a paper, which was patterned into the proposed donut-shape of the kirigami by the box cutter, and we demonstrated its stretchable and deformable capabilities for the muscle. However, it was uncertain whether the micro-scale donut-kirigami device shows these device properties or not. We explored them through fabricating the device by using the microfabrication process and the device characterizations, and we confirmed that the fabricated device exhibited the expected deformation against our thought," explains the first author of the article, Ph.D. candidate Yusuke Morikawa.

The donut-shaped kirigami device still needs further improvements in terms of durability and the dense array of the microelectrodes. Moreover, the influence of the device implantations to the biological tissues should be clarified if used for a long period. However, it is expected that the proposed device is applicable to an EMG based human-machine-interface and contributes to the improvement of the quality of life of amputees.

For the first time, researchers can track biological molecules with unprecedented speed and precision thanks to the use of multi-metallic nanoparticles.

The researchers published their results on October 17 in ACS Photonics, a journal of the American Chemical Society.

Nanoparticles are used to track the movements of biological molecules isolated from cells and also in living cells, such as the mechanisms related to intracelluar transport, cell signaling, and other processes. Researchers have traditionally used gold nanoparticles to track these movements, but, in imaging, they could only show one color: green. Now, scientists can see more than green through the use of gold, silver and gold-silver alloy nanoparticles.

"Gold nanoparticles are very powerful tools used to precisely track the fast motion of biomolecules," said Ryota Iino, paper author and professor at the Institute for Molecular Science in the National Institutes of Natural Sciences. "However, the imaging was previously limited to monochromatic green. In this study, by using gold, silver and silver-gold nanoparticles, we have succeeded in extending the color palette--between purple and green--of high-speed and high-precision imaging of biomolecules."

Other tagging techniques, such as organic fluorescent dyes, can extend the color palette to include reds, but they tend to display as weaker colors than the sharp and strong showing that metallic nanoparticles give off. Metallic nanoparticles are also more stable than organic dyes, meaning they remain visible as they move with the tagged biomolecule for a long period.

"Nanoparticles show much stronger signals, and they don't blink in the same way organic dyes can," Iino said. "Different nanoparticles also strongly scatter the light at different wavelengths, meaning they show up as visibly different colors when imaged."

The team is now working on extending the imaging color palette even further with newly engineered nanoparticles. They also hope to use even much smaller nanoparticles to have a better understanding of all molecular mechanisms in functioning cells.

Osaka, Japan - Almost from the moment DNA was discovered, the ability to fix or remove disease-causing genes in affected patients has been something of a holy grail of medicine. Now that this goal is within reach, researchers are working to fine-tune the technology to ensure safe and effective gene editing with no unwanted downstream effects.

In a study published this month in Nature Communications, Japanese researchers led by Osaka University describe a new genome editing approach that brings us much closer to achieving the dream of eliminating a host of diseases caused by faults in our DNA.

Most modern gene editing techniques rely on CRISPR technology—short for "clusters of regularly interspaced short palindromic repeats"—adapted from bacterial anti-viral defense systems. Essentially, CRISPR-associated proteins (Cas) can be directed to specific regions of the genome, where they make precise cuts in the DNA. This approach can be used to completely eliminate regions of faulty DNA or to introduce new DNA by supplying an altered blueprint that is followed by the cell when repairing the DNA break.

There are two main classes of CRISPR systems, Class 1 and Class 2, that are distinguished by the number of helper proteins needed to cut the DNA. While most gene editing approaches use single-component Class 2 CRISPR systems, very little is known about the utility of multi-component Class 1 systems in eukaryotic gene editing.

"Class 2 CRISPR systems, particularly those using the Cas9 or Cas12a enzymes, are widely used for eukaryotic genome editing," says lead author of the study Hiroyuki Morisaka. "However, these systems aren't perfect: as well as introducing unintended mutations, genome editing efficiencies using these methods can be somewhat variable."

The researchers therefore decided to investigate whether Class 1 CRISPR systems could offer a more efficient and safer alternative.

Using a Cas3 protein-based Class 1 CRISPR system, the team successfully demonstrated both DNA deletions and insertions in human cells. Notably, the Cas3 protein induced unidirectional deletions of large sections of DNA, setting it apart from Class 2 enzymes which usually need help to achieve such large genome edits. Most importantly though, Cas3 achieved more efficient genome editing than Cas9, with no prominent off-target effects.

To confirm the therapeutic potential of the system, the researchers carried out Cas3-based repair of the DMD gene in induced pluripotent stem cells from a patient with Duchenne muscular dystrophy.

"Our results suggest that this Cas3-based method offers a superior alternative to Class 2 CRISPR gene editing systems," says senior author Tomoji Mashimo. "As well as its obvious therapeutic uses, we envisage potential applications in drug discovery, disease prevention, and crop improvement."

Rhythm is a fundamental aspect of music, dance and language. However, we do not know to what extent our rhythmic skills depend on ancient evolutionary mechanisms that may be present in other animals.

"In our study, we explored whether other animals can detect an isochronous beat (in which all signals are separated by the same interval) and distinguish non-isochronous beats, regardless of other irrelevant features such as tempo", assert Alexandre Celma-Miralles and Juan Manuel Toro, ICREA research professor with the Department of Information and Communication Technologies (DTIC), and members of the Language and Comparative Cognition research group (LCC) at the Center for Brain and Cognition (CBC) at UPF.

The perception of temporal regularities is essential to synchronize to music and dance. The researchers explored the detection of isochrony in two mammal species for which they trained rats (Rattus norvegicus) and humans to discriminate sound sequences with regular intervals from sound sequences with irregular intervals. The researchers started from the assumption that that the detection of regularity may not rely on vocal learning skills and that both rats and humans distinguish regular from irregular stimuli.

The study used four different tempi in the training sessions and introduced two new tempi in the tests. They then compared the behavioural responses of the two species. They discovered that both rats and humans responded more to new, regular sequences than to irregular ones. Thus, as the authors point out: "In our experiments, we find that species that are very distant from humans, that do not produce complex vocalizations, like rats, have this ability". Therefore, the lack of difference between the responses of rats and those of humans may imply that the two species are able to detect regularity, regardless of the involvement of any vocal learning ability.

In summary, this study suggests that detecting temporal regularities in sequences of sounds may have ancient evolutionary roots and could rely on timing mechanisms present in distantly related mammals.

This suggests that rhythmic perception in humans has strong evolutionary roots that may be linked to more general mechanisms of temporal perception. This study represents a breakthrough in the understanding of the biological roots of rhythmic perception and opens the door to identifying the neural substrates, common across the species, that enhance musical cognition.

Researchers from the National Astronomical Observatories of the Chinese Academy of Science (NAOC), Peking University and Tsinghua University have found a special population of dwarf galaxies that could mainly consist baryons within radii of up to tens of thousands of light-years. This contrasts with the normal expectation that such regions should instead be dominated by dark matter.

This study may challenge the formation theory of dwarf galaxies in the framework of standard cosmology and may provide new clues to the nature of dark matter. The results were published in Nature Astronomy on Nov. 26, 2019.

In standard cosmology, the Universe is dominated by cold dark matter and dark energy, while baryons only occupy 4.6% by mass. Galaxies form and evolve in systems dominated by dark matter (Fig. 1). In high-mass systems, the baryonic fraction may reach the universal value, i.e., 4.6%. In low-mass systems, the baryonic fraction may be much lower due to their shallow gravitational potential.

The satellite dwarf galaxies in our Local Group are found to be dominated by dark matter down to radii of a few thousand light-years. However, statistical studies of the dynamics of dwarf galaxies beyond the Local Group previously had been hampered by the extreme faintness of such systems.

Multi-wavelength data have recently made such studies possible, however.

By taking advantage of the release of 40% of the data from the Arecibo Legacy Fast (ALFA) catalogue and the Seventh Data Release of the Sloan Digital Sky Survey, a research group led by Prof. GUO Qi from NAOC has found 19 dwarf galaxies that are dominated by baryons at radii far beyond their half-optical radii ( typically a few thousand light-years). Normally, the dark matter-to-baryon mass ratio reaches 10-1000 for "typical" dwarf galaxies. Notably, most of these baryon-dominated dwarf galaxies are isolated galaxies, free from the influence of nearby bright galaxies and high-density environments.

"This result is very hard to explain using the standard galaxy formation model in the context of concordance cosmology, and thus encourages people to revisit the nature of dark matter," said Prof. GUO.

Instead of the standard cold dark matter model, a warm dark matter model or fuzzy dark matter model might be more in line with the formation of this particular population of dwarf galaxies. Alternatively, some extreme astrophysical processes may also be responsible.

Further observations are required to understand the formation of these particular baryon-dominated dwarf galaxies.